format-version: 1.2 data-version: 2013-01-31 date: 04:01:2013 10:31 saved-by: haendel auto-generated-by: OBO-Edit 2.2 subsetdef: abnormal_slim "Abnormal/normal slim" subsetdef: absent_slim "Absent/present slim" subsetdef: attribute_slim "Attribute slim" subsetdef: cell_quality "cell_quality" subsetdef: cyclostome_subset "cyclostome structures" subsetdef: defined_by_ordinal_series "classes that are defined by relative position counting from first in a series of elements along an axis in an individual organism rather than by strict homology" subsetdef: developmental_classification "developmental_classification" subsetdef: disjointness_axiom_removed "A class which has a weakened disjointness axiom, to avoid inconsistency. These are kept separately in the uberon_disjoint_from_strict ontology." subsetdef: disposition_slim "Disposition slim" subsetdef: dubious_grouping "Indicates that subclasses in AOs may be inappropriately linked" subsetdef: early_development "A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes." subsetdef: emapa_ehdaa2 "derived from the union of EHDAA2 and EMAPA - still to be checked" subsetdef: functional_classification "functional_classification" subsetdef: goslim_aspergillus "Aspergillus GO slim" subsetdef: goslim_candida "Candida GO slim" subsetdef: goslim_generic "Generic GO slim" subsetdef: goslim_goa "GOA and proteome slim" subsetdef: goslim_metagenomics "Metagenomics GO slim" subsetdef: goslim_pir "PIR GO slim" subsetdef: goslim_plant "Plant GO slim" subsetdef: goslim_pombe "Fission yeast GO slim" subsetdef: goslim_yeast "Yeast GO slim" subsetdef: gosubset_prok "Prokaryotic GO subset" subsetdef: grouping_class "Subset consisting of classes creating for grouping purposes" subsetdef: high_level_annotation_qc "High-level terms not to be used for direct annotation" subsetdef: inconsistent_with_fma "classes that have some inconsistency with FMA" subsetdef: inherited_grouping_class "A grouping class that originates in two or more separate anatomical ontologies. Includes 'region of X' type terms" subsetdef: loose_concept "loose concept" subsetdef: major_organ "somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads" subsetdef: metazoa_core "core classes typically found across metazoa. one purpose is to create a rough set of terms that could be used to start a new metazoan AO. Note this subset is not yet fully fleshed out" subsetdef: mf_needs_review "Catalytic activity terms in need of attention" subsetdef: mpath_slim "Pathology slim" subsetdef: non_informative "abstract class brought in to group ontology classes but not informative" subsetdef: organ_slim "organs, excluding individual muscles and skeletal elements" subsetdef: phenotype_rcn "A subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMA" subsetdef: relational_slim "Relational slim: types of quality that require an additional entity in order to exist" subsetdef: scalar_slim "Scalar slim" subsetdef: termgenie_unvetted "Terms created by TermGenie that do not follow a template and require additional vetting by editors" subsetdef: uberon_slim "Uberon slim - somewhat arbitrary subset that excludes obscure terms and deep compositional terms" subsetdef: ubprop:upper_level "abstract upper-level terms not directly useful for analysis" subsetdef: unverified_taxonomic_grouping "Indicates that the class encompasses classes from other AOs that have not been verified" subsetdef: unvetted "" subsetdef: upper_level "abstract upper-level terms not directly useful for analysis" subsetdef: upper_ontology_conflict "Terms in this subset group together terms from different anatomy ontologies that have conflicting upper ontology/CARO assignments. For example, in FMA the naris is immaterial and in ZFA it is an organism subdivision." subsetdef: value_slim "Value slim" subsetdef: vertebrate_core "core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO" subsetdef: vessel_or_tree "A term classified differently in FMA due to its treatment of branching structures - to be reviewed and revised by editors" subsetdef: virus_checked "Viral overhaul terms" synonymtypedef: ABBREVIATION "abbreviation" synonymtypedef: ATTRIBUTION_REQUIRED "expert consultation and attribution required" synonymtypedef: BRAND_NAME "BRAND NAME" synonymtypedef: DEPRECATED "A historic synonym, no longer encouraged" synonymtypedef: DEVELOPMENTAL "developmental term" synonymtypedef: DUBIOUS "dubious or contested synonym" synonymtypedef: FORMULA "FORMULA" synonymtypedef: HOMOLOGY "a synonym made on the basis of a possibly homologous structure in another species" synonymtypedef: HUMAN_PREFERRED "preferred term when talking about an instance of this class in Homo sapiens" synonymtypedef: InChI "InChI" synonymtypedef: InChIKey "InChIKey" synonymtypedef: INCONSISTENT "indicates that a synonym is used in an inconsistent or confusing way, typically between species" synonymtypedef: INN "INN" synonymtypedef: IUPAC_NAME "IUPAC NAME" synonymtypedef: LATIN "latin term" synonymtypedef: PLURAL "plural term" synonymtypedef: PRO-short-label "Unique short label for PRO terms for display purposes" EXACT synonymtypedef: PSI-MOD-label "Unique short label curated by PSI-MOD" EXACT synonymtypedef: SENSU "taxonomic disambiguation" synonymtypedef: SMILES "SMILES" synonymtypedef: systematic_synonym "Systematic synonym" EXACT default-namespace: cl treat-xrefs-as-equivalent: BILA treat-xrefs-as-equivalent: BSPO treat-xrefs-as-equivalent: CARO treat-xrefs-as-equivalent: GO treat-xrefs-as-equivalent: NIF_GrossAnatomy treat-xrefs-as-equivalent: OG treat-xrefs-as-equivalent: VSAO remark: $Revision: 1.113 $ See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo. ontology: cl treat-xrefs-as-reverse-genus-differentia: AAO part_of NCBITaxon:8292 treat-xrefs-as-reverse-genus-differentia: FBbt part_of NCBITaxon:7227 treat-xrefs-as-reverse-genus-differentia: FMA part_of NCBITaxon:9606 treat-xrefs-as-reverse-genus-differentia: HAO part_of NCBITaxon:7399 treat-xrefs-as-reverse-genus-differentia: KUPO part_of NCBITaxon:9606 treat-xrefs-as-reverse-genus-differentia: MA part_of NCBITaxon:10088 treat-xrefs-as-reverse-genus-differentia: MFO part_of NCBITaxon:8089 treat-xrefs-as-reverse-genus-differentia: ncithesaurus part_of NCBITaxon:40674 treat-xrefs-as-reverse-genus-differentia: SPD part_of NCBITaxon:6893 treat-xrefs-as-reverse-genus-differentia: TADS part_of NCBITaxon:6939 treat-xrefs-as-reverse-genus-differentia: TAO part_of NCBITaxon:32443 treat-xrefs-as-reverse-genus-differentia: TGMA part_of NCBITaxon:44484 treat-xrefs-as-reverse-genus-differentia: WBbt part_of NCBITaxon:6237 treat-xrefs-as-reverse-genus-differentia: XAO part_of NCBITaxon:8353 treat-xrefs-as-reverse-genus-differentia: ZFA part_of NCBITaxon:7954 treat-xrefs-as-has-subclass: EHDAA treat-xrefs-as-has-subclass: EHDAA2 treat-xrefs-as-has-subclass: EMAPA [Term] id: CHEBI:23367 name: molecular entity namespace: chebi_ontology def: "Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity." [] synonym: "entidad molecular" RELATED [IUPAC:] synonym: "entidades moleculares" RELATED [IUPAC:] synonym: "entite moleculaire" RELATED [IUPAC:] synonym: "molecular entities" RELATED [IUPAC:] synonym: "molecular entity" EXACT IUPAC_NAME [IUPAC:] synonym: "molekulare Entitaet" RELATED [ChEBI:] is_a: CHEBI:24431 ! chemical entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:24431 name: chemical entity namespace: chebi_ontology def: "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances." [] property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:24651 name: hydroxides namespace: chebi_ontology def: "Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-))." [] is_a: CHEBI:25806 ! oxygen molecular entity is_a: CHEBI:33608 ! hydrogen molecular entity is_a: CHEBI:37577 ! heteroatomic molecular entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:25179 name: melanin namespace: chebi_ontology alt_id: CHEBI:6727 is_a: CHEBI:26195 ! polyphenol property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:25806 name: oxygen molecular entity namespace: chebi_ontology synonym: "oxygen molecular entities" RELATED [ChEBI:] synonym: "oxygen molecular entity" EXACT [ChEBI:] is_a: CHEBI:33304 ! chalcogen molecular entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:26195 name: polyphenol namespace: chebi_ontology def: "Any of the group of vegetable chemical substances, characterized by the presence of more than one phenolic group." [] synonym: "polyphenols" RELATED [ChEBI:] is_a: CHEBI:33822 ! organic hydroxy compound property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:33243 name: natural product namespace: chebi_ontology synonym: "natural products" RELATED [ChEBI:] is_a: CHEBI:50860 ! organic molecular entity [Term] id: CHEBI:33304 name: chalcogen molecular entity namespace: chebi_ontology def: "Any p-block molecular entity containing a chalcogen." [] synonym: "chalcogen compounds" RELATED [ChEBI:] synonym: "chalcogen molecular entities" RELATED [ChEBI:] synonym: "chalcogen molecular entity" EXACT [ChEBI:] is_a: CHEBI:33675 ! p-block molecular entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:33579 name: main group molecular entity namespace: chebi_ontology def: "A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table." [] synonym: "main group compounds" RELATED [ChEBI:] synonym: "main group molecular entities" RELATED [ChEBI:] is_a: CHEBI:23367 ! molecular entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:33582 name: carbon group molecular entity namespace: chebi_ontology synonym: "carbon group molecular entities" RELATED [ChEBI:] synonym: "carbon group molecular entity" EXACT [ChEBI:] is_a: CHEBI:33675 ! p-block molecular entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:33608 name: hydrogen molecular entity namespace: chebi_ontology synonym: "hydrogen compounds" RELATED [ChEBI:] synonym: "hydrogen molecular entities" RELATED [ChEBI:] is_a: CHEBI:33674 ! s-block molecular entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:33674 name: s-block molecular entity namespace: chebi_ontology def: "An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element." [] synonym: "s-block compounds" RELATED [ChEBI:] synonym: "s-block molecular entities" RELATED [ChEBI:] synonym: "s-block molecular entity" EXACT [ChEBI:] is_a: CHEBI:33579 ! main group molecular entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:33675 name: p-block molecular entity namespace: chebi_ontology def: "A p-block molecular entity is a molecular entity containing one or more atoms of a p-block element." [] synonym: "p-block compounds" RELATED [ChEBI:] synonym: "p-block molecular entities" RELATED [ChEBI:] synonym: "p-block molecular entitiy" RELATED [ChEBI:] is_a: CHEBI:33579 ! main group molecular entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:33822 name: organic hydroxy compound namespace: chebi_ontology def: "An organic compound having at least one hydroxy group attached to a carbon atom." [] synonym: "hydroxy compounds" EXACT IUPAC_NAME [IUPAC:] synonym: "organic hydroxy compounds" RELATED [ChEBI:] is_a: CHEBI:24651 ! hydroxides is_a: CHEBI:50860 ! organic molecular entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:36357 name: polyatomic entity namespace: chebi_ontology def: "Any molecular entity consisting of more than one atom." [] synonym: "polyatomic entities" RELATED [ChEBI:] is_a: CHEBI:23367 ! molecular entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:37577 name: heteroatomic molecular entity namespace: chebi_ontology def: "A molecular entity consisting of two or more chemical elements." [] synonym: "chemical compound" RELATED [ChEBI:] synonym: "heteroatomic molecular entities" RELATED [ChEBI:] is_a: CHEBI:36357 ! polyatomic entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:50860 name: organic molecular entity namespace: chebi_ontology alt_id: CHEBI:25700 alt_id: CHEBI:33244 def: "Any molecular entity that contains carbon." [] synonym: "organic compounds" RELATED [ChEBI:] synonym: "organic entity" RELATED [ChEBI:] synonym: "organic molecular entities" RELATED [ChEBI:] is_a: CHEBI:33582 ! carbon group molecular entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CL:0000000 name: cell namespace: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). subset: ubprop:upper_level xref: FMA:68646 xref: GO:0005623 xref: KUPO:0000002 xref: VHOG:0001533 xref: WBbt:0004017 xref: XAO:0003012 [Term] id: CL:0000001 name: primary cultured cell namespace: cell def: "A cultured cell that is freshly isolated from some source organism and not yet passaged." [ReO:mhb] comment: Covers cells actively being cultured or stored in a quiescent state for future use. synonym: "primary cell culture cell" EXACT [] synonym: "primary cell line cell" RELATED [] synonym: "unpassaged cultured cell" EXACT [] xref: BTO:0002290 is_a: CL:0000010 ! cultured cell [Term] id: CL:0000002 name: immortal cell line cell namespace: cell def: "A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite growth/propagation in vitro as part of a immortal cell line." [ReO:mhb] comment: Covers cells actively being cultured or stored in a quiescent state for future use. synonym: "continuous cell line cell" EXACT [] synonym: "permanent cell line cell" EXACT [] is_a: CL:0007014 ! cell line cell [Term] id: CL:0000003 name: native cell namespace: cell def: "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)." [CARO:mah] comment: To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). subset: ubprop:upper_level synonym: "cell in vivo" NARROW [] xref: CARO:0000013 is_a: CL:0000000 ! cell [Term] id: CL:0000004 name: cell by organism namespace: cell def: "A classification of cells by the organisms within which they are contained." [FB:ma] comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified by its species. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate. is_obsolete: true consider: CL:0000000 consider: CL:0000003 consider: CL:0001034 [Term] id: CL:0000005 name: fibroblast neural crest derived namespace: cell is_a: CL:0000057 ! fibroblast relationship: develops_from CL:0000008 ! migratory cranial neural crest cell [Term] id: CL:0000006 name: neuronal receptor cell namespace: cell synonym: "neuronal receptor cell (sensu Animalia)" EXACT [] is_a: CL:0000197 ! receptor cell is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception [Term] id: CL:0000007 name: early embryonic cell namespace: cell def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] is_a: CL:0002321 ! embryonic cell [Term] id: CL:0000008 name: migratory cranial neural crest cell namespace: cell is_a: CL:0000333 ! migratory neural crest cell [Term] id: CL:0000009 name: fusiform initial namespace: cell alt_id: CL:0000274 def: "Obsolete. Use PO:0000079 from Plant Ontology instead. An elongated cell with approximately wedge-shaped ends, found in the vascular cambium, which gives rise to the elements of the axial system in the secondary vascular tissues." [ISBN:0471245208] comment: replaced_by: PO:0000079 synonym: "xylem initial" RELATED [] synonym: "xylem mother cell" RELATED [] is_obsolete: true [Term] id: CL:0000010 name: cultured cell namespace: cell def: "A cell in vitro that is or has been maintained or propagated as part of a cell culture." [ReO:mhb] comment: Covers cells actively being cultured or stored in a quiescent state for future use. The class has been re-labeled to 'cultured cell' instead of 'cell line cell', as this class intends to cover cultured cells of multicellular and unicellular organisms, and both immortal and mortal cultured cells. 'Cell line' has different meanings to different people, in some cases referring to a culture that has been passaged, and in others referring to cultures that are immortal. 'Cell line cell' is included, however, as a narrow synonym. synonym: "cell line cell" NARROW [] is_a: CL:0000578 ! experimentally modified cell in vitro [Term] id: CL:0000011 name: migratory trunk neural crest cell namespace: cell is_a: CL:0000333 ! migratory neural crest cell [Term] id: CL:0000012 name: cell by class namespace: cell comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate. is_obsolete: true consider: CL:0000000 consider: CL:0000003 consider: CL:0001034 [Term] id: CL:0000013 name: dentine secreting cell namespace: cell is_obsolete: true consider: CL:0000140 [Term] id: CL:0000014 name: germ line stem cell namespace: cell synonym: "germline stem cell" EXACT [] is_a: CL:0000034 ! stem cell is_a: CL:0000039 ! germ line cell intersection_of: CL:0000039 ! germ line cell intersection_of: capable_of GO:0017145 ! stem cell division relationship: capable_of GO:0017145 ! stem cell division [Term] id: CL:0000015 name: male germ cell namespace: cell xref: FMA:72290 xref: MA:0002765 xref: ncithesaurus:Spermatogenic_Cell xref: VHOG:0001531 is_a: CL:0000586 ! germ cell intersection_of: CL:0000586 ! germ cell intersection_of: capable_of GO:0007283 ! spermatogenesis relationship: capable_of GO:0007283 ! spermatogenesis [Term] id: CL:0000016 name: male germ line stem cell namespace: cell is_a: CL:0000014 ! germ line stem cell is_a: CL:0000015 ! male germ cell [Term] id: CL:0000017 name: spermatocyte namespace: cell def: "A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids." [GOC:tfm, MESH:A05.360.490.890.880] xref: BTO:0001275 xref: EMAPA:31484 xref: FBbt:00004936 xref: FMA:84049 xref: WBbt:0006799 is_a: CL:0000015 ! male germ cell is_a: CL:0002625 ! seminiferous tubule epithelial cell intersection_of: CL:0000015 ! male germ cell intersection_of: capable_of GO:0048137 ! spermatocyte division relationship: capable_of GO:0048137 ! spermatocyte division relationship: develops_from CL:0000020 ! spermatogonium [Term] id: CL:0000018 name: spermatid namespace: cell def: "A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa." [MESH:A05.360.490.890.860] synonym: "nematoblast" EXACT [] xref: BTO:0001274 xref: EMAPA:31486 xref: FBbt:00004942 xref: FMA:72294 xref: WBbt:0006800 is_a: CL:0000015 ! male germ cell is_a: CL:0000413 ! haploid cell is_a: CL:0002625 ! seminiferous tubule epithelial cell intersection_of: CL:0000015 ! male germ cell intersection_of: capable_of GO:0001675 ! acrosome assembly intersection_of: capable_of GO:0007288 ! sperm axoneme assembly intersection_of: capable_of GO:0007289 ! spermatid nucleus differentiation intersection_of: has_quality PATO:0001375 ! haploid relationship: capable_of GO:0001675 ! acrosome assembly relationship: capable_of GO:0007288 ! sperm axoneme assembly relationship: capable_of GO:0007289 ! spermatid nucleus differentiation relationship: develops_from CL:0000657 ! secondary spermatocyte relationship: has_quality PATO:0001375 ! haploid [Term] id: CL:0000019 name: sperm namespace: cell def: "A mature male germ cell that develops from a spermatid." [GOC:tfm, MESH:A05.360.490.890] synonym: "sperm cell" EXACT [] synonym: "spermatozoid" EXACT [] synonym: "spermatozoon" EXACT [] xref: BTO:0001277 xref: BTO:0002046 xref: FBbt:00004954 xref: FMA:67338 xref: WBbt:0006798 is_a: CL:0000219 ! motile cell is_a: CL:0000408 ! male gamete intersection_of: CL:0000408 ! male gamete intersection_of: capable_of GO:0030317 ! sperm motility intersection_of: capable_of GO:0048240 ! sperm capacitation relationship: capable_of GO:0030317 ! sperm motility relationship: capable_of GO:0048240 ! sperm capacitation relationship: develops_from CL:0000018 ! spermatid [Term] id: CL:0000020 name: spermatogonium namespace: cell def: "An euploid male germ cell of an early stage of spermatogenesis." [MESH:A05.360.490.890.900] xref: BTO:0000958 xref: EMAPA:31482 xref: FBbt:00004935 xref: FMA:72291 is_a: CL:0000015 ! male germ cell is_a: CL:0002625 ! seminiferous tubule epithelial cell intersection_of: CL:0000015 ! male germ cell intersection_of: has_quality PATO:0001394 ! diploid intersection_of: has_quality PATO:0001501 ! immature relationship: has_quality PATO:0001394 ! diploid relationship: has_quality PATO:0001501 ! immature [Term] id: CL:0000021 name: female germ cell namespace: cell def: "Female germ cell is a germ cell that supports female gamete production." [GOC:tfm, PMID:11023867, PMID:20454446] xref: MA:0000388 xref: ncithesaurus:Egg xref: VHOG:0001530 is_a: CL:0000586 ! germ cell intersection_of: CL:0000586 ! germ cell intersection_of: capable_of GO:0048477 ! oogenesis relationship: capable_of GO:0048477 ! oogenesis [Term] id: CL:0000022 name: female germ line stem cell namespace: cell is_a: CL:0000014 ! germ line stem cell is_a: CL:0000021 ! female germ cell intersection_of: CL:0000021 ! female germ cell intersection_of: capable_of GO:0017145 ! stem cell division relationship: capable_of GO:0017145 ! stem cell division [Term] id: CL:0000023 name: oocyte namespace: cell def: "A female germ cell that has entered meiosis." [GOC:tfm, ISBN:0721662544] synonym: "oogonium" RELATED [] xref: BTO:0000964 xref: FBbt:00004886 xref: FMA:18644 xref: WBbt:0006797 is_a: CL:0000021 ! female germ cell intersection_of: CL:0000021 ! female germ cell intersection_of: participates_in GO:0007143 ! female meiosis relationship: participates_in GO:0007143 ! female meiosis [Term] id: CL:0000024 name: oogonial cell namespace: cell def: "An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes." [GOC:tfm, ISBN:0721662544] xref: FMA:83673 is_a: CL:0000021 ! female germ cell intersection_of: CL:0000021 ! female germ cell intersection_of: capable_of GO:0007067 ! mitosis relationship: capable_of GO:0007067 ! mitosis relationship: develops_from CL:0000670 ! primordial germ cell [Term] id: CL:0000025 name: egg namespace: cell def: "A female gamete where meiosis has progressed to metaphase II and is able to participate in fertilization." [GOC:tfm, ISBN:0721662544] synonym: "mature oocyte" EXACT [] synonym: "ovum" EXACT [] xref: BTO:0000369 xref: BTO:0003801 xref: FBbt:00000034 xref: FMA:67343 xref: MA:0000388 is_a: CL:0000023 ! oocyte is_a: CL:0000675 ! female gamete intersection_of: CL:0000675 ! female gamete intersection_of: capable_of GO:0009566 ! fertilization intersection_of: participates_in GO:0007143 ! female meiosis relationship: capable_of GO:0009566 ! fertilization relationship: develops_from CL:0000655 ! secondary oocyte relationship: participates_in GO:0007143 ! female meiosis [Term] id: CL:0000026 name: invertebrate nurse cell namespace: cell def: "A germline cell that contributes to the development of the oocyte by transferring cytoplasm directly to oocyte." [GOC:tfm, PMID:15848391] synonym: "nurse cell" RELATED [] xref: BTO:0000953 xref: FBbt:00004878 is_a: CL:0000039 ! germ line cell is_a: CL:0000412 ! polyploid cell relationship: develops_from CL:0000722 ! cystoblast [Term] id: CL:0000027 name: smooth muscle cell neural crest derived namespace: cell is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: develops_from CL:0000333 ! migratory neural crest cell relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: develops_from CL:0000333 ! migratory neural crest cell [Term] id: CL:0000028 name: CNS neuron (sensu Nematoda and Protostomia) namespace: cell is_a: CL:0000540 ! neuron relationship: develops_from CL:0000338 ! neuroblast (sensu Nematoda and Protostomia) [Term] id: CL:0000029 name: neuron neural crest derived namespace: cell is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: develops_from CL:0000333 ! migratory neural crest cell relationship: develops_from CL:0000333 ! migratory neural crest cell relationship: develops_from CL:0002676 ! neural crest derived neuroblast [Term] id: CL:0000030 name: glioblast namespace: cell xref: FBbt:00005145 is_a: CL:0000055 ! non-terminally differentiated cell relationship: develops_from CL:0000133 ! neurectodermal cell [Term] id: CL:0000031 name: neuroblast namespace: cell xref: BTO:0000930 xref: FBbt:00005146 xref: FMA:70563 is_a: CL:0000047 ! neuronal stem cell is_a: CL:0000055 ! non-terminally differentiated cell [Term] id: CL:0000032 name: neuroplacodal cell namespace: cell def: "A cell of a platelike structure, especially a thickened plate of ectoderm in the early embryo, from which a sense organ develops." [GOC:tfm, ISBN:0618947256] synonym: "neural placode cell" EXACT [] is_a: CL:0002321 ! embryonic cell relationship: develops_from CL:0000114 ! surface ectodermal cell [Term] id: CL:0000033 name: apocrine cell namespace: cell def: "An apocrine cell is a secretory cell characterized loss of part of the cytoplasm during the process of secretion - secretions are budded off through the plasma membrane producing membrane bound vesicles containing the secreted substance." [GOC:tfm, ISBN:0721662544] is_a: CL:0000151 ! secretory cell [Term] id: CL:0000034 name: stem cell namespace: cell def: "A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." [GOC:tfm, MESH:A11.872] xref: FMA:63368 is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: capable_of GO:0017145 ! stem cell division relationship: capable_of GO:0017145 ! stem cell division [Term] id: CL:0000035 name: single fate stem cell namespace: cell def: "A stem cell that self-renews as well as give rise to a single mature cell type." [GOC:tfm] synonym: "unipotent stem cell" EXACT [] synonym: "unipotential stem cell" EXACT [] xref: FMA:70569 is_a: CL:0000723 ! somatic stem cell [Term] id: CL:0000036 name: epithelial fate stem cell namespace: cell is_a: CL:0000035 ! single fate stem cell [Term] id: CL:0000037 name: hematopoietic stem cell namespace: cell def: "A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119." [GOC:add, GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Hematopoietic_stem_cell, PMID:19022770] comment: Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. synonym: "blood forming stem cell" EXACT [] synonym: "colony forming unit hematopoietic" RELATED [] synonym: "hemopoietic stem cell" EXACT [] synonym: "HSC" EXACT [] xref: BTO:0000725 xref: FMA:70337 xref: FMA:86475 xref: VHOG:0001485 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0000988 ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: capable_of GO:0002244 ! hematopoietic progenitor cell differentiation intersection_of: capable_of GO:0048103 ! somatic stem cell division intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G intersection_of: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 relationship: capable_of GO:0002244 ! hematopoietic progenitor cell differentiation relationship: capable_of GO:0048103 ! somatic stem cell division relationship: develops_from CL:0000566 ! angioblastic mesenchymal cell relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G relationship: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 [Term] id: CL:0000038 name: erythroid progenitor cell namespace: cell def: "A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative)." [GOC:add, ISBN:0721601464] synonym: "BFU-E" RELATED [] synonym: "blast forming unit erythroid" RELATED [] synonym: "burst forming unit erythroid" RELATED [] synonym: "CFU-E" RELATED [] synonym: "colony forming unit erythroid" RELATED [] synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030218 ! erythrocyte differentiation intersection_of: has_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G relationship: capable_of GO:0030218 ! erythrocyte differentiation relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell relationship: has_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G [Term] id: CL:0000039 name: germ line cell namespace: cell def: "A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring." [GOC:tfm, ISBN:0721662544] comment: Originally this term had some plant germ line cell children. subset: ubprop:upper_level is_a: CL:0000548 ! animal cell disjoint_from: CL:0002371 ! somatic cell relationship: capable_of GO:0022414 ! reproductive process [Term] id: CL:0000040 name: monoblast namespace: cell def: "A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus." [GOC:add, http://en.wikipedia.org/wiki/Monoblast, http://www.copewithcytokines.de, PMID:1104740] comment: Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. synonym: "CFU-M" RELATED [] synonym: "colony forming unit macrophage" RELATED [] synonym: "colony forming unit monocyte" RELATED [] synonym: "monocyte stem cell" RELATED [] xref: FMA:83553 is_a: CL:0002194 ! monopoietic cell intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part CP:0000028 ! basophilic cytoplasm intersection_of: has_part GO:0000791 ! euchromatin intersection_of: has_part GO:0005730 ! nucleolus intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: capable_of GO:0030224 ! monocyte differentiation relationship: develops_from CL:0002009 ! macrophage dendritic cell progenitor relationship: has_part CP:0000028 ! basophilic cytoplasm relationship: has_part GO:0000791 ! euchromatin relationship: has_part GO:0005730 ! nucleolus relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M [Term] id: CL:0000041 name: mature eosinophil namespace: cell def: "A fully differentiated eosinophil, a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Cells are also differentiated from other granulocytes by a small nuclear-to-cytoplasm ratio (1:3). This cell type is CD49d-positive." [GOC:add, GOC:dsd, GOC:tfm, http://www.cap.org, ISBN:0721601464] comment: Eosinophils are CD125-positive (IL-5R), GM-CSFR-positive, IL-3R-positive, VLA4-positive. They can also express MHC Class I & II, CD4, CD9, CD11a, CD11b, CD11c, CD13, CD15, CD16, CD17, CD18, CD24, CD25,CD28, CD29, CD32, CD33, CD35, CD37, CD39, CD43, CD44, CD45, CD45RB, CD45RO, CD46, CD47, CD48, CD49d, CD49f, CD50, CD52, CD53, CD54, CD55, CD58, CD59, CD62L, CD63, CD65, CD66, CD69, CD71, CD76, CD80, CD81, CD82, CD86, CD87, CD88, CD89, CD92, CD95, CD97, CD98, CD99, CD100, CD101, CD116, CD117, CD119, CD120, CD123, CD124, CD125, CD131, CD137, CD139, CD148, CD149, CD151, CD153, CD156, CD162, CD161, CD162, CD165, CD174, CD182, CD183, CD191, CD192, CD193, CD196, CD213, IL9R, ad integrin, beta-7 integrin, FceRI, IL13Ra1, TGFbR, PAFR, LTB4R, C3aR, CystLT1R, CystLT2R, fMLPR, CRTH2 (PGD2 receptor), histamine 4R, IDO, KYN, PAR-2, Siglec-8, Siglec-10, LIR1, LIR2, LIR3, LIR7, TLR7, TLR8, and VLA-4. Eosinophils can also secrete CXCL1, eotaxin-1, GM-CSF, IL-2, IL-3, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12, IL-13, IL-16, IL-18, IFN-gamma, LTC4, MIP-1alpha, NGF, PAF, RANTES, substance P, TGF-alpha, TGF-beta, TNF-alpha, and VIP. synonym: "mature eosinocyte" EXACT [] synonym: "mature eosinophil leucocyte" EXACT [] synonym: "mature eosinophil leukocyte" EXACT [] synonym: "polymorphonuclear leucocyte" BROAD [] synonym: "polymorphonuclear leukocyte" BROAD [] is_a: CL:0000771 ! eosinophil is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000771 ! eosinophil intersection_of: capable_of GO:0002495 ! antigen processing and presentation of peptide antigen via MHC class II intersection_of: capable_of GO:0002540 ! leukotriene production involved in inflammatory response intersection_of: capable_of GO:0045730 ! respiratory burst intersection_of: has_part CP:0000025 ! lobed nucleus intersection_of: has_part PR:000007152 ! eosinophil peroxidase intersection_of: has_part PR:000007857 ! erythroid transcription factor intersection_of: has_part PR:000007858 ! endothelial transcription factor GATA-2 intersection_of: has_part PR:000014046 ! non-secretory ribonuclease intersection_of: has_part PR:000014047 ! eosinophil cationic protein intersection_of: has_part PR:000022006 ! eosinophil granule major basic protein intersection_of: has_plasma_membrane_part PR:000009129 ! integrin alpha-4 relationship: capable_of GO:0002495 ! antigen processing and presentation of peptide antigen via MHC class II relationship: capable_of GO:0002540 ! leukotriene production involved in inflammatory response relationship: capable_of GO:0045730 ! respiratory burst relationship: develops_from CL:0000774 ! band form eosinophil relationship: has_part CP:0000025 ! lobed nucleus relationship: has_part PR:000007152 ! eosinophil peroxidase relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: has_part PR:000014046 ! non-secretory ribonuclease relationship: has_part PR:000014047 ! eosinophil cationic protein relationship: has_part PR:000022006 ! eosinophil granule major basic protein relationship: has_plasma_membrane_part PR:000009129 ! integrin alpha-4 [Term] id: CL:0000042 name: neutrophilic myeloblast namespace: cell def: "A myeloblast committed to the neutrophil lineage. This cell type is GATA-1 positive, C/EBPa-positive, AML-1-positive, c-myb-positive and has low expression of PU.1 transcription factor." [GOC:add, ISBN:0721601464, PMID:12560239, PMID:15514007] comment: These cells are CD11b-negative, CD15-negative, CD16-negative, CD35-negative, CD49d-positive, CD68-positive, lactotransferrin-negative, and fMLP receptor-negative. They are found in the Band 3 fraction. synonym: "neutrophilic granuloblast" RELATED [] is_a: CL:0000834 ! neutrophil progenitor cell is_a: CL:0000835 ! myeloblast intersection_of: CL:0000835 ! myeloblast intersection_of: capable_of GO:0030223 ! neutrophil differentiation intersection_of: has_part PR:000001944 ! transcription factor PU.1 intersection_of: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha intersection_of: has_part PR:000007857 ! erythroid transcription factor intersection_of: has_part PR:000010799 ! myb proto-oncogene protein intersection_of: has_part PR:000014362 ! runt-related transcription factor 1 relationship: capable_of GO:0030223 ! neutrophil differentiation relationship: develops_from CL:0000834 ! neutrophil progenitor cell relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000010799 ! myb proto-oncogene protein relationship: has_part PR:000014362 ! runt-related transcription factor 1 [Term] id: CL:0000043 name: mature basophil namespace: cell alt_id: CL:0000739 def: "A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation." [GOC:add, GOC:dsd, GOC:tfm, http://www.cap.org, ISBN:0721601464, PMID:18466030, PMID:19231594, PMID:20837449] comment: Mature basophils are also capable of producing IL-3, IL-5, IL-6, IL-8, IL-13, IL-25, CCL22, tslp, vegf, and LTC4. synonym: "mature basophil leucocyte" EXACT [] synonym: "mature basophil leukocyte" EXACT [] synonym: "polymorphonuclear leucocyte" BROAD [] synonym: "polymorphonuclear leukocyte" BROAD [] xref: BTO:0001026 is_a: CL:0000767 ! basophil is_a: CL:0002242 ! nucleate cell is_a: CL:0002274 ! histamine secreting cell intersection_of: CL:0000767 ! basophil intersection_of: capable_of GO:0002349 ! histamine production involved in inflammatory response intersection_of: capable_of GO:0002351 ! serotonin production involved in inflammatory response intersection_of: capable_of GO:0002830 ! positive regulation of type 2 immune response intersection_of: capable_of GO:0008015 ! blood circulation intersection_of: capable_of GO:0032616 ! interleukin-13 production intersection_of: capable_of GO:0032633 ! interleukin-4 production intersection_of: capable_of GO:0048295 ! positive regulation of isotype switching to IgE isotypes intersection_of: has_part CP:0000025 ! lobed nucleus relationship: capable_of GO:0002349 ! histamine production involved in inflammatory response relationship: capable_of GO:0002351 ! serotonin production involved in inflammatory response relationship: capable_of GO:0002830 ! positive regulation of type 2 immune response relationship: capable_of GO:0008015 ! blood circulation relationship: capable_of GO:0032616 ! interleukin-13 production relationship: capable_of GO:0032633 ! interleukin-4 production relationship: capable_of GO:0048295 ! positive regulation of isotype switching to IgE isotypes relationship: develops_from CL:0000770 ! band form basophil relationship: has_part CP:0000025 ! lobed nucleus [Term] id: CL:0000045 name: thymus processed stem cell namespace: cell def: "OBSOLETE (was not defined before being made obsolete)." [] comment: Consider using term 'pro-T cell ; CL:0000827' or the term 'thymocyte ; CL:0000893' or one of its children instead. is_obsolete: true [Term] id: CL:0000046 name: bursa processed stem cell namespace: cell def: "OBSOLETE (was not defined before being made obsolete)." [] comment: Consider using term 'pro-B cell ; CL:0000826' or the term 'immature B cell ; CL:0000816 or one of its children instead. is_obsolete: true [Term] id: CL:0000047 name: neuronal stem cell namespace: cell def: "Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors." [GOC:tfm, http://en.wikipedia.org/wiki/Neural_stem_cell, MESH:D058953, PMID:15247488] synonym: "neural stem cell" EXACT [] synonym: "NSC" EXACT [] xref: BTO:0002881 xref: FMA:86684 is_a: CL:0000048 ! multi fate stem cell intersection_of: CL:0000048 ! multi fate stem cell intersection_of: part_of UBERON:0001017 ! central nervous system relationship: develops_from CL:0000133 ! neurectodermal cell relationship: part_of UBERON:0001017 ! central nervous system [Term] id: CL:0000048 name: multi fate stem cell namespace: cell def: "A stem cell that can give rise to multiple lineages of cells." [GOC:add] synonym: "multi-fate stem cell" EXACT [] synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] synonym: "multipotent stem cell" EXACT [] xref: FMA:84789 is_a: CL:0000723 ! somatic stem cell intersection_of: CL:0000723 ! somatic stem cell intersection_of: capable_of GO:0030154 ! cell differentiation relationship: capable_of GO:0030154 ! cell differentiation [Term] id: CL:0000049 name: common myeloid progenitor namespace: cell def: "A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1." [GOC:add, GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Common_myeloid_progenitor, ISBN:0878932437, MESH:D023461, PMCID:PMC2212039, PMID:10724173, PMID:16551251, PMID:16647566] comment: CMP are reportedly CD16-positive, CD32-positive, CD38-positive, CD45RA-negative, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. synonym: "CFU-GEMM" RELATED [ISBN:0878932437] synonym: "CFU-S" RELATED [ISBN:0878932437] synonym: "CMP" EXACT [ISBN:0878932437] synonym: "colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte" RELATED [ISBN:0878932437] synonym: "common myeloid precursor" EXACT [] synonym: "multipotential myeloid stem cell" RELATED [ISBN:0878932437] synonym: "myeloid stem cell" RELATED [ISBN:0878932437] synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] xref: BTO:0004730 is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0002573 ! myeloid leukocyte differentiation intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation intersection_of: has_part PR:000001944 ! transcription factor PU.1 intersection_of: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha intersection_of: has_part PR:000007857 ! erythroid transcription factor intersection_of: has_part PR:000007858 ! endothelial transcription factor GATA-2 intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell disjoint_from: CL:0000051 ! common lymphoid progenitor disjoint_from: CL:0000557 ! granulocyte monocyte progenitor cell relationship: capable_of GO:0002573 ! myeloid leukocyte differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule [Term] id: CL:0000050 name: megakaryocyte-erythroid progenitor cell namespace: cell def: "A progenitor cell committed to the megakaryocyte and erythroid lineages." [GOC:add, GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell, MESH:D055015, PMID:16647566] comment: MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. synonym: "CFU-EM" EXACT [] synonym: "CFU-MegE" EXACT [] synonym: "colony forming unit erythroid megakaryocyte" EXACT [] synonym: "Meg/E progenitor" EXACT [] synonym: "megakaryocyte/erythrocyte progenitor" EXACT [] synonym: "megakaryocyte/erythroid progenitor cell" EXACT [] synonym: "MEP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030218 ! erythrocyte differentiation intersection_of: capable_of GO:0030219 ! megakaryocyte differentiation disjoint_from: CL:0000557 ! granulocyte monocyte progenitor cell disjoint_from: CL:0002009 ! macrophage dendritic cell progenitor relationship: capable_of GO:0030218 ! erythrocyte differentiation relationship: capable_of GO:0030219 ! megakaryocyte differentiation relationship: develops_from CL:0000049 ! common myeloid progenitor [Term] id: CL:0000051 name: common lymphoid progenitor namespace: cell alt_id: CL:0000044 def: "A oligopotent progenitor cell committed to the lymphoid lineage." [GOC:add, GOC:dsd, GOC:tfm, PMID:10407577, PMID:16551251] comment: CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative. synonym: "CLP" EXACT [] synonym: "committed lymphopoietic stem cell" RELATED [] synonym: "common lymphocyte precursor" EXACT [] synonym: "common lymphocyte progenitor" EXACT [] synonym: "common lymphoid precursor" EXACT [] synonym: "early lymphocyte progenitor" RELATED [] synonym: "ELP" RELATED [] synonym: "lymphoid stem cell" RELATED [] synonym: "lymphopoietic stem cell" RELATED [] is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030098 ! lymphocyte differentiation relationship: capable_of GO:0030098 ! lymphocyte differentiation [Term] id: CL:0000052 name: totipotent stem cell namespace: cell def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 is_a: CL:0000723 ! somatic stem cell [Term] id: CL:0000054 name: bone matrix secreting cell namespace: cell is_a: CL:0000151 ! secretory cell [Term] id: CL:0000055 name: non-terminally differentiated cell namespace: cell def: "A precursor cell with a limited number of potential fates." [SANBI:mhl] comment: define using PATO mulit-potent or oligopotent? synonym: "blast cell" EXACT [] xref: BTO:0000125 xref: FMA:84782 is_a: CL:0000003 ! native cell [Term] id: CL:0000056 name: myoblast namespace: cell def: "A precursor cell of the myogenic lineage that develops from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes." [GOC:tfm, MESH:A11.635] xref: BTO:0000222 xref: FBbt:00005083 xref: FMA:70335 xref: VHOG:0001529 is_a: CL:0000680 ! muscle precursor cell relationship: develops_from CL:0000355 ! muscle stem cell [Term] id: CL:0000057 name: fibroblast namespace: cell def: "A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped." [http://en.wikipedia.org/wiki/Fibroblast, ISBN:0517223651, MESH:A11.329.228, MESH:D005347] comment: These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. xref: BTO:0000452 xref: FMA:63877 xref: VHOG:0001482 is_a: CL:0002320 ! connective tissue cell relationship: develops_from CL:0000134 ! mesenchymal cell [Term] id: CL:0000058 name: chondroblast namespace: cell def: "Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell." [GO_REF:0000034, GOC:tfm, ISBN:0618947256] synonym: "chrondoplast" EXACT [] xref: BTO:0003607 xref: FMA:66783 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0002320 ! connective tissue cell relationship: develops_from CL:0007009 ! prechondroblast relationship: produces UBERON:0002418 ! cartilage tissue [Term] id: CL:0000059 name: ameloblast namespace: cell alt_id: CL:0000053 alt_id: CL:0000139 def: "Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell." [GO_REF:0000034, GOC:tfm, MESH:A11.436.107] comment: non-encoded relationship from VSAO produces VSAO:0000066 synonym: "amelocyte" EXACT [] synonym: "enamel secreting cell" EXACT [] xref: BTO:0001663 xref: FMA:70576 is_a: CL:0000146 ! simple columnar epithelial cell is_a: CL:0000151 ! secretory cell relationship: adjacent_to UBERON:0001763 ! odontogenic papilla relationship: capable_of GO:0097186 ! amelogenesis relationship: develops_from CL:0007000 ! preameloblast relationship: part_of UBERON:0005176 ! tooth enamel organ relationship: produces UBERON:0001752 ! enamel [Term] id: CL:0000060 name: odontoblast namespace: cell def: "Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell." [GO_REF:0000034, ISBN:0618947256] comment: legacy def: One of the cells forming the outer surface of dental pulp that produces tooth dentin. xref: BTO:0001769 xref: FMA:62999 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0002159 ! general ecto-epithelial cell relationship: develops_from CL:0007003 ! preodontoblast relationship: part_of UBERON:0005176 ! tooth enamel organ relationship: produces UBERON:0001751 ! dentine [Term] id: CL:0000061 name: cementoblast namespace: cell alt_id: CL:0000859 def: "Skeletogenic cell that produces cementum (a bony substance that covers the root of a tooth), is part of the odontogenic papilla, and develops from a precementoblast cell." [GO_REF:0000034, ISBN:0781733901] comment: Legacy def: A cell of ectomesenchymal origin that aids in the formation the cementum layer on the roots of teeth. synonym: "cementum secreting cell" EXACT [] xref: FMA:63002 is_a: CL:0000062 ! osteoblast is_a: CL:0000151 ! secretory cell relationship: develops_from CL:0007002 ! precementoblast relationship: part_of UBERON:0005176 ! tooth enamel organ relationship: produces UBERON:0001753 ! cementum [Term] id: CL:0000062 name: osteoblast namespace: cell def: "Skeletogenic cell that secretes osteoid, is capable of producing mineralized (hydroxyapatite) matrix, is located adjacent to or within osteoid tissue, and arises from the transformation of a preosteoblast cell." [GO_REF:0000034, MESH:A11.329.629] comment: non-encoded relationships from VSAO - capable_of_producing VSAO:0000020 xref: BTO:0001593 xref: FMA:66780 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0002320 ! connective tissue cell relationship: develops_from CL:0007010 ! preosteoblast relationship: produces UBERON:0008883 ! osteoid [Term] id: CL:0000063 name: cell by histology namespace: cell def: "A classification of cells by their microscopic appearance." [FB:ma, GOC:tfm] comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified by its microscopic appearance. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate. is_obsolete: true consider: CL:0000000 consider: CL:0000003 consider: CL:0001034 [Term] id: CL:0000064 name: ciliated cell namespace: cell def: "A cell that has a filiform extrusion of the cell surface." [GOC:tfm] xref: VHOG:0001532 xref: XAO:0000031 is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: has_plasma_membrane_part GO:0005929 ! cilium relationship: has_plasma_membrane_part GO:0005929 ! cilium [Term] id: CL:0000065 name: ependymal cell namespace: cell def: "A neurectoderm derived cell that lines the neural lumen." [GOC:tfm, JB:jb, PMID:9550134] synonym: "ependymocyte" EXACT [] xref: BTO:0001724 xref: FMA:70550 is_a: CL:0000067 ! ciliated epithelial cell is_a: CL:0000710 ! neurecto-epithelial cell relationship: has_plasma_membrane_part GO:0005929 ! cilium [Term] id: CL:0000066 name: epithelial cell namespace: cell def: "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina." [FB:ma, GOC:tfm, MESH:A11.436] synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CARO:0000077 xref: FBbt:00000124 xref: FMA:66768 xref: WBbt:0003672 is_a: CL:0000548 ! animal cell [Term] id: CL:0000067 name: ciliated epithelial cell namespace: cell def: "An epithelial cell that has a cillia." [GOC:tfm] xref: FMA:70605 is_a: CL:0000064 ! ciliated cell is_a: CL:0000075 ! columnar/cuboidal epithelial cell intersection_of: CL:0000075 ! columnar/cuboidal epithelial cell intersection_of: has_plasma_membrane_part GO:0005929 ! cilium relationship: has_plasma_membrane_part GO:0005929 ! cilium [Term] id: CL:0000068 name: duct epithelial cell namespace: cell is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000069 name: branched duct epithelial cell namespace: cell is_a: CL:0000068 ! duct epithelial cell [Term] id: CL:0000070 name: epithelial cell of gland namespace: cell is_obsolete: true [Term] id: CL:0000071 name: blood vessel endothelial cell namespace: cell def: "An endothelial cell that lines the vasculature." [GOC:tfm] synonym: "cuboidal endothelial cell of vascular tree" EXACT [] is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0004638 ! blood vessel endothelium relationship: develops_from CL:0002546 ! embryonic blood vessel endothelial progenitor cell relationship: part_of UBERON:0004638 ! blood vessel endothelium [Term] id: CL:0000072 name: non-branched duct epithelial cell namespace: cell is_a: CL:0000068 ! duct epithelial cell relationship: develops_from CL:0000222 ! mesodermal cell [Term] id: CL:0000073 name: barrier epithelial cell namespace: cell is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000074 name: epithem cell namespace: cell def: "Obsolete. Use PO:0000066 from Plant Ontology instead. A cell that constitutes the mesophyll of a hydathode and is located between the xylem endings and the epidermis. Proposed to be involved in the retrieval of solutes from the xylem sap." [ISBN:0471245208, PMID:12662305] comment: replaced_by: PO:0000066 is_obsolete: true [Term] id: CL:0000075 name: columnar/cuboidal epithelial cell namespace: cell is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000076 name: squamous epithelial cell namespace: cell is_a: CL:0000066 ! epithelial cell [Term] id: CL:0000077 name: mesothelial cell namespace: cell def: "A flattened epithelial cell of mesenchymal origin that lines the serous cavity." [GOC:tfm, ISBN:0721662544] synonym: "mesotheliocyte" EXACT [] xref: FMA:66773 is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000213 ! lining cell relationship: develops_from CL:0000222 ! mesodermal cell [Term] id: CL:0000078 name: peridermal cell namespace: cell is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000079 name: stratified epithelial cell namespace: cell is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell relationship: develops_from CL:0000357 ! stratified epithelial stem cell [Term] id: CL:0000080 name: circulating cell namespace: cell def: "A cell which moves among different tissues of the body, via blood, lymph, or other medium." [GOC:add] is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: part_of UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0000179 ! haemolymphatic fluid [Term] id: CL:0000081 name: blood cell namespace: cell def: "A cell found predominately in the blood." [GOC:add, GOC:tfm] xref: FMA:62844 is_a: CL:0000988 ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: capable_of GO:0008015 ! blood circulation relationship: capable_of GO:0008015 ! blood circulation [Term] id: CL:0000082 name: epithelial cell of lung namespace: cell xref: BTO:0004299 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0000115 ! lung epithelium relationship: part_of UBERON:0002048 ! lung [Term] id: CL:0000083 name: epithelial cell of pancreas namespace: cell def: "An epithelial cell of the pancreas." [GOC:tfm] xref: BTO:0000028 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001264 ! pancreas relationship: develops_from CL:0000223 ! endodermal cell relationship: part_of UBERON:0001264 ! pancreas [Term] id: CL:0000084 name: T cell namespace: cell alt_id: CL:0000804 alt_id: CL:0000812 def: "A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex." [GOC:add, GOC:tfm, ISBN:0781735149] synonym: "immature T cell" RELATED [] synonym: "mature T cell" RELATED [] synonym: "T lymphocyte" EXACT [] synonym: "T-cell" EXACT [] synonym: "T-lymphocyte" EXACT [] xref: BTO:0000782 xref: FMA:62870 xref: VHOG:0001479 is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0002456 ! T cell mediated immunity disjoint_from: CL:0000623 ! natural killer cell disjoint_from: CL:0000945 ! lymphocyte of B lineage relationship: capable_of GO:0002456 ! T cell mediated immunity relationship: develops_from CL:0000827 ! pro-T cell [Term] id: CL:0000085 name: germ line stem cell (sensu Vertebrata) namespace: cell is_a: CL:0000014 ! germ line stem cell [Term] id: CL:0000086 name: germ line stem cell (sensu Nematoda and Protostomia) namespace: cell xref: FBbt:00004861 is_a: CL:0000014 ! germ line stem cell [Term] id: CL:0000087 name: male germ line stem cell (sensu Nematoda and Protostomia) namespace: cell xref: FBbt:00004929 is_a: CL:0000016 ! male germ line stem cell is_a: CL:0000086 ! germ line stem cell (sensu Nematoda and Protostomia) [Term] id: CL:0000088 name: female germ line stem cell (sensu Nematoda and Protostomia) namespace: cell xref: FBbt:00004873 is_a: CL:0000022 ! female germ line stem cell is_a: CL:0000086 ! germ line stem cell (sensu Nematoda and Protostomia) [Term] id: CL:0000089 name: male germ line stem cell (sensu Vertebrata) namespace: cell is_a: CL:0000016 ! male germ line stem cell is_a: CL:0000085 ! germ line stem cell (sensu Vertebrata) [Term] id: CL:0000090 name: female germ line stem cell (sensu Vertebrata) namespace: cell is_a: CL:0000022 ! female germ line stem cell is_a: CL:0000085 ! germ line stem cell (sensu Vertebrata) [Term] id: CL:0000091 name: Kupffer cell namespace: cell def: "A tissue-resident macrophage of the reticuloendothelial system found on the luminal surface of the hepatic sinusoids involved in erythrocyte clearance. Markers include F4/80+, CD11b-low, CD68-positive, sialoadhesin-positive, CD163/SRCR-positive. Irregular, with long processes including lamellipodia extending into the sinusoid lumen, have flattened nucleus with cytoplasm containing characteristic invaginations of the plasma membrane (vermiform bodies); lie within the sinusoid lumen attached to the endothelial surface; derived from the bone marrow, form a major part of the body's mononuclear phagocyte system." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0517223651, MESH:A11.329.372.588, PMID:15771589, PMID:17105582] comment: Markers: Mouse: F4/80+, CD11b-low, CD68+, sialoadhesin+, CD163/SRCR+; role or process: immune, antigen-presentation, clearance of senescent erythrocytes, iron metabolism. Kupffer cells are also reportedly C3aR-positive, CD14-low, CD54-positive, CD88-positive, and CD284-positive. They are also capable of producing IL-1, IL-6, TNF-alpha, nitric oxide, PGD2, PGE2, PGF2alpha, and TXA2. synonym: "hepatic macrophage" EXACT [] synonym: "littoral cell of hepatic sinusoid" EXACT [] synonym: "liver macrophage" EXACT [] synonym: "macrophagocytus stellatus" EXACT [] synonym: "stellate cell of von Kupffer" EXACT [] synonym: "von Kupffer cell" EXACT [] xref: BTO:0000685 xref: FMA:14656 is_a: CL:0000864 ! tissue-resident macrophage intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0034102 ! erythrocyte clearance intersection_of: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 intersection_of: has_plasma_membrane_part PR:000001925 ! scavenger receptor cysteine-rich type 1 protein M130 intersection_of: has_plasma_membrane_part PR:000002064 ! macrosialin intersection_of: part_of UBERON:0001281 ! hepatic sinusoid relationship: capable_of GO:0034102 ! erythrocyte clearance relationship: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 relationship: has_plasma_membrane_part PR:000001925 ! scavenger receptor cysteine-rich type 1 protein M130 relationship: has_plasma_membrane_part PR:000002064 ! macrosialin relationship: part_of UBERON:0001281 ! hepatic sinusoid [Term] id: CL:0000092 name: osteoclast namespace: cell def: "A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149, PMID:10428500, PMID:15055519, PMID:17380158] comment: Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid. synonym: "chondroclast" RELATED [] xref: BTO:0000968 xref: FMA:66781 is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0001035 ! bone cell intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0045453 ! bone resorption intersection_of: has_part PR:000001850 ! cathepsin K intersection_of: has_part PR:000001937 ! tartrate-resistant acid phosphatase type 5 intersection_of: has_part PR:000001944 ! transcription factor PU.1 intersection_of: has_part PR:000007597 ! proto-oncogene c-Fos intersection_of: has_part PR:000011178 ! nuclear factor NF-kappa-B p100 subunit intersection_of: has_plasma_membrane_part PR:000001954 ! tumor necrosis factor receptor superfamily member 11A intersection_of: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor intersection_of: part_of UBERON:0001474 ! bone relationship: capable_of GO:0045453 ! bone resorption relationship: develops_from CL:0000576 ! monocyte relationship: has_part PR:000001850 ! cathepsin K relationship: has_part PR:000001937 ! tartrate-resistant acid phosphatase type 5 relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000007597 ! proto-oncogene c-Fos relationship: has_part PR:000011178 ! nuclear factor NF-kappa-B p100 subunit relationship: has_plasma_membrane_part PR:000001954 ! tumor necrosis factor receptor superfamily member 11A relationship: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor relationship: part_of UBERON:0001474 ! bone [Term] id: CL:0000093 name: osteochondroclast namespace: cell def: "OBSOLETE (was not defined before being made obsolete)." [] comment: Consider using 'osteoclast ; CL:0000092' instead. is_obsolete: true [Term] id: CL:0000094 name: granulocyte namespace: cell def: "A leukocyte with abundant granules in the cytoplasm." [GOC:amm, GOC:tfm, http://en.wikipedia.org/wiki/Granulocyte, MESH:A11.118.637.415, MESH:D006098] synonym: "granular leucocyte" EXACT [] synonym: "granular leukocyte" EXACT [] synonym: "polymorphonuclear leukocyte" EXACT [] xref: BTO:0000539 xref: BTO:0001026 xref: FMA:62854 is_a: CL:0000081 ! blood cell is_a: CL:0000766 ! myeloid leukocyte intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0008015 ! blood circulation intersection_of: has_part GO:0030141 ! secretory granule intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001332 ! carcinoembryonic antigen-related cell adhesion molecule 8 intersection_of: has_plasma_membrane_part PR:000001969 ! urokinase plasminogen activator surface receptor intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: capable_of GO:0008015 ! blood circulation relationship: has_part GO:0030141 ! secretory granule relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001332 ! carcinoembryonic antigen-related cell adhesion molecule 8 relationship: has_plasma_membrane_part PR:000001969 ! urokinase plasminogen activator surface receptor relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain [Term] id: CL:0000095 name: neuron associated cell namespace: cell is_a: CL:0002319 ! neural cell relationship: develops_from CL:0000133 ! neurectodermal cell [Term] id: CL:0000096 name: mature neutrophil namespace: cell def: "A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive." [GOC:add, GOC:tfm, http://www.cap.org, MESH:A11.118.637.415.583, MESH:D009504, PMID:11138776, PMID:12560239, PMID:15514007, PMID:7880385] comment: Neutrophils are also capable of secreting GRO-alpha, IL-1beta, IL-1ra, IL-3, IL-12, IP-10, MIG, MIP-1alpha, MIP-1beta, TGF-beta, TNF-alpha, VEGF, and anti-microbial peptides. They can positively influence the chemotaxis of basophils, T-cells, monocytes, macrophages, dendritic cells, and other neutrophils. Neutrophils are also CD35-positive, CD64-positive, CD89-positive, CD184-positive, and fMLP receptor-positive Ly-6G-positive (mouse), TLR2-low, TLR4-low, and lineage-negative (CD2, CD3, CD5, CD9, CD19, CD36, CD49d, CD56, CD61, CD235a (glycophorin-A)). synonym: "mature neutrocyte" EXACT [] synonym: "mature neutrophil leucocyte" EXACT [] synonym: "mature neutrophil leukocyte" EXACT [] synonym: "mature neutrophilic leucocyte" EXACT [] synonym: "mature neutrophilic leukocyte" EXACT [] synonym: "PMN" EXACT [] synonym: "poly" BROAD [] synonym: "polymorphonuclear leucocyte" BROAD [] synonym: "polymorphonuclear leukocyte" BROAD [] synonym: "polymorphonuclear neutrophil" EXACT [] synonym: "polynuclear neutrophilic leucocyte" EXACT [] synonym: "polynuclear neutrophilic leukocyte" EXACT [] xref: BTO:0003473 is_a: CL:0000234 ! phagocyte is_a: CL:0000775 ! neutrophil is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000775 ! neutrophil intersection_of: capable_of GO:0002536 ! respiratory burst involved in inflammatory response intersection_of: capable_of GO:0002690 ! positive regulation of leukocyte chemotaxis intersection_of: capable_of GO:0006909 ! phagocytosis intersection_of: capable_of GO:0032637 ! interleukin-8 production intersection_of: has_part CP:0000000 ! neutrophillic cytoplasm intersection_of: has_part CP:0000025 ! lobed nucleus intersection_of: has_part GO:0070820 ! tertiary granule intersection_of: has_plasma_membrane_part PR:000001256 ! high affinity interleukin-8 receptor A intersection_of: has_plasma_membrane_part PR:000001257 ! high affinity interleukin-8 receptor B intersection_of: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 intersection_of: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III intersection_of: has_plasma_membrane_part PR:000001879 ! leukosialin intersection_of: has_plasma_membrane_part PR:000001944 ! transcription factor PU.1 intersection_of: has_plasma_membrane_part PR:000007597 ! proto-oncogene c-Fos intersection_of: lacks_part PR:000009978 ! lactotransferrin intersection_of: lacks_part PR:000010543 ! myeloperoxidase intersection_of: lacks_part PR:000010799 ! myb proto-oncogene protein relationship: capable_of GO:0002536 ! respiratory burst involved in inflammatory response relationship: capable_of GO:0002690 ! positive regulation of leukocyte chemotaxis relationship: capable_of GO:0006909 ! phagocytosis relationship: capable_of GO:0032637 ! interleukin-8 production relationship: develops_from CL:0000560 ! band form neutrophil relationship: has_part CP:0000000 ! neutrophillic cytoplasm relationship: has_part CP:0000025 ! lobed nucleus relationship: has_part GO:0070820 ! tertiary granule relationship: has_plasma_membrane_part PR:000001256 ! high affinity interleukin-8 receptor A relationship: has_plasma_membrane_part PR:000001257 ! high affinity interleukin-8 receptor B relationship: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 relationship: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: has_plasma_membrane_part PR:000001879 ! leukosialin relationship: has_plasma_membrane_part PR:000001944 ! transcription factor PU.1 relationship: has_plasma_membrane_part PR:000007597 ! proto-oncogene c-Fos relationship: lacks_part PR:000009978 ! lactotransferrin relationship: lacks_part PR:000010543 ! myeloperoxidase relationship: lacks_part PR:000010799 ! myb proto-oncogene protein [Term] id: CL:0000097 name: mast cell namespace: cell def: "A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development." [GOC:add, GOC:dsd, GOC:tfm, ISBN:068340007X, MESH:A11.329.427, MESH:D008407, PMCID:PMC1312421, PMCID:PMC2855166, PMID:15153310, PMID:16455980, PMID:19671378, PMID:212366338, PMID:9354811] comment: Mast cells are generally integrin beta-7-negative and positive for TLR2, TLR3, TLR4, TLR5, TLR7, TLR9, C3aR, C5aR, CR3, CR4, VEGF, FGF2, and renin. They can express MHC Class I and II on their surface. Activated murine mast cells (IgE+Antigen) were capable of expressing the following co-stimulatory molecules: CD95 (Fas), CD120b, CD137 (4-1BB), CD153 (CD30L), CD154 (CD40L), GITR, ICOSL, OX40L, PD-L1, and PD-L2. Note that there was some mouse strain variation. Mast cells have also been demonstrated to produce bFGF, CCL2, CCL4, CCL5, CCL11, CCL20, CXCL2, CXCL8, CXCL10, GM-CSF, IFN-gamma, IL-1, IL-2, IL-3, IL-8, IL-10, IL-11, IL-12, IL-13, IL-16, IL-25, IL-18, MIP-1, prostaglandin D2, SCF, TGF-beta, TNF-alpha, TSLP, VEGF, and XCL1. They express the transcription factors Transcription factors AP-1, GATA1, MITF, Notch2, PIAS3, PU.1, and STAT5. synonym: "histaminocyte" EXACT [] synonym: "labrocyte" EXACT [ISBN:0721601464] synonym: "mastocyte" EXACT [ISBN:0721601464] synonym: "tissue basophil" RELATED [ISBN:068340007X] xref: BTO:0000830 xref: FMA:66784 is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0002274 ! histamine secreting cell intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0002349 ! histamine production involved in inflammatory response intersection_of: capable_of GO:0002539 ! prostaglandin production involved in inflammatory response intersection_of: capable_of GO:0002660 ! positive regulation of peripheral tolerance induction intersection_of: capable_of GO:0002690 ! positive regulation of leukocyte chemotaxis intersection_of: capable_of GO:0002830 ! positive regulation of type 2 immune response intersection_of: capable_of GO:0030210 ! heparin biosynthetic process intersection_of: has_high_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor intersection_of: has_high_plasma_membrane_amount PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha intersection_of: has_part GO:0030141 ! secretory granule intersection_of: has_plasma_membrane_part PR:000001255 ! chemokine receptor CCR3 intersection_of: has_plasma_membrane_part PR:000006169 ! cell surface glycoprotein CD200 receptor 3 intersection_of: lacks_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain relationship: capable_of GO:0002349 ! histamine production involved in inflammatory response relationship: capable_of GO:0002539 ! prostaglandin production involved in inflammatory response relationship: capable_of GO:0002660 ! positive regulation of peripheral tolerance induction relationship: capable_of GO:0002690 ! positive regulation of leukocyte chemotaxis relationship: capable_of GO:0002830 ! positive regulation of type 2 immune response relationship: capable_of GO:0030210 ! heparin biosynthetic process relationship: develops_from CL:0000831 ! mast cell progenitor relationship: has_high_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor relationship: has_high_plasma_membrane_amount PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha relationship: has_part GO:0030141 ! secretory granule relationship: has_plasma_membrane_part PR:000001255 ! chemokine receptor CCR3 relationship: has_plasma_membrane_part PR:000006169 ! cell surface glycoprotein CD200 receptor 3 relationship: lacks_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain [Term] id: CL:0000098 name: sensory epithelial cell namespace: cell def: "A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells." [GOC:tfm, ISBN:0517223651, ISBN:0721662544] comment: The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710). synonym: "neuroepithelial cell" BROAD [] xref: BTO:0004301 is_a: CL:0000066 ! epithelial cell is_a: CL:0000197 ! receptor cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000099 name: interneuron namespace: cell def: "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions." [GOC:tfm, MESH:A08.663.358] xref: BTO:0003811 xref: FBbt:00005125 xref: FMA:67313 xref: WBbt:0005113 is_a: CL:0000540 ! neuron [Term] id: CL:0000100 name: motor neuron namespace: cell def: "An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes movement." [MESH:A08.663.655.500, PMID:16875686] synonym: "anterior horn cell" EXACT [] synonym: "motoneuron" EXACT [] xref: BTO:0000312 xref: FMA:83617 xref: WBbt:0005409 is_a: CL:0000527 ! efferent neuron [Term] id: CL:0000101 name: sensory neuron namespace: cell def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [ISBN:0721662544] xref: BTO:0001037 xref: FBbt:00005124 xref: FMA:84649 xref: WBbt:0005759 is_a: CL:0000526 ! afferent neuron [Term] id: CL:0000102 name: polymodal neuron namespace: cell is_a: CL:0000540 ! neuron [Term] id: CL:0000103 name: bipolar neuron namespace: cell def: "A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body." [GOC:tfm, ISBN:0444009442] xref: FMA:67282 is_a: CL:0000099 ! interneuron [Term] id: CL:0000104 name: multipolar neuron namespace: cell def: "Neuron with an axon and two or more dendrites." [FMA:67287, GOC:tfm] xref: FMA:67287 is_a: CL:0000540 ! neuron [Term] id: CL:0000105 name: pseudounipolar neuron namespace: cell def: "Neuron with two neurites that are fused grossly when they protrude from the soma and bifurcate a short distance from the soma." [FMA:67305, GOC:tfm] xref: FMA:67305 is_a: CL:0000540 ! neuron [Term] id: CL:0000106 name: unipolar neuron namespace: cell def: "Neuron with one neurite that extends from the cell body." [FMA:67278, GOC:nv] xref: FMA:67278 is_a: CL:0000540 ! neuron [Term] id: CL:0000107 name: autonomic neuron namespace: cell def: "A neruon whose cell body is within an autonomic ganglion." [GOC:tfm] xref: FMA:80121 is_a: CL:0000540 ! neuron [Term] id: CL:0000108 name: cholinergic neuron namespace: cell def: "A neuron that uses acetylcholine as a vesicular neurotransmitter." [GOC:tfm] xref: BTO:0004902 xref: FMA:84796 xref: WBbt:0006840 is_a: CL:0000540 ! neuron [Term] id: CL:0000109 name: adrenergic neuron namespace: cell is_a: CL:0000540 ! neuron [Term] id: CL:0000110 name: peptidergic neuron namespace: cell is_a: CL:0000540 ! neuron [Term] id: CL:0000111 name: peripheral neuron namespace: cell def: "A neuron that is part of nerve found outside the central nervous system." [ISBN:0721662544] xref: FMA:84664 is_a: CL:0000540 ! neuron [Term] id: CL:0000112 name: columnar neuron namespace: cell synonym: "columnar neuron" RELATED [] is_a: CL:0000540 ! neuron [Term] id: CL:0000113 name: mononuclear phagocyte namespace: cell def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:0781735149] xref: BTO:0001433 is_a: CL:0000226 ! single nucleate cell is_a: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: has_quality PATO:0001407 ! mononucleate relationship: has_quality PATO:0001407 ! mononucleate [Term] id: CL:0000114 name: surface ectodermal cell namespace: cell synonym: "cell of surface ectoderm" EXACT [] synonym: "surface ectoderm cell" EXACT [] xref: FMA:72552 is_a: CL:0000221 ! ectodermal cell [Term] id: CL:0000115 name: endothelial cell namespace: cell def: "An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm." [GOC:tfm, http://en.wikipedia.org/wiki/Endothelial_cell, https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3364936&group_id=36855, MESH:D042783, PMID:21275341] comment: From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: FMA:66772 is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell [Term] id: CL:0000116 name: pioneer neuron namespace: cell def: "Pioneer neurons establish a pathway in the developing central nervous system and then undergo programmed cell death once the adult axons, which follow them, have made connections with the target site. Thus, they are a transient cell type involved in axon guidance." [GOC:cvs, GOC:tfm] xref: FBbt:00005128 is_a: CL:0000540 ! neuron [Term] id: CL:0000117 name: CNS neuron (sensu Vertebrata) namespace: cell is_a: CL:0000540 ! neuron relationship: develops_from CL:0000337 ! neuroblast (sensu Vertebrata) [Term] id: CL:0000118 name: basket cell namespace: cell is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) [Term] id: CL:0000119 name: Golgi cell namespace: cell is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) [Term] id: CL:0000120 name: granule cell namespace: cell xref: BTO:0003393 is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) [Term] id: CL:0000121 name: Purkinje cell namespace: cell def: "The output neuron of the cerebellar cortex." [MESH:A08.186.211.132.810.428.200.212.600] synonym: "Purkinje neuron" EXACT [] synonym: "Purkinje's cell" EXACT [] xref: BTO:0001011 xref: FMA:67969 is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) is_a: CL:0000527 ! efferent neuron [Term] id: CL:0000122 name: stellate cell namespace: cell xref: BTO:0002316 is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) [Term] id: CL:0000123 name: neuron associated cell (sensu Vertebrata) namespace: cell is_a: CL:0000095 ! neuron associated cell relationship: develops_from CL:0000333 ! migratory neural crest cell [Term] id: CL:0000124 name: glial cell (sensu Nematoda and Protostomia) namespace: cell xref: FBbt:00005144 is_a: CL:0000125 ! glial cell [Term] id: CL:0000125 name: glial cell namespace: cell def: "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons." [MESH:A08.637] synonym: "neuroglia" RELATED [] synonym: "neuroglial cell" EXACT [] xref: BTO:0002606 xref: FMA:54536 is_a: CL:0000095 ! neuron associated cell relationship: develops_from CL:0000030 ! glioblast [Term] id: CL:0000126 name: macroglial cell namespace: cell def: "A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together." [GOC:tfm, ISBN:0721662544] synonym: "macrogliocyte" EXACT [] xref: BTO:0000771 xref: FMA:54538 is_a: CL:0000243 ! glial cell (sensu Vertebrata) relationship: develops_from CL:0000339 ! glioblast (sensu Vertebrata) [Term] id: CL:0000127 name: astrocyte namespace: cell def: "A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury." [GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Astrocyte, MESH:A08.637.200, MESH:D001253, PMID:11746784, PMID:12162730, PMID:12898703, PMID:20942978] comment: Astrocytes are reportedly CD68-negative, CD121a-positive, CD184-positive, CD192-positive, CRF-positive, EGFR-positive, GFAP-positive, GLUT1-positive, MBP-negative, and NGFR-positive. synonym: "astrocytic glia" EXACT [] xref: BTO:0000099 xref: FMA:54537 is_a: CL:0000128 ! oligodendrocyte intersection_of: CL:0000126 ! macroglial cell intersection_of: has_part UBERON:0001023 ! dendrite intersection_of: part_of UBERON:0001017 ! central nervous system relationship: has_part UBERON:0001023 ! dendrite relationship: part_of UBERON:0001017 ! central nervous system [Term] id: CL:0000128 name: oligodendrocyte namespace: cell def: "A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system." [http://en.wikipedia.org/wiki/Oligodendrocyte, MESH:A08.637.600, MESH:D009836] comment: Oligodendrocytes are reportedly MDP-positive and CD4-negative. synonym: "oligodendroglia" RELATED [] synonym: "OLs" EXACT [PMID:8734446] xref: BTO:0000962 xref: FMA:54540 is_a: CL:0000126 ! macroglial cell intersection_of: CL:0000126 ! macroglial cell intersection_of: part_of UBERON:0001017 ! central nervous system relationship: develops_from CL:0002453 ! oligodendrocyte precursor cell relationship: part_of UBERON:0001017 ! central nervous system [Term] id: CL:0000129 name: microglial cell namespace: cell def: "A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive." [GOC:add, GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Microglia, ISBN:0721601464, MESH:D017628, PMID:11517395, PMID:12430718, PMID:14561199, PMID:14612429, PMID:16177057, PMID:19461673, PMID:2089275] comment: Markers: Mouse: CD11b+, F4/80+, CD68+. They represent ~12% of the cells in the CNS, but they are not uniformly distributed within the CNS. A normal adult mouse brain has approximately 3.5x10e6 microglia. Microglia are also reportedly CD3-negative, CD4-positive, CD8-negative, CD11b-positive, CD11c-high, CD14-negative, CD19-negative, CD45-low, CD56-negative, CD163-negative, CD200R-positive, CD281-positive, CD282-positive, CD283-positive, CD284-positive, CD285-positive, CD286-positive, CD287-positive, CD288-positive, CD289-positive, Gr1-negative, nestin-positive, and PU.1-positive. synonym: "brain macrophage" BROAD [] synonym: "brain-resident macrophage" EXACT [] synonym: "hortega cells" EXACT [http://www.copewithcytokines.de/] synonym: "MF.microglia.CNS" RELATED [] synonym: "microglia" EXACT [] synonym: "microgliocyte" EXACT [http://www.copewithcytokines.de/] xref: BTO:0000078 xref: BTO:0000962 xref: FMA:54539 xref: FMA:54540 is_a: CL:0000243 ! glial cell (sensu Vertebrata) is_a: CL:0000878 ! central nervous system macrophage intersection_of: CL:0000243 ! glial cell (sensu Vertebrata) intersection_of: capable_of GO:0045087 ! innate immune response intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 intersection_of: has_plasma_membrane_part PR:000002064 ! macrosialin intersection_of: part_of UBERON:0001017 ! central nervous system relationship: capable_of GO:0045087 ! innate immune response relationship: develops_from CL:0002453 ! oligodendrocyte precursor cell relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 relationship: has_plasma_membrane_part PR:000002064 ! macrosialin relationship: part_of UBERON:0001017 ! central nervous system [Term] id: CL:0000130 name: neuron associated cell (sensu Nematoda and Protostomia) namespace: cell is_a: CL:0000095 ! neuron associated cell [Term] id: CL:0000131 name: gut endothelial cell namespace: cell is_a: CL:0000115 ! endothelial cell relationship: develops_from CL:0000223 ! endodermal cell [Term] id: CL:0000132 name: corneal endothelial cell namespace: cell def: "Cell of the single layer of large flattened cells covering the surface of the cornea." [GOC:tfm, MESH:A09.371.060.067.31] xref: FMA:70614 is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000710 ! neurecto-epithelial cell relationship: develops_from CL:0000008 ! migratory cranial neural crest cell [Term] id: CL:0000133 name: neurectodermal cell namespace: cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] synonym: "neurectoderm cell" EXACT [] is_a: CL:0000221 ! ectodermal cell [Term] id: CL:0000134 name: mesenchymal cell namespace: cell alt_id: CL:0002452 def: "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. This cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." [FB:ma, GOC:dsd, http://en.wikipedia.org/wiki/Mesenchymal_stem_cell, http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells, PMCID:PMC2613570, PMID:10102814j, PMID:16923606, PMID:17986482, PMID:19960544] comment: Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. synonym: "BMSC" NARROW [] synonym: "bone marrow stromal cells" NARROW [] synonym: "CFU-F" RELATED [] synonym: "colony-forming unit-fibroblast" NARROW [] synonym: "marrow stromal cells" NARROW [PMID:11378515] synonym: "mesenchymal precursor cell" RELATED [] synonym: "mesenchymal progenitor cells" RELATED PLURAL [MESH:D044982] synonym: "mesenchymal stem cell" RELATED [] synonym: "mesenchymal stromal cell" RELATED [] synonym: "mesenchymal stromal cells" RELATED PLURAL [] synonym: "MSC" RELATED [PMID:11378515] synonym: "stem cells, mesenchymal" RELATED PLURAL [MESH:D044982] xref: BTO:0002625 xref: BTO:0003298 xref: FMA:70546 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0000219 ! motile cell is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0002320 ! connective tissue cell intersection_of: capable_of GO:0001649 ! osteoblast differentiation intersection_of: capable_of GO:0016477 ! cell migration intersection_of: capable_of GO:0030182 ! neuron differentiation intersection_of: capable_of GO:0030855 ! epithelial cell differentiation intersection_of: capable_of GO:0045444 ! fat cell differentiation intersection_of: capable_of GO:0055007 ! cardiac muscle cell differentiation intersection_of: capable_of GO:0060591 ! chondroblast differentiation intersection_of: has_plasma_membrane_part PR:000001345 ! endoglin intersection_of: has_plasma_membrane_part PR:000001800 ! 5'-nucleotidase intersection_of: has_plasma_membrane_part PR:000001843 ! Thy-1 membrane glycoprotein intersection_of: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex intersection_of: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: lacks_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C relationship: capable_of GO:0001649 ! osteoblast differentiation relationship: capable_of GO:0016477 ! cell migration relationship: capable_of GO:0030182 ! neuron differentiation relationship: capable_of GO:0030855 ! epithelial cell differentiation relationship: capable_of GO:0045444 ! fat cell differentiation relationship: capable_of GO:0055007 ! cardiac muscle cell differentiation relationship: capable_of GO:0060591 ! chondroblast differentiation relationship: has_plasma_membrane_part PR:000001345 ! endoglin relationship: has_plasma_membrane_part PR:000001800 ! 5'-nucleotidase relationship: has_plasma_membrane_part PR:000001843 ! Thy-1 membrane glycoprotein relationship: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: lacks_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C [Term] id: CL:0000135 name: fibrocyte namespace: cell def: "An inactive fibroblast; cytoplasm is sparse, endoplasmic reticulum is scanty with flattened nucleus. Term used by some histologists; when fibroblasts become relatively inactive in fiber formation. However, this cell has the potential for fibrogenesis in quiescent connective tissue of the adult, as well as during development, other histologists prefer to use the term fibroblast in all circumstances. These cells represent ~0.5% of peripheral blood leukocytes." [GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Fibrocyte, ISBN:0412046911, ISBN:0517223651, PMID:11641248, PMID:15010326, PMID:17607298, PMID:18222966, PMID:8790603, PMID:9551999] comment: Cultured human fibrocytes are MHCI-positive, MHCII-positive, CD1a-negative, CD3-negative, CD4-negative, CD8-negative, CD10-negative, CD11b-positive, CD13-positive, CD14-negative, CD16-negative, CD18-positive, CD19-negative, CD25-negative, CD29-positive, CD32-positive, CD33-negative, CD34-positive, CD38-negative, CD40-positive, CD44-negative, CD45RO-positive, CD49a-positive, CD49b-positive, CD49c-negative, CD49d-negative, CD49e-positive, CD49f-negative, CD56-negative, CD58-positive, CD61-positive, CD64-positive, CD70-negative, CD71-positive, CD80-positive, CD83-negative, CD86-positive, CD103-negative, CD105-positive, CD181-positive, CD182-negative, CD183-positive, CD184-positive, CD185-negative, CD186-negative, CD191-positive, CD192-negative, CD193-positive, CD194-positive, CD195-positive, CD196-negative, CD197-positive, CD199-positive, desmin-negative, F4/80-positive, Gr1-positive, LSP-1-positive, MHCI-positive, MHCII-positive, alpha-SMA-negative, TCRab-negative, TCRgd-negative, and vimentin-positive. Fibrocytes are also capable of secreting angiogenin, bFGF, CCL2, CCL3, CCL4, CCL8, CXCL1, type I collagen, type III collagen, CTGF, fibronectin, GM-CSF, IL-1a, IL-6, IL-8, IL-10, M-CSF, MMP-9, PDGF-A, TGF-alpha, TGF-beta1, TNF-alpha, and VEGF-A. xref: FMA:63879 is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: capable_of GO:0002495 ! antigen processing and presentation of peptide antigen via MHC class II intersection_of: capable_of GO:0045766 ! positive regulation of angiogenesis relationship: capable_of GO:0002495 ! antigen processing and presentation of peptide antigen via MHC class II relationship: capable_of GO:0045766 ! positive regulation of angiogenesis relationship: develops_from CL:0000057 ! fibroblast [Term] id: CL:0000136 name: fat cell namespace: cell alt_id: CL:0000450 def: "A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides." [MESH:A11.329.114] synonym: "adipocyte" EXACT [] synonym: "adipose cell" EXACT [] xref: BTO:0000443 xref: FMA:63880 is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0002320 ! connective tissue cell relationship: develops_from CL:0000134 ! mesenchymal cell [Term] id: CL:0000137 name: osteocyte namespace: cell def: "A mature osteoblast that has become embedded in the bone matrix. They occupy a small cavity, called lacuna, in the matrix and are connected to adjacent osteocytes via protoplasmic projections called canaliculi." [GOC:tfm, MESH:A11.329.629.500] comment: VSAO relationship simplified OBO_REL:integral_part_of VSAO:0000118 synonym: "bone cell" BROAD [] xref: BTO:0002038 xref: FMA:66779 xref: VSAO:0000124 is_a: CL:0001035 ! bone cell relationship: develops_from CL:0001040 ! non-terminally differentiated osteoblast relationship: part_of UBERON:0002481 ! bone tissue [Term] id: CL:0000138 name: chondrocyte namespace: cell def: "Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell." [GO_REF:0000034, MESH:A11.329.171] synonym: "cartilage cell" EXACT [] xref: BTO:0000249 xref: FMA:66782 is_a: CL:0000153 ! GAG secreting cell is_a: CL:0000667 ! collagen secreting cell relationship: develops_from CL:0000058 ! chondroblast [Term] id: CL:0000140 name: odontocyte namespace: cell def: "Skeletogenic cell that secretes dentine matrix, is derived from odontogenic papilla. Embedded in dentine tissue, and is the transformation of a non-terminally differentiated odontoblast cell." [GO_REF:0000034] is_a: CL:0002320 ! connective tissue cell relationship: develops_from CL:0000060 ! odontoblast relationship: develops_from CL:0000134 ! mesenchymal cell relationship: produces UBERON:0001751 ! dentine [Term] id: CL:0000141 name: cementocyte namespace: cell def: "An osteocytelike cell with numerous processes, trapped in a lacuna in the cement of the tooth." [ISBN:0781733901] comment: CHECK: wikipedia says that cementocytes no longer produce cementum, but the phenoscape def is: Skeletogenic cell that produces cementum, is part of the odontogenic papilla, and is a transformation of a cementoblast cell (no change to existing def). xref: FMA:63003 is_a: CL:0000137 ! osteocyte relationship: develops_from CL:0000061 ! cementoblast relationship: part_of UBERON:0005176 ! tooth enamel organ [Term] id: CL:0000142 name: hyalocyte namespace: cell def: "A cell occurring in the peripheral part of the vitreous body of the eye that may be responsible for production of hyaluronic acid and collagen." [GOC:tfm, PMID:19073178] synonym: "vitreous cell" RELATED [] xref: BTO:0004271 xref: FMA:70620 is_a: CL:0000499 ! stromal cell [Term] id: CL:0000143 name: guidepost cell namespace: cell is_a: CL:0000130 ! neuron associated cell (sensu Nematoda and Protostomia) [Term] id: CL:0000144 name: cell by function namespace: cell def: "A classification of cells by their primary end goal or behavior." [FB:ma] comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified by its function or behavior. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate. is_obsolete: true consider: CL:0000000 consider: CL:0000003 consider: CL:0001034 [Term] id: CL:0000145 name: professional antigen presenting cell namespace: cell def: "A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response." [GOC:add, ISBN:0781735149] comment: Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells. synonym: "APC" BROAD [] is_a: CL:0000473 ! defensive cell [Term] id: CL:0000146 name: simple columnar epithelial cell namespace: cell is_a: CL:0000075 ! columnar/cuboidal epithelial cell [Term] id: CL:0000147 name: pigment cell namespace: cell def: "A pigment cell is a cell that contains pigment granules." [GOC:tfm] synonym: "chromatocyte" EXACT [] synonym: "chromatophore" EXACT [] xref: VHOG:0001678 is_a: CL:0000325 ! stuff accumulating cell [Term] id: CL:0000148 name: melanocyte namespace: cell alt_id: CL:0000572 def: "A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance." [SANBI:mhl] synonym: "melanophore" NARROW [] xref: BTO:0000847 xref: FMA:70545 xref: VHOG:0001679 is_a: CL:0000147 ! pigment cell is_a: CL:0000710 ! neurecto-epithelial cell intersection_of: CL:0000147 ! pigment cell intersection_of: has_part GO:0042470 ! melanosome relationship: develops_from CL:0000541 ! melanoblast relationship: has_part GO:0042470 ! melanosome [Term] id: CL:0000149 name: visual pigment cell namespace: cell synonym: "pigment cell" BROAD [] is_a: CL:0000147 ! pigment cell [Term] id: CL:0000150 name: glandular epithelial cell namespace: cell def: "A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules." [GOC:tfm] xref: FMA:86494 is_a: CL:0000066 ! epithelial cell is_a: CL:0000151 ! secretory cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000151 name: secretory cell namespace: cell def: "A cell that specializes in controlled release of one or more substances." [GOC:tfm, ISBN:0721662544] xref: BTO:0003659 xref: FMA:86916 is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: capable_of GO:0032940 ! secretion by cell relationship: capable_of GO:0032940 ! secretion by cell [Term] id: CL:0000152 name: exocrine cell namespace: cell def: "A cell of an exocrine gland, i.e. a gland that discharges its secretion via a duct." [ISBN:0198547684] xref: FMA:16014 is_a: CL:0000151 ! secretory cell [Term] id: CL:0000153 name: GAG secreting cell namespace: cell def: "A cell that secretes glycosaminoglycans." [GOC:tfm] synonym: "hyaluronic acid secreting cell" EXACT [] is_a: CL:0000327 ! extracellular matrix secreting cell is_a: CL:0000447 ! carbohydrate secreting cell [Term] id: CL:0000154 name: protein secreting cell namespace: cell is_a: CL:0000151 ! secretory cell [Term] id: CL:0000155 name: peptic cell namespace: cell def: "A cell that is usually basal in position, cuboidal with round nucleus, short microvilli, secretes pepsinogen." [GOC:tfm] synonym: "chief cell of stomach" EXACT [] synonym: "gastric chief cell" EXACT [] synonym: "pepsinogen secreting cell" EXACT [] synonym: "zymogenic cell" EXACT [] xref: FMA:62902 is_a: CL:0000154 ! protein secreting cell is_a: CL:0002659 ! glandular cell of stomach [Term] id: CL:0000156 name: antibody secreting cell namespace: cell def: "OBSOLETE: A cell of the lymphoid series that can react with antigen to produce specific cell products called antibodies. Various cell subpopulations, often B cells, can be defined, based on the different classes of immunoglobulins that they synthesize." [] comment: Consider using 'B cell ; CL:0000236' or one of its children instead. is_obsolete: true [Term] id: CL:0000157 name: surfactant secreting cell namespace: cell def: "A cell that specializes in secretion of surfactant in the alveoli of the lung." [GOC:tfm, ISBN:0721662544] is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0043129 ! surfactant homeostasis relationship: capable_of GO:0043129 ! surfactant homeostasis [Term] id: CL:0000158 name: Clara cell namespace: cell def: "Epithelial progenitor cell of the lung. Clara cells are dome-shaped with short microvilli but no cilia. They function to protect the bronchiolar epithelium. Clara cells also multiply and differentiate into ciliated cells to regenerate the bronchiolar epithelium." [GOC:tfm, PMID:12107102, PMID:7905712] synonym: "bronchiolar non-ciliated cell" EXACT [] synonym: "Clara cell of bronchiole" EXACT [] xref: BTO:0004811 xref: FMA:14119 is_a: CL:0000157 ! surfactant secreting cell is_a: CL:0002328 ! bronchial epithelial cell intersection_of: CL:0002328 ! bronchial epithelial cell intersection_of: capable_of GO:0032940 ! secretion by cell intersection_of: capable_of GO:0043129 ! surfactant homeostasis intersection_of: has_plasma_membrane_part GO:0005902 ! microvillus intersection_of: has_quality PATO:0001789 ! domed relationship: capable_of GO:0032940 ! secretion by cell relationship: capable_of GO:0043129 ! surfactant homeostasis relationship: has_plasma_membrane_part GO:0005902 ! microvillus relationship: has_quality PATO:0001789 ! domed [Term] id: CL:0000159 name: seromucus secreting cell namespace: cell is_a: CL:0000151 ! secretory cell [Term] id: CL:0000160 name: goblet cell namespace: cell def: "A cell of the epithelial lining that produce and secrete mucins." [MESH:A03.492.411.369.320] synonym: "chalice cell" EXACT [] xref: BTO:0001540 xref: FMA:13148 is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000319 ! mucus secreting cell [Term] id: CL:0000161 name: acid secreting cell namespace: cell is_a: CL:0000151 ! secretory cell [Term] id: CL:0000162 name: parietal cell namespace: cell def: "A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl." [GOC:tfm, ISBN:0517223651] synonym: "oxyntic cell" EXACT [] xref: BTO:0001780 xref: FMA:62901 is_a: CL:0000161 ! acid secreting cell is_a: CL:0002659 ! glandular cell of stomach [Term] id: CL:0000163 name: endocrine cell namespace: cell def: "A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions." [MESH:A06.407] synonym: "endocrinocyte" EXACT [] xref: FMA:83809 is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0046879 ! hormone secretion relationship: capable_of GO:0046879 ! hormone secretion [Term] id: CL:0000164 name: enteroendocrine cell namespace: cell def: "An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas." [GOC:tfm, SANBI:mhl] xref: BTO:0003865 xref: FMA:62930 is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000163 ! endocrine cell [Term] id: CL:0000165 name: neuroendocrine cell namespace: cell def: "An endocrine cell that has the specialized function to produce and secrete hormones in response to neuronal signals." [MESH:A06.688] synonym: "neurosecretory cell" EXACT [] xref: BTO:0002691 xref: FMA:83810 is_a: CL:0000163 ! endocrine cell is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000710 ! neurecto-epithelial cell [Term] id: CL:0000166 name: chromaffin cell namespace: cell def: "A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system." [MESH:A06.224.161] synonym: "phaeochromocyte" EXACT [] xref: BTO:0000259 xref: FMA:69263 is_a: CL:0000568 ! APUD cell relationship: develops_from CL:0000333 ! migratory neural crest cell [Term] id: CL:0000167 name: peptide hormone secreting cell namespace: cell is_a: CL:0000163 ! endocrine cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0030072 ! peptide hormone secretion relationship: capable_of GO:0030072 ! peptide hormone secretion [Term] id: CL:0000168 name: insulin secreting cell namespace: cell xref: BTO:0000783 is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0030073 ! insulin secretion relationship: capable_of GO:0030073 ! insulin secretion [Term] id: CL:0000169 name: type B pancreatic cell namespace: cell def: "A cell that secretes insulin and is located towards the center of the islets of Langerhans." [GOC:tfm, http://en.wikipedia.org/wiki/Pancreatic_b_cell, ISBN:0517223651] comment: Pancreatic beta cells are also reportedly CD284-positive. Upon activation, they upregulate their CD14 expression. synonym: "B-cell of pancreatic islet" EXACT [FMA:70586] synonym: "beta cell" BROAD [ZFA:0009102] synonym: "beta cell islet" RELATED [MA:0002419] synonym: "beta cell of pancreatic islet" EXACT [FMA:70586] synonym: "insulin-secreting cell" EXACT [FMA:70586] synonym: "pancreatic B cell" EXACT [] synonym: "pancreatic B-cell" EXACT [FMA:70586] synonym: "pancreatic beta cell" EXACT [FMA:70586] synonym: "pancreatic islet core" EXACT [MA:0002419] synonym: "type B enteroendocrine cell" EXACT [FMA:70586] xref: BTO:0000783 xref: EV:0200009 xref: FMA:70586 xref: MA:0002419 xref: ncithesaurus:Beta_Cell is_a: CL:0000083 ! epithelial cell of pancreas is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000168 ! insulin secreting cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: capable_of GO:0030073 ! insulin secretion intersection_of: part_of UBERON:0000006 ! islet of Langerhans relationship: capable_of GO:0030073 ! insulin secretion relationship: develops_from CL:0002351 ! progenitor cell of endocrine pancreas relationship: part_of UBERON:0000006 ! islet of Langerhans [Term] id: CL:0000170 name: glucagon secreting cell namespace: cell def: "A cell that secretes glucagon." [GOC:tfm] synonym: "glucagon-secreting cell" EXACT [] xref: FMA:84045 is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0070091 ! glucagon secretion relationship: capable_of GO:0070091 ! glucagon secretion [Term] id: CL:0000171 name: pancreatic A cell namespace: cell def: "A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon." [GOC:tfm, ISBN:0721662544] synonym: "alpha cell of iselt of Langerhans" EXACT [] synonym: "pancreatic alpha cell" EXACT [] xref: BTO:0000990 xref: FMA:70585 is_a: CL:0002067 ! type A enterocrine cell relationship: capable_of GO:0070091 ! glucagon secretion relationship: develops_from CL:0002351 ! progenitor cell of endocrine pancreas [Term] id: CL:0000172 name: somatostatin secreting cell namespace: cell is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0070253 ! somatostatin secretion relationship: capable_of GO:0070253 ! somatostatin secretion [Term] id: CL:0000173 name: pancreatic D cell namespace: cell def: "A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin." [FMA:0517223651, GOC:tfm] synonym: "D-cell of pancreatic islet" EXACT [] synonym: "delta cell of islet" EXACT [] synonym: "delta cell of pancreatic islet" EXACT [] synonym: "pancreatic D-cell" EXACT [] synonym: "pancreatic delta cell" EXACT [] synonym: "somatostatin-secreting pancreatic cell" EXACT [] xref: BTO:0000803 xref: FMA:70587 is_a: CL:0000502 ! type D enteroendocrine cell relationship: develops_from CL:0002351 ! progenitor cell of endocrine pancreas [Term] id: CL:0000174 name: steroid hormone secreting cell namespace: cell is_a: CL:0000163 ! endocrine cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0035929 ! steroid hormone secretion relationship: capable_of GO:0035929 ! steroid hormone secretion [Term] id: CL:0000175 name: luteal cell namespace: cell def: "A progesterone secreting cell in the corpus luteum. The large luteal cells develop from the granulosa cells. The small luteal cells develop from the theca cells." [MESH:A05.360.319.114.630.278.400] synonym: "lutein cell" EXACT [] xref: BTO:0003939 xref: FMA:18688 is_a: CL:0000179 ! progesterone secreting cell is_a: CL:0002132 ! stromal cell of ovary relationship: capable_of GO:0042701 ! progesterone secretion relationship: part_of UBERON:0002512 ! corpus luteum [Term] id: CL:0000176 name: ecdysteroid secreting cell namespace: cell is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0045457 ! ecdysteroid secretion relationship: capable_of GO:0045457 ! ecdysteroid secretion [Term] id: CL:0000177 name: testosterone secreting cell namespace: cell is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0035936 ! testosterone secretion relationship: capable_of GO:0035936 ! testosterone secretion [Term] id: CL:0000178 name: Leydig cell namespace: cell def: "A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis." [GOC:tfm, PMID:12050120] comment: Note that the Amphibian Anatomy Ontology (AA) has a class 'leydig cells' but this is unrelated synonym: "interstitial cell" BROAD [] synonym: "interstitial cell of Leydig" EXACT [] xref: BTO:0000755 xref: EMAPA:29655 xref: FMA:72297 is_a: CL:0000177 ! testosterone secreting cell relationship: part_of UBERON:0005212 ! testis interstitial tissue [Term] id: CL:0000179 name: progesterone secreting cell namespace: cell is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0042701 ! progesterone secretion relationship: capable_of GO:0042701 ! progesterone secretion [Term] id: CL:0000180 name: estradiol secreting cell namespace: cell is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0035938 ! estradiol secretion relationship: capable_of GO:0035938 ! estradiol secretion [Term] id: CL:0000181 name: metabolising cell namespace: cell def: "A cell whose primary function is intermediary metabolism." [FB:ma] is_a: CL:0000003 ! native cell [Term] id: CL:0000182 name: hepatocyte namespace: cell def: "The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated." [GOC:tfm, http://en.wikipedia.org/wiki/Hepatocyte, ISBN:0412046911, MESH:A11.436.348, PMID:19717280] comment: Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive. xref: BTO:0000575 xref: FMA:14515 is_a: CL:0000066 ! epithelial cell is_a: CL:0000181 ! metabolising cell is_a: CL:0000417 ! endopolyploid cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002107 ! liver relationship: develops_from CL:0000134 ! mesenchymal cell relationship: develops_from CL:0000223 ! endodermal cell relationship: part_of UBERON:0002107 ! liver [Term] id: CL:0000183 name: contractile cell namespace: cell def: "A cell whose primary function is to shorten." [FB:ma] is_a: CL:0000003 ! native cell [Term] id: CL:0000185 name: myoepithelial cell namespace: cell def: "Contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament." [GOC:tfm, ISBN:0721662544] synonym: "basket epithelial cell" EXACT [] synonym: "myoepitheliocyte" EXACT [] xref: BTO:0002309 xref: FMA:67799 is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0000183 ! contractile cell relationship: develops_from CL:0000222 ! mesodermal cell [Term] id: CL:0000186 name: myofibroblast cell namespace: cell def: "An animal cell that has characteristics of both a fibroblast cell and a smooth muscle cell." [GOC:dsd, GOC:tfm, MESH:D058628, PMID:19800625, PMID:20630469] comment: Myofibroblasts are alpha-SMA-positive, CD34-negative, CD45-negative. They are reportedly capable of secreting IL-1beta, IL-6, and TNF-alpha. synonym: "MFB" EXACT [PMID:8731193] is_a: CL:0000183 ! contractile cell is_a: CL:0000548 ! animal cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000187 name: muscle cell namespace: cell def: "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." [MESH:A11.620] synonym: "muscle fiber" EXACT [] synonym: "myocyte" EXACT [] xref: BTO:0000888 xref: BTO:0000902 xref: FBbt:00005074 xref: FMA:67328 xref: WBbt:0003675 is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000548 ! animal cell is_a: CL:0002371 ! somatic cell relationship: develops_from CL:0000056 ! myoblast [Term] id: CL:0000188 name: skeletal muscle cell namespace: cell def: "A somatic cell located in skeletal muscle." [GOC:tfm] xref: BTO:0004392 xref: FMA:9727 is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue relationship: part_of UBERON:0001134 ! skeletal muscle tissue [Term] id: CL:0000189 name: slow muscle cell namespace: cell def: "A muscle cell that develops tension more slowly than a fast-twitch fiber." [GOC:tfm, ISBN:0323052908] synonym: "slow muscle fiber" EXACT [ISBN:0815316208] xref: FMA:84448 is_a: CL:0002372 ! myotube relationship: develops_from CL:0000857 ! slow muscle myoblast [Term] id: CL:0000190 name: fast muscle cell namespace: cell def: "A muscle cell that can develop high tension rapidly. It is usually innervated by a single alpha neuron ." [GOC:tfm, ISBN:0323052908] synonym: "glycolytic muscle fiber" EXACT [] is_a: CL:0002372 ! myotube relationship: develops_from CL:0000858 ! fast muscle myoblast [Term] id: CL:0000192 name: smooth muscle cell namespace: cell alt_id: CL:0000191 def: "A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast)." [http://en.wikipedia.org/wiki/Smooth_muscle_cell, MESH:A11.620.520, MESH:D032389, PMID:9315361] synonym: "myocytes, smooth muscle" EXACT [MESH:D032389] synonym: "non-striated muscle cell" EXACT [] synonym: "SMCs" EXACT [PMID:9315361] synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: FMA:14072 is_a: CL:0000187 ! muscle cell relationship: develops_from CL:0000514 ! smooth muscle myoblast [Term] id: CL:0000193 name: cardiac muscle cell (sensu Arthopoda) namespace: cell alt_id: CL:0000466 def: "A striated muscle cell found in the heart. They develop from cardiac myoblasts." [MESH:A11.620.500] is_a: CL:0000228 ! multinucleate cell is_a: CL:0000746 ! cardiac muscle cell relationship: develops_from CL:0000465 ! cardioblast (sensu Arthropoda) [Term] id: CL:0000194 name: nodal cardiac cell namespace: cell comment: Consider CL:0002072. is_obsolete: true [Term] id: CL:0000195 name: Purkinje fiber namespace: cell is_obsolete: true [Term] id: CL:0000196 name: flight muscle cell namespace: cell is_a: CL:0000187 ! muscle cell is_a: CL:0000228 ! multinucleate cell [Term] id: CL:0000197 name: receptor cell namespace: cell is_a: CL:0000003 ! native cell [Term] id: CL:0000198 name: pain receptor cell namespace: cell def: "The peripheral receptor for pain. Includes receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. All mammalian nociceptors are free nerve endings." [MESH:A08.800.550.700.650] comment: Editor note: request detection of stimulus involved in sensory perception of pain; add develops_from relationship synonym: "nociceptor" EXACT [] synonym: "nocireceptor" EXACT [] is_a: CL:0000006 ! neuronal receptor cell [Term] id: CL:0000199 name: mechanoreceptor cell namespace: cell def: "A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system." [MESH:A08.800.550.700.500] synonym: "mechanoreceptor" EXACT [MP:0000972] is_a: CL:0000006 ! neuronal receptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050974 ! detection of mechanical stimulus involved in sensory perception relationship: capable_of GO:0050974 ! detection of mechanical stimulus involved in sensory perception [Term] id: CL:0000200 name: touch receptor cell namespace: cell is_a: CL:0000199 ! mechanoreceptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050976 ! detection of mechanical stimulus involved in sensory perception of touch relationship: capable_of GO:0050976 ! detection of mechanical stimulus involved in sensory perception of touch [Term] id: CL:0000202 name: auditory hair cell namespace: cell alt_id: CL:0000201 def: "A mechanoreceptor cell located in the inner ear that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system." [MESH:A08.663.650.250] comment: In mammals these cells are located in the organ of Corti. synonym: "auditory receptor cell" EXACT [] synonym: "cochlear hair cell" EXACT [] synonym: "inner ear hair cell" EXACT [GO:0060119] synonym: "inner ear receptor cell" EXACT [GO:0060119] xref: FMA:62364 is_a: CL:0001035 ! bone cell is_a: CL:0002374 ! ear hair cell is_a: CL:0002491 ! auditory epithelial cell relationship: capable_of GO:0050910 ! detection of mechanical stimulus involved in sensory perception of sound relationship: part_of UBERON:0002227 ! spiral organ of cochlea [Term] id: CL:0000203 name: gravity sensitive cell namespace: cell is_a: CL:0000199 ! mechanoreceptor cell intersection_of: CL:0000006 ! neuronal receptor cell intersection_of: capable_of GO:0070999 ! detection of mechanical stimulus involved in sensory perception of gravity relationship: capable_of GO:0070999 ! detection of mechanical stimulus involved in sensory perception of gravity [Term] id: CL:0000204 name: acceleration receptive cell namespace: cell is_a: CL:0000006 ! neuronal receptor cell [Term] id: CL:0000205 name: thermoreceptor cell namespace: cell def: "A cellular receptor which mediates the sense of temperature. Thermoreceptor cells in vertebrates are mostly located under the skin. In mammals there are separate types of thermoreceptors for cold and for warmth and pain receptor cells which detect cold or heat extreme enough to cause pain." [GOC:tfm, MESH:A08.800.550.700.840, MP:0000971] is_a: CL:0000006 ! neuronal receptor cell intersection_of: CL:0000006 ! neuronal receptor cell intersection_of: capable_of GO:0050960 ! detection of temperature stimulus involved in thermoception relationship: capable_of GO:0050960 ! detection of temperature stimulus involved in thermoception [Term] id: CL:0000206 name: chemoreceptor cell namespace: cell def: "A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood." [MESH:A08.800.550.700.120] is_a: CL:0000006 ! neuronal receptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050907 ! detection of chemical stimulus involved in sensory perception relationship: capable_of GO:0050907 ! detection of chemical stimulus involved in sensory perception [Term] id: CL:0000207 name: olfactory receptor cell namespace: cell synonym: "olfactory receptor neuron" EXACT [] synonym: "olfactory sensory neuron" EXACT [] synonym: "Schultze's cell" EXACT [] xref: BTO:0004185 xref: FMA:67860 is_a: CL:0000206 ! chemoreceptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050911 ! detection of chemical stimulus involved in sensory perception of smell relationship: capable_of GO:0050911 ! detection of chemical stimulus involved in sensory perception of smell [Term] id: CL:0000208 name: pH receptor cell namespace: cell is_a: CL:0000206 ! chemoreceptor cell [Term] id: CL:0000209 name: taste receptor cell namespace: cell def: "A cell type found in the spherical or ovoid clusters of receptor cells found mainly in the epithelium of the tongue and constituting the end organs of the sense of taste." [GOC:tfm, ISBN:0618947256] synonym: "taste bud cell" EXACT [] xref: FMA:67910 is_a: CL:0000098 ! sensory epithelial cell is_a: CL:0000206 ! chemoreceptor cell is_a: CL:0002076 ! endo-epithelial cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050912 ! detection of chemical stimulus involved in sensory perception of taste relationship: capable_of GO:0050912 ! detection of chemical stimulus involved in sensory perception of taste [Term] id: CL:0000210 name: photoreceptor cell namespace: cell def: "A cell specialized to detect and transduce light." [MESH:A08.663.650.650] xref: BTO:0001060 xref: FBbt:00004211 xref: FMA:86740 is_a: CL:0000006 ! neuronal receptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception [Term] id: CL:0000211 name: electrically active cell namespace: cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] is_a: CL:0000003 ! native cell [Term] id: CL:0000212 name: absorptive cell namespace: cell def: "A cell that takes up and metabolizes substances." [CL:CVS] is_a: CL:0000003 ! native cell [Term] id: CL:0000213 name: lining cell namespace: cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] synonym: "boundary cell" EXACT [] is_a: CL:0000215 ! barrier cell [Term] id: CL:0000214 name: synovial cell namespace: cell def: "A meso-epithelial cell that lies between the cartilaginous fibers in the synovial membrane of a joint and produces hyaluronic acid." [GOC:tfm, ISBN:0721662544, PMID:17942474] synonym: "hyaluronic acid secreting cell" EXACT [] synonym: "synoviocyte" EXACT [] xref: BTO:0003652 xref: FMA:66786 is_a: CL:0000153 ! GAG secreting cell is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell intersection_of: CL:0002078 ! meso-epithelial cell intersection_of: part_of UBERON:0002018 ! synovial membrane of synovial joint relationship: part_of UBERON:0002018 ! synovial membrane of synovial joint [Term] id: CL:0000215 name: barrier cell namespace: cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] is_a: CL:0000003 ! native cell [Term] id: CL:0000216 name: Sertoli cell namespace: cell def: "A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier." [MESH:A05.360.444.849.789] xref: BTO:0001238 xref: FMA:72298 xref: VHOG:0001348 is_a: CL:0000511 ! androgen binding protein secreting cell is_a: CL:0000630 ! supportive cell is_a: CL:0002625 ! seminiferous tubule epithelial cell intersection_of: CL:0000630 ! supportive cell intersection_of: part_of UBERON:0001343 ! seminiferous tubule of testis relationship: part_of UBERON:0001343 ! seminiferous tubule of testis [Term] id: CL:0000217 name: insulating cell namespace: cell is_a: CL:0000215 ! barrier cell [Term] id: CL:0000218 name: myelinating Schwann cell namespace: cell def: "A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons." [GOC:cvs, GOC:tfm, MESH:A08.637.800] synonym: "neurilemmal cell" EXACT [] synonym: "peripheral neuroglial cell" BROAD [] synonym: "Schwann cell" BROAD [] xref: FMA:62121 is_a: CL:0000217 ! insulating cell is_a: CL:0000328 ! myelin accumulating cell is_a: CL:0002573 ! Schwann cell relationship: develops_from CL:0002377 ! immature Schwann cell [Term] id: CL:0000219 name: motile cell namespace: cell def: "A cell that moves by its own activities." [FB:ma] is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: capable_of GO:0048870 ! cell motility relationship: capable_of GO:0048870 ! cell motility [Term] id: CL:0000220 name: cell by lineage namespace: cell comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell in a multicellular organiam, apart from a zygote, can potentially be classified by its lineage. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate. is_obsolete: true consider: CL:0000000 consider: CL:0000003 consider: CL:0001034 [Term] id: CL:0000221 name: ectodermal cell namespace: cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:A16.254.425.273] synonym: "ectoderm cell" EXACT [] xref: FMA:72549 is_a: CL:0002321 ! embryonic cell relationship: part_of UBERON:0000924 ! ectoderm [Term] id: CL:0000222 name: mesodermal cell namespace: cell def: "A cell of the middle germ layer of the embryo." [MESH:A16.254.425.660] synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 is_a: CL:0002321 ! embryonic cell relationship: part_of UBERON:0000926 ! mesoderm [Term] id: CL:0000223 name: endodermal cell namespace: cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:A16.254.425.407] synonym: "endoderm cell" EXACT [] xref: FMA:72555 is_a: CL:0002321 ! embryonic cell relationship: part_of UBERON:0000925 ! endoderm [Term] id: CL:0000224 name: cell by nuclear number namespace: cell def: "A classification of cells by the number of their nuclei." [FB:ma, GOC:tfm] comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified by its nuclear number (note that this term was previously used as a parent class of enucleate cell). If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate. is_obsolete: true consider: CL:0000000 consider: CL:0000003 consider: CL:0001034 [Term] id: CL:0000225 name: anucleate cell namespace: cell def: "A cell that lacks a nucleus." [FB:ma] synonym: "non-nucleated cell" EXACT [] xref: FMA:68647 is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: has_quality PATO:0001405 ! anucleate relationship: has_quality PATO:0001405 ! anucleate [Term] id: CL:0000226 name: single nucleate cell namespace: cell def: "A cell with a single nucleus." [FB:ma, GOC:tfm] is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: has_quality PATO:0001407 ! mononucleate relationship: has_quality PATO:0001407 ! mononucleate [Term] id: CL:0000227 name: binucleate cell namespace: cell is_a: CL:0000228 ! multinucleate cell intersection_of: CL:0000003 ! native cell intersection_of: has_quality PATO:0001406 ! binucleate relationship: has_quality PATO:0001406 ! binucleate [Term] id: CL:0000228 name: multinucleate cell namespace: cell def: "A cell with more than one nucleus." [FB:ma] synonym: "syncitium" EXACT [] synonym: "syncytial cell" EXACT [] synonym: "syncytium" EXACT [] xref: AEO:0000203 xref: WBbt:0008074 is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: has_quality PATO:0001908 ! multinucleate relationship: has_quality PATO:0001908 ! multinucleate [Term] id: CL:0000229 name: lymphoblast namespace: cell def: "OBSOLETE (was not defined before being made obsolete)." [] comment: Refers to an activated mature lymphocyte phenotype rather than a distinct cell type; consider using 'lymphocyte ; CL:0000542' or one of its children instead. is_obsolete: true [Term] id: CL:0000230 name: T lymphoblast namespace: cell def: "OBSOLETE (was not defined before being made obsolete)." [] comment: Refers to an activated mature T lymphocyte phenotype rather than a distinct cell type; consider using 'T cell ; CL:0000084' or one of its children instead. is_obsolete: true [Term] id: CL:0000231 name: B lymphoblast namespace: cell def: "OBSOLETE (was not defined before being made obsolete)." [] comment: Refers to an activated mature B lymphocyte phenotype rather than a distinct cell type; consider using 'B cell ; CL:0000236' or one of its children instead. is_obsolete: true [Term] id: CL:0000232 name: erythrocyte namespace: cell def: "A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen." [GOC:tfm, MESH:A11.118.290] synonym: "RBC" EXACT [] synonym: "red blood cell" EXACT [] xref: BTO:0000424 xref: FMA:81100 is_a: CL:0000081 ! blood cell is_a: CL:0000329 ! oxygen accumulating cell is_a: CL:0000764 ! erythroid lineage cell intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0008015 ! blood circulation intersection_of: capable_of GO:0015671 ! oxygen transport intersection_of: has_quality PATO:0002039 ! biconcave intersection_of: lacks_part GO:0005840 ! ribosome intersection_of: lacks_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 relationship: capable_of GO:0008015 ! blood circulation relationship: capable_of GO:0015671 ! oxygen transport relationship: develops_from CL:0000558 ! reticulocyte relationship: has_quality PATO:0002039 ! biconcave relationship: lacks_part GO:0005840 ! ribosome relationship: lacks_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 [Term] id: CL:0000233 name: platelet namespace: cell def: "A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation." [GOC:add, GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Platelet, MESH:A11.118.188, MESH:D001792, PMID:11110672, PMID:16987572, PMID:17204662, PMID:17479180, PMID:20414831] comment: Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, CCR4-positive, CCR5-negative, CCR6-negative, CCR7-negative, CCR8-negative, CCR9-negative, CCR10-negative, CD16-positive, CD23-positive, CD32-positive, CD40-positive, CD41-positive CD42-positive, CD61-positive, CD62P-positive, CD64-positive, CD89-positive, CD102-positive, CD147-positive (activated platelets), CD154-positive (activated platelets), CD162-positive, CD209, CD282-positive, CD284-positive, CD289-positive, CD181-negative, CD182-negative, CD183-negative, CD184-positive, CLEC2-positive, GPVI-positive, JAMC-positive, PAR1-positive, PAR2-negative, PAR3-positive, PAR4-positive, TSP1-positive, and TXA2R-positive. Platelets can reportedly produce CCL2, CCL3, CCL5, CCL7, CCL17, CD40L, CXCL1, CXCL4, CXCL4L1, CXCL5, CXCL7, CXCL8, CXCL12, EGF, factor V, factor VII, factor XI, factor XIII, bFGF, histamine, IGF-1, IL-1beta, PAI-1, PDGF, plasminogen, protein S, serotonin, TGF-beta, TFPI, VEGF, and vWF. synonym: "anucleate thrombocyte" EXACT [] synonym: "blood platelet" EXACT [] synonym: "enucleate thrombocyte" EXACT [] xref: BTO:0000132 xref: FMA:62851 is_a: CL:0000081 ! blood cell is_a: CL:0000225 ! anucleate cell is_a: CL:0000458 ! serotonin secreting cell is_a: CL:0000763 ! myeloid cell intersection_of: CL:0000763 ! myeloid cell intersection_of: capable_of GO:0007596 ! blood coagulation intersection_of: capable_of GO:0008015 ! blood circulation intersection_of: has_quality PATO:0001405 ! anucleate intersection_of: has_quality PATO:0001874 ! discoid relationship: capable_of GO:0007596 ! blood coagulation relationship: capable_of GO:0008015 ! blood circulation relationship: develops_from CL:0000556 ! megakaryocyte relationship: has_quality PATO:0001405 ! anucleate relationship: has_quality PATO:0001874 ! discoid [Term] id: CL:0000234 name: phagocyte namespace: cell def: "Any cell capable of ingesting particulate matter via phagocytosis." [GOC:add, ISBN:0721601464] xref: BTO:0001044 xref: FMA:83806 is_a: CL:0000219 ! motile cell is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0000473 ! defensive cell intersection_of: CL:0000003 ! native cell intersection_of: capable_of GO:0006909 ! phagocytosis relationship: capable_of GO:0006909 ! phagocytosis [Term] id: CL:0000235 name: macrophage namespace: cell def: "A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells." [GO_REF:0000031, GOC:add, GOC:tfm, PMID:16213494, PMID:1919437] comment: Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid. synonym: "histiocyte" EXACT [] xref: BTO:0000801 xref: FMA:63261 xref: FMA:83585 is_a: CL:0000234 ! phagocyte is_a: CL:0000766 ! myeloid leukocyte intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0006909 ! phagocytosis intersection_of: capable_of GO:0031268 ! pseudopodium organization relationship: capable_of GO:0006909 ! phagocytosis relationship: capable_of GO:0031268 ! pseudopodium organization relationship: develops_from CL:0000576 ! monocyte [Term] id: CL:0000236 name: B cell namespace: cell def: "A lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149] synonym: "B lymphocyte" EXACT [] synonym: "B-cell" EXACT [] synonym: "B-lymphocyte" EXACT [] xref: BTO:0000776 xref: FMA:62869 xref: VHOG:0001480 is_a: CL:0000945 ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: capable_of GO:0019724 ! B cell mediated immunity relationship: capable_of GO:0019724 ! B cell mediated immunity relationship: develops_from CL:0000826 ! pro-B cell [Term] id: CL:0000237 name: keratinizing barrier epithelial cell namespace: cell is_a: CL:0000240 ! stratified squamous epithelial cell is_a: CL:0000311 ! keratin accumulating cell relationship: develops_from CL:0000114 ! surface ectodermal cell [Term] id: CL:0000238 name: non keratinizing barrier epithelial cell namespace: cell is_a: CL:0000240 ! stratified squamous epithelial cell [Term] id: CL:0000239 name: brush border epithelial cell namespace: cell is_a: CL:0000075 ! columnar/cuboidal epithelial cell [Term] id: CL:0000240 name: stratified squamous epithelial cell namespace: cell is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000079 ! stratified epithelial cell [Term] id: CL:0000241 name: stratified cuboidal epithelial cell namespace: cell is_a: CL:0000079 ! stratified epithelial cell [Term] id: CL:0000242 name: Merkel cell namespace: cell def: "A modified epidermal cell located in the stratum basale. They are found mostly in areas where sensory perception is acute. Merkel cells are closely associated with an expanded terminal bulb of an afferent myelinated nerve fiber." [MESH:A08.800.550.700.500.425] synonym: "Merkel's cell" EXACT [] xref: FMA:70548 is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) is_a: CL:0000312 ! keratinocyte [Term] id: CL:0000243 name: glial cell (sensu Vertebrata) namespace: cell def: "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Form the myelin insulation of nervous pathways, guide neuronal migration during development, and exchange metabolites with neurons. Neuroglia have high-affinity transmitter uptake systems, voltage-dependent and transmitter-gated ion channels, and can release transmitters, but their role in signaling (as in many other functions) is unclear." [MESH:A08.637] is_a: CL:0000125 ! glial cell relationship: develops_from CL:0000339 ! glioblast (sensu Vertebrata) [Term] id: CL:0000244 name: transitional epithelial cell namespace: cell def: "A cell characteristically found lining hollow organs that are subject to great mechanical change due to contraction and distention; originally thought to represent a transition between stratified squamous and columnar epithelium." [GOC:tfm, ISBN:0721662544] xref: FMA:66778 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000245 name: passage cell namespace: cell def: "Obsolete. Use PO:0000353 from Plant Ontology instead. Cell in exodermis or endodermis that remains thin walled when the associated cells develop thick secondary walls. Has casparian strip in endodermis." [ISBN:0471245208] comment: replaced_by: PO:0000353 is_obsolete: true [Term] id: CL:0000246 name: Mauthner neuron namespace: cell is_a: CL:0000099 ! interneuron [Term] id: CL:0000247 name: Rohon-Beard neuron namespace: cell def: "Type of neuron that is a primary mechanosensory cell, with peripheral neurites innervating the skin with free nerve endings." [VHOG:0001484] synonym: "RB neuron" RELATED [VHOG:0001484] synonym: "Rohon Beard cell" EXACT [VHOG:0001484] synonym: "Rohon-Beard cell" EXACT [] xref: AAO:0010316 xref: EFO:0003711 xref: VHOG:0001484 is_a: CL:0000531 ! primary sensory neuron [Term] id: CL:0000248 name: microsporocyte namespace: cell def: "Obsolete. Use PO:0020047 from Plant Ontology instead. A diploid (2n) cell that undergoes meiosis and forms four haploid (1n) microspores; also called microspore mother cell and, in seed plants, pollen mother cell." [ISBN:0471245208] comment: replaced_by: PO:0020047 synonym: "pollen mother cell" EXACT [] synonym: "primary sporogenous cell" EXACT [] is_obsolete: true [Term] id: CL:0000249 name: hatching gland cell namespace: cell is_a: CL:0000151 ! secretory cell [Term] id: CL:0000250 name: megaspore namespace: cell def: "Obsolete. Use PO:0020019 from Plant Ontology instead. A haploid (1n) spore developing into a female gametophyte in heterosporous plants." [ISBN:0471245208] comment: replaced_by: PO:0020019 is_obsolete: true [Term] id: CL:0000251 name: extramedullary cell namespace: cell is_a: CL:0000101 ! sensory neuron [Term] id: CL:0000252 name: microspore namespace: cell def: "Obsolete. Use PO:0020048 from Plant Ontology instead. A haploid (1n) spore developing into a male gametophyte in heterosporous plants; the uninucleate pollen grain in seed plants." [ISBN:0471245208] comment: replaced_by: PO:0020048 is_obsolete: true [Term] id: CL:0000253 name: eurydendroid cell namespace: cell is_a: CL:0000527 ! efferent neuron [Term] id: CL:0000254 name: egg cell namespace: cell def: "Obsolete. Use PO:0020094 from Plant Ontology instead. The female gamete of plants." [TAIR:lr] comment: replaced_by: PO:0020094 synonym: "female gametophyte egg cell" EXACT [] is_obsolete: true [Term] id: CL:0000255 name: eukaryotic cell namespace: cell is_a: CL:0000003 ! native cell disjoint_from: CL:0000520 ! prokaryotic cell [Term] id: CL:0000256 name: uric acid accumulating cell namespace: cell is_a: CL:0000325 ! stuff accumulating cell [Term] id: CL:0000257 name: Mycetozoan cell namespace: cell is_a: CL:0000255 ! eukaryotic cell [Term] id: CL:0000258 name: fiber tracheid namespace: cell def: "Obsolete. Use PO:0000355 from Plant Ontology instead. A fiber like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit like apertures." [ISBN:0471245208] comment: replaced_by: PO:0000355 is_obsolete: true [Term] id: CL:0000259 name: aggregate cell namespace: cell def: "Differentiating cell composing the aggregate that has acquired adhesive properties." [DictyBase:DDB] is_a: CL:0000263 ! vegetative cell (sensu Mycetozoa) [Term] id: CL:0000260 name: mucilage cell namespace: cell def: "Obsolete. Use PO:0000373 from Plant Ontology instead. Cell containing mucilages or gums or similar carbohydrate material characterized by the property of swelling in water." [ISBN:0471245208] comment: replaced_by: PO:0000373 is_obsolete: true [Term] id: CL:0000261 name: anterior cell namespace: cell is_a: CL:0000263 ! vegetative cell (sensu Mycetozoa) [Term] id: CL:0000262 name: guard mother cell namespace: cell def: "Obsolete. Use PO:0000351 from Plant Ontology instead. An epidermal cell that divides to produce the guard cells." [ISBN:0471245208] comment: replaced_by: PO:0000351 is_obsolete: true [Term] id: CL:0000263 name: vegetative cell (sensu Mycetozoa) namespace: cell def: "Unicellular haploid myxamoebae that feeds on bacteria and divides by binary fission." [DictyBase:DDB] synonym: "amoeba" EXACT [] is_a: CL:0000257 ! Mycetozoan cell [Term] id: CL:0000264 name: phloem initial namespace: cell def: "Obsolete. Use PO:0000400 from Plant Ontology instead. A cambial cell on the phloem side of the cambial zone that is the source of one or more cells arising by periclinal divisions and differentiating into phloem elements with or without additional divisions in various planes." [ISBN:0471245208] comment: replaced_by: PO:0000400 synonym: "phloem mother cell" EXACT [] is_obsolete: true [Term] id: CL:0000265 name: anterior like cell namespace: cell def: "Cell that has properties of anterior cells (for e.g., accumulate vital dyes in autophagic vesicles) but that is are scattered throughout the rear of the slug. Some but not all these cells express the ecmA gene and/or the ecmB gene. ALCs maintain an amoeboid appearance during culmination. ALCs that express the ecmO promoter have been called pstO/ALC." [DictyBase:DDB] synonym: "ALC" EXACT [] is_a: CL:0000263 ! vegetative cell (sensu Mycetozoa) [Term] id: CL:0000266 name: meristemoid namespace: cell def: "Obsolete. Use PO:0004011 from Plant Ontology instead. A cell constituting an active locus of meristematic activity in a tissue composed of somewhat older, differentiating cells." [ISBN:0471245208] comment: replaced_by: PO:0004011 is_obsolete: true [Term] id: CL:0000267 name: prespore cell namespace: cell def: "Cell that is undergoing differentiation to become a spore." [DictyBase:DDB] is_a: CL:0000263 ! vegetative cell (sensu Mycetozoa) [Term] id: CL:0000268 name: sieve element namespace: cell def: "Obsolete. Consult Plant Ontology instead. The cell in the phloem tissue concerned with mainly longitudinal conduction of food materials. Classified into sieve cell and sieve tube member." [ISBN:0471245208] is_obsolete: true [Term] id: CL:0000269 name: prestalk cell namespace: cell is_a: CL:0000263 ! vegetative cell (sensu Mycetozoa) [Term] id: CL:0000270 name: subsidiary cell namespace: cell def: "Obsolete. Use PO:0000284 from Plant Ontology instead. An epidermal cell associated with a stoma and at least morphologically distinguishable from the epidermal cells composing the groundmass of the tissue." [ISBN:047124520] comment: replaced_by: PO:0000284 is_obsolete: true [Term] id: CL:0000271 name: prestalk A cell namespace: cell def: "Cell expressing the ecmA marker from a promoter region that is proximal to the ATG (ecmAO promoter). They are located at the anterior-most region of the slug. During culmination pstA cells differentiate into pstAB cells." [DictyBase:DDB] synonym: "pstA" EXACT [] synonym: "pstAO" EXACT [] is_a: CL:0000269 ! prestalk cell [Term] id: CL:0000272 name: cambial initial namespace: cell def: "OBSOLETE, use term from Plant Ontology. A cell localized in the vascular cambium or phellogen. Its periclinal division can contribute cells either to the outside or to the inside of the axis; in vascular cambium, classified into fusiform initials (source of axial cells of xylem and phloem) and ray initials (source of the ray cells)." [ISBN:0471245208] comment: replaced_by PO:0000295 is_obsolete: true [Term] id: CL:0000273 name: prestalk AB cell namespace: cell def: "Cell that expresses both ecmA and ecmB either simultaneously or sequentially. During culmination pstA differentiate into pstAB cells." [DictyBase:DDB] synonym: "pstAB" EXACT [] is_a: CL:0000269 ! prestalk cell [Term] id: CL:0000275 name: prestalk B cell namespace: cell def: "Cell expressing ecmB but not ecmA. Most pstB cells are located at the very rear of the slug (rearguard region). These cells form part of the basal disc of the fruiting body. If a migratory slug is formed, these cells are left behind." [DictyBase:DDB] synonym: "pstB" EXACT [] is_a: CL:0000269 ! prestalk cell [Term] id: CL:0000276 name: sclerenchyma cell namespace: cell def: "Obsolete. Use PO:0000077 from Plant Ontology instead. Cell variable in form and size, being more or less thick, often lignified, secondary walls. Belongs to the category of subcells and may or may not be devoid of protoplast at maturity." [ISBN:0471245208] comment: replaced_by: PO:0000077 is_obsolete: true [Term] id: CL:0000277 name: obsolete prestalk I cell namespace: cell def: "Initial population of prestalk cells that activate the ecmA promoter at the mound stage and that presumably further differentiate into pstA and pstO cells." [DictyBase:DDB] comment: This cell type does not exist in Dictyostelium. it has been long deleted in their anatomy ontology. is_obsolete: true replaced_by: DDANAT:0000406 [Term] id: CL:0000278 name: central cell namespace: cell def: "Obsolete. Use PO:0020090 from Plant Ontology instead. OBSOLETED, use term from Plant Ontology. A cell containing the two polar nuclei which, after double fertilization, will develop into the endosperm." [TAIR:lr] comment: replaced_by: PO:0020090 is_obsolete: true [Term] id: CL:0000279 name: prestalk 0 cell namespace: cell def: "Cell that express ecmA at a very low level. Located at the posterior half of the prestalk zone. Expresses ecmA from the distal region of its promoter (ecmO)." [DictyBase:DDB] is_a: CL:0000269 ! prestalk cell [Term] id: CL:0000280 name: generative cell namespace: cell def: "Obsolete. Use PO:0020097 from Plant Ontology instead. The cell that will give rise to the generative nuclei which will participate in fertilization." [TAIR:lr] comment: replaced_by: PO:0020097 is_obsolete: true [Term] id: CL:0000281 name: pstAB/ALC namespace: cell def: "Anterior-like cell expressing both ecmA and ecmB." [DictyBase:DDB] is_a: CL:0000265 ! anterior like cell [Term] id: CL:0000282 name: trichome namespace: cell def: "Obsolete. Use PO:0000282 from Plant Ontology instead. An outgrowth from the epidermis. Trichomes vary in size and complexity and include hairs, scales, and other structures and may be glandular. In Arabidopsis, patterning of trichome development is not random but does not appear to be lineage-based like stomata." [ISBN:0471245208, PMID:10938806] comment: replaced_by: PO:0000282 is_obsolete: true [Term] id: CL:0000283 name: pstO/ALC namespace: cell def: "Anterior-like cell that expresses the ecmO promoter and that can move to the position normally occupied by the pstO cells." [DictyBase:DDB] is_a: CL:0000265 ! anterior like cell [Term] id: CL:0000284 name: companion cell namespace: cell def: "Obsolete. Use PO:0000071 from Plant Ontology instead. A specialized parenchyma cell associated with a sieve-tube member in angiosperm phloem and arising from the same mother cell as the sieve-tube member." [ISBN:0879015322] comment: replaced_by: PO:0000071 is_obsolete: true [Term] id: CL:0000285 name: stalk cell namespace: cell def: "Vacuolated cell located at the center of the stalk tube that has a cell wall composed of cellulose and that die upon terminal differentiation. Stalk cells provide structural support for the fruiting body." [DictyBase:DDB] is_a: CL:0000263 ! vegetative cell (sensu Mycetozoa) [Term] id: CL:0000286 name: hyphal cell namespace: cell def: "A cell of a filament of a fungal mycelium." [ISBN:08199377X] is_a: CL:0000521 ! fungal cell [Term] id: CL:0000287 name: eye photoreceptor cell namespace: cell is_a: CL:0000210 ! photoreceptor cell [Term] id: CL:0000288 name: synergid namespace: cell def: "Obsolete. Use PO:0000191 from Plant Ontology instead. A cell in the micropylar end of the embryo sac associated with the egg in the egg apparatus of angiosperms. Plays a vital role in fertilization." [ISBN:047125208] comment: replaced_by: PO:0000191 is_obsolete: true [Term] id: CL:0000289 name: chemotactic amoeboid cell (sensu Mycetozoa) namespace: cell def: "Starved cell that secretes and responds to chemoattractants (cAMP)." [DictyBase:DDB] is_a: CL:0000263 ! vegetative cell (sensu Mycetozoa) is_a: CL:0000732 ! amoeboid cell [Term] id: CL:0000290 name: xylem fiber cell namespace: cell def: "Obsolete. Use PO:0000274 from Plant Ontology instead. A fiber of the xylem tissue, Two types are recognized in the secondary xylem: fiber tracheids and libriform fibers." [ISBN:0471245208] comment: replaced_by: PO:0000274 is_obsolete: true [Term] id: CL:0000291 name: spore (sensu Mycetozoa) namespace: cell def: "Dormant cell protected by a tri-layer spore coat. The spore has an elliptical shape and is approximately 6-9 microns by 3 microns." [DDB_REF:5048, DictyBase:DDB, PMID:4338436] xref: DDANAT:0000414 is_a: CL:0000263 ! vegetative cell (sensu Mycetozoa) [Term] id: CL:0000292 name: guard cell namespace: cell def: "Obsolete. Use PO:0000293 from Plant Ontology instead. One of a pair of cells flanking the stomatal pore and causing the opening and closing of the pore by changes in turgor." [ISBN:0471245208] comment: replaced_by: PO:0000293 synonym: "stomatal guard cell" EXACT [] is_obsolete: true [Term] id: CL:0000293 name: structural cell namespace: cell def: "A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism." [TAIR:sr] is_a: CL:0000003 ! native cell [Term] id: CL:0000294 name: sieve cell namespace: cell def: "Obsolete. Consult Plant Ontology instead. A type of sieve element that has relatively undifferentiated sieve areas (with narrow pores), rather uniform in structure on all walls; that is, there are no sieve plates. Typical of gymnosperms and lower vascular plants." [ISBN:0471245208] is_obsolete: true [Term] id: CL:0000295 name: somatotropin secreting cell namespace: cell alt_id: CL:0000471 def: "A peptide hormone secreting cell that produces growth hormone, somatotropin." [GOC:tfm, SANBI:mhl] synonym: "growth hormone secreting cell" EXACT [] synonym: "somatotrophin secreting cell" EXACT [] is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0030252 ! growth hormone secretion relationship: capable_of GO:0030252 ! growth hormone secretion [Term] id: CL:0000296 name: vegetative cell namespace: cell def: "Obsolete. Use PO:0020099 from Plant Ontology instead. Cell type formed after the first mitotic division of the microgametophye, The nucleus of this cell migrates to the tip of the pollen tube after germination and disintegrates when the pollen tube penetrates the nucellus." [ISBN:0140514031, TAIR:lr] comment: replaced_by: PO:0020099 is_obsolete: true [Term] id: CL:0000297 name: socket cell namespace: cell def: "Obsolete. Use PO:0000115 from Plant Ontology instead. A cell that surrounds a trichome and provides support for the trichome." [PMID:10938806] comment: replaced_by: PO:0000115 is_obsolete: true [Term] id: CL:0000298 name: xylem element namespace: cell def: "Obsolete. Use PO:0000273 from Plant Ontology instead. A cell composing the xylem." [ISBN:0471245208] comment: replaced_by: PO:0000273 is_obsolete: true [Term] id: CL:0000299 name: trichoblast namespace: cell def: "OBSOLETED. Commonly used for a cell in root epidermis that gives rise to a root hair. The daughter cell produced by the asymmetric division of a root epidermal cell that gives rise to a root hair." [ISBN:0471245208] comment: Obsoleted. Use trichoblast from the plant ontology (PO:0000262). is_obsolete: true [Term] id: CL:0000300 name: gamete namespace: cell def: "A mature sexual reproductive cell having a single set of unpaired chromosomes." [GOC:tfm, ISBN:0721662544] synonym: "haploid germ cell" RELATED [] synonym: "haploid nucleated cell" EXACT [] xref: FBbt:00005412 xref: FMA:18649 is_a: CL:0000413 ! haploid cell is_a: CL:0000586 ! germ cell intersection_of: CL:0000586 ! germ cell intersection_of: capable_of GO:0009566 ! fertilization intersection_of: has_quality PATO:0001375 ! haploid relationship: capable_of GO:0009566 ! fertilization relationship: has_quality PATO:0001375 ! haploid [Term] id: CL:0000301 name: pole cell namespace: cell xref: FBbt:00000092 is_a: CL:0000670 ! primordial germ cell [Term] id: CL:0000302 name: IgM B cell namespace: cell def: "OBSOLETE (was not defined before being made obsolete)." [] comment: Not a differentiation state per se; consider using 'B cell ; CL:0000236' or one of its children instead. is_obsolete: true [Term] id: CL:0000303 name: IgG B cell namespace: cell def: "OBSOLETE (was not defined before being made obsolete)." [] comment: Not a differentiation state per se, and IgG isotypes vary by species; consider using 'B cell ; CL:0000236' or one of its children instead. is_obsolete: true [Term] id: CL:0000304 name: IgA B cell namespace: cell def: "OBSOLETE (was not defined before being made obsolete)." [] comment: Not a differentiation state per se, and IgA isotypes vary by species. Consider using 'B cell ; CL:0000236' or one of its children instead. is_obsolete: true [Term] id: CL:0000305 name: IgE B cell namespace: cell def: "OBSOLETE (was not defined before being made obsolete)." [] comment: Not a differentiation state per se; consider using 'B cell ; CL:0000236' or one of its children instead. is_obsolete: true [Term] id: CL:0000306 name: crystallin accumulating cell namespace: cell synonym: "lens cell" EXACT [] xref: FBbt:00004193 is_a: CL:0000325 ! stuff accumulating cell [Term] id: CL:0000307 name: tracheal epithelial cell namespace: cell alt_id: CL:1000474 def: "An epithelial cell found in the trachea." [GOC:tfm] synonym: "tracheocyte" EXACT [] xref: FBbt:00005038 xref: FMA:74793 is_a: CL:0002202 ! epithelial cell of tracheobronchial tree intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0003126 ! trachea relationship: develops_from CL:0000377 ! tracheoblast relationship: part_of UBERON:0003126 ! trachea [Term] id: CL:0000308 name: metal ion accumulating cell namespace: cell is_a: CL:0000325 ! stuff accumulating cell [Term] id: CL:0000309 name: copper accumulating cell namespace: cell synonym: "cuprophilic cell" EXACT [] is_a: CL:0000308 ! metal ion accumulating cell [Term] id: CL:0000310 name: iron accumulating cell namespace: cell is_a: CL:0000308 ! metal ion accumulating cell [Term] id: CL:0000311 name: keratin accumulating cell namespace: cell is_a: CL:0000325 ! stuff accumulating cell [Term] id: CL:0000312 name: keratinocyte namespace: cell alt_id: CL:0002185 def: "An epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell." [GOC:dsd, http://en.wikipedia.org/wiki/Keratinocyte, MESH:A11.436.397, MESH:D015603, PMID:15582983, PMID:15749908, PMID:19727116] comment: Keratinocytes are reportedly CDw210a-negative, CDw210b-positive, CD281-positive, CD282-positive, CD285-positive, IL22Ra1-positive, Human keratinocytes are reportedly capable of secreting BD-2, BD-3, hCAP-18, CXCL1, CXCL5, CXCL8, elafin, MMP-3, NGAL, PDGF-A, S100A7, S100A8, and S100A9. Transcription factors: STAT3-positive. synonym: "keratinized cell of epidermis" EXACT [] synonym: "malpighian cell" EXACT [] xref: BTO:0000667 xref: FMA:62879 is_a: CL:0000237 ! keratinizing barrier epithelial cell is_a: CL:0000362 ! epidermal cell intersection_of: CL:0000237 ! keratinizing barrier epithelial cell intersection_of: capable_of GO:0002775 ! antimicrobial peptide production intersection_of: capable_of GO:0002776 ! antimicrobial peptide secretion intersection_of: capable_of GO:0090023 ! positive regulation of neutrophil chemotaxis intersection_of: part_of UBERON:0001003 ! epidermis relationship: capable_of GO:0002775 ! antimicrobial peptide production relationship: capable_of GO:0002776 ! antimicrobial peptide secretion relationship: capable_of GO:0090023 ! positive regulation of neutrophil chemotaxis relationship: part_of UBERON:0001003 ! epidermis [Term] id: CL:0000313 name: serous secreting cell namespace: cell def: "Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid." [GOC:tfm, ISBN:0517223651, ISBN:0721662544] synonym: "serous cell" EXACT [] xref: BTO:0003687 xref: FMA:62511 is_a: CL:0000159 ! seromucus secreting cell [Term] id: CL:0000314 name: milk secreting cell namespace: cell is_a: CL:0000151 ! secretory cell [Term] id: CL:0000315 name: tears secreting cell namespace: cell def: "A cell secreting tears, the fluid secreted by the lacrimal glands. This fluid moistens the conjunctiva and cornea." [MESH:A12.200.882] is_a: CL:0000151 ! secretory cell [Term] id: CL:0000316 name: ray initial namespace: cell def: "Obsolete. Use PO:0000082 from Plant Ontology instead. OBSOLETE, use term from Plant Ontology. A meristemic ray cell in the vascular cambium that gives rise to ray cells of the secondary xylem and secondary phloem." [ISBN:0471245208] comment: replaced_by: PO:0000082 is_obsolete: true [Term] id: CL:0000317 name: sebum secreting cell namespace: cell def: "A cell secreting sebun, an oily substance secreted by sebaceous glands, composed of keratin, fat, and cellular debris." [MESH:A12.200.702] is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: part_of UBERON:0001821 ! sebaceous gland relationship: part_of UBERON:0001821 ! sebaceous gland [Term] id: CL:0000318 name: sweat secreting cell namespace: cell def: "A cell secreting sweat, the fluid excreted by the sweat glands of mammals. It consists of water containing sodium chloride, phosphate, urea, ammonia, and other waste products." [MESH:A12.200.849] is_a: CL:0000150 ! glandular epithelial cell [Term] id: CL:0000319 name: mucus secreting cell namespace: cell synonym: "mucous cell" EXACT [] xref: BTO:0003689 is_a: CL:0000159 ! seromucus secreting cell relationship: capable_of GO:0070254 ! mucus secretion [Term] id: CL:0000320 name: megasporocyte namespace: cell def: "Obsolete. Use PO:0000431 from Plant Ontology instead. A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores; also called megaspore mother cell." [ISBN:0471245208] comment: replaced_by: PO:0000431 synonym: "archesporial cell" EXACT [] synonym: "megaspore mother cell" EXACT [] is_obsolete: true [Term] id: CL:0000321 name: seminal fluid secreting cell namespace: cell is_a: CL:0000151 ! secretory cell [Term] id: CL:0000322 name: pneumocyte namespace: cell def: "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates." [GOC:tfm, PMID:20054144] synonym: "alveolar epithelial cell" EXACT [] synonym: "pneumonocyte" EXACT [] xref: BTO:0000395 xref: FMA:62499 is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0002202 ! epithelial cell of tracheobronchial tree intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002299 ! alveolus of lung relationship: part_of UBERON:0002299 ! alveolus of lung relationship: part_of UBERON:0004821 ! pulmonary alveolus epithelium [Term] id: CL:0000323 name: lysozyme secreting cell namespace: cell is_a: CL:0000154 ! protein secreting cell [Term] id: CL:0000324 name: metanephric mesenchyme stem cell namespace: cell is_a: CL:0000134 ! mesenchymal cell relationship: develops_from CL:0000222 ! mesodermal cell [Term] id: CL:0000325 name: stuff accumulating cell namespace: cell def: "A cell that is specialised to accumulate a particular substance(s)." [FB:ma] subset: ubprop:upper_level is_a: CL:0000003 ! native cell [Term] id: CL:0000326 name: glycogen accumulating cell namespace: cell is_a: CL:0000325 ! stuff accumulating cell [Term] id: CL:0000327 name: extracellular matrix secreting cell namespace: cell is_a: CL:0000151 ! secretory cell is_a: CL:0000499 ! stromal cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0070278 ! extracellular matrix constituent secretion relationship: capable_of GO:0070278 ! extracellular matrix constituent secretion [Term] id: CL:0000328 name: myelin accumulating cell namespace: cell is_a: CL:0000325 ! stuff accumulating cell [Term] id: CL:0000329 name: oxygen accumulating cell namespace: cell is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: capable_of GO:0015671 ! oxygen transport relationship: capable_of GO:0015671 ! oxygen transport [Term] id: CL:0000330 name: collenchymal cell namespace: cell def: "Obsolete. Use PO:0000075 from Plant Ontology instead. An elongated living cell with unevenly thickened nonlignified primary walls." [ISBN:0471245208] comment: replaced_by: PO:0000075 is_obsolete: true [Term] id: CL:0000331 name: tracheid namespace: cell def: "Obsolete. Use PO:0000301 from Plant Ontology instead. A tracheary element of the xylem that has no perforations, as contrasted with a vessel member. May occur in primary and in secondary xylem. May have any kind of secondary wall thickening found in tracheary elements." [ISBN:0471245208] comment: replaced_by: PO:0000301 is_obsolete: true [Term] id: CL:0000332 name: atrichoblast namespace: cell def: "OBSOLETE, use term from Plant Ontology. A cell formed after asymmetric division of root epidermal cell that does not give rise to a root hair." [ISBN:0387987819] comment: replaced_by: PO:0020090 synonym: "non-hair cell" RELATED [] is_obsolete: true [Term] id: CL:0000333 name: migratory neural crest cell namespace: cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [MESH:A16.254.600] xref: FMA:86667 is_a: CL:0000219 ! motile cell is_a: CL:0002321 ! embryonic cell relationship: develops_from CL:0000133 ! neurectodermal cell relationship: develops_from CL:0007004 ! premigratory neural crest cell [Term] id: CL:0000334 name: vegetative cell (sensu Fungi) namespace: cell synonym: "yeast-form" RELATED [] xref: BTO:0002307 xref: FAO:0000032 is_a: CL:0000521 ! fungal cell [Term] id: CL:0000335 name: mesenchyme condensation cell namespace: cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] is_a: CL:0000134 ! mesenchymal cell [Term] id: CL:0000336 name: adrenal medulla chromaffin cell namespace: cell alt_id: CL:1000422 def: "A cell found within the adrenal medulla that secrete biogenic amine hormones upon stimulation." [GOC:tfm, http://www.britannica.com/EBchecked/topic/6405/adrenal-gland] synonym: "medullary chromaffin cell of adrenal gland" EXACT [FMA:69262] xref: FMA:69262 is_a: CL:0000457 ! biogenic amine secreting cell is_a: CL:1000426 ! chromaffin cell of adrenal gland intersection_of: CL:0000166 ! chromaffin cell intersection_of: part_of UBERON:0001236 ! adrenal medulla relationship: develops_from CL:0000011 ! migratory trunk neural crest cell relationship: part_of UBERON:0001236 ! adrenal medulla [Term] id: CL:0000337 name: neuroblast (sensu Vertebrata) namespace: cell def: "An embryonic cell that develops into a nerve cell or neuron." [FMA:70563] is_a: CL:0000031 ! neuroblast [Term] id: CL:0000338 name: neuroblast (sensu Nematoda and Protostomia) namespace: cell synonym: "neuroblast" BROAD [] is_a: CL:0000031 ! neuroblast [Term] id: CL:0000339 name: glioblast (sensu Vertebrata) namespace: cell def: "An early neural cell developing from the early ependymal cell of the neural tube." [GOC:tfm, ISBN:0618947256] synonym: "spongioblast" EXACT [] xref: FMA:70564 is_a: CL:0000030 ! glioblast is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) [Term] id: CL:0000340 name: glioblast (sensu Nematoda and Protostomia) namespace: cell is_a: CL:0000030 ! glioblast is_a: CL:0000130 ! neuron associated cell (sensu Nematoda and Protostomia) [Term] id: CL:0000341 name: pigment cell (sensu Nematoda and Protostomia) namespace: cell is_a: CL:0000147 ! pigment cell [Term] id: CL:0000342 name: pigment cell (sensu Vertebrata) namespace: cell def: "Any animal cell containing pigment granules." [GOC:tfm, ISBN:0721662544] is_a: CL:0000147 ! pigment cell [Term] id: CL:0000343 name: visual pigment cell (sensu Vertebrata) namespace: cell def: "A pigment cell that is capable of detecting light stimulus that is involved in visual perception." [GOC:tfm] xref: FMA:63846 is_a: CL:0000149 ! visual pigment cell is_a: CL:0000342 ! pigment cell (sensu Vertebrata) intersection_of: CL:0000342 ! pigment cell (sensu Vertebrata) intersection_of: capable_of GO:0050908 ! detection of light stimulus involved in visual perception relationship: capable_of GO:0050908 ! detection of light stimulus involved in visual perception [Term] id: CL:0000344 name: non-visual cell (sensu Vertebrata) namespace: cell is_obsolete: true [Term] id: CL:0000345 name: dental papilla cell namespace: cell def: "A small mass of condensed mesenchyme in the enamel organ; it differentiates into the dentin and dental pulp." [GOC:tfm, ISBN:0721662544] is_a: CL:0000134 ! mesenchymal cell relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001763 ! odontogenic papilla [Term] id: CL:0000346 name: hair follicle dermal papilla cell namespace: cell def: "A specialized mesenchymal cell that resides in the dermal papilla located at the bottom of hair follicles. This cell plays a pivotal roles in hair formation, growth, and cycling." [GOC:tfm, PMID:9893172] is_a: CL:0000134 ! mesenchymal cell intersection_of: CL:0000134 ! mesenchymal cell intersection_of: part_of UBERON:0000412 ! dermal papilla relationship: develops_from CL:0000333 ! migratory neural crest cell relationship: part_of UBERON:0000412 ! dermal papilla [Term] id: CL:0000347 name: scleral cell namespace: cell def: "A cell of the sclera of the eye." [GOC:add] is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001773 ! sclera relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001773 ! sclera [Term] id: CL:0000348 name: choroidal cell of the eye namespace: cell def: "A cell of the choroid of the eye." [GOC:add] is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001776 ! optic choroid relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001776 ! optic choroid [Term] id: CL:0000349 name: extraembryonic cell namespace: cell is_a: CL:0000548 ! animal cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000548 ! animal cell intersection_of: part_of UBERON:0000478 ! extraembryonic structure relationship: part_of UBERON:0000478 ! extraembryonic structure [Term] id: CL:0000350 name: amnioserosal cell namespace: cell is_a: CL:0000349 ! extraembryonic cell intersection_of: CL:0000349 ! extraembryonic cell intersection_of: part_of UBERON:0010302 ! amnioserosa relationship: part_of UBERON:0010302 ! amnioserosa [Term] id: CL:0000351 name: trophoblast cell namespace: cell def: "A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface." [GOC:tfm, MESH:A11.936] synonym: "trophoblastic cell" EXACT [] xref: FMA:83028 is_a: CL:0000349 ! extraembryonic cell intersection_of: CL:0000349 ! extraembryonic cell intersection_of: part_of UBERON:0000358 ! blastocyst relationship: part_of UBERON:0000358 ! blastocyst [Term] id: CL:0000352 name: epiblast cell namespace: cell def: "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." [GOC:tfm, ISBN:0618947256] is_a: CL:0000052 ! totipotent stem cell [Term] id: CL:0000353 name: blastoderm cell namespace: cell def: "An undifferentiated cell produced by early cleavages of the fertilized egg (zygote)." [MESH:A11.104] synonym: "blastomere" EXACT [] xref: BTO:0001473 xref: FMA:72551 is_a: CL:0000007 ! early embryonic cell [Term] id: CL:0000354 name: blastemal cell namespace: cell synonym: "blastema cell" EXACT [] xref: ncithesaurus:Blastemal_Cell is_a: CL:0000048 ! multi fate stem cell [Term] id: CL:0000355 name: muscle stem cell namespace: cell def: "A multifate stem cell found in skeletal muscle than can differentiate into many different cell types. Distinct cell type from satellite cell." [PMID:18282570] xref: FMA:86767 is_a: CL:0000048 ! multi fate stem cell intersection_of: CL:0000048 ! multi fate stem cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue relationship: part_of UBERON:0001134 ! skeletal muscle tissue [Term] id: CL:0000356 name: hair matrix stem cell namespace: cell is_a: CL:0000035 ! single fate stem cell [Term] id: CL:0000357 name: stratified epithelial stem cell namespace: cell is_a: CL:0000036 ! epithelial fate stem cell [Term] id: CL:0000358 name: sphincter associated smooth muscle cell namespace: cell def: "A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning." [GOC:cjm] is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0004590 ! sphincter muscle relationship: part_of UBERON:0004590 ! sphincter muscle [Term] id: CL:0000359 name: vascular associated smooth muscle cell namespace: cell def: "A smooth muscle cell assocatiated with the vasculature." [GOC:dsd, GOC:tfm] synonym: "vascular smooth muscle cell" EXACT [] synonym: "VSMC" EXACT [] is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0002049 ! vasculature relationship: part_of UBERON:0002049 ! vasculature [Term] id: CL:0000360 name: morula cell namespace: cell def: "A cell of the early embryo at the developmental stage in which the blastomeres, resulting from repeated mitotic divisions of the fertilized ovum (zygote), form a compact cell mass." [MESH:A16.254.270.550] is_a: CL:0000007 ! early embryonic cell relationship: part_of UBERON:0000085 ! morula [Term] id: CL:0000361 name: gastrula cell namespace: cell def: "A cell of the embryo in the early stage following the blastula, characterized by morphogenetic cell movements, cell differentiation, and the formation of the three germ layers." [MESH:A16.254.412] is_a: CL:0000007 ! early embryonic cell relationship: part_of UBERON:0004734 ! gastrula [Term] id: CL:0000362 name: epidermal cell namespace: cell alt_id: CL:1000396 def: "An epithelial cell of the integument (the outer layer of an organism)." [Flybase:dsj, MA:ma] synonym: "cell of epidermis" EXACT [FMA:62411] synonym: "epithelial cell of skin" NARROW [FMA:62411] xref: BTO:0001470 xref: FMA:62411 is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001003 ! epidermis relationship: part_of UBERON:0001003 ! epidermis [Term] id: CL:0000363 name: axial cell namespace: cell def: "Obsolete. Use PO:0000081 from Plant Ontology instead. OBSOLETE, use term from the Plant Ontology. A secondary vascular cell that develops from the fusiform cambial initials and oriented with their longest diameter parallel with the main axis of stem or root. These cells make up the axial system, also known as vertical or longitudinal system." [ISBN:0471245208] comment: replaced_by: PO:0000081 is_obsolete: true [Term] id: CL:0000364 name: ray cell namespace: cell def: "Obsolete. Consult Plant Ontology. A cell that develops from the ray initial and composes all rays (panels of tissue variable in height and width, formed by the ray initials in the vascular cambium and extending radially in the secondary xylem and secondary phloem) in the secondary vascular tissues." [ISBN:0471245208] is_obsolete: true [Term] id: CL:0000365 name: zygote namespace: cell def: "Diploid cell produced by the fusion of sperm cell nucleus and egg cell." [ISBN:0471245208] xref: BTO:0000854 xref: EHDAA2:0004546 xref: FMA:72395 is_a: CL:0000007 ! early embryonic cell [Term] id: CL:0000366 name: sperm cell (sensu Viridiplantae) namespace: cell def: "Obsolete. Use PO:0000084 from Plant Ontology instead. Male gamete, part of male germ unit." [ISBN:0471245208] comment: replaced_by: PO:0000084 synonym: "gametophyte sperm cell" RELATED [] synonym: "male gametophyte sperm cell" RELATED [] synonym: "pollen germ cell " RELATED [] is_obsolete: true [Term] id: CL:0000367 name: sheath cell (sensu Nematoda) namespace: cell synonym: "glial cell (sensu Nematoda)" RELATED [] is_a: CL:0000619 ! support cell (sensu Nematoda) [Term] id: CL:0000368 name: myrosin cell namespace: cell def: "Obsolete. Use PO:0000352 from Plant Ontology instead. Cell containing glucosinolates ('mustard oil glucosides') and myrosinases, enzymes hydrolyzing the glucosinolates. Occurs in eleven dicotyledon families, the two largest of which are the Brassicaceae and Euphorbiaceae." [ISBN:0471245208] comment: replaced_by: PO:0000352 is_obsolete: true [Term] id: CL:0000370 name: transfer cell namespace: cell def: "Obsolete. Use PO:0000078 from Plant Ontology instead. Parenchyma cell with the wall ingrowth (or invaginations) that increase the surface of the plasmalemma. Appears to be specialized for short-distance transfer of solutes." [ISBN:0471245208] comment: replaced_by: PO:0000078 synonym: "intermediary cell" RELATED [] is_obsolete: true [Term] id: CL:0000371 name: protoplast namespace: cell def: "The cell protoplasm after removal of the cell wall." [ISBN:08199377X] is_a: CL:0000578 ! experimentally modified cell in vitro [Term] id: CL:0000372 name: tormogen cell namespace: cell def: "An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization that forms a socket around the base of a cuticular specialization produced by a trichogen cell." [ISBN:978-0801481253] synonym: "socket cell" BROAD [ISBN:978-0801481253] xref: FBbt:00005171 is_a: CL:0000463 ! epidermal cell (sensu arthropoda) [Term] id: CL:0000373 name: histoblast namespace: cell xref: FBbt:00001789 is_a: CL:0000146 ! simple columnar epithelial cell [Term] id: CL:0000374 name: trichogen cell namespace: cell def: "An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization, often in the form of a hair, bristle, peg or scale. The base of this specialization is often surrounded by a socket produced by a closely associated tormogen cell." [ISBN:978-0801481253] synonym: "hair cell" BROAD [] xref: BTO:0004744 xref: FBbt:00005169 is_a: CL:0000463 ! epidermal cell (sensu arthropoda) [Term] id: CL:0000375 name: osteoprogenitor cell namespace: cell xref: BTO:0002051 is_obsolete: true replaced_by: CL:0007010 [Term] id: CL:0000376 name: humidity receptor cell namespace: cell is_a: CL:0000006 ! neuronal receptor cell [Term] id: CL:0000377 name: tracheoblast namespace: cell is_a: CL:0000069 ! branched duct epithelial cell [Term] id: CL:0000378 name: support cell (sensu Nematoda and Protostomia) namespace: cell is_a: CL:0000630 ! supportive cell [Term] id: CL:0000379 name: sensory processing neuron namespace: cell is_a: CL:0000540 ! neuron [Term] id: CL:0000380 name: thecogen cell namespace: cell def: "The support cell that makes the thecogen dendritic cap - a cuticle-like matrix around the tip of the eo-dendrite and which encloses the soma of the eo-neuron." [Fbbt:00005173] synonym: "fly sheath cell" EXACT [] is_a: CL:0000378 ! support cell (sensu Nematoda and Protostomia) [Term] id: CL:0000381 name: neurosecretory neuron namespace: cell xref: FBbt:00005130 is_a: CL:0000527 ! efferent neuron [Term] id: CL:0000382 name: scolopidium namespace: cell synonym: "scolopale cell" EXACT [] xref: FBbt:00005217 is_a: CL:0000378 ! support cell (sensu Nematoda and Protostomia) [Term] id: CL:0000383 name: nephrogenic mesenchyme stem cell namespace: cell is_a: CL:0000134 ! mesenchymal cell relationship: develops_from CL:0000134 ! mesenchymal cell [Term] id: CL:0000384 name: ligament cell namespace: cell is_a: CL:0000630 ! supportive cell [Term] id: CL:0000385 name: prohemocyte (sensu Nematoda and Protostomia) namespace: cell xref: FBbt:00005062 is_a: CL:0000390 ! blood cell (sensu Nematoda and Protostomia) [Term] id: CL:0000386 name: attachment cell namespace: cell is_a: CL:0000630 ! supportive cell [Term] id: CL:0000387 name: hemocyte (sensu Nematoda and Protostomia) namespace: cell xref: FBbt:00005063 is_a: CL:0000519 ! phagocyte (sensu Nematoda and Protostomia) relationship: capable_of GO:0035010 {source="PMID:18025161"} ! encapsulation of foreign target relationship: develops_from CL:0000385 ! prohemocyte (sensu Nematoda and Protostomia) [Term] id: CL:0000388 name: tendon cell namespace: cell def: "A fibrocyte that is part of a tendon." [GOC:tfm] synonym: "muscle attachment cell" EXACT [] synonym: "tenocyte" RELATED [] is_a: CL:0000135 ! fibrocyte is_a: CL:0000386 ! attachment cell intersection_of: CL:0000135 ! fibrocyte intersection_of: part_of UBERON:0000043 ! tendon relationship: part_of UBERON:0000043 ! tendon [Term] id: CL:0000389 name: socket cell (sensu Nematoda) namespace: cell is_a: CL:0000619 ! support cell (sensu Nematoda) is_a: CL:0000658 ! cuticle secreting cell [Term] id: CL:0000390 name: blood cell (sensu Nematoda and Protostomia) namespace: cell is_a: CL:0000081 ! blood cell [Term] id: CL:0000391 name: podocyte (sensu Diptera) namespace: cell def: "An insect immune cell that develops from plasmatocyte." [PMID:12930778] xref: FBbt:00001688 is_a: CL:0000387 ! hemocyte (sensu Nematoda and Protostomia) relationship: develops_from CL:0000394 ! plasmatocyte [Term] id: CL:0000392 name: crystal cell namespace: cell xref: FMA:63847 is_a: CL:0000391 ! podocyte (sensu Diptera) [Term] id: CL:0000393 name: electrically responsive cell namespace: cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] is_a: CL:0000211 ! electrically active cell [Term] id: CL:0000394 name: plasmatocyte namespace: cell xref: FBbt:00001685 is_a: CL:0000387 ! hemocyte (sensu Nematoda and Protostomia) [Term] id: CL:0000395 name: procrystal cell namespace: cell xref: FBbt:00001689 is_a: CL:0000387 ! hemocyte (sensu Nematoda and Protostomia) [Term] id: CL:0000396 name: lamellocyte namespace: cell xref: FBbt:00001687 is_a: CL:0000394 ! plasmatocyte [Term] id: CL:0000397 name: ganglion interneuron namespace: cell is_a: CL:0000099 ! interneuron [Term] id: CL:0000398 name: polygonal cell namespace: cell xref: FBbt:00001691 is_a: CL:0000387 ! hemocyte (sensu Nematoda and Protostomia) [Term] id: CL:0000399 name: phloem element namespace: cell def: "Obsolete. Consult Plant Ontology instead. OBSOLETED, not defined prior to obsoletion." [GOC:tfm] is_obsolete: true [Term] id: CL:0000400 name: pavement cell namespace: cell def: "Obsolete. Use PO:0000332 from Plant Ontology instead. An epidermal cell with a characteristic convoluted anticlinal cell wall that gives a jigsaw like appearance to the lamina." [ISBN:087694289] comment: replaced_by: PO:0000332 is_obsolete: true [Term] id: CL:0000401 name: macrophage (sensu Diptera) namespace: cell xref: FBbt:00001686 is_a: CL:0000394 ! plasmatocyte [Term] id: CL:0000402 name: CNS interneuron namespace: cell is_a: CL:0000099 ! interneuron is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) [Term] id: CL:0000404 name: electrically signaling cell namespace: cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] is_a: CL:0000211 ! electrically active cell [Term] id: CL:0000405 name: neuroepidermoblast namespace: cell xref: FBbt:00005148 is_a: CL:0000338 ! neuroblast (sensu Nematoda and Protostomia) [Term] id: CL:0000406 name: CNS short range interneuron namespace: cell is_a: CL:0000402 ! CNS interneuron [Term] id: CL:0000407 name: scolopidial ligament cell namespace: cell xref: FBbt:00005221 is_a: CL:0000384 ! ligament cell [Term] id: CL:0000408 name: male gamete namespace: cell xref: BTO:0001277 is_a: CL:0000015 ! male germ cell is_a: CL:0000300 ! gamete intersection_of: CL:0000015 ! male germ cell intersection_of: capable_of GO:0009566 ! fertilization intersection_of: has_quality PATO:0001375 ! haploid relationship: capable_of GO:0009566 ! fertilization relationship: has_quality PATO:0001375 ! haploid [Term] id: CL:0000409 name: scolopidial sheath cell namespace: cell xref: FBbt:00005219 is_a: CL:0000618 ! sheath cell [Term] id: CL:0000410 name: CNS long range interneuron namespace: cell is_a: CL:0000402 ! CNS interneuron [Term] id: CL:0000411 name: flatworm hypodermal cell namespace: cell def: "An epithelial cell of the hypodermis of flatworms." [GOC:tfm, http://www.wormatlas.org/hermaphrodite/hypodermis/mainframe.htm] xref: WBbt:0007846 is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000228 ! multinucleate cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000412 name: polyploid cell namespace: cell def: "A cell whose nucleus, or nuclei, each contain more than two haploid genomes." [FB:ma] is_a: CL:0000003 ! native cell [Term] id: CL:0000413 name: haploid cell namespace: cell def: "A cell whose nucleus contains a single haploid genome." [FB:ma, GOC:tfm] is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: has_quality PATO:0001375 ! haploid relationship: has_quality PATO:0001375 ! haploid [Term] id: CL:0000414 name: cell by ploidy namespace: cell def: "A classification of cells by the number of haploid genome equivalents of their nucleus or nuclei." [FB:ma, GOC:tfm] comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell with chromosomes can be classified by its ploidy. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), eukaryotic cell (CL:0000255) or cell in vitro (CL:0001034) as appropriate. is_obsolete: true consider: CL:0000000 consider: CL:0000003 consider: CL:0000255 consider: CL:0001034 [Term] id: CL:0000415 name: diploid cell namespace: cell def: "A cell whose nucleus has two haploid genomes." [FB:ma] xref: FMA:72300 is_a: CL:0000003 ! native cell [Term] id: CL:0000416 name: polytene cell namespace: cell is_a: CL:0000412 ! polyploid cell [Term] id: CL:0000417 name: endopolyploid cell namespace: cell is_a: CL:0000412 ! polyploid cell [Term] id: CL:0000418 name: arcade cell namespace: cell def: "An epithelial cell found in C. elegans that firmly hold the outer body wall and the lips to the inner cylinder of the pharynx in a manner that keeps these organs from breaking apart, while still giving each organ freedom of movement during feeding." [GOC:tfm, http://www.wormatlas.org/ver1/handbook/hypodermis/hypsupportother.htm#arcadecells] xref: WBbt:0005793 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000419 name: seam cell namespace: cell def: "An epithelial fate stem cell found in flatworms." [GOC:tfm, http://www.wormatlas.org/hermaphrodite/seam%20cells/mainframe.htm] xref: BTO:0003039 is_a: CL:0000036 ! epithelial fate stem cell [Term] id: CL:0000420 name: syncytial epithelial cell namespace: cell is_a: CL:0000066 ! epithelial cell is_a: CL:0000228 ! multinucleate cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000421 name: coelomocyte namespace: cell def: "A free floating cell, including amebocytes and eleocytes, in the coelom of certain animals, especially annelids." [GOC:tfm, ISBN:0721662544] xref: BTO:0002856 xref: WBbt:0005751 is_a: CL:0000080 ! circulating cell is_a: CL:0000519 ! phagocyte (sensu Nematoda and Protostomia) [Term] id: CL:0000422 name: mitogenic signaling cell namespace: cell def: "A cell whose primary function is to cause growth by stimulating cell division in its immediate cellular environment." [FB:ma] is_a: CL:0000003 ! native cell [Term] id: CL:0000423 name: tip cell namespace: cell is_a: CL:0000422 ! mitogenic signaling cell [Term] id: CL:0000424 name: excretory cell namespace: cell def: "A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids." [GOC:tfm, PMID:19783135] xref: WBbt:0005812 is_a: CL:0000151 ! secretory cell [Term] id: CL:0000425 name: pore cell namespace: cell def: "Forms the terminal part of the cuticle-lined excretory duct of C. elegans." [JB:jb] is_a: CL:0000658 ! cuticle secreting cell [Term] id: CL:0000426 name: scaffold cell namespace: cell is_a: CL:0000445 ! apoptosis fated cell [Term] id: CL:0000427 name: GLR cell namespace: cell def: "A scaffolding cell type found in C. elegans, this cell plays a supportive role to the muscle arms. May also have an endocrine role." [GOC:tfm, http://wormatlas.psc.edu/hermaphrodite/muscleGLR/mainframe.htm] is_a: CL:0002320 ! connective tissue cell [Term] id: CL:0000428 name: yolk cell namespace: cell is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0000349 ! extraembryonic cell [Term] id: CL:0000429 name: imaginal disc cell namespace: cell is_a: CL:0000146 ! simple columnar epithelial cell [Term] id: CL:0000430 name: xanthophore namespace: cell def: "A pigment cell derived from the neural crest. Contains cartenoid pigments in structures called pterinosomes or xanthosomes. This gives an appearance ranging from a golden yellow to orange and red." [SANBI:mhl] is_a: CL:0000147 ! pigment cell relationship: develops_from CL:0005002 ! xanthoblast [Term] id: CL:0000431 name: iridophore namespace: cell def: "A pigment cell derived from the neural crest. The cell contains flat light-reflecting platelets, probably of guanine, in stacks called reflecting platets or iridisomes. The color-generating components produce a silver, gold, or iridescent color." [SANBI:mhl] synonym: "guanophore" RELATED [] is_a: CL:0000147 ! pigment cell relationship: develops_from CL:0005001 ! iridoblast [Term] id: CL:0000432 name: reticular cell namespace: cell def: "Large, stellate fibroblast found along the network of collagen fibers of the reticulum of the spleen; synthesize the matrix components of the reticulum." [GOC:tfm, http://en.wikipedia.org/wiki/Reticular_cell, ISBN:0517223651] synonym: "reticulum cell" EXACT [] xref: FMA:62877 is_a: CL:0000057 ! fibroblast [Term] id: CL:0000433 name: functional megaspore namespace: cell def: "Obsolete. Use PO:0000244 from Plant Ontology instead. In monosporic and bisporic megasporogenesis: the megaspore(s) that will undergo megagametogenesis." [TAIR:lr] comment: replaced_by: PO:0000244 is_obsolete: true [Term] id: CL:0000434 name: eccrine cell namespace: cell def: "A secretory cell that discharges its product without loss of cytoplasm." [ISBN:0198547684] is_a: CL:0000150 ! glandular epithelial cell [Term] id: CL:0000435 name: alkali secreting cell namespace: cell is_a: CL:0000151 ! secretory cell [Term] id: CL:0000436 name: vaginal lubricant secreting cell namespace: cell is_a: CL:0000151 ! secretory cell relationship: part_of UBERON:0000996 ! vagina [Term] id: CL:0000437 name: gonadtroph namespace: cell def: "A rounded cell that is usually situated next to sinusoids; secretes follicular stimulating hormone (FSH) and luteinizing hormone (LH)." [GOC:tfm, http://en.wikipedia.org/wiki/Gonadotroph, ISBN:0517223651] synonym: "delta basophil" EXACT [] synonym: "follicle stimulating hormone secreting cell" EXACT [] synonym: "gonadotrope" EXACT [] synonym: "gonadotrope cell" EXACT [] synonym: "gonadotroph" EXACT [] synonym: "gonadotropic cell" EXACT [] synonym: "pituitary delta cell" EXACT [] xref: BTO:0002482 xref: FMA:83100 is_a: CL:0000438 ! luteinizing hormone secreting cell is_a: CL:0000639 ! basophil cell of pars distalis of adenohypophysis [Term] id: CL:0000438 name: luteinizing hormone secreting cell namespace: cell def: "A peptide hormone secreting cell pituitary that produces luteinizing hormone." [GOC:tfm] is_a: CL:0000163 ! endocrine cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0032275 ! luteinizing hormone secretion relationship: capable_of GO:0032275 ! luteinizing hormone secretion [Term] id: CL:0000439 name: prolactin secreting cell namespace: cell def: "A peptide hormone cell that secretes prolactin." [GOC:tfm, SANBI:mhl] is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0070459 ! prolactin secretion relationship: capable_of GO:0070459 ! prolactin secretion [Term] id: CL:0000440 name: melanocyte stimulating hormone secreting cell namespace: cell def: "A cell of the intermediate pituitary that produces melanocyte stimulating hormone." [SANBI:mhl] synonym: "melanotrope" EXACT [] synonym: "melanotroph" EXACT [] xref: BTO:0002277 is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0036160 ! melanocyte-stimulating hormone secretion relationship: capable_of GO:0036160 ! melanocyte-stimulating hormone secretion [Term] id: CL:0000441 name: follicle stem cell namespace: cell xref: FBbt:00004903 is_a: CL:0000036 ! epithelial fate stem cell [Term] id: CL:0000442 name: follicular dendritic cell namespace: cell def: "A cell with extensive dendritic processes found in the B cell areas (primary follicles and germinal centers) of lymphoid tissue. They are unrelated to the dendritic cell associated with T cells. Follicular dendritic cells have Fc receptors and C3b receptors, but unlike other dendritic cells, they do not process or present antigen in a way that allows recognition by T cells. Instead, they hold antigen in the form of immune complexes on their surfaces for long periods and can present antigen to B cells during an immune response." [ISBN:127520252] comment: Due to its unique lineage and distinct function, this is not a type of dendritic cell; CL:0000451. xref: BTO:0004267 xref: FMA:83037 is_a: CL:0000473 ! defensive cell [Term] id: CL:0000443 name: calcitonin secreting cell namespace: cell is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0036161 ! calcitonin secretion relationship: capable_of GO:0036161 ! calcitonin secretion [Term] id: CL:0000444 name: obliquely striated muscle cell namespace: cell is_a: CL:0000737 ! striated muscle cell [Term] id: CL:0000445 name: apoptosis fated cell namespace: cell is_a: CL:0000003 ! native cell [Term] id: CL:0000446 name: chief cell of parathyroid gland namespace: cell def: "An epithelial cell of the parathyroid gland that is arranged in wide, irregular interconnecting columns; responsible for the synthesis and secretion of parathyroid hormone." [FMA:69078, GOC:tfm, ISBN:0517223651] synonym: "parathyroid chief cell" EXACT [] synonym: "parathyroid gland chief cell" EXACT [] synonym: "parathyroid hormone secreting cell" EXACT [] synonym: "principal cell of parathyroid gland" EXACT [] xref: BTO:0004712 xref: FMA:69078 is_a: CL:0000167 ! peptide hormone secreting cell is_a: CL:0002260 ! epithelial cell of parathyroid gland [Term] id: CL:0000447 name: carbohydrate secreting cell namespace: cell is_a: CL:0000151 ! secretory cell [Term] id: CL:0000448 name: white fat cell namespace: cell def: "Fat cells with light coloration and few mitochondria. They contain a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole." [GOC:tfm, MESH:A11.329.114.500] synonym: "white adipocyte" RELATED [] synonym: "white adipose cell" EXACT [] synonym: "white fat cell" EXACT [] xref: FMA:83434 is_a: CL:0000136 ! fat cell relationship: develops_from CL:0002334 ! preadipocyte relationship: part_of UBERON:0001347 ! white adipose tissue [Term] id: CL:0000449 name: brown fat cell namespace: cell def: "A cell from the thermogenic form of adipose tissue found in newborns of many species, including humans, and in hibernating mammals. Brown fat is capable of rapid liberation of energy and seems to be important in the maintenance of body temperature immediately after birth and upon waking from hibernation." [MESH:A10.165.114.322] synonym: "brown adipocyte" EXACT [] synonym: "brown adipose cell" EXACT [] xref: FMA:83435 is_a: CL:0000136 ! fat cell relationship: develops_from CL:0002335 ! brown preadipocyte relationship: part_of UBERON:0001348 ! brown adipose tissue [Term] id: CL:0000451 name: dendritic cell namespace: cell def: "A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative)." [GOC:add, ISBN:0781735149] synonym: "interdigitating cell" RELATED [] synonym: "veiled cell" RELATED [] xref: BTO:0002042 xref: FMA:83036 is_a: CL:0000738 ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: capable_of GO:0001816 ! cytokine production intersection_of: capable_of GO:0019882 ! antigen processing and presentation intersection_of: capable_of GO:0045580 ! regulation of T cell differentiation intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 disjoint_from: CL:0000542 ! lymphocyte relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0019882 ! antigen processing and presentation relationship: capable_of GO:0045580 ! regulation of T cell differentiation relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 [Term] id: CL:0000452 name: thyroid hormone secreting cell namespace: cell is_a: CL:0000163 ! endocrine cell [Term] id: CL:0000453 name: Langerhans cell namespace: cell def: "Langerhans cell is a conventional dendritic cell that has plasma membrane part CD207. A Langerhans cell is a stellate dendritic cell of myeloid origin, that appears clear on light microscopy and has a dark-staining, indented nucleus and characteristic inclusions (Birbeck granules) in the cytoplasm; Langerhans cells are found principally in the stratum spinosum of the epidermis, but they also occur in other stratified epithelia and have been identified in the lung, lymph nodes, spleen, and thymus." [GO_REF:0000031, GOC:add, GOC:amm, ISBN:0721601464, ISBN:0781735149, PMCID:PMC2346585, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000021 )(PMID:19243617). These cells are also CD1a-high, CD14-negative, CD207-positive (langerin), CD324-positive (E-cadherin), and DCIR-positive. They reside in the epidermis. synonym: "Langerhans' cell" EXACT [] synonym: "LC" EXACT [] xref: BTO:0000705 xref: FMA:63072 is_a: CL:0000990 ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: capable_of GO:0002828 ! regulation of type 2 immune response intersection_of: has_plasma_membrane_part PR:000001293 ! C-type lectin domain family 4 member K relationship: capable_of GO:0002828 ! regulation of type 2 immune response relationship: develops_from CL:0000763 ! myeloid cell relationship: has_plasma_membrane_part PR:000001293 ! C-type lectin domain family 4 member K [Term] id: CL:0000454 name: epinephrine secreting cell namespace: cell def: "A cell capable of producing epinephrine. Epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme, which is expressed in the adrenal glands, androgenic neurons, and in other cell types." [GOC:tfm, PMID:12438093] synonym: "adrenaline secreting cell" EXACT [GO:0048242] synonym: "epinephrin secreting cell" EXACT [] is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0048242 ! epinephrine secretion relationship: capable_of GO:0048242 ! epinephrine secretion [Term] id: CL:0000455 name: starch sheath cell namespace: cell def: "Obsolete. Use PO:0004531 from Plant Ontology instead. A cell characterized by conspicuous and rather stable accumulation of starch." [ISBN:044174520] comment: replaced_by: PO:0004531 is_obsolete: true [Term] id: CL:0000456 name: mineralocorticoid secreting cell namespace: cell is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0035931 ! mineralocorticoid secretion relationship: capable_of GO:0035931 ! mineralocorticoid secretion [Term] id: CL:0000457 name: biogenic amine secreting cell namespace: cell is_a: CL:0000163 ! endocrine cell [Term] id: CL:0000458 name: serotonin secreting cell namespace: cell def: "A cell type that secretes 5-Hydroxytryptamine (serotonin)." [GOC:tfm, PMID:19630576] synonym: "5-HT secreting cell" EXACT [] synonym: "5-Hydroxytryptamine secreting cell" EXACT [] is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0001820 ! serotonin secretion relationship: capable_of GO:0001820 ! serotonin secretion [Term] id: CL:0000459 name: norepinephrin secreting cell namespace: cell def: "A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme." [GOC:tfm, ISBN:068340007X] synonym: "noradrenalin secreting cell" EXACT [] is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0048243 ! norepinephrine secretion relationship: capable_of GO:0048243 ! norepinephrine secretion [Term] id: CL:0000460 name: glucocorticoid secreting cell namespace: cell is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0035933 ! glucocorticoid secretion relationship: capable_of GO:0035933 ! glucocorticoid secretion [Term] id: CL:0000462 name: adepithelial cell namespace: cell xref: FBbt:00003219 is_a: CL:0000680 ! muscle precursor cell [Term] id: CL:0000463 name: epidermal cell (sensu arthropoda) namespace: cell def: "An epidermal cell that secretes chitinous cuticle from its apical side." [FlyBase:ds, ISBN:ISBN\:978-0801481253] comment: While insect epidermis is generally columnar/cuboidal, there are certainly well studied cases where it is not (e.g.- Rhodnius prolixus when starved). So it would be safer to add this as a differentium for particular species where this is known. -DSJ. is_a: CL:0000362 ! epidermal cell relationship: develops_from CL:0000464 ! epidermoblast [Term] id: CL:0000464 name: epidermoblast namespace: cell def: "An epidermal progenitor cell that arises from neuroectoderm and in turn gives rise to the epidermal sheath of ventral and cephalic regions." [GOC:tfm, PMID:7576311] xref: FBbt:00004994 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000710 ! neurecto-epithelial cell relationship: develops_from CL:0000114 ! surface ectodermal cell [Term] id: CL:0000465 name: cardioblast (sensu Arthropoda) namespace: cell xref: FBbt:00001666 is_a: CL:0000513 ! cardiac muscle myoblast [Term] id: CL:0000467 name: adrenocorticotropic hormone secreting cell namespace: cell alt_id: CL:0000640 def: "A peptide hormone secreting cell that produces adrenocorticotropin, or corticotropin." [GOC:tfm, SANBI:mhl] synonym: "ACTH secreting cell" EXACT [GO:0051458] synonym: "adrenocorticotrophic hormone secreting cell" EXACT [] synonym: "corticotrophin hormone secreting cell" EXACT [] synonym: "corticotropin hormone secreting cell" EXACT [] synonym: "corticotropin secreting cell" EXACT [GO:0051458] is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0051458 ! corticotropin secretion relationship: capable_of GO:0051458 ! corticotropin secretion [Term] id: CL:0000468 name: neuroglioblast namespace: cell xref: FBbt:00005147 is_a: CL:0000047 ! neuronal stem cell is_a: CL:0000055 ! non-terminally differentiated cell [Term] id: CL:0000469 name: ganglion mother cell namespace: cell xref: FBbt:00005149 is_a: CL:0000468 ! neuroglioblast [Term] id: CL:0000470 name: digestive enzyme secreting cell namespace: cell is_a: CL:0000154 ! protein secreting cell [Term] id: CL:0000472 name: chlorenchyma cell namespace: cell def: "Obsolete. Use PO:0000076 from Plant Ontology instead. OBSOLETE, use term from Plant Ontology. Parenchyma cells containing chloroplasts; a component of leaf mesophyll and other green parenchyma tissue." [ISBN:0471245208] comment: replaced_by: PO:0000076 is_obsolete: true [Term] id: CL:0000473 name: defensive cell namespace: cell def: "A cell whose primary function is to protect the organism." [JB:jb] is_a: CL:0000003 ! native cell [Term] id: CL:0000474 name: pericardial nephrocyte namespace: cell def: "an insect renal cell that filters hemolymph and is found with other pericardial nephrocytes in two rows flanking the dorsal vessel." [FBbt:00003184, GO:0061320, GOC:tfm, PMID:19783135] synonym: "pericardial cell" NARROW [FBbt:00005058, GO:0061320] xref: FBbt:00005058 is_a: CL:0000519 ! phagocyte (sensu Nematoda and Protostomia) is_a: CL:0002520 ! nephrocyte [Term] id: CL:0000475 name: degenerate megaspore namespace: cell def: "Obsolete. Use PO:0000245 from Plant Ontology instead. In monosporic and bisporic megasporogenesis: the megaspore(s) that do not participate in megagametogenesis." [TAIR:lr] comment: replaced_by: PO:0000245 is_obsolete: true [Term] id: CL:0000476 name: thyrotroph namespace: cell def: "A basophil cell of the anterior pituitary that produces thyroid stimulating hormone, thyrotrophin. This cell type is elongated, polygonal and lie in clusters towards the adenohypophyseal center." [ISBN:0517223651, SANBI:mhl] synonym: "beta-basophil" EXACT [] synonym: "thyroid stimulating hormone secreting cell" EXACT [] synonym: "thyrotrope" EXACT [] xref: FMA:83099 is_a: CL:0000639 ! basophil cell of pars distalis of adenohypophysis relationship: capable_of GO:0070460 ! thyroid-stimulating hormone secretion [Term] id: CL:0000477 name: follicle cell namespace: cell comment: Editors note: check this. Currently used in goxp synonym: "ovarian follicle cell" EXACT [GO:0007297] xref: FBbt:00004904 is_a: CL:0000075 ! columnar/cuboidal epithelial cell relationship: develops_from CL:0000441 ! follicle stem cell [Term] id: CL:0000478 name: oxytocin stimulating hormone secreting cell namespace: cell def: "A peptide hormone secreting cell that secretes oxytocin stimulating hormone" [GO:tfm] is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000479 name: vasopressin stimulating hormone secreting cell namespace: cell def: "A peptide hormone secreting cell that secretes vasopressin stimulating hormone" [GO:tfm] is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000480 name: secretin stimulating hormone secreting cell namespace: cell def: "A peptide hormone secreting cell that secretes secretin stimulating hormone" [GO:tfm] is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000481 name: cholecystokin stimulating hormone secreting cell namespace: cell def: "A peptide hormone secreting cell that secretes cholecystokin stimulating hormone" [GO:tfm] is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000482 name: juvenile hormone secreting cell namespace: cell def: "An endocrine cell that secretes juvenile hormone." [GO:tfm] is_a: CL:0000163 ! endocrine cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0045443 ! juvenile hormone secretion relationship: capable_of GO:0045443 ! juvenile hormone secretion [Term] id: CL:0000483 name: bombesin stimulating hormone secreting cell namespace: cell def: "A peptide hormone secreting cell that secretes cholecystokin stimulating hormone" [GO:tfm] is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000484 name: connective tissue type mast cell namespace: cell def: "Mast cell subtype whose granules contain both the serine proteases tryptase and chymase. These cells are primarily found in connective tissue, such as the peritoneal cavity, skin, and intestinal submucosa. Their development is T-cell independent." [GOC:add, GOC:dsd, GOC:tfm, PMID:19923473, PMID:9354811] comment: They are CD88-positive. The cytoplasmic granules contain high levels of histamine and heparin (mouse) or major neutral proteases, tryptase, chymase, carboxypeptidase A, and cathepsin G (humans). Reportedly, they cannot produce leukotrienes (LTC4) and IL-4. They are reportedly very heterogeneous depending upon location and can convert to the MC(T) phenotype. synonym: "MC(TC)" EXACT [] synonym: "MCTC" EXACT [] synonym: "TC mast cells" EXACT [] is_a: CL:0000097 ! mast cell is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0000097 ! mast cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue [Term] id: CL:0000485 name: mucosal type mast cell namespace: cell def: "Mast cell subtype that contains only the serine protease trypase in its granules. These cells are primarily found in mucosal tissue, such as intestinal mucosa and alveoli. They depend upon T-cells for development of phenotype." [GOC:add, GOC:dsd, PMID:19923473, PMID:9354811] comment: They are CD88-negative. The cytoplasmic granules contain low levels of histamine and high levels of chondroitin sulfate (mouse) or major neutral proteases and tryptase (humans). Additionally, they can produce leukotrienes (LTC4), IL-5, IL-6, and low levels of IL-4. They are reportedly very heterogeneous depending upon location and can convert to the MC(T) phenotype. synonym: "MC(T)" EXACT [] synonym: "MCT" EXACT [] synonym: "T mast cells" EXACT [] is_a: CL:0000097 ! mast cell intersection_of: CL:0000097 ! mast cell intersection_of: capable_of GO:0002540 ! leukotriene production involved in inflammatory response intersection_of: part_of UBERON:0001961 ! mucosa-associated lymphoid tissue relationship: capable_of GO:0002540 ! leukotriene production involved in inflammatory response relationship: part_of UBERON:0001961 ! mucosa-associated lymphoid tissue [Term] id: CL:0000486 name: garland cell namespace: cell def: "A large binucleate cell that forms a 'garland' around the anterior end of the proventriculus (cardia) at its junction with the esophagus in both adults and larvae flies. Each cell is surrounded by a basement membrane and there are numerous micro-invaginations (lacunae) extending from the surface into the cytoplasm. At the mouth of each lacuna is a doubled filament forming a specialised filtration system (diaphragm). The filtrate is endocytosed from the lacunae." [fbbt:00005059, GOC:tfm, PMID:19783135] synonym: "garland nephrocyte" BROAD [GO:0061321] xref: BTO:0004596 xref: FBbt:00005059 is_a: CL:0000227 ! binucleate cell is_a: CL:0000519 ! phagocyte (sensu Nematoda and Protostomia) is_a: CL:0002520 ! nephrocyte [Term] id: CL:0000487 name: oenocyte namespace: cell def: "A large secretory cell found in clusters underlying the epidermis of the abdominal segments of larval abdominal segments." [GOC:bf, PMID:11171397] xref: FBbt:00004995 is_a: CL:0000151 ! secretory cell [Term] id: CL:0000488 name: visible light photoreceptor cell namespace: cell def: "A photoreceptor cell that detects visible light." [GOC:tfm] is_a: CL:0000210 ! photoreceptor cell [Term] id: CL:0000489 name: scotopic photoreceptor cell namespace: cell is_a: CL:0000210 ! photoreceptor cell [Term] id: CL:0000490 name: photopic photoreceptor cell namespace: cell is_a: CL:0000488 ! visible light photoreceptor cell [Term] id: CL:0000491 name: cytotoxic T cell namespace: cell def: "OBSOLETE: A cell responsible for spontaneous cytotoxicity of a variety of tumor cells without prior immunization. These natural killer cells are found in non-immune humans and experimental animals and are thought by some to be the same as killer cells (killing by antibody-dependent cell cytotoxicity), but they can also kill in the absence of antibody." [] comment: This term had an incorrect definition and was overly broad. Consider using 'cytotoxic T cell ; CL:0000910' (in most cases) or another lymphocyte cell type if cytotoxicity is shown to be part of the cell's phenotype in a particular experimental situation. is_obsolete: true [Term] id: CL:0000492 name: CD4-positive helper T cell namespace: cell def: "A CD4-positive, alpha-beta T cell that cooperates with other lymphocytes via direct contact or cytokine release to initiate a variety of immune functions." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, ISBN:0781735149, MESH:A11.118.637.555.567.569.200.400] synonym: "CD4-positive helper T lymphocyte" EXACT [] synonym: "CD4-positive helper T-cell" EXACT [] synonym: "CD4-positive helper T-lymphocyte" EXACT [] synonym: "CD4-positive T-helper cell" EXACT [] xref: FMA:70572 is_a: CL:0000624 ! CD4-positive, alpha-beta T cell is_a: CL:0000912 ! helper T cell intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0001816 ! cytokine production relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell relationship: has_completed GO:0030217 ! T cell differentiation [Term] id: CL:0000493 name: regulatory T cell namespace: cell def: "OBSOLETE: Subpopulation of CD4+ cells which induce CD8+ suppressor T cells to suppress antibody production by B cells. They also stimulate other cellular immune responses." [] comment: This term was defined too narrowly; consider using the term 'regulatory T cell ; CL:0000815' instead. is_obsolete: true [Term] id: CL:0000494 name: UV sensitive photoreceptor cell namespace: cell def: "A photoreceptor cell that detects ultraviolet light." [GOC:tfm] is_a: CL:0000210 ! photoreceptor cell [Term] id: CL:0000495 name: blue sensitive photoreceptor cell namespace: cell def: "A photoreceptor cell that is sensitive to blue light." [GO:tfm] is_a: CL:0000490 ! photopic photoreceptor cell [Term] id: CL:0000496 name: green sensitive photoreceptor cell namespace: cell def: "A photoreceptor cell that is sensitive to green light." [GO:tfm] is_a: CL:0000490 ! photopic photoreceptor cell [Term] id: CL:0000497 name: red sensitive photoreceptor cell namespace: cell def: "A photoreceptor cell that is sensitive to red light." [GO:tfm] is_a: CL:0000490 ! photopic photoreceptor cell [Term] id: CL:0000498 name: inhibitory interneuron namespace: cell def: "An interneuron (also called relay neuron, association neuron or local circuit neuron) is a multipolar neuron which connects afferent neurons and efferent neurons in neural pathways. Like motor neurons, interneuron cell bodies are always located in the central nervous system (CNS)." [GOC:tfm, http://en.wikipedia.org/wiki/Interneuron] xref: FMA:84776 is_a: CL:0000099 ! interneuron [Term] id: CL:0000499 name: stromal cell namespace: cell def: "A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere." [GOC:tfm, MESH:A11.329.830] xref: BTO:0002064 xref: FMA:83624 is_a: CL:0002320 ! connective tissue cell relationship: develops_from CL:0000134 ! mesenchymal cell [Term] id: CL:0000500 name: follicular epithelial cell namespace: cell is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000501 name: granulosa cell namespace: cell def: "A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors." [MESH:A05.360.319.114.630.535.200] synonym: "granulosa cell of ovary" EXACT [] xref: BTO:0000542 xref: FMA:18718 is_a: CL:0000174 ! steroid hormone secreting cell is_a: CL:0002174 ! follicular cell of ovary [Term] id: CL:0000502 name: type D enteroendocrine cell namespace: cell def: "A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin." [MESH:A03.492.766.440.175] synonym: "D cell" EXACT [] xref: FMA:62935 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000172 ! somatostatin secreting cell [Term] id: CL:0000503 name: theca cell namespace: cell def: "A flattened stroma cell forming a sheath or theca outside the basal lamina lining the mature ovarian follicle. Thecal interstitial or stromal cells are steroidogenic, and produce primarily androgens which serve as precusors of estrogens in the granulosa cells." [MESH:A05.360.319.114.630.535.400] xref: BTO:0002850 xref: FMA:18690 is_a: CL:0000499 ! stromal cell is_a: CL:0000593 ! androgen secreting cell [Term] id: CL:0000504 name: enterochromaffin-like cell namespace: cell def: "A enteroendocrine cell part of the glands of the gastric mucosa. They produce histamine and peptides such as chromogranins. This cell type respond to gastrin by releasing histamine which acts as a paracrine stimulator of the release of hydrochloric acid from the gastric parietal cells." [GOC:tfm, MESH:A06.224.365] comment: Consider enterochromaffin cell (CL:0002065). For several years this cell type was "enterochromaffin cell" despite a MESH dbxref and a free text definition that clearly meant enterochromaffin-like cell. synonym: "ECL" EXACT [] xref: BTO:0002692 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0002274 ! histamine secreting cell [Term] id: CL:0000505 name: substance P secreting cell namespace: cell def: "A peptide hormone secreting cell that secretes substance P." [GO:tfm] is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000506 name: enkephalin secreting cell namespace: cell def: "An endorphine cell that secretes enkephalin." [GO:tfm] is_a: CL:0000507 ! endorphin secreting cell [Term] id: CL:0000507 name: endorphin secreting cell namespace: cell def: "A peptide hormone secreting cell that secretes endorphin." [GO:tfm] is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000508 name: type G enteroendocrine cell namespace: cell def: "An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli." [GOC:tfm, ISBN:0517223651, MESH:A03.492.766.440.300] synonym: "G cell " EXACT [] xref: BTO:0004108 xref: FMA:67609 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000506 ! enkephalin secreting cell is_a: CL:0000509 ! gastrin secreting cell [Term] id: CL:0000509 name: gastrin secreting cell namespace: cell def: "A peptide hormone secreting cell that secretes gastrin." [GO:tfm] is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000510 name: paneth cell namespace: cell def: "An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix." [GOC:tfm, ISBN:0517223651, MESH:A03.492.411.369.700] xref: BTO:0000993 xref: FMA:62897 is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000323 ! lysozyme secreting cell is_a: CL:0002563 ! intestinal epithelial cell intersection_of: CL:0000150 ! glandular epithelial cell intersection_of: part_of UBERON:0001277 ! intestinal epithelium relationship: part_of UBERON:0001277 ! intestinal epithelium [Term] id: CL:0000511 name: androgen binding protein secreting cell namespace: cell def: "A peptide hormone secreting cell that secretes androgen binding protein." [GO:tfm] is_a: CL:0000154 ! protein secreting cell [Term] id: CL:0000512 name: paracrine cell namespace: cell def: "A paracrine cell is a secretory cell that secretes an agonist into intercellular spaces in which it diffuses to a target cell other than that which produced it." [GOC:tfm, ISBN:0198529171] is_a: CL:0000151 ! secretory cell [Term] id: CL:0000513 name: cardiac muscle myoblast namespace: cell alt_id: CL:0000714 def: "A precursor cell destined to differentiate into cardiac muscle cell." [GOC:tfm, MESH:A11.635.470] xref: FMA:84797 is_a: CL:0000056 ! myoblast [Term] id: CL:0000514 name: smooth muscle myoblast namespace: cell def: "A precursor cell destined to differentiate into smooth muscle myocytes." [GOC:tfm, MESH:A11.635.510, MESH:D032390] synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] synonym: "satellite cell" RELATED [] xref: FMA:84798 is_a: CL:0000056 ! myoblast [Term] id: CL:0000515 name: skeletal muscle myoblast namespace: cell def: "A myoblast that differentiates into skeletal muscle fibers." [SANBI:mhl] synonym: "skeletal myoblast" EXACT [] xref: FMA:84799 is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue relationship: part_of UBERON:0001134 ! skeletal muscle tissue [Term] id: CL:0000516 name: perineuronal satellite cell namespace: cell def: "A non-neuronal cell that surrounds the neuronal cell bodies of the ganglia." [GOC:tfm, MESH:A08.340.685] synonym: "perineural satellite cell" EXACT [] synonym: "perineuronal satellite oligodendroglial cell" EXACT [] synonym: "satellite oligodendrocyte" EXACT [] xref: FMA:54550 is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) is_a: CL:0000243 ! glial cell (sensu Vertebrata) relationship: develops_from CL:0000339 ! glioblast (sensu Vertebrata) [Term] id: CL:0000517 name: macrophage derived foam cell namespace: cell def: "A type of foam cell derived from a macrophage containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions." [GOC:add, PMID:20213546] is_a: CL:0000891 ! foam cell relationship: develops_from CL:0000235 ! macrophage [Term] id: CL:0000518 name: phagocyte (sensu Vertebrata) namespace: cell def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] is_a: CL:0000234 ! phagocyte [Term] id: CL:0000519 name: phagocyte (sensu Nematoda and Protostomia) namespace: cell def: "A phagocyte from organisms in the Nematoda or Protostomia clades." [GOC:tfm] is_a: CL:0000234 ! phagocyte [Term] id: CL:0000520 name: prokaryotic cell namespace: cell is_a: CL:0000003 ! native cell [Term] id: CL:0000521 name: fungal cell namespace: cell is_a: CL:0000255 ! eukaryotic cell disjoint_from: CL:0000548 ! animal cell [Term] id: CL:0000522 name: spore namespace: cell def: "The reproductive structure of bacteria, fungi and cryptograms." [ISBN:08199377X] is_obsolete: true [Term] id: CL:0000523 name: mononuclear cytotrophoblast cell namespace: cell def: "A cell from the inner layer of the trophoblast of the early mammalian embryo that gives rise to the outer surface and villi of the chorion. Mononuclear crytoblasts fuse to give rise to a multinuclear cytotrophoblast." [GOC:tfm, ISBN:0323052908] synonym: "Langhans' cell" EXACT [] xref: FMA:83042 is_a: CL:0000351 ! trophoblast cell [Term] id: CL:0000524 name: spheroplast namespace: cell def: "A cell, usually of bacteria or yeast, which has partially lost its cell wall." [MESH:A11.868] synonym: "sphaeroplast" EXACT [] is_a: CL:0000371 ! protoplast [Term] id: CL:0000525 name: syncytiotrophoblast cell namespace: cell def: "A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo. It It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy." [GOC:tfm, ISBN:0323052908] synonym: "plasmidotrophoblast" EXACT [] synonym: "syncytial trophoblast" EXACT [] synonym: "syntrophoblast" EXACT [] xref: FMA:83043 is_a: CL:0000228 ! multinucleate cell is_a: CL:0000351 ! trophoblast cell [Term] id: CL:0000526 name: afferent neuron namespace: cell def: "A neuron which conveys sensory information centrally from the periphery." [GOC:tfm, MESH:A08.663.650] synonym: "input neuron" EXACT [] xref: FMA:87653 is_a: CL:0000540 ! neuron [Term] id: CL:0000527 name: efferent neuron namespace: cell def: "A neuron which sends impulses peripherally to activate muscles or secretory cells." [MESH:A08.663.655] synonym: "output neuron" EXACT [] is_a: CL:0000540 ! neuron [Term] id: CL:0000528 name: nitrergic neuron namespace: cell def: "A nerve cell where transmission is mediated by nitric oxide." [MESH:A08.663.748] xref: FMA:84792 is_a: CL:0000540 ! neuron [Term] id: CL:0000529 name: pigmented epithelial cell namespace: cell is_a: CL:0000710 ! neurecto-epithelial cell [Term] id: CL:0000530 name: primary neuron namespace: cell is_a: CL:0000540 ! neuron [Term] id: CL:0000531 name: primary sensory neuron namespace: cell is_a: CL:0000101 ! sensory neuron is_a: CL:0000530 ! primary neuron [Term] id: CL:0000532 name: CAP motoneuron namespace: cell is_a: CL:0000533 ! primary motor neuron [Term] id: CL:0000533 name: primary motor neuron namespace: cell xref: FMA:83619 is_a: CL:0000100 ! motor neuron is_a: CL:0000530 ! primary neuron [Term] id: CL:0000534 name: primary interneuron namespace: cell is_a: CL:0000099 ! interneuron is_a: CL:0000530 ! primary neuron [Term] id: CL:0000535 name: secondary neuron namespace: cell is_a: CL:0000540 ! neuron [Term] id: CL:0000536 name: secondary motor neuron namespace: cell xref: FMA:83620 is_a: CL:0000100 ! motor neuron is_a: CL:0000535 ! secondary neuron [Term] id: CL:0000537 name: antipodal cell namespace: cell def: "Obsolete. Use PO:0020093 from Plant Ontology instead. OBSOLETE, use term from plant ontology. A cell located at the chalazal end of the mature embryo sac in angiosperms." [ISBN:047125208] comment: replaced_by: PO:0020093 is_obsolete: true [Term] id: CL:0000538 name: epidermal initial namespace: cell def: "Obsolete. Use PO:0000349 from Plant Ontology instead. A relatively unspecialized cell that will give rise to specialized cell types of the epidermis." [TAIR:lr] comment: replaced_by: PO:0000349 is_obsolete: true [Term] id: CL:0000539 name: idioblast namespace: cell def: "A cell in a tissue that markedly differs in form, size, or contents from other cells in the same tissue." [ISBN:0471245208] is_obsolete: true [Term] id: CL:0000540 name: neuron namespace: cell def: "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [http://en.wikipedia.org/wiki/Neuron, MESH:A08.663, MESH:D009474] comment: These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: FBbt:00005106 xref: FMA:54527 xref: VHOG:0001483 xref: WBbt:0003679 is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: develops_from CL:0000031 ! neuroblast [Term] id: CL:0000541 name: melanoblast namespace: cell def: "A cell that originates from the neural crest and differentiates into a pigment cell." [GOC:tfm, SANBI:mhl] comment: Derived from UBERON:0002342 neural crest. xref: BTO:0003217 xref: FMA:83377 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000710 ! neurecto-epithelial cell relationship: develops_from CL:0000333 ! migratory neural crest cell [Term] id: CL:0000542 name: lymphocyte namespace: cell def: "A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." [GOC:add, ISBN:0683073696, ISBN:0781735149] comment: Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) xref: BTO:0000775 xref: FMA:62863 xref: VHOG:0001535 is_a: CL:0002087 ! nongranular leukocyte is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000738 ! leukocyte intersection_of: has_part CP:0000000 ! neutrophillic cytoplasm intersection_of: has_part CP:0000037 ! increased nucleus size intersection_of: has_part GO:0000792 ! heterochromatin intersection_of: lacks_part GO:0030141 ! secretory granule disjoint_from: CL:0000766 ! myeloid leukocyte relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: has_part CP:0000000 ! neutrophillic cytoplasm relationship: has_part CP:0000037 ! increased nucleus size relationship: has_part GO:0000792 ! heterochromatin relationship: lacks_part GO:0030141 ! secretory granule [Term] id: CL:0000543 name: sieve tube member namespace: cell def: "Obsolete. Use PO:0000289 from Plant Ontology instead. One of the series of cellular components of a sieve tube. It shows a more or less pronounced differentiation between sieve plates (wide pores) and lateral sieve areas (narrow pores). Also sieve tube element and the obsolete sieve tube segment." [ISBN:0471245208] comment: replaced_by: PO:0000289 synonym: "sieve tube element" EXACT [] is_obsolete: true [Term] id: CL:0000544 name: slowly adapting mechanoreceptor cell namespace: cell is_a: CL:0000199 ! mechanoreceptor cell [Term] id: CL:0000545 name: T-helper 1 cell namespace: cell def: "A CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive and produces interferon-gamma." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19375293, PMID:20303875] synonym: "helper T cell type 1" EXACT [] synonym: "T helper cells type 1" EXACT [PMID:9419219] synonym: "T(H)-1 cell" EXACT [] synonym: "Th1 cell" EXACT [] synonym: "Th1 T cell" EXACT [] synonym: "Th1 T lymphocyte" EXACT [] synonym: "Th1 T-cell" EXACT [] synonym: "Th1 T-lymphocyte" EXACT [] xref: BTO:0001678 xref: FMA:84382 is_a: CL:0000492 ! CD4-positive helper T cell intersection_of: CL:0000492 ! CD4-positive helper T cell intersection_of: capable_of GO:0032609 ! interferon-gamma production intersection_of: has_part PR:000001835 ! T-box transcription factor TBX21 relationship: capable_of GO:0032609 ! interferon-gamma production relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell relationship: has_part PR:000001835 ! T-box transcription factor TBX21 [Term] id: CL:0000546 name: T-helper 2 cell namespace: cell def: "A CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive and produces interleukin-4." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19375293, PMID:20103781] synonym: "helper T cell type 2" EXACT [] synonym: "T helper cells type 2" EXACT [PMID:9419219] synonym: "T(H)-2 cell" EXACT [] synonym: "Th2 cell" EXACT [] synonym: "Th2 T cell" EXACT [] synonym: "Th2 T lymphocyte" EXACT [] synonym: "Th2 T-cell" EXACT [] synonym: "Th2 T-lymphocyte" EXACT [] xref: BTO:0001679 xref: FMA:84385 is_a: CL:0000492 ! CD4-positive helper T cell intersection_of: CL:0000492 ! CD4-positive helper T cell intersection_of: capable_of GO:0032633 ! interleukin-4 production intersection_of: has_part PR:000001941 ! trans-acting T-cell-specific transcription factor GATA-3 relationship: capable_of GO:0032633 ! interleukin-4 production relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell relationship: has_part PR:000001941 ! trans-acting T-cell-specific transcription factor GATA-3 [Term] id: CL:0000547 name: proerythroblast namespace: cell def: "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers." [ISBN:0721601464, MESH:A11.118.290.350.200, PMID:1638021] synonym: "pronormoblast" RELATED [] synonym: "rubriblast" EXACT [ISBN:0721601464] xref: FMA:83518 is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: has_part CP:0000028 ! basophilic cytoplasm intersection_of: has_part CP:0000037 ! increased nucleus size intersection_of: has_part GO:0005634 ! nucleus intersection_of: has_part GO:0005730 ! nucleolus intersection_of: has_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G relationship: develops_from CL:0000038 ! erythroid progenitor cell relationship: has_part CP:0000028 ! basophilic cytoplasm relationship: has_part CP:0000037 ! increased nucleus size relationship: has_part GO:0005634 ! nucleus relationship: has_part GO:0005730 ! nucleolus relationship: has_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G [Term] id: CL:0000548 name: animal cell namespace: cell subset: ubprop:upper_level is_a: CL:0000255 ! eukaryotic cell [Term] id: CL:0000549 name: basophilic erythroblast namespace: cell def: "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers." [GOC:tfm, ISBN:0721601464] synonym: "basophilic normoblast" EXACT [ISBN:0721601464] synonym: "early erythroblast" EXACT [ISBN:0721601464] synonym: "early normoblast" EXACT [ISBN:0721601464] synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 is_a: CL:0000765 ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CP:0000028 ! basophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin intersection_of: has_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 relationship: develops_from CL:0000547 ! proerythroblast relationship: has_part CP:0000028 ! basophilic cytoplasm relationship: has_part GO:0000792 ! heterochromatin relationship: has_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 [Term] id: CL:0000550 name: polychromatophilic erythroblast namespace: cell def: "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers." [ISBN:0721601464] synonym: "intermediate erythroblast" EXACT [ISBN:0721601464] synonym: "intermediate normoblast" EXACT [ISBN:0721601464] synonym: "polychromatic erythroblast" EXACT [ISBN:0721601464] synonym: "polychromatic normoblast" EXACT [ISBN:0721601464] synonym: "polychromatophilic normoblast" EXACT [ISBN:0721601464] synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 is_a: CL:0000765 ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CP:0000035 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin intersection_of: has_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 relationship: develops_from CL:0000549 ! basophilic erythroblast relationship: has_part CP:0000035 ! polychromatophilic cytoplasm relationship: has_part GO:0000792 ! heterochromatin relationship: has_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 [Term] id: CL:0000551 name: unimodal nocireceptor namespace: cell is_a: CL:0000198 ! pain receptor cell [Term] id: CL:0000552 name: orthochromatic erythroblast namespace: cell def: "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated." [ISBN:0721601464] synonym: "acidophilic erythroblast" EXACT [ISBN:0721601464] synonym: "eosinophilic erythroblast" EXACT [ISBN:0721601464] synonym: "late erythoblast" EXACT [] synonym: "orthochromatic normoblast" EXACT [ISBN:0721601464] synonym: "pyknotic eto enrythroblast" EXACT [ISBN:0721601464] xref: FMA:84646 is_a: CL:0000765 ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CP:0000027 ! acidophilic cytoplasm intersection_of: participates_in GO:0030263 ! apoptotic chromosome condensation relationship: develops_from CL:0000550 ! polychromatophilic erythroblast relationship: has_part CP:0000027 ! acidophilic cytoplasm relationship: participates_in GO:0030263 ! apoptotic chromosome condensation [Term] id: CL:0000553 name: megakaryocyte progenitor cell namespace: cell def: "The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative)." [GOC:dsd, GOC:tfm, ISBN:0721601464] comment: Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. synonym: "CFU-Meg" EXACT [PMID:11722431, PMID:12482498] synonym: "colony-forming unit-megakaryocyte" EXACT [] synonym: "Meg-CFC" EXACT [PMCID:PMC1794060] synonym: "megacaryoblast" EXACT [] synonym: "megacaryocyte progenitor cell" EXACT [] synonym: "megakaryoblast" EXACT [] synonym: "megakaryocytic progenitor cell" EXACT [PMID:12482498] synonym: "MkP" EXACT [PMID:21116988] synonym: "promegacaryocyte" RELATED [] synonym: "promegakaryocyte" RELATED [] xref: BTO:0001164 xref: FMA:84235 is_a: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0007113 ! endomitotic cell cycle intersection_of: capable_of GO:0030219 ! megakaryocyte differentiation intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G intersection_of: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 relationship: capable_of GO:0007113 ! endomitotic cell cycle relationship: capable_of GO:0030219 ! megakaryocyte differentiation relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G relationship: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 [Term] id: CL:0000554 name: gastrin stimulating hormone secreting cell namespace: cell def: "A peptide hormone secreting cell that secretes gastrin stimulating hormone." [GOC:tfm] is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000555 name: neuronal brush cell namespace: cell is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) [Term] id: CL:0000556 name: megakaryocyte namespace: cell def: "A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm." [http://en.wikipedia.org/wiki/Megakaryocyte, ISBN:0721601464, MESH:D008533] comment: Megakaryocytes are reportedly CD181-positive and CD182-positive. synonym: "megacaryocyte" EXACT [] synonym: "megalocaryocyte" EXACT [] synonym: "megalokaryocyte" EXACT [] xref: BTO:0000843 xref: FMA:83555 is_a: CL:0000763 ! myeloid cell is_a: CL:0002092 ! bone marrow cell intersection_of: CL:0000763 ! myeloid cell intersection_of: has_quality PATO:0001393 ! euploid intersection_of: part_of UBERON:0002371 ! bone marrow disjoint_from: CL:0000764 ! erythroid lineage cell relationship: develops_from CL:0000553 ! megakaryocyte progenitor cell relationship: has_quality PATO:0001393 ! euploid relationship: part_of UBERON:0002371 ! bone marrow [Term] id: CL:0000557 name: granulocyte monocyte progenitor cell namespace: cell def: "A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1." [GO_REF:0000031, GOC:amm, GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/CFU-GM, http://www.copewithcytokines.de, ISBN:0721601464, MESH:D055014, PMCID:PMC2213186, PMCID:PMC548021, PMID:16551251, PMID:16647566] comment: Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. synonym: "CFU-C , Colony forming unit in culture" BROAD [http://www.copewithcytokines.de] synonym: "CFU-GM" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "colony forming unit granulocyte macrophage" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "GMP" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "granulocyte-macrophage progenitor" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "granulocyte/monocyte precursor" EXACT [] synonym: "granulocyte/monocyte progenitor" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell is_a: CL:0002092 ! bone marrow cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030225 ! macrophage differentiation intersection_of: capable_of GO:0030851 ! granulocyte differentiation intersection_of: has_part PR:000001944 ! transcription factor PU.1 intersection_of: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha intersection_of: has_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain intersection_of: lacks_part PR:000007857 ! erythroid transcription factor intersection_of: lacks_part PR:000007858 ! endothelial transcription factor GATA-2 intersection_of: part_of UBERON:0002371 ! bone marrow relationship: capable_of GO:0030225 ! macrophage differentiation relationship: capable_of GO:0030851 ! granulocyte differentiation relationship: develops_from CL:0000049 ! common myeloid progenitor relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain relationship: lacks_part PR:000007857 ! erythroid transcription factor relationship: lacks_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: part_of UBERON:0002371 ! bone marrow [Term] id: CL:0000558 name: reticulocyte namespace: cell def: "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds." [GOC:add, GOC:tfm, PMID:15946868, PMID:2037622] xref: BTO:0001173 is_a: CL:0000764 ! erythroid lineage cell intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular vesicular exosome assembly intersection_of: has_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G relationship: capable_of GO:0071971 ! extracellular vesicular exosome assembly relationship: develops_from CL:0000552 ! orthochromatic erythroblast relationship: has_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G [Term] id: CL:0000559 name: promonocyte namespace: cell def: "A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules." [GOC:tfm, ISBN:0721601464] comment: Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. xref: BTO:0004657 xref: FMA:83551 is_a: CL:0002194 ! monopoietic cell intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: capable_of GO:0030224 ! monocyte differentiation relationship: develops_from CL:0000040 ! monoblast relationship: has_part GO:0042582 ! azurophil granule relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M [Term] id: CL:0000560 name: band form neutrophil namespace: cell def: "A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative." [GOC:add, GOC:dsd, GOC:tfm, http://www.cap.org, ISBN:0721601464, PMID:10618520, PMID:12560239, PMID:15514007] comment: They are found in the Band 1 fraction. synonym: "band" BROAD [] synonym: "band cell" BROAD [] synonym: "band form" BROAD [] synonym: "rod neutrophil" EXACT [] synonym: "stab cell" BROAD [] is_a: CL:0000776 ! immature neutrophil is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000776 ! immature neutrophil intersection_of: has_part CP:0000039 ! banded nucleus intersection_of: has_part PR:000001944 ! transcription factor PU.1 intersection_of: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha intersection_of: has_part PR:000007597 ! proto-oncogene c-Fos intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001337 ! complement receptor type 1 intersection_of: has_plasma_membrane_part PR:000001580 ! fMet-Leu-Phe receptor intersection_of: lacks_part PR:000009978 ! lactotransferrin intersection_of: lacks_part PR:000010799 ! myb proto-oncogene protein intersection_of: lacks_plasma_membrane_part PR:000009129 ! integrin alpha-4 intersection_of: lacks_plasma_membrane_part PR:000010543 ! myeloperoxidase relationship: develops_from CL:0000582 ! neutrophilic metamyelocyte relationship: has_part CP:0000039 ! banded nucleus relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000007597 ! proto-oncogene c-Fos relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001337 ! complement receptor type 1 relationship: has_plasma_membrane_part PR:000001580 ! fMet-Leu-Phe receptor relationship: lacks_part PR:000009978 ! lactotransferrin relationship: lacks_part PR:000010799 ! myb proto-oncogene protein relationship: lacks_plasma_membrane_part PR:000009129 ! integrin alpha-4 relationship: lacks_plasma_membrane_part PR:000010543 ! myeloperoxidase [Term] id: CL:0000561 name: amacrine cell namespace: cell def: "Interneuron of the vertebrate retina. They integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. They lack large axons." [GOC:tfm, MESH:A08.663.358.050] comment: Not clear if this term overlaps with retinal bipolar neuron (CL:0000748). synonym: "amacrine neuron" EXACT [] xref: BTO:0004044 xref: FBbt:00005127 xref: FMA:67766 is_a: CL:0000099 ! interneuron [Term] id: CL:0000562 name: nucleate erythrocyte namespace: cell def: "An erythrocyte having a nucleus." [GOC:add, GOc:tfm] synonym: "RBC" BROAD [] synonym: "red blood cell" BROAD [] is_a: CL:0000232 ! erythrocyte is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000232 ! erythrocyte intersection_of: has_part GO:0005634 ! nucleus relationship: develops_from CL:0002421 ! nucleated reticulocyte relationship: has_part GO:0005634 ! nucleus [Term] id: CL:0000563 name: endospore namespace: cell def: "A rounded, inactive form that certain bacteria assume under conditions of extreme temperature, dryness, or lack of food. The bacterium develops a waterproof cell wall that protects it from being dried out or damaged." [GOC:tfm, ISBN:0618947256] synonym: "bacterial spore" EXACT [] xref: BTO:0002779 is_a: CL:0000520 ! prokaryotic cell [Term] id: CL:0000564 name: neutrophilic promyelocyte namespace: cell def: "A promyelocyte committed to the neutrophil lineage. This cell type is GATA-1-positive, C/EBPa-positive, AML-1-positive, MPO-positive, has low expression of PU.1 transcription factor and lacks lactotransferrin expression." [GOC:add, GOC:dsd, GOC:tfm, ISBN:0721601464, PMID:12560239, PMID:15514007] comment: These cells are CD11b-negative, CD15-positive, CD16-negative, CD49d-positive, CD68-positive, CD35-negative, and fMLP receptor-negative. They are found in the Band 3 fraction. synonym: "neutrophilic premyelocyte" EXACT [] synonym: "neutrophilic progranulocyte" EXACT [] xref: FMA:84196 is_a: CL:0000834 ! neutrophil progenitor cell is_a: CL:0000836 ! promyelocyte intersection_of: CL:0000836 ! promyelocyte intersection_of: capable_of GO:0030223 ! neutrophil differentiation intersection_of: has_part PR:000001944 ! transcription factor PU.1 intersection_of: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha intersection_of: has_part PR:000007857 ! erythroid transcription factor intersection_of: has_part PR:000010543 ! myeloperoxidase intersection_of: has_part PR:000014362 ! runt-related transcription factor 1 intersection_of: lacks_part PR:000009978 ! lactotransferrin relationship: capable_of GO:0030223 ! neutrophil differentiation relationship: develops_from CL:0000042 ! neutrophilic myeloblast relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000010543 ! myeloperoxidase relationship: has_part PR:000014362 ! runt-related transcription factor 1 relationship: lacks_part PR:000009978 ! lactotransferrin [Term] id: CL:0000565 name: fat body cell namespace: cell def: "A cell whose primary function is intermediary metabolism." [FB:ma] is_a: CL:0000181 ! metabolising cell [Term] id: CL:0000566 name: angioblastic mesenchymal cell namespace: cell def: "A mesenchymal stem cell capable of developing into blood vessel endothelium." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] is_a: CL:0000134 ! mesenchymal cell intersection_of: CL:0000134 ! mesenchymal cell intersection_of: has_plasma_membrane_part PR:000001444 ! cadherin-5 intersection_of: has_plasma_membrane_part PR:000002112 ! vascular endothelial growth factor receptor 2 intersection_of: has_plasma_membrane_part PR:000016043 ! T-cell acute lymphocytic leukemia protein 1 relationship: develops_from CL:0000134 ! mesenchymal cell relationship: has_plasma_membrane_part PR:000001444 ! cadherin-5 relationship: has_plasma_membrane_part PR:000002112 ! vascular endothelial growth factor receptor 2 relationship: has_plasma_membrane_part PR:000016043 ! T-cell acute lymphocytic leukemia protein 1 [Term] id: CL:0000567 name: polymodal nocireceptor namespace: cell is_a: CL:0000198 ! pain receptor cell [Term] id: CL:0000568 name: APUD cell namespace: cell def: "A cell that originates in the neural crest, that has certain cytochemical and ultrastructural characteristics and is found scattered throughout the body; types include melanocytes, the cells of the chromaffin system, and cells in the hypothalamus, hypophysis, thyroid, parathyroids, lungs, gastrointestinal tract, and pancreas. This cell type concentrates the amino acid precursors of certain amines and decarboxylate them, forming amines that function as regulators and neurotransmitters. This cell type produces substances such as epinephrine, norepinephrine, dopamine, serotonin, enkephalin, somatostatin, neurotensin, and substance P, the actions of which may affect contiguous cells, nearby groups of cells, or distant cells, thus functioning as local or systemic hormones. The name is an acronym for amine precursor uptake and decarboxylation cell." [GOC:tfm, ISBN:0721662544, MESH:A11.070] synonym: "amine precursor uptake and decarboxylation cell" EXACT [] xref: BTO:0003866 xref: FMA:83114 is_a: CL:0000165 ! neuroendocrine cell [Term] id: CL:0000569 name: cardiac mesenchymal cell namespace: cell def: "A mesenchymal cell found in the developing heart." [PMID:18816864] is_a: CL:0000134 ! mesenchymal cell is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000134 ! mesenchymal cell intersection_of: part_of UBERON:0000948 ! heart relationship: develops_from CL:0000011 ! migratory trunk neural crest cell relationship: part_of UBERON:0000948 ! heart [Term] id: CL:0000570 name: parafollicular cell namespace: cell def: "A neuroepithelial cells that occurs singly or in small groups, close to the outer follicular borders but within the follicular basement membrane of the thyroid. Expresses a form of the neural cell adhesion molecule (N-CAM) on their surface. Secrets calcitonin, 5-hydroxytryptamine and dopamine." [GOC:tfm, ISBN:0517223651] synonym: "C cell" EXACT [] synonym: "C cell of thyroid gland" EXACT [FMA:68653] synonym: "clear cell of thyroid gland" EXACT [FMA:68653] synonym: "parafollicular cell of thyroid gland" EXACT [FMA:68653] synonym: "thyroid parafollicular cell" EXACT [FMA:68653] xref: FMA:68653 xref: SCTID:176770005 is_a: CL:0000443 ! calcitonin secreting cell is_a: CL:0000458 ! serotonin secreting cell is_a: CL:0000710 ! neurecto-epithelial cell intersection_of: CL:0000710 ! neurecto-epithelial cell intersection_of: capable_of GO:0001820 ! serotonin secretion intersection_of: capable_of GO:0014046 ! dopamine secretion intersection_of: has_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: capable_of GO:0001820 ! serotonin secretion relationship: capable_of GO:0014046 ! dopamine secretion relationship: develops_from CL:0000333 ! migratory neural crest cell relationship: has_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: part_of UBERON:0001747 ! parenchyma of thyroid gland [Term] id: CL:0000571 name: leucophore namespace: cell def: "A pigment cell derived from the neural crest. Contains uric acid or other purine crystals deposited in stacks called leucosomes. The crystals reflect light and this gives a white appearance under white light." [SANBI:mhl] is_a: CL:0000147 ! pigment cell relationship: develops_from CL:0005003 ! leucoblast [Term] id: CL:0000573 name: retinal cone cell namespace: cell def: "One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision." [MESH:A08.663.650.650.670.100] xref: BTO:0001036 xref: FMA:67748 is_a: CL:0000287 ! eye photoreceptor cell relationship: develops_from CL:0002672 ! retinal progenitor cell [Term] id: CL:0000574 name: erythrophore namespace: cell def: "A pigment cell derived from the neural crest. Contains pteridine and/or carotenoid pigments in structures called pterinosomes or erythrosomes. This gives an orange to red appearance." [SANBI:mhl] is_a: CL:0000147 ! pigment cell relationship: develops_from CL:0005004 ! pigment erythroblast [Term] id: CL:0000575 name: corneal epithelial cell namespace: cell alt_id: CL:1000431 def: "An epithelial cell of the cornea." [GOC:tfm] synonym: "epithelial cell of cornea" EXACT [FMA:70551] xref: BTO:0004298 xref: FMA:70551 is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0000964 ! cornea relationship: part_of UBERON:0000964 ! cornea [Term] id: CL:0000576 name: monocyte namespace: cell def: "Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells." [GO_REF:0000031, MESH:A11.118.637.555.652] comment: Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid. xref: BTO:0000876 xref: FMA:62864 is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0002087 ! nongranular leukocyte intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0030225 ! macrophage differentiation intersection_of: capable_of GO:0030316 ! osteoclast differentiation intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation intersection_of: lacks_part GO:0030141 ! secretory granule relationship: capable_of GO:0030225 ! macrophage differentiation relationship: capable_of GO:0030316 ! osteoclast differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: develops_from CL:0000559 ! promonocyte relationship: lacks_part GO:0030141 ! secretory granule [Term] id: CL:0000577 name: type EC enteroendocrine cell namespace: cell alt_id: CL:0002065 def: "A subtype of enteroendocrine cells found in the gastrointestinal mucosa, particularly in the glands of pyloric antrum; duodenum; and ileum. These cell type secretes serotonin and some neurotransmitters including enkephalins and substance P. Their secretory granules stain readily with silver (argentaffin stain)." [MESH:A03.492.766.440.250, PMID:9505449] synonym: "argentaffin cell" EXACT [] synonym: "enterochromaffin cell" EXACT [] synonym: "Kulchitsky cell" EXACT [] xref: FMA:62934 xref: FMA:83132 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000166 ! chromaffin cell is_a: CL:0000458 ! serotonin secreting cell is_a: CL:0000506 ! enkephalin secreting cell [Term] id: CL:0000578 name: experimentally modified cell in vitro namespace: cell def: "A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure." [FB:ma, ReO:mhb] comment: This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12 is_a: CL:0001034 ! cell in vitro [Term] id: CL:0000579 name: border follicle cell namespace: cell xref: FBbt:00004905 is_a: CL:0000477 ! follicle cell [Term] id: CL:0000580 name: neutrophilic myelocyte namespace: cell def: "A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and neutrophil-specific granules has started. No nucleolus is present. This cell type is CD13-positive, CD16-negative, integrin alpha-M-positive, CD15-positive, CD33-positive, CD24-positive, C/EBP-a-positive, C/EBPe-positive, PU.1-positive, lactotransferrin-positive, myeloperoxidase-positive and NGAL-positive." [GOC:add, GOC:dsd, GOC:tfm, http://www.cap.org, ISBN:0721601464, PMID:10618520, PMID:12560239, PMID:15514007] comment: These cells are also CD15-positive, CD35-negative, CD49d-positive, and fMLP receptor-negative. They are found in the Band 2 fraction. xref: BTO:0003455 xref: FMA:83540 is_a: CL:0000776 ! immature neutrophil is_a: CL:0002087 ! nongranular leukocyte is_a: CL:0002193 ! myelocyte intersection_of: CL:0000776 ! immature neutrophil intersection_of: has_part CP:0000027 ! acidophilic cytoplasm intersection_of: has_part GO:0042582 ! azurophil granule intersection_of: has_part PR:000001944 ! transcription factor PU.1 intersection_of: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha intersection_of: has_part PR:000005310 ! CCAAT/enhancer-binding protein epsilon intersection_of: has_part PR:000009725 ! neutrophil gelatinase-associated lipocalin intersection_of: has_part PR:000009978 ! lactotransferrin intersection_of: has_part PR:000010543 ! myeloperoxidase intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 intersection_of: has_plasma_membrane_part PR:000001892 ! CD33 molecule intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part PR:000002031 ! aminopeptidase N intersection_of: lacks_part GO:0070820 ! tertiary granule intersection_of: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: develops_from CL:0000564 ! neutrophilic promyelocyte relationship: has_part CP:0000027 ! acidophilic cytoplasm relationship: has_part GO:0042582 ! azurophil granule relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000005310 ! CCAAT/enhancer-binding protein epsilon relationship: has_part PR:000009725 ! neutrophil gelatinase-associated lipocalin relationship: has_part PR:000009978 ! lactotransferrin relationship: has_part PR:000010543 ! myeloperoxidase relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 relationship: has_plasma_membrane_part PR:000001892 ! CD33 molecule relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000002031 ! aminopeptidase N relationship: lacks_part GO:0070820 ! tertiary granule relationship: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III [Term] id: CL:0000581 name: peritoneal macrophage namespace: cell def: "A macrophage resident in the peritoneum under non-inflammatory conditions. Markers include F4/80-high, CD11b-high, CD68-positive, SIGNR1-positive, CD115-high, MHC-II-negative, and Dectin-1-positive." [MESH:A11.329.372.630, PMID:15771589, PMID:19201820] comment: Markers: Mouse: F4/80-high, CD11b-high, CD68+, SIGNR1+, Dectin-1+. xref: BTO:0001034 xref: FMA:83025 is_a: CL:0000864 ! tissue-resident macrophage intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0042742 ! defense response to bacterium intersection_of: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M intersection_of: has_high_plasma_membrane_amount PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 intersection_of: has_high_plasma_membrane_amount PR:000002062 ! macrophage colony-stimulating factor 1 receptor intersection_of: has_plasma_membrane_part PR:000001807 ! C-type lectin domain family 7 member A intersection_of: has_plasma_membrane_part PR:000002064 ! macrosialin intersection_of: has_plasma_membrane_part PR:000006172 ! CD209 molecule-like protein B intersection_of: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex intersection_of: located_in UBERON:0001179 ! peritoneal cavity relationship: capable_of GO:0042742 ! defense response to bacterium relationship: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: has_high_plasma_membrane_amount PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 relationship: has_high_plasma_membrane_amount PR:000002062 ! macrophage colony-stimulating factor 1 receptor relationship: has_plasma_membrane_part PR:000001807 ! C-type lectin domain family 7 member A relationship: has_plasma_membrane_part PR:000002064 ! macrosialin relationship: has_plasma_membrane_part PR:000006172 ! CD209 molecule-like protein B relationship: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: located_in UBERON:0001179 ! peritoneal cavity [Term] id: CL:0000582 name: neutrophilic metamyelocyte namespace: cell def: "A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and the band form neutrophil. The protein synthesis seen in earlier stages decreases or stops; the nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare; and the cytoplasm becomes amphophilic like that of a mature granulocyte. This cell type is integrin alpha-M-positive, CD13-negative, CD15-positive, CD16-positive, CD33-positive, CD24-positive, fMLP receptor-negative and has expression of C/EBP-a, C/EBP-e, PU.1 transcription factor, lactotransferrin, myeloperoxidase and neutrophil gelatinase associated lipocalin." [GOC:add, GOC:dsd, GOC:tfm, http://www.cap.org, ISBN:0721601464, PMID:10618520, PMID:12560239, PMID:15514007] comment: These cells are also CD35-negative, CD49d-positive, and fMLP receptor-negative. They are found in the Band 2 fraction. synonym: "juvenile neutrophil" EXACT [] xref: FMA:84197 is_a: CL:0000776 ! immature neutrophil is_a: CL:0002192 ! metamyelocyte is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000776 ! immature neutrophil intersection_of: has_part CP:0000027 ! acidophilic cytoplasm intersection_of: has_part CP:0000040 ! reniform nucleus intersection_of: has_part GO:0000792 ! heterochromatin intersection_of: has_part GO:0042582 ! azurophil granule intersection_of: has_part GO:0070820 ! tertiary granule intersection_of: has_part PR:000001944 ! transcription factor PU.1 intersection_of: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha intersection_of: has_part PR:000005310 ! CCAAT/enhancer-binding protein epsilon intersection_of: has_part PR:000009725 ! neutrophil gelatinase-associated lipocalin intersection_of: has_part PR:000009978 ! lactotransferrin intersection_of: has_part PR:000010543 ! myeloperoxidase intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 intersection_of: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III intersection_of: has_plasma_membrane_part PR:000001892 ! CD33 molecule intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part PR:000002031 ! aminopeptidase N intersection_of: lacks_plasma_membrane_part PR:000001580 ! fMet-Leu-Phe receptor relationship: develops_from CL:0000580 ! neutrophilic myelocyte relationship: has_part CP:0000027 ! acidophilic cytoplasm relationship: has_part CP:0000040 ! reniform nucleus relationship: has_part GO:0000792 ! heterochromatin relationship: has_part GO:0042582 ! azurophil granule relationship: has_part GO:0070820 ! tertiary granule relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000005310 ! CCAAT/enhancer-binding protein epsilon relationship: has_part PR:000009725 ! neutrophil gelatinase-associated lipocalin relationship: has_part PR:000009978 ! lactotransferrin relationship: has_part PR:000010543 ! myeloperoxidase relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 relationship: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: has_plasma_membrane_part PR:000001892 ! CD33 molecule relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000002031 ! aminopeptidase N relationship: lacks_plasma_membrane_part PR:000001580 ! fMet-Leu-Phe receptor [Term] id: CL:0000583 name: alveolar macrophage namespace: cell def: "A tissue-resident macrophage found in the alveoli of the lungs. Ingests small inhaled particles resulting in degradation and presentation of the antigen to immunocompetent cells. Markers include F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative." [GO_REF:0000031, GOC:ana, GOC:dsd, GOC:tfm, MESH:A11.329.372.600] comment: Markers: Mouse: F4/80mid, CD11b-/low, CD11c+, CD68+, sialoadhesin+, dectin-1+, MR+, CX3CR1-. synonym: "dust cell" EXACT [] synonym: "MF.Lu" RELATED [] xref: BTO:0000802 xref: FMA:83023 is_a: CL:0000864 ! tissue-resident macrophage intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0019882 ! antigen processing and presentation intersection_of: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001013 ! integrin alpha-X intersection_of: has_plasma_membrane_part PR:000001807 ! C-type lectin domain family 7 member A intersection_of: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 intersection_of: has_plasma_membrane_part PR:000001931 ! sialoadhesin intersection_of: has_plasma_membrane_part PR:000002064 ! macrosialin intersection_of: has_plasma_membrane_part PR:000002972 ! macrophage mannose receptor 1 intersection_of: lacks_plasma_membrane_part PR:000001206 ! CX3C chemokine receptor 1 intersection_of: part_of UBERON:0002299 ! alveolus of lung relationship: capable_of GO:0019882 ! antigen processing and presentation relationship: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001013 ! integrin alpha-X relationship: has_plasma_membrane_part PR:000001807 ! C-type lectin domain family 7 member A relationship: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 relationship: has_plasma_membrane_part PR:000001931 ! sialoadhesin relationship: has_plasma_membrane_part PR:000002064 ! macrosialin relationship: has_plasma_membrane_part PR:000002972 ! macrophage mannose receptor 1 relationship: lacks_plasma_membrane_part PR:000001206 ! CX3C chemokine receptor 1 relationship: part_of UBERON:0002299 ! alveolus of lung [Term] id: CL:0000584 name: enterocyte namespace: cell def: "An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen." [SANBI:mhl] xref: BTO:0000398 xref: FMA:62122 is_a: CL:0000239 ! brush border epithelial cell is_a: CL:0000677 ! gut absorptive cell is_a: CL:0002563 ! intestinal epithelial cell [Term] id: CL:0000585 name: null cell namespace: cell def: "OBSOLETE: A class of lymphocytes characterized by the lack of surface markers specific for either T or B cells." [] comment: This term is rather archaic; consider using 'natural killer cell ; CL:0000623', 'pro-B cell ; CL:0000826', 'pro-T cell ; CL:0000827', or other appropriate lymphocyte-related term depending on the context. is_obsolete: true [Term] id: CL:0000586 name: germ cell namespace: cell def: "The reproductive cell in multicellular organisms." [MESH:A05.360.490] xref: BTO:0000535 xref: VHOG:0001534 xref: WBbt:0006796 is_a: CL:0000039 ! germ line cell intersection_of: CL:0000039 ! germ line cell intersection_of: capable_of GO:0048609 ! multicellular organismal reproductive process relationship: capable_of GO:0048609 ! multicellular organismal reproductive process [Term] id: CL:0000587 name: cold sensing thermoreceptor cell namespace: cell def: "A thermoreceptor cell that detects reduced temperatures." [GOC:tfm] is_a: CL:0000205 ! thermoreceptor cell [Term] id: CL:0000588 name: odontoclast namespace: cell def: "A specialized osteoclast associated with the absorption and removal of cementum." [GOC:add, MESH:A11.329.679] xref: BTO:0002516 xref: FMA:83027 is_a: CL:0000092 ! osteoclast intersection_of: CL:0000092 ! osteoclast intersection_of: capable_of GO:0042483 ! negative regulation of odontogenesis relationship: capable_of GO:0042483 ! negative regulation of odontogenesis [Term] id: CL:0000589 name: cochlear inner hair cell namespace: cell def: "A bulbous cell that is medially placed in one row in the organ of Corti. In contrast to the outer hair cells, the inner hair cells are fewer in number, have fewer sensory hairs, and are less differentiated." [MESH:A08.663.650.250.250] synonym: "inner hair cell" BROAD [] xref: BTO:0003667 xref: FMA:62365 is_a: CL:0000202 ! auditory hair cell [Term] id: CL:0000590 name: small luteal cell namespace: cell def: "A progesterone secreting cell in the corpus luteum that develops from theca cells." [GOC:tfm, MESH:A05.360.319.114.630.278.400] synonym: "small lutein cell" EXACT [] synonym: "theca lutein cell" EXACT [] xref: BTO:0002850 xref: FMA:18690 is_a: CL:0000175 ! luteal cell relationship: develops_from CL:0000503 ! theca cell [Term] id: CL:0000591 name: warmth sensing thermoreceptor cell namespace: cell def: "A thermoreceptor cell that detects reduced temperatures." [GOC:tfm] is_a: CL:0000205 ! thermoreceptor cell [Term] id: CL:0000592 name: large luteal cell namespace: cell def: "A large, progesterone secreting cell in the corpus luteum that develops from the granulosa cells." [GOC:tfm, MESH:A05.360.319.114.630.278.400] synonym: "granulosa lutein cell" EXACT [] synonym: "granulosoluteocytus" RELATED [] xref: FMA:18689 is_a: CL:0000175 ! luteal cell is_a: CL:0000177 ! testosterone secreting cell relationship: develops_from CL:0000501 ! granulosa cell [Term] id: CL:0000593 name: androgen secreting cell namespace: cell def: "A steroid hormone secreting cell that secretes androgen." [GOC:tfm] is_a: CL:0000174 ! steroid hormone secreting cell [Term] id: CL:0000594 name: skeletal muscle satellite cell namespace: cell def: "An elongated, spindle-shaped, quiescent myoblast that are located between the basal lamina and the plasmalemma of the muscle fibres. They are thought to play a role in muscle repair and regeneration." [GOC:tfm, MESH:A11.635.500.700] is_a: CL:0000035 ! single fate stem cell is_a: CL:0000188 ! skeletal muscle cell is_a: CL:0000680 ! muscle precursor cell [Term] id: CL:0000595 name: enucleate erythrocyte namespace: cell def: "An erythrocyte lacking a nucleus." [GOC:add, GOC:tfm] synonym: "RBC" BROAD [] synonym: "red blood cell" BROAD [] is_a: CL:0000232 ! erythrocyte intersection_of: CL:0000232 ! erythrocyte intersection_of: lacks_part GO:0005634 ! nucleus relationship: develops_from CL:0002422 ! enucleated reticulocyte relationship: lacks_part GO:0005634 ! nucleus [Term] id: CL:0000596 name: sexual spore namespace: cell def: "A spore formed following meiosis. Sometimes following meiosis, prospores may undergo one or more rounds of mitosis before they are fully mature." [FAO:0000017, GOC:tfm, SGD:clt] synonym: "meiotically-derived spore" EXACT [] xref: FAO:0000017 is_a: CL:0002369 ! fungal spore [Term] id: CL:0000597 name: microconidium namespace: cell def: "The smaller of two types of asexual spores formed by some fungi. An ovoid to pear-shaped asexual spore that contains very little cytoplasm and organelles, is uninucleate, and forms in vegetative hypae within a mycelium. Micronidia are extruded from the hyphal cell wall." [GOC:tfm, ISBN:0471940526, PMID:8357339, SGD:clt] xref: FAO:0000028 is_a: CL:0002381 ! uninucleate conidium [Term] id: CL:0000598 name: pyramidal cell namespace: cell def: "A projection neuron in the cerebral cortex and the hippocampus. Pyramidal cells have a pyramid-shaped soma with the apex and an apical dendrite pointed toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their cortical region." [GOC:tfm, MESH:A08.186.211.577.405.700] synonym: "projection neuron" EXACT [] synonym: "pyramidal neuron" EXACT [] xref: BTO:0003102 xref: FMA:67310 xref: FMA:86775 xref: NIF_Cell:sao862606388 is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) [Term] id: CL:0000599 name: conidium namespace: cell def: "An asexual, nonmotile spore formed by higher fungi; conidia are usually made from the side or tip of specialized sporogenous cells and do not form by progressive cleavage of the cytoplasm." [ISBN:08199377X, PMID:2524423, PMID:9529886, SGD:clt] xref: BTO:0000283 xref: FAO:0000024 is_a: CL:0000605 ! fungal asexual spore [Term] id: CL:0000600 name: heterokaryon namespace: cell def: "A fungal cell with two or more genetically distinct nuclei." [ISBN:08199377X] is_a: CL:0000228 ! multinucleate cell is_a: CL:0000521 ! fungal cell [Term] id: CL:0000601 name: outer hair cell namespace: cell def: "A mechanoreceptor in the organ of Corti. In mammals the outer hair cells are arranged in three rows which are further from the modiolus than the single row of inner hair cells. The motile properties of the outer hair cells may contribute actively to tuning the sensitivity and frequency selectivity of the cochlea." [MESH:A08.663.650.250.315] synonym: "cochlear outer hair cell" EXACT [] xref: BTO:0003666 xref: FMA:62366 is_a: CL:0000202 ! auditory hair cell [Term] id: CL:0000602 name: pressoreceptor cell namespace: cell def: "A receptor in the vascular system, particularly the aorta and carotid sinus, which is sensitive to stretch of the vessel walls." [MESH:A08.800.050.800.900.700] is_a: CL:1000082 ! stretch receptor cell [Term] id: CL:0000603 name: dikaryon namespace: cell def: "A fungal cell with two genetically distinct haploid nuclei." [ISBN:08199377X] is_a: CL:0000227 ! binucleate cell is_a: CL:0000600 ! heterokaryon [Term] id: CL:0000604 name: retinal rod cell namespace: cell def: "One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision." [MESH:A08.663.650.650.670.650] xref: BTO:0001024 xref: FMA:67747 is_a: CL:0000287 ! eye photoreceptor cell relationship: develops_from CL:0002672 ! retinal progenitor cell [Term] id: CL:0000605 name: fungal asexual spore namespace: cell def: "A spore formed following mitosis or mitoses." [GOC:tfm, PMID:2524423, PMID:9529886, SGD:clt] xref: FAO:0000023 is_a: CL:0002369 ! fungal spore [Term] id: CL:0000606 name: macroconidium namespace: cell def: "The larger of two types of asexual spores formed by some fungi; usually round or oblong." [GOC:tfm, ISBN:0471940526, SGD:clt] xref: FAO:0000038 is_a: CL:0000599 ! conidium [Term] id: CL:0000607 name: ascospore namespace: cell def: "A thick walled spore that stores and protects one or more nuclei following sexual reproduction in an Ascomycete." [GOC:tfm, ISBN:08199377X, SGD:clt] xref: BTO:0000097 xref: FAO:0000020 is_a: CL:0000596 ! sexual spore [Term] id: CL:0000608 name: zygospore namespace: cell def: "A thick walled, sexual, resting spore formed by Zygomycetes; sometimes refers to the spore and the multi-layered cell wall that encloses the spore, the zygosporangium." [ISBN:0471940526, ISBN:08199377X, SGD:clt] xref: FAO:0000040 is_a: CL:0000596 ! sexual spore [Term] id: CL:0000609 name: vestibular hair cell namespace: cell def: "A mechanoreceptor located in the acoustic maculae and the semicircular canals that mediates the sense of balance, movement, and head position. The vestibular hair cells are connected to accessory structures in such a way that movements of the head displace their stereocilia. This influences the membrane potential of the cells which relay information about movements via the vestibular part of the vestibulocochlear nerve to the brain stem." [GOC:tfm, MESH:A08.663.650.250.380] synonym: "vestibular receptor cell" EXACT [] xref: FMA:62351 is_a: CL:0002374 ! ear hair cell [Term] id: CL:0000610 name: plant cell namespace: cell comment: This term was obsoleted as it is redundant with PO:0009002 in the cell ontology (PO) is_obsolete: true consider: PO:0009002 [Term] id: CL:0000611 name: eosinophil progenitor cell namespace: cell comment: These cells are CD34-positive, CD45RA-negative, CD71-negative, and lineage-negative (CD2, CD3 epsilon, CD4, CD5, CD8a, CD14, CD19, CD20, integrin alpha-M, NCAM-1, SCA-1, Ly6G, Ly76). synonym: "CFU-Eo" RELATED [] synonym: "colony forming unit eosinophil" RELATED [] synonym: "EoP" EXACT [PMCID:PMC2212039, PMCID:PMC2626675] synonym: "eosinophil stem cell" RELATED [] is_a: CL:0002191 ! granulocytopoietic cell intersection_of: CL:0002191 ! granulocytopoietic cell intersection_of: capable_of GO:0030222 ! eosinophil differentiation intersection_of: has_part PR:000001944 ! transcription factor PU.1 intersection_of: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha intersection_of: has_part PR:000007857 ! erythroid transcription factor intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: has_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain intersection_of: has_plasma_membrane_part PR:000001867 ! interleukin-5 receptor subunit alpha intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G intersection_of: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 relationship: capable_of GO:0030222 ! eosinophil differentiation relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: has_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain relationship: has_plasma_membrane_part PR:000001867 ! interleukin-5 receptor subunit alpha relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G relationship: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 [Term] id: CL:0000612 name: eosinophilic myelocyte namespace: cell def: "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte;in this stage, production of primary granules is complete and eosinophil-specific granules has started. No nucleolus is present. These cells are integrin alpha-M-positive, CD13-positive, CD15-positive, CD16-negative, CD24-positive, and CD33-positive." [GOC:add, GOC:dsd, http://www.cap.org, ISBN:0721601464, PMID:19622087] xref: BTO:0003454 xref: FMA:83542 is_a: CL:0000772 ! immature eosinophil is_a: CL:0002087 ! nongranular leukocyte is_a: CL:0002193 ! myelocyte intersection_of: CL:0000772 ! immature eosinophil intersection_of: has_part GO:0042582 ! azurophil granule intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 intersection_of: has_plasma_membrane_part PR:000001892 ! CD33 molecule intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part PR:000002031 ! aminopeptidase N intersection_of: lacks_part GO:0070820 ! tertiary granule intersection_of: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: has_part GO:0042582 ! azurophil granule relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 relationship: has_plasma_membrane_part PR:000001892 ! CD33 molecule relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000002031 ! aminopeptidase N relationship: lacks_part GO:0070820 ! tertiary granule relationship: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III [Term] id: CL:0000613 name: basophil progenitor cell namespace: cell def: "A progenitor cell committed to the basophil lineage. This cell lacks hematopoietic lineage markers (lin-negative) and is CD34-positive, T1/ST2-low, CD117-negative, and FceRIa-high. This cell also expresses Gata-1, Gata-2 and C/EBPa." [GOC:add, GOC:dsd, http://www.copewithcytokines.de, PMCID:PMC1312421] comment: BaP are also CD13-low and integrin beta-7-low. They are lin-negative (CD2, CD3e, CD4, CD5, CD8, CD11b, CD14, CD19, CD20, ly6g, ly76, and NCAM-1). They also lack expression of mast cell protease 1 (MCP-1) and microphthalmia-associated transcription factor (mitf). synonym: "BaP" EXACT [] synonym: "basophilic stem cell" RELATED [] synonym: "CFU-Bas" RELATED [] synonym: "colony forming unit basophil" RELATED [] is_a: CL:0002191 ! granulocytopoietic cell intersection_of: CL:0002191 ! granulocytopoietic cell intersection_of: capable_of GO:0030221 ! basophil differentiation intersection_of: has_high_plasma_membrane_amount PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha intersection_of: has_low_plasma_membrane_amount PR:000016401 ! transmembrane emp24 domain-containing protein 1 intersection_of: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha intersection_of: has_part PR:000007857 ! erythroid transcription factor intersection_of: has_part PR:000007858 ! endothelial transcription factor GATA-2 intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: lacks_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G intersection_of: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 relationship: capable_of GO:0030221 ! basophil differentiation relationship: develops_from CL:0002028 ! basophil mast progenitor cell relationship: has_high_plasma_membrane_amount PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha relationship: has_low_plasma_membrane_amount PR:000016401 ! transmembrane emp24 domain-containing protein 1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: lacks_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G relationship: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 [Term] id: CL:0000614 name: basophilic myelocyte namespace: cell def: "A basophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and basophil-specific granules has started. No nucleolus is present. Markers are being integrin alpha-M-positive, fucosyltransferase FUT4-positive, CD33-positive, CD24-positive, aminopeptidase N-positive." [GOC:add, GOC:tfm, http://www.cap.org, ISBN:0721601464, PMID:18466030] xref: BTO:0003456 xref: FMA:83543 is_a: CL:0000768 ! immature basophil is_a: CL:0002087 ! nongranular leukocyte intersection_of: CL:0000768 ! immature basophil intersection_of: has_part GO:0042582 ! azurophil granule intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 intersection_of: has_plasma_membrane_part PR:000001892 ! CD33 molecule intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part PR:000002031 ! aminopeptidase N intersection_of: lacks_part GO:0005730 ! nucleolus intersection_of: lacks_part GO:0070820 ! tertiary granule intersection_of: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: develops_from CL:0000830 ! basophilic promyelocyte relationship: has_part GO:0042582 ! azurophil granule relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 relationship: has_plasma_membrane_part PR:000001892 ! CD33 molecule relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000002031 ! aminopeptidase N relationship: lacks_part GO:0005730 ! nucleolus relationship: lacks_part GO:0070820 ! tertiary granule relationship: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III [Term] id: CL:0000615 name: basidiospore namespace: cell def: "A thick walled spore containing one or more haploid nuclei produced by sexual reproduction in an Basidiomycete; formed externally on extrusions of the basidium." [GOC:clt, ISBN:0471940526, ISBN:08199377X] xref: BTO:0002166 xref: FAO:0000021 is_a: CL:0000596 ! sexual spore [Term] id: CL:0000616 name: sporangiospore namespace: cell def: "A walled spore produced in a sporangium." [ISBN:08199377X] is_obsolete: true [Term] id: CL:0000617 name: GABAergic neuron namespace: cell def: "A neuron that uses GABA as a vesicular neurotransmitter" [GOC:tfm] synonym: "GABA-ergic neuron" EXACT [] xref: FMA:84788 xref: WBbt:0005190 is_a: CL:0000540 ! neuron [Term] id: CL:0000618 name: sheath cell namespace: cell is_a: CL:0000075 ! columnar/cuboidal epithelial cell [Term] id: CL:0000619 name: support cell (sensu Nematoda) namespace: cell is_a: CL:0000124 ! glial cell (sensu Nematoda and Protostomia) is_a: CL:0000378 ! support cell (sensu Nematoda and Protostomia) [Term] id: CL:0000620 name: zoospore namespace: cell def: "A sporangiospore that is motile, having flagella." [ISBN:08199377X] xref: FAO:0000039 is_obsolete: true [Term] id: CL:0000621 name: fusion competent myoblast namespace: cell is_a: CL:0000056 ! myoblast [Term] id: CL:0000622 name: acinar cell namespace: cell def: "A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus)." [GOC:tfm, http://www.copewithcytokines.de] synonym: "acinic cell" EXACT [] synonym: "acinous cell" EXACT [] xref: FMA:83625 is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000154 ! protein secreting cell relationship: part_of UBERON:0009842 ! acinus [Term] id: CL:0000623 name: natural killer cell namespace: cell def: "A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells." [GOC:add, ISBN:0781735149, PMID:15771571] synonym: "large granular lymphocyte" BROAD [] synonym: "NK cell" EXACT [] synonym: "null cell" BROAD [] xref: BTO:0000914 xref: BTO:0004716 xref: FMA:63147 xref: FMA:83601 xref: VHOG:0001697 is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0002228 ! natural killer cell mediated immunity intersection_of: capable_of GO:0050776 ! regulation of immune response intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: capable_of GO:0002228 ! natural killer cell mediated immunity relationship: capable_of GO:0050776 ! regulation of immune response relationship: develops_from CL:0000825 ! pro-NK cell relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon [Term] id: CL:0000624 name: CD4-positive, alpha-beta T cell namespace: cell def: "A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor." [GOC:add, ISBN:0781735149] synonym: "CD4-positive, alpha-beta T lymphocyte" EXACT [] synonym: "CD4-positive, alpha-beta T-cell" EXACT [] synonym: "CD4-positive, alpha-beta T-lymphocyte" EXACT [] is_a: CL:0000791 ! mature alpha-beta T cell intersection_of: CL:0000791 ! mature alpha-beta T cell intersection_of: has_plasma_membrane_part PR:000001004 ! CD4 molecule disjoint_from: CL:0000625 ! CD8-positive, alpha-beta T cell relationship: has_plasma_membrane_part PR:000001004 ! CD4 molecule [Term] id: CL:0000625 name: CD8-positive, alpha-beta T cell namespace: cell def: "A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor." [GOC:add, GOC:tfm, ISBN:0781735149] synonym: "CD8-positive, alpha-beta T lymphocyte" EXACT [] synonym: "CD8-positive, alpha-beta T-cell" EXACT [] synonym: "CD8-positive, alpha-beta T-lymphocyte" EXACT [] is_a: CL:0000791 ! mature alpha-beta T cell intersection_of: CL:0000791 ! mature alpha-beta T cell intersection_of: has_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 relationship: has_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 [Term] id: CL:0000626 name: olfactory granule cell namespace: cell def: "Granule cell that is part of the olfactory bulb." [GOC:mah] is_a: CL:0000120 ! granule cell [Term] id: CL:0000627 name: transporting cell namespace: cell def: "A cell involved in transporting nutrients, minerals, water, gases and other chemicals between cells for a variety of purposes including conveying nutrition to other tissues, removing waste products from the tissues, conveying gases for respiration, distributing heat and repelling invasion of foreign substances." [TAIR:sr] is_a: CL:0000003 ! native cell [Term] id: CL:0000628 name: photosynthetic cell namespace: cell def: "A cell that can perform photosynthesis, in which carbohydrates are synthesized from carbon dioxide and water, using light as the energy source." [TAIR:sr] comment: see PMID:21177950, The making of a photosynthetic animal. is_a: CL:0000003 ! native cell [Term] id: CL:0000629 name: storage cell namespace: cell def: "A cell that is specialized to store a particular substance(s), which is(are) later released from the store for a particular purpose." [FB:ma] is_a: CL:0000325 ! stuff accumulating cell [Term] id: CL:0000630 name: supportive cell namespace: cell def: "A cell whose primary function is to support other cell types." [FB:ma, GOC:tfm] xref: BTO:0002315 xref: FMA:86947 xref: ZFA:0000688 is_a: CL:0000003 ! native cell [Term] id: CL:0000631 name: labyrinth supporting cell namespace: cell def: "Cells forming a framework supporting the organ of Corti. Specific cells are those of Claudius, Deiters and Hensen." [MESH:A09.246.631.246.577.543] is_a: CL:0000630 ! supportive cell [Term] id: CL:0000632 name: hepatic stellate cell namespace: cell def: "A cell that is found in the perisinusoidal space of the liver that is capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components that can contribute to liver fibrosis. This activated state has a myofibroblast-like phenotype, though it's not clear in the literature if this is terminally differentiated. This cell type comprises approximately 8-15% of total cells in the liver." [GOC:dsd, http://en.wikipedia.org/wiki/Hepatic_stellate_cell, MESH:D055166, PMID:12808230, PMID:17239632, PMID:18222966, PMID:9302568] comment: Hepatic stellate cells are CD271-positive, desmin-positive, DDR-2-positive, GFAP-positive, synamin-positive, synaptophysin-positive, vimentin-positive, They are capable of producing angiotensin II, fibronectin, laminin, MMP-1, MMP-2, MMP-3, MMP-9, MMP-11, TGF-beta1, TIMP-1, TIMP-2, type I collagen, type III collagen, type IV collagen, and type VI collagen. synonym: "fat-storing cell" RELATED [] synonym: "hepatic perisinusoidal cell" EXACT [] synonym: "Ito cell" EXACT [] synonym: "lipocyte" RELATED [] synonym: "perisinusoidal cell" EXACT [] synonym: "vitamin A-storing cells" RELATED [PMID:12808230] xref: BTO:0002741 xref: FMA:67763 is_a: CL:0000057 ! fibroblast is_a: CL:0000327 ! extracellular matrix secreting cell intersection_of: CL:0002320 ! connective tissue cell intersection_of: has_plasma_membrane_part PR:000007939 ! glial fibrillary acidic protein intersection_of: part_of UBERON:0002107 ! liver relationship: has_plasma_membrane_part PR:000007939 ! glial fibrillary acidic protein relationship: part_of UBERON:0002107 ! liver [Term] id: CL:0000633 name: Hensen cell namespace: cell def: "A tall supporting cell that is arranged in rows adjacent to the last row of outer phalangeal cells. This cell type constitutes the outer border of the organ of Corti." [GOC:tfm, ISBN:0721662544] synonym: "cell of Hensen" EXACT [] synonym: "external limiting cell of organ of Corti" EXACT [] synonym: "Hensen's cell" EXACT [] xref: FMA:79799 is_a: CL:0002490 ! organ of Corti supporting cell [Term] id: CL:0000634 name: Claudius cell namespace: cell def: "A cuboidal cell which along with Boettcher's cells form the floor of the external spiral sulcus, external to the organ of Corti." [GOC:tfm, ISBN:0721662544] synonym: "cell of Claudius" EXACT [] synonym: "external supporting cell of Claudius" EXACT [] synonym: "external supporting cell of vestibular epithelium" EXACT [] xref: FMA:79802 is_a: CL:0002315 ! supporting cell of cochlea [Term] id: CL:0000635 name: Deiter's cell namespace: cell def: "The outer phalangeal cells of the organ of Corti. This cell holds the base of the hair cell in a cup-shaped depression." [GOC:tfm, http://www.britannica.com/EBchecked/topic/156177/Deiters-cell, ISBN:0721662544] synonym: "Deiters cell" EXACT [] synonym: "outer phalangeal cell" EXACT [] xref: FMA:75725 is_a: CL:0002165 ! phalangeal cell [Term] id: CL:0000636 name: Mueller cell namespace: cell xref: BTO:0003064 is_a: CL:0000127 ! astrocyte [Term] id: CL:0000637 name: chromophil cell of anterior pituitary gland namespace: cell def: "A cell that stains readily in the anterior pituitary gland." [GOC:tfm, ISBN:0618947256] xref: FMA:83089 is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000166 ! chromaffin cell is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000166 ! chromaffin cell intersection_of: part_of UBERON:0002196 ! adenohypophysis relationship: part_of UBERON:0002196 ! adenohypophysis [Term] id: CL:0000638 name: acidophil cell of pars distalis of adenohypophysis namespace: cell def: "An acidophilic chromophil cell that of the anterior pituitary gland." [GOC:tfm] synonym: "acidophil cell of pars anterior of adenohypophysis" EXACT [] synonym: "acidophil of pars anterior of adenohypophysis" EXACT [] synonym: "acidophil of pars distalis of adenohypophysis" EXACT [] synonym: "pituitary alpha cell" EXACT [] xref: FMA:83093 is_a: CL:0000637 ! chromophil cell of anterior pituitary gland [Term] id: CL:0000639 name: basophil cell of pars distalis of adenohypophysis namespace: cell def: "A basophillic chromophil cell that of the anterior pituitary gland." [GOC:tfm] synonym: "basophil cell of anterior lobe of hypophysis" EXACT [] synonym: "beta cell" RELATED [] synonym: "pituitary beta cell" RELATED [] xref: FMA:83094 is_a: CL:0000637 ! chromophil cell of anterior pituitary gland [Term] id: CL:0000641 name: chromophobe cell namespace: cell def: "A cell that is resistant to stains." [GOC:tfm] synonym: "chromophobic cell" EXACT [] xref: FMA:83626 is_a: CL:0000163 ! endocrine cell [Term] id: CL:0000642 name: folliculostellate cell namespace: cell def: "A supportive cell of the vertebrate pituitary that provides macromolecular transport and secretes hormones." [JB:jb] is_a: CL:0000163 ! endocrine cell is_a: CL:0000630 ! supportive cell [Term] id: CL:0000644 name: Bergmann glial cell namespace: cell def: "Type of radial astrocyte in the cerebellar cortex that have their cell bodies in the Purkinje cell layer and processes that extend into the molecular layer, terminating with bulbous endfeet at the pial surface. Bergmann glia express high densities of glutamate transporters that limit diffusion of the neurotransmitter glutamate during its release from synaptic terminals. Besides their role in early development of the cerebellum, Bergmann glia are also required for the pruning or addition of synapses." [GOC:tfm, http://www.neurolex.org/wiki/Category\:Bergmann_Glial_Cell] synonym: "Bergmann astrocyte" EXACT [] synonym: "Bergmann glial cell of cerebellum" EXACT [] xref: FMA:54559 is_a: CL:0000127 ! astrocyte [Term] id: CL:0000645 name: pituicyte namespace: cell def: "A cell with long processes running parallel to adjacent axons in the proximal infundibulum of the neurohypophysis. These processes form a three-dimensional network among the axons of the hypothalamic neurosecretory cells and are connected by gap junctions which provide for their metabolic coupling. This cell type constitutes most of the nonexcitable tissue in the neurohypophsis; function may include possibly acting as an intermediate in the modulation of oxytocin and vasopressin release. This cell type is highly variable in size and shape and commonly contain lipid droplets and deposits of lipochrome pigment." [http://en.wikipedia.org/wiki/Pituicyte, ISBN:0412046911, ISBN:0517223651] xref: BTO:0003793 xref: FMA:83503 is_a: CL:0000127 ! astrocyte [Term] id: CL:0000646 name: basal cell namespace: cell def: "Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament." [GOC:tfm, ISBN:0517223651] xref: BTO:0000939 xref: FMA:62516 is_a: CL:0000036 ! epithelial fate stem cell [Term] id: CL:0000647 name: multinucleated giant cell namespace: cell def: "A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes." [GOC:add, GOC:tfm, ISBN:0702022918, ISBN:0702024783] comment: Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this. synonym: "foreign body giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "Langerhans giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "macrophage polykaryon" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "multinucleate giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "syncytial giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] xref: BTO:0003107 xref: FMA:83035 is_a: CL:0000228 ! multinucleate cell is_a: CL:0000766 ! myeloid leukocyte intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: has_quality PATO:0001908 ! multinucleate intersection_of: participates_in GO:0002432 ! granuloma formation intersection_of: participates_in GO:0002544 ! chronic inflammatory response relationship: develops_from CL:0000235 ! macrophage relationship: has_quality PATO:0001908 ! multinucleate relationship: participates_in GO:0002432 ! granuloma formation relationship: participates_in GO:0002544 ! chronic inflammatory response [Term] id: CL:0000648 name: kidney granular cell namespace: cell alt_id: CL:0000461 def: "A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation." [GOC:cvs, GOC:tfm, PMID:11457727] synonym: "JG cell" EXACT [] synonym: "juxtaglomerular cell" BROAD [] synonym: "renin secreting cell" EXACT [] xref: FMA:84138 is_a: CL:0000154 ! protein secreting cell is_a: CL:0000192 ! smooth muscle cell is_a: CL:1000618 ! juxtaglomerular complex cell [Term] id: CL:0000649 name: prickle cell namespace: cell alt_id: CL:0002186 def: "A cell with delicate radiating processes known as desmosomes that form intercellular bridges between other cells of this type. This cell type forms the stratum spinosum (prickle cell layer. A function of this cell is to generate keratin." [GOC:tfm, ISBN:0721662544, ISBN:0815332181] synonym: "prickle cell of epidermis" EXACT [] xref: FMA:69059 is_a: CL:0000312 ! keratinocyte [Term] id: CL:0000650 name: mesangial cell namespace: cell def: "A cell type that encapsulates the capillaries and venules in the kidney. This cell secretes mesangial matrix that provides the structural support for the capillaries." [GOC:tfm, http://www.copewithcytokines.de/cope.cgi?key=mesangial%20cells] xref: BTO:0000853 xref: FMA:70972 is_a: CL:0000669 ! pericyte cell relationship: develops_from CL:0000134 ! mesenchymal cell [Term] id: CL:0000651 name: neck cell namespace: cell def: "A mucus-secreting cell, with numerous apical secretory vesicles containing mucins; nucleus are basally displaced; numerous at the neck of mucus secreting glands" [GOC:tfm] synonym: "mucous neck cell" EXACT [] is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000319 ! mucus secreting cell [Term] id: CL:0000652 name: pinealocyte namespace: cell def: "This cell type produces and secretes melatonin and forms the pineal parenchyma. Extending from each cell body, which has a spherical, oval or lobulated mucleus, are one or more tortuous basophilic processes, containing parallel microtubules known as synaptic ribbons. These processes end in expanded terminal buds near capillaries or less, frequently, ependymal cells of the pineal recess. The terminal buds contain granular endoplasmic reticulum, mitochondria and electron-dense cored vesicles, which store monoamines and polypeptide hormones, release of which appears to require sympathetic innervation." [GOC:tfm, http://en.wikipedia.org/wiki/Pinealocyte, ISBN:0517223651, PMID:16687276] xref: BTO:0001068 xref: FMA:83417 is_a: CL:0000163 ! endocrine cell is_a: CL:0000710 ! neurecto-epithelial cell [Term] id: CL:0000653 name: glomerular visceral epithelial cell namespace: cell def: "A glomerular visceral epithelial cell is a specialized kidney epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells." [GOC:tfm] comment: GO has podocyte as a related synonym due to concern this may refer to more than one cell type. However, this did not turn up in my search. If podocyte does refer to more than one cell type, then we should classify the synonym to 'related'[tfm]. synonym: "epithelial cell of visceral layer of glomerular capsule" BROAD [FMA:70967] synonym: "glomerular podocyte" EXACT [FMA:70967] synonym: "podocyte" EXACT [] xref: BTO:0002295 is_a: CL:0002522 ! renal filtration cell is_a: CL:1000451 ! epithelial cell of visceral layer of glomerular capsule relationship: part_of UBERON:0005751 ! visceral layer of glomerular capsule [Term] id: CL:0000654 name: primary oocyte namespace: cell def: "A primary oocyte is an oocyte that has not completed female meosis I." [GOC:tfm, ISBN:0721662544] synonym: "primary oogonium" RELATED [] xref: BTO:0000512 xref: FMA:18645 is_a: CL:0000023 ! oocyte intersection_of: CL:0000023 ! oocyte intersection_of: has_not_completed GO:0007126 ! meiosis relationship: develops_from CL:0000024 ! oogonial cell relationship: has_not_completed GO:0007126 ! meiosis [Term] id: CL:0000655 name: secondary oocyte namespace: cell def: "A secondary oocyte is an oocyte that has not completed meiosis II." [GOC:tfm, ISBN:0721662544] synonym: "primary oogonium" RELATED [] xref: BTO:0003094 xref: FMA:18646 is_a: CL:0000023 ! oocyte intersection_of: CL:0000023 ! oocyte intersection_of: has_not_completed GO:0007147 ! female meiosis II relationship: develops_from CL:0000654 ! primary oocyte relationship: has_not_completed GO:0007147 ! female meiosis II [Term] id: CL:0000656 name: primary spermatocyte namespace: cell def: "A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes." [GOC:tfm, ISBN:0721662544] xref: BTO:0001115 xref: FMA:72292 is_a: CL:0000017 ! spermatocyte intersection_of: CL:0000017 ! spermatocyte intersection_of: capable_of GO:0007140 ! male meiosis intersection_of: has_quality PATO:0001394 ! diploid relationship: capable_of GO:0007140 ! male meiosis relationship: has_quality PATO:0001394 ! diploid [Term] id: CL:0000657 name: secondary spermatocyte namespace: cell def: "One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids." [GOC:tfm, ISBN:0721662544] xref: BTO:0000709 xref: FBbt:00004941 xref: FMA:72293 is_a: CL:0000017 ! spermatocyte is_a: CL:0000413 ! haploid cell intersection_of: CL:0000017 ! spermatocyte intersection_of: capable_of GO:0007142 ! male meiosis II intersection_of: has_quality PATO:0001375 ! haploid relationship: capable_of GO:0007142 ! male meiosis II relationship: develops_from CL:0000656 ! primary spermatocyte relationship: has_quality PATO:0001375 ! haploid [Term] id: CL:0000658 name: cuticle secreting cell namespace: cell def: "An epithelial cell that secretes cuticle." [GOC:tfm] is_a: CL:0000066 ! epithelial cell is_a: CL:0000327 ! extracellular matrix secreting cell [Term] id: CL:0000659 name: eggshell secreting cell namespace: cell def: "An extracellular matrix secreting cell that secretes eggshell." [GOC:tfm] is_a: CL:0000327 ! extracellular matrix secreting cell is_a: CL:0000500 ! follicular epithelial cell [Term] id: CL:0000660 name: glycocalyx secreting cell namespace: cell def: "An extracellular matrix secreting cell that secretes glycocalyx." [GOC:tfm] is_a: CL:0000327 ! extracellular matrix secreting cell [Term] id: CL:0000661 name: distal tip cell (sensu Nematoda) namespace: cell is_a: CL:0000422 ! mitogenic signaling cell [Term] id: CL:0000662 name: neuroglioblast (sensu Nematoda) namespace: cell is_a: CL:0000468 ! neuroglioblast [Term] id: CL:0000663 name: valve cell namespace: cell is_a: CL:0000003 ! native cell [Term] id: CL:0000664 name: closable valve cell namespace: cell is_a: CL:0000185 ! myoepithelial cell is_a: CL:0000663 ! valve cell [Term] id: CL:0000665 name: permanently open valve cell namespace: cell is_a: CL:0000663 ! valve cell [Term] id: CL:0000666 name: fenestrated cell namespace: cell synonym: "window cell" EXACT [] is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000667 name: collagen secreting cell namespace: cell def: "An extracellular matrix secreting cell that secretes collagen." [GOC:tfm] is_a: CL:0000327 ! extracellular matrix secreting cell [Term] id: CL:0000668 name: obsolete parenchymal cell namespace: cell def: "The cell characteristic of an organ, as distinguished from associated connective or supporting tissues." [ISBN:0471245208] comment: OBSOLETE: Term was made obsolete to avoid confusion with plant parenchymal cell. Cell type has a similar but slightly different meaning in botany (plants): see PO:0000074. xref: BTO:0002174 xref: FMA:84638 is_obsolete: true [Term] id: CL:0000669 name: pericyte cell namespace: cell alt_id: CL:0000184 def: "An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. Pericytes are present in capillaries where proper adventitia and muscle layer are missing (thus distingushing this cell type from adventitial cells). They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells." [GOC:dsd, GOC:tfm, ISBN:0721662544, MESH:D020286, PMID:16807374, PMID:17986482, PMID:20024907] comment: Pericytes are CD10-positive, CD13-positive, CD31-negative, CD45-negative, CD106-positive, CD117-negative, CD140-positive, CD144-negative, CD146-positive, CD271-positive, CD325-positive, NG2-positive, RGS5-positive, SMA-positive, and desmin-positive. A subpopulation is CD248-positive. They are also capable of producing angiopoietin 1, CXCL12, TGF-beta, and VEGF-A. synonym: "adventitial cell" RELATED [] synonym: "adventitial reticular cell" EXACT [] synonym: "ARC" EXACT [PMID:17986482] synonym: "cell of Rouget" EXACT [] synonym: "pericyte" EXACT [] synonym: "pericyte of Rouget" EXACT [] xref: BTO:0002441 xref: FMA:63174 is_a: CL:0000183 ! contractile cell is_a: CL:0000630 ! supportive cell is_a: CL:0002320 ! connective tissue cell [Term] id: CL:0000670 name: primordial germ cell namespace: cell def: "A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells." [GOC:tfm, PMID:1381289] synonym: "gonocyte" EXACT [] synonym: "primitive germ cell" EXACT [] xref: FMA:70567 is_a: CL:0000039 ! germ line cell is_a: CL:0000219 ! motile cell intersection_of: CL:0000039 ! germ line cell intersection_of: capable_of GO:0048870 ! cell motility intersection_of: part_of UBERON:0000922 ! embryo relationship: capable_of GO:0048870 ! cell motility relationship: part_of UBERON:0000922 ! embryo [Term] id: CL:0000671 name: centripetally migrating follicle cell namespace: cell xref: FBbt:00004906 is_a: CL:0000477 ! follicle cell [Term] id: CL:0000672 name: tracheary element namespace: cell def: "Obsolete. Use PO:0000290 from Plant Ontology instead. A water conducting cell, tracheid or vessel member." [ISBN:0471245208] comment: replaced_by: PO:0000290 is_obsolete: true [Term] id: CL:0000673 name: Kenyon cell namespace: cell is_a: CL:0000028 ! CNS neuron (sensu Nematoda and Protostomia) [Term] id: CL:0000674 name: interfollicle cell namespace: cell synonym: "fly stalk cell" EXACT [] xref: FBbt:00004910 is_a: CL:0000075 ! columnar/cuboidal epithelial cell [Term] id: CL:0000675 name: female gamete namespace: cell def: "A mature sexual reproductive cell of the female germline." [GOC:tfm] is_a: CL:0000021 ! female germ cell is_a: CL:0000300 ! gamete intersection_of: CL:0000021 ! female germ cell intersection_of: has_quality PATO:0001375 ! haploid relationship: has_quality PATO:0001375 ! haploid [Term] id: CL:0000676 name: cap cell namespace: cell xref: BTO:0001033 is_a: CL:0000378 ! support cell (sensu Nematoda and Protostomia) [Term] id: CL:0000677 name: gut absorptive cell namespace: cell def: "Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules." [JB:jb] is_a: CL:0000212 ! absorptive cell [Term] id: CL:0000678 name: commisural neuron namespace: cell is_a: CL:0000372 ! tormogen cell [Term] id: CL:0000679 name: glutamatergic neuron namespace: cell xref: WBbt:0006829 is_a: CL:0000540 ! neuron [Term] id: CL:0000680 name: muscle precursor cell namespace: cell is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0002371 ! somatic cell relationship: develops_from CL:0000222 ! mesodermal cell [Term] id: CL:0000681 name: radial glial cell namespace: cell def: "A transient cell present only in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration." [GOC:dph] is_a: CL:0000337 ! neuroblast (sensu Vertebrata) relationship: develops_from CL:0000133 ! neurectodermal cell [Term] id: CL:0000682 name: M cell namespace: cell def: "An absorptive cell of the gut epithelium that endocytoses microorganisms and intact macromolecules from the gut lumen and transports them to the subepithelial space where they are presented to antigen-presenting cells and lymphocytes." [GOC:jb, GOC:tfm] synonym: "M-cell" EXACT [] synonym: "microfold cell" EXACT [] xref: BTO:0003600 xref: FMA:62929 is_a: CL:0000066 ! epithelial cell is_a: CL:0000473 ! defensive cell is_a: CL:0000627 ! transporting cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000683 name: ependymoglial cell namespace: cell def: "A cell that transports hormones from neurosecretory cells. This nerve cell is characterized by bipolar shape and endfeet that contact a basal lamina around blood vessels, and/or the pia mater or vitreous body of the eye and additionally contact the ventricular surface or sub-retinal space." [http://neurolex.org/wiki/Category\:Ependymoglial_Cell, JB:jb] synonym: "ependymal astrocyte" EXACT [] is_a: CL:0000127 ! astrocyte [Term] id: CL:0000684 name: littoral cell of liver namespace: cell is_a: CL:0000077 ! mesothelial cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000685 name: meristematic cell namespace: cell def: "Obsolete. Use PO:0004010 from Plant Ontology instead. A cell synthesizing protoplasm and producing new cells by division and with only a primary cell wall." [PO:0004010] comment: replaced_by: PO:0004010 is_obsolete: true [Term] id: CL:0000686 name: cerebrospinal fluid secreting cell namespace: cell def: "A columnar/cuboidal epithelial cell that secretes cerebrospinal fluid." [GOC:tfm] is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0000151 ! secretory cell relationship: develops_from CL:0000333 ! migratory neural crest cell [Term] id: CL:0000687 name: R1 photoreceptor cell namespace: cell is_a: CL:0000287 ! eye photoreceptor cell is_a: CL:0000488 ! visible light photoreceptor cell [Term] id: CL:0000688 name: perijunctional fibroblast namespace: cell def: "A fibroblast-like cell that provides support at neuromuscular junctions in vertebrates and are localized outside the synaptic basal lamina." [JB:jb] is_a: CL:0000057 ! fibroblast is_a: CL:0000630 ! supportive cell [Term] id: CL:0000689 name: myoendocrine cell namespace: cell def: "A cell with both myofibrils and secretory granules." [JB:jb] is_a: CL:0000163 ! endocrine cell [Term] id: CL:0000690 name: R2 photoreceptor cell namespace: cell is_a: CL:0000287 ! eye photoreceptor cell is_a: CL:0000488 ! visible light photoreceptor cell [Term] id: CL:0000691 name: stellate interneuron namespace: cell is_a: CL:0000099 ! interneuron [Term] id: CL:0000692 name: terminal Schwann cell namespace: cell def: "A neuroglial cell of the peripheral nervous system inside the basal lamina of the neuromuscular junction providing chemical and physical support to the synapse." [JB:jb, PMID:16136171] synonym: "Schwann cell" BROAD [] is_a: CL:0000630 ! supportive cell is_a: CL:0002376 ! non-myelinating Schwann cell [Term] id: CL:0000693 name: neuroglioform cell namespace: cell def: "A stellate interneuron having 7-10 dendrites that may branch." [JB:jb] synonym: "spiderweb cell" EXACT [] is_a: CL:0000691 ! stellate interneuron [Term] id: CL:0000694 name: R3 photoreceptor cell namespace: cell is_a: CL:0000287 ! eye photoreceptor cell is_a: CL:0000488 ! visible light photoreceptor cell [Term] id: CL:0000695 name: Cajal-Retzius cell namespace: cell def: "One of a transient population of pioneering neurons in the cerebral cortex. These cells are slender bipolar cells of the developing marginal zone. One feature of these cells in mammals is that they express the Reelin gene." [PMID:10600995, PMID:9728912] is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) [Term] id: CL:0000696 name: PP cell namespace: cell def: "A cell that stores and secretes pancreatic polypeptide hormone." [GOC:tfm, JB:jb, PMID:15153415] synonym: "type F enteroendocrine cell" EXACT [] xref: FMA:62938 xref: FMA:83409 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000697 name: R4 photoreceptor cell namespace: cell is_a: CL:0000287 ! eye photoreceptor cell is_a: CL:0000488 ! visible light photoreceptor cell [Term] id: CL:0000698 name: paraganglial cell namespace: cell is_obsolete: true [Term] id: CL:0000699 name: paraganglial type 1 cell namespace: cell def: "A type of glomus or chief cell, is sensitive to hypoxia and produce catecholamines." [GOC:tfm] is_a: CL:0000165 ! neuroendocrine cell [Term] id: CL:0000700 name: dopaminergic neuron namespace: cell def: "A neuron that releases dopamine as a neurotransmitter." [GOC:dhill] synonym: "dopaminergic cell" EXACT [] xref: BTO:0004032 xref: FMA:84787 xref: WBbt:0006746 is_a: CL:0000540 ! neuron [Term] id: CL:0000701 name: paraganglia type 2 cell namespace: cell def: "Supports paraganglial type 1 cell." [JB:jb] is_a: CL:0000630 ! supportive cell [Term] id: CL:0000702 name: R5 photoreceptor cell namespace: cell is_a: CL:0000287 ! eye photoreceptor cell is_a: CL:0000488 ! visible light photoreceptor cell [Term] id: CL:0000703 name: sustentacular cell namespace: cell def: "Cell that provides some or all mechanical, nutritional and phagocytic support to their neighbors." [JB:jb] xref: BTO:0002315 is_a: CL:0000630 ! supportive cell [Term] id: CL:0000704 name: endothelial tip cell namespace: cell def: "A specialized endothelial cell that senses extracellular signals and guides the directed growth of blood vessels." [PMID:15376331] is_a: CL:0000071 ! blood vessel endothelial cell [Term] id: CL:0000705 name: R6 photoreceptor cell namespace: cell is_a: CL:0000287 ! eye photoreceptor cell is_a: CL:0000488 ! visible light photoreceptor cell [Term] id: CL:0000706 name: choroid plexus epithelial cell namespace: cell alt_id: CL:1000430 def: "Specialized ependymal cell that produces the cerebrospinal fluid from the blood and secretes it into the lumen of the brain and spinal chord." [GOC:add, GOC:tfm, JB:jb, PMID:9550134] synonym: "epithelial cell of choroid plexus" EXACT [] xref: FMA:70549 is_a: CL:0000065 ! ependymal cell is_a: CL:0000627 ! transporting cell intersection_of: CL:0000065 ! ependymal cell intersection_of: part_of UBERON:0001886 ! choroid plexus relationship: part_of UBERON:0001886 ! choroid plexus [Term] id: CL:0000707 name: R7 photoreceptor cell namespace: cell is_a: CL:0000287 ! eye photoreceptor cell is_a: CL:0000494 ! UV sensitive photoreceptor cell [Term] id: CL:0000708 name: leptomeningeal cell namespace: cell def: "Stromal cell that forms the internal covering of the vertebrate brain and produces ECM for this and the choroid plexus." [JB:jb] synonym: "leptomemingeal cell" RELATED [] is_a: CL:0000327 ! extracellular matrix secreting cell intersection_of: CL:0000327 ! extracellular matrix secreting cell intersection_of: part_of UBERON:0003210 ! blood-cerebrospinal fluid barrier relationship: part_of UBERON:0003210 ! blood-cerebrospinal fluid barrier [Term] id: CL:0000709 name: R8 photoreceptor cell namespace: cell is_a: CL:0000287 ! eye photoreceptor cell is_a: CL:0000488 ! visible light photoreceptor cell [Term] id: CL:0000710 name: neurecto-epithelial cell namespace: cell def: "Epithelial cells derived from neural plate and neural crest." [GOC:tfm] comment: The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098). synonym: "neuroepithelial cell" BROAD [] xref: BTO:0004301 xref: FMA:70557 is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002077 ! ecto-epithelial cell relationship: develops_from CL:0000133 ! neurectodermal cell [Term] id: CL:0000711 name: cumulus cell namespace: cell def: "Cumulus cell is a specialized granulosa cell that surrounds and nourishes the oocyte. This cell-type surrounds the fully-grown oocyte to form a cumulus-oocyte complex (abbr. COC). The terms cumulus oophorus cells, cumulus granulosa cells, cumulus oophorous granulosa cells, granulosa-cumulus cells are used to make a distinction between this cell and the other functionally different subpopulation of granulosa cells at the wall of the Graafian follicle." [GOC:tfm, http://www.copewithcytokines.org/cope.cgi?key=cumulus%20cells] xref: BTO:0002236 is_a: CL:0000154 ! protein secreting cell is_a: CL:0002174 ! follicular cell of ovary relationship: develops_from CL:0000501 ! granulosa cell [Term] id: CL:0000712 name: stratum granulosum cell namespace: cell is_a: CL:0000362 ! epidermal cell [Term] id: CL:0000713 name: corona radiata cell namespace: cell is_a: CL:0000711 ! cumulus cell [Term] id: CL:0000715 name: embryonic crystal cell namespace: cell is_a: CL:0000392 ! crystal cell is_a: CL:0000736 ! embryonic gland hemocyte [Term] id: CL:0000716 name: lymph gland crystal cell namespace: cell is_a: CL:0000392 ! crystal cell is_a: CL:0000735 ! lymph gland hemocyte [Term] id: CL:0000717 name: fusimotor neuron namespace: cell def: "A subset of motor neurons that innervates intrafusal muscle fibers and has small diameter axons." [PMID:15582775] is_a: CL:0000100 ! motor neuron [Term] id: CL:0000718 name: cone cell (sensu Endopterygota) namespace: cell is_a: CL:0000306 ! crystallin accumulating cell [Term] id: CL:0000719 name: posterior cone cell (sensu Endopterygota) namespace: cell is_a: CL:0000718 ! cone cell (sensu Endopterygota) [Term] id: CL:0000720 name: anterior cone cell (sensu Endopterygota) namespace: cell is_a: CL:0000718 ! cone cell (sensu Endopterygota) [Term] id: CL:0000721 name: equatorial cone cell (sensu Endopterygota) namespace: cell is_a: CL:0000718 ! cone cell (sensu Endopterygota) [Term] id: CL:0000722 name: cystoblast namespace: cell is_a: CL:0000586 ! germ cell [Term] id: CL:0000723 name: somatic stem cell namespace: cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] xref: FMA:63368 is_a: CL:0000034 ! stem cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000034 ! stem cell intersection_of: capable_of GO:0048103 ! somatic stem cell division relationship: capable_of GO:0048103 ! somatic stem cell division [Term] id: CL:0000724 name: heterocyst namespace: cell def: " A differentiated cell that functions as a site of nitrogen fixation under aerobic conditions." [MA:ma] xref: BTO:0000600 is_a: CL:0000520 ! prokaryotic cell is_a: CL:0000725 ! nitrogen fixing cell [Term] id: CL:0000725 name: nitrogen fixing cell namespace: cell is_a: CL:0000003 ! native cell [Term] id: CL:0000726 name: chlamydospore namespace: cell def: "An asexual 1-celled spore (primarily for perennation, not dissemination). Originates endogenously and singly within part of a pre-existing cell by the contraction of the protoplast. Possesses an inner secondary and often thickened hyaline or brown wall, usually impregnated with hydrophobic material." [GOC:tfm, ISBN:085199377X] comment: Considering obsoleting as sometimes used to refer to protozoans too. But reference indicates term was intended for fungus. is_a: CL:0000605 ! fungal asexual spore [Term] id: CL:0000727 name: primary pigment cell namespace: cell is_a: CL:0001658 ! visual pigment cell (sensu Nematoda and Protostomia) [Term] id: CL:0000728 name: secondary pigment cell namespace: cell is_a: CL:0001658 ! visual pigment cell (sensu Nematoda and Protostomia) [Term] id: CL:0000729 name: tertiary pigment cell namespace: cell is_a: CL:0001658 ! visual pigment cell (sensu Nematoda and Protostomia) [Term] id: CL:0000730 name: leading edge cell namespace: cell def: "A cell at the front of a migrating epithelial sheet." [MA:ma] is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000731 name: urothelial cell namespace: cell def: "A cell of a layer of transitional epithelium in the wall of the bladder, ureter, and renal pelvis, external to the lamina propria." [GOC:tfm, MA:ma] synonym: "bladder transitional cell" NARROW [] synonym: "transitional epithelial cell of urinary bladder" NARROW [] synonym: "urinary tract transitional epithelial cell" NARROW [] xref: FMA:84127 is_a: CL:0000244 ! transitional epithelial cell intersection_of: CL:0000244 ! transitional epithelial cell intersection_of: part_of UBERON:0000365 ! urothelium relationship: part_of UBERON:0000365 ! urothelium [Term] id: CL:0000732 name: amoeboid cell namespace: cell is_a: CL:0000219 ! motile cell [Term] id: CL:0000733 name: lymph gland plasmatocyte namespace: cell is_a: CL:0000394 ! plasmatocyte is_a: CL:0000735 ! lymph gland hemocyte [Term] id: CL:0000734 name: embryonic gland plasmatocyte namespace: cell is_a: CL:0000394 ! plasmatocyte is_a: CL:0000736 ! embryonic gland hemocyte [Term] id: CL:0000735 name: lymph gland hemocyte namespace: cell is_a: CL:0000387 ! hemocyte (sensu Nematoda and Protostomia) [Term] id: CL:0000736 name: embryonic gland hemocyte namespace: cell is_a: CL:0000387 ! hemocyte (sensu Nematoda and Protostomia) [Term] id: CL:0000737 name: striated muscle cell namespace: cell def: "Muscle cell which has as its direct parts myofilaments organized into sarcomeres." [GOC:tfm, ISBN:0721662544] xref: BTO:0002916 xref: FMA:86936 is_a: CL:0000187 ! muscle cell [Term] id: CL:0000738 name: leukocyte namespace: cell def: "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." [GOC:add, GOC:tfm, ISBN:978-0-323-05290-0] synonym: "immune cell" EXACT [] synonym: "leucocyte" EXACT [] synonym: "white blood cell" EXACT [] xref: BTO:0000751 xref: FMA:62852 is_a: CL:0000219 ! motile cell is_a: CL:0000988 ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: capable_of GO:0001667 ! ameboidal cell migration relationship: capable_of GO:0001667 ! ameboidal cell migration relationship: develops_from CL:0000037 ! hematopoietic stem cell [Term] id: CL:0000740 name: retinal ganglion cell namespace: cell def: "The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve." [GOC:dph] synonym: "gangliocyte" EXACT [] synonym: "ganglion cell of retina" EXACT [] synonym: "RGC" EXACT [] xref: BTO:0001800 xref: FMA:67765 is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) [Term] id: CL:0000741 name: spinal accessory motor neuron namespace: cell def: "A motor neuron that is located in the cervical region of the spinal cord and selectively innervates the sternocleidmastoid or trapezius muscle. Unlike other motor neurons, they extend axons dorsally along lateral margins of the spinal cord." [PMID:16267219] synonym: "SACMN" EXACT [] is_a: CL:0000100 ! motor neuron [Term] id: CL:0000742 name: periarticular chondrocyte namespace: cell def: "A round chondrocyte that first differentiates in the late embryonic growth plate of bone." [PMID:15951842] is_a: CL:0000138 ! chondrocyte intersection_of: CL:0000138 ! chondrocyte intersection_of: part_of UBERON:0010996 ! articular cartilage of joint relationship: part_of UBERON:0010996 ! articular cartilage of joint [Term] id: CL:0000743 name: hypertrophic chondrocyte namespace: cell def: "Chondrocyte that is terminally differentiated, produces type X collagen, is large in size, and often associated with the replacement of cartilage by bone (endochondral ossification)." [GO_REF:0000034, PMID:15951842] comment: is hypertrophic pathological or normal? and can it be described using a pato term? is_a: CL:0000138 ! chondrocyte [Term] id: CL:0000744 name: columnar chondrocyte namespace: cell def: "A columnar chondrocyte that differentiates in the late embryonic growth plate of bone. Columnar chondrocytes vigorously proliferate and form columns in the growth plate." [PMID:15951842] is_a: CL:0000138 ! chondrocyte [Term] id: CL:0000745 name: horizontal cell namespace: cell def: "A neuron that laterally connects other neurons in the inner nuclear layer of the retina." [ISBN:0195088433] xref: BTO:0004120 is_a: CL:0000099 ! interneuron [Term] id: CL:0000746 name: cardiac muscle cell namespace: cell alt_id: FMA:83808 def: "Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei." [GOC:mtg_cardiacconduct_nov11, GOC:tfm, ISBN:0323052908] synonym: "cardiac muscle fiber" EXACT [GO:0048739] synonym: "cardiac myocyte" EXACT [] synonym: "cardiocyte" BROAD [] synonym: "cardiomyocyte" EXACT [] synonym: "heart muscle cell" EXACT [] xref: BTO:0001539 xref: FMA:14067 is_a: CL:0000737 ! striated muscle cell is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000737 ! striated muscle cell intersection_of: part_of UBERON:0007100 ! circulatory organ relationship: develops_from CL:0000513 ! cardiac muscle myoblast relationship: part_of UBERON:0007100 ! circulatory organ [Term] id: CL:0000747 name: cyanophore namespace: cell def: "A pigment cell derived from the neural crest. Contains blue pigment of unknown chemical composition in fibrous organelles termed cyanosomes. This gives a blue appearance." [SANBI:mhl] synonym: "blue chromatophore" RELATED [] is_a: CL:0000147 ! pigment cell relationship: develops_from CL:0005005 ! cyanoblast [Term] id: CL:0000748 name: retinal bipolar neuron namespace: cell def: "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner plexiform layer." [PMID:14689473] is_a: CL:0000103 ! bipolar neuron [Term] id: CL:0000749 name: ON-bipolar cell namespace: cell def: "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner half of the inner plexiform layer. These cells depolarize in response to light stimulation of their corresponding photoreceptors." [PMID:14689473] is_a: CL:0000748 ! retinal bipolar neuron [Term] id: CL:0000750 name: OFF-bipolar cell namespace: cell def: "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the outer half of the inner plexiform layer. These cells hyperpolarize in response to light stimulation of their corresponding photoreceptors." [PMID:14689473] is_a: CL:0000748 ! retinal bipolar neuron [Term] id: CL:0000751 name: rod bipolar cell namespace: cell def: "A bipolar neuron found in the retina and having connections with rod photoreceptor cells and neurons in the inner plexiform layer." [GOC:tfm, PMID:14689473] xref: FMA:67750 is_a: CL:0000749 ! ON-bipolar cell [Term] id: CL:0000752 name: cone retinal bipolar cell namespace: cell def: "A bipolar neuron found in the retina and having connections with cone photoreceptor cells and neurons in the inner plexiform layer." [PMID:14689473] is_a: CL:0000748 ! retinal bipolar neuron [Term] id: CL:0000753 name: type 1 cone bipolar cell (sensu Mus) namespace: cell def: "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell body of these cells is in the middle of the inner plexiform layer. The dendritic tree is stout and the axon terminates in sublamina 1. The axonal terminal is wide and has only a few varicosities." [PMID:14689473] synonym: "DB1 cone bipolar cell" EXACT [] is_a: CL:0000750 ! OFF-bipolar cell is_a: CL:0000752 ! cone retinal bipolar cell [Term] id: CL:0000754 name: type 2 cone bipolar cell (sensu Mus) namespace: cell def: "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is not well filled and the dendrites are more delicate than in type 1 cells. The axon terminal is bushier and exhibits a dense plexus of varicosities in the inner part of sublamina 1." [PMID:14689473] synonym: "FMB cone bipolar cell" EXACT [] is_a: CL:0000750 ! OFF-bipolar cell is_a: CL:0000752 ! cone retinal bipolar cell [Term] id: CL:0000755 name: type 3 cone bipolar cell (sensu Mus) namespace: cell def: "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is delicate and the dendritic tips appear small when compared with type 1 cells. The axon terminal is stratified and restricted to sublamina 2 of the inner plexiform layer." [PMID:14689473] synonym: "DB2 cone bipolar cell" EXACT [] is_a: CL:0000750 ! OFF-bipolar cell is_a: CL:0000752 ! cone retinal bipolar cell [Term] id: CL:0000756 name: type 4 cone bipolar cell (sensu Mus) namespace: cell def: "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell has a diffuse axon terminal with varicosities in sublaminae 1 and 2 of the inner plexiform layer." [PMID:14689473] synonym: "DB3 cone bipolar cell" EXACT [] is_a: CL:0000750 ! OFF-bipolar cell is_a: CL:0000752 ! cone retinal bipolar cell [Term] id: CL:0000757 name: type 5 cone bipolar cell (sensu Mus) namespace: cell def: "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is restricted to sublamina 3 of the inner plexiform layer. It is narrowly stratified and branched. The dendritic tree has many delicate branches." [PMID:14689473] synonym: "DB4 cone bipolar cell" EXACT [] is_a: CL:0000749 ! ON-bipolar cell is_a: CL:0000752 ! cone retinal bipolar cell [Term] id: CL:0000758 name: type 6 cone bipolar cell (sensu Mus) namespace: cell def: "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The cell has a loose, delicate axon terminal that opens in sublamina 3 of the inner plexiform layer and descends into sublamina 4." [PMID:14689473] synonym: "DB5 cone bipolar cell" EXACT [] is_a: CL:0000749 ! ON-bipolar cell is_a: CL:0000752 ! cone retinal bipolar cell [Term] id: CL:0000759 name: type 7 cone bipolar cell (sensu Mus) namespace: cell def: "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is narrowly stratified and are found just below a calretinin-expressing band in sublamina 4 of the inner plexiform layer." [PMID:14689473] synonym: "IMB cone bipolar cell" EXACT [] is_a: CL:0000749 ! ON-bipolar cell is_a: CL:0000752 ! cone retinal bipolar cell [Term] id: CL:0000760 name: type 8 cone bipolar cell (sensu Mus) namespace: cell def: "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. This cell has the widest dendritic field and the widest axon terminal of all retinal bipolar cells. The axon terminal is delicate and stratified through sublaminae 4 and 5 of the inner plexiform layer." [PMID:14689473] synonym: "DB6 cone bipolar cell" EXACT [] is_a: CL:0000749 ! ON-bipolar cell is_a: CL:0000752 ! cone retinal bipolar cell [Term] id: CL:0000761 name: type 9 cone bipolar cell (sensu Mus) namespace: cell def: "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The dendritic tree is wide and the dendritic convergence indicates cone selectivity. The axon terminal is sparsely branched and terminates in sublamina 5 of the inner plexiform layer." [PMID:14689473] synonym: "BB cone bipolar cell" EXACT [] is_a: CL:0000749 ! ON-bipolar cell is_a: CL:0000752 ! cone retinal bipolar cell [Term] id: CL:0000762 name: nucleated thrombocyte namespace: cell def: "A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates." [GOC:add, GOC:tfm, PMID:16360205] comment: Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals. is_a: CL:0000226 ! single nucleate cell is_a: CL:0000763 ! myeloid cell intersection_of: CL:0000763 ! myeloid cell intersection_of: capable_of GO:0007596 ! blood coagulation intersection_of: has_quality PATO:0001407 ! mononucleate relationship: capable_of GO:0007596 ! blood coagulation relationship: develops_from CL:0000828 ! thromboblast relationship: has_quality PATO:0001407 ! mononucleate [Term] id: CL:0000763 name: myeloid cell namespace: cell def: "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." [GOC:add] xref: BTO:0001441 is_a: CL:0000988 ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: develops_from CL:0000049 ! common myeloid progenitor relationship: develops_from CL:0000049 ! common myeloid progenitor [Term] id: CL:0000764 name: erythroid lineage cell namespace: cell alt_id: CL:0002156 def: "A immature or mature cell in the lineage leading to and including erythrocytes." [GOC:add, GOC:tfm] comment: Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. synonym: "erythropoietic cell" EXACT [] xref: FMA:62845 xref: FMA:83516 is_a: CL:0000763 ! myeloid cell [Term] id: CL:0000765 name: erythroblast namespace: cell def: "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers." [GOC:add, ISBN:0721601464, PMID:18174176] synonym: "normoblast" EXACT [] xref: BTO:0001571 xref: FMA:83504 is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0030218 ! erythrocyte differentiation intersection_of: has_part GO:0005634 ! nucleus intersection_of: lacks_part GO:0005730 ! nucleolus intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G relationship: capable_of GO:0030218 ! erythrocyte differentiation relationship: develops_from CL:0000547 ! proerythroblast relationship: has_part GO:0005634 ! nucleus relationship: lacks_part GO:0005730 ! nucleolus relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G [Term] id: CL:0000766 name: myeloid leukocyte namespace: cell def: "A cell of the monocyte, granulocyte, or mast cell lineage." [GOC:add] is_a: CL:0000738 ! leukocyte is_a: CL:0000763 ! myeloid cell intersection_of: CL:0000738 ! leukocyte intersection_of: develops_from CL:0000049 ! common myeloid progenitor relationship: develops_from CL:0000049 ! common myeloid progenitor [Term] id: CL:0000767 name: basophil namespace: cell def: "Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive." [GOC:add, GOC:amm, GOC:dsd, GOC:tfm, ISBN:0721601464, MESH:D001491, PMCID:PMC2626675, PMID:11927641, PMID:19741522, PMID:21236338, PMID:9933081] comment: Matures in the bone marrow and account for <1% of leukocytes in the peripheral blood, spleen, and bone marrow. Basophils are described as being CD11a-positive, CD11b-positive, CD13-positive, CD15-positive, CD18-positive, CD21-positive, CD25-positive, CD29-positive, CD35-positive, CD40-positive, CD40L-positive, CD44-positive, CD45R-negative, CD46-positive, CD49a-positive, CD49b-positive, CD49d-positive, CD55-positive, CD59-positive, CD62L-positive, CD63-positive, CD69-positive, CD90-negative, CD116-positive, CD117-negative, CD124-positive, CD125-positive, CD131-positive, CD161-positive, CD184-positive, CD191-positive, CD192-positive, CD197-positive, CD200R3-positive, CD218-positive, CD282-positive, CD284-positive, CD289-positive, CD290-positive, CD294-positive, natural killer cell receptor 2B4-positive, smad1-positive, CD3-negative, CD4-negative, CD7-negative, CD8-negative, CD14-negative, CD15-negative, CD16-negative, CD19-negative, CD20-negative, CD34-negative, CD36-negative, CD45R-negative, CD56-negative, CD57-negative, CD235a-negative, and GR1-negative. Transcription factors- GATA1-positive, PU.1-positive. synonym: "basophilic leucocyte" EXACT [] synonym: "basophilic leukocyte" EXACT [] synonym: "polymorphonuclear leucocyte" BROAD [] synonym: "polymorphonuclear leukocyte" BROAD [] xref: BTO:0000129 xref: FMA:62862 is_a: CL:0000094 ! granulocyte intersection_of: CL:0000094 ! granulocyte intersection_of: has_high_plasma_membrane_amount PR:000001255 ! chemokine receptor CCR3 intersection_of: has_high_plasma_membrane_amount PR:000001865 ! interleukin-3 receptor class 2 alpha chain intersection_of: has_high_plasma_membrane_amount PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha intersection_of: has_plasma_membrane_part PR:000001344 ! ectonucleotide pyrophosphatase/phosphodiesterase family member 3 intersection_of: has_plasma_membrane_part PR:000001950 ! tumor necrosis factor ligand superfamily member 5 relationship: has_high_plasma_membrane_amount PR:000001255 ! chemokine receptor CCR3 relationship: has_high_plasma_membrane_amount PR:000001865 ! interleukin-3 receptor class 2 alpha chain relationship: has_high_plasma_membrane_amount PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha relationship: has_plasma_membrane_part PR:000001344 ! ectonucleotide pyrophosphatase/phosphodiesterase family member 3 relationship: has_plasma_membrane_part PR:000001950 ! tumor necrosis factor ligand superfamily member 5 [Term] id: CL:0000768 name: immature basophil namespace: cell def: "Any of the immature forms of a basophil, in which basophilic specific granules are present but other phenotypic features of the mature form may be lacking." [GOC:add, ISBN:0721601464] synonym: "immature basophilic leucocyte" EXACT [] synonym: "immature basophilic leukocyte" EXACT [] is_a: CL:0000767 ! basophil intersection_of: CL:0000767 ! basophil intersection_of: lacks_part CP:0000025 ! lobed nucleus relationship: develops_from CL:0000830 ! basophilic promyelocyte relationship: lacks_part CP:0000025 ! lobed nucleus [Term] id: CL:0000769 name: basophilic metamyelocyte namespace: cell def: "A basophil precursor in the granulocytic series, being a cell intermediate in development between a basophilic myelocyte and a band form basophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are CD11b-positive, CD15-positive, CD16-positive, CD24-positive, CD33-positive, and CD13-positive." [GOC:tfm, ISBN:0721601464, PMID:18466030] xref: FMA:84198 is_a: CL:0000768 ! immature basophil is_a: CL:0002192 ! metamyelocyte is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000768 ! immature basophil intersection_of: has_part CP:0000040 ! reniform nucleus intersection_of: has_part GO:0000792 ! heterochromatin intersection_of: has_part GO:0042582 ! azurophil granule intersection_of: has_part GO:0070820 ! tertiary granule intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 intersection_of: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III intersection_of: has_plasma_membrane_part PR:000001892 ! CD33 molecule intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part PR:000002031 ! aminopeptidase N relationship: develops_from CL:0000614 ! basophilic myelocyte relationship: has_part CP:0000040 ! reniform nucleus relationship: has_part GO:0000792 ! heterochromatin relationship: has_part GO:0042582 ! azurophil granule relationship: has_part GO:0070820 ! tertiary granule relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 relationship: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: has_plasma_membrane_part PR:000001892 ! CD33 molecule relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000002031 ! aminopeptidase N [Term] id: CL:0000770 name: band form basophil namespace: cell def: "A late basophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature basophil." [GOC:add, http://www.cap.org, ISBN:0721601464, PMID:18466030] is_a: CL:0000768 ! immature basophil is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000768 ! immature basophil intersection_of: has_part CP:0000039 ! banded nucleus relationship: develops_from CL:0000769 ! basophilic metamyelocyte relationship: has_part CP:0000039 ! banded nucleus [Term] id: CL:0000771 name: eosinophil namespace: cell def: "Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive." [GOC:add, GOC:amm, GOC:dsd, GOC:tfm, ISBN:0721601464, PMCID:PMC2626675, PMID:10914487, PMID:1662676] comment: Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48-positive, CD69-positive, CD192-negative, MBP1-positive, MBP2-positive, TLR2-negative, TLR4-negative, and lineage-negative (B220, CD2, CD14, CD19, CD56, CD71, CD117, CD123, CD235a (glycophorin A), and TER119). The cytokines IL-3, IL-5, and GM-CSF are involved in their development and differentiation. Usually considered CD16-negative, CD16 is observed on eosinophilic metamyelocyte. synonym: "eosinocyte" EXACT [] synonym: "eosinophilic granulocyte" EXACT [] synonym: "eosinophilic leucocyte" EXACT [] synonym: "eosinophilic leukocyte" EXACT [] synonym: "polymorphonuclear leucocyte" BROAD [] synonym: "polymorphonuclear leukocyte" BROAD [] xref: BTO:0000399 xref: FMA:62861 is_a: CL:0000094 ! granulocyte intersection_of: CL:0000094 ! granulocyte intersection_of: has_plasma_membrane_part PR:000001254 ! chemokine receptor CCR1 intersection_of: has_plasma_membrane_part PR:000001255 ! chemokine receptor CCR3 intersection_of: has_plasma_membrane_part PR:000001307 ! CD44 molecule intersection_of: has_plasma_membrane_part PR:000001343 ! CD69 molecule intersection_of: has_plasma_membrane_part PR:000005178 ! CD9 molecule relationship: has_plasma_membrane_part PR:000001254 ! chemokine receptor CCR1 relationship: has_plasma_membrane_part PR:000001255 ! chemokine receptor CCR3 relationship: has_plasma_membrane_part PR:000001307 ! CD44 molecule relationship: has_plasma_membrane_part PR:000001343 ! CD69 molecule relationship: has_plasma_membrane_part PR:000005178 ! CD9 molecule [Term] id: CL:0000772 name: immature eosinophil namespace: cell def: "Any of the immature forms of an eosinophil, in which eosinophilic specific granules are present but other phenotypic features of the mature form may be lacking." [GOC:add, ISBN:0721601464] synonym: "immature eosinocyte" EXACT [] synonym: "immature eosinophilic leucocyte" EXACT [] synonym: "immature eosinophilic leukocyte" EXACT [] is_a: CL:0000771 ! eosinophil intersection_of: CL:0000771 ! eosinophil intersection_of: lacks_part CP:0000025 ! lobed nucleus relationship: develops_from CL:0000833 ! eosinophilic promyelocyte relationship: lacks_part CP:0000025 ! lobed nucleus [Term] id: CL:0000773 name: eosinophilic metamyelocyte namespace: cell def: "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a eosinophilic myelocyte and a band form eosinophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are integrin alpha-M-positive, fucosyltransferase FUT4-positive, low affinity immunoglobulin gamma Fc region receptor III-positive, CD33-positive, CD24-positive and aminopeptidase N-negative." [GOC:add, GOC:tfm, ISBN:0721601464, PMID:19622087] is_a: CL:0000772 ! immature eosinophil is_a: CL:0002192 ! metamyelocyte is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000772 ! immature eosinophil intersection_of: has_part CP:0000027 ! acidophilic cytoplasm intersection_of: has_part CP:0000040 ! reniform nucleus intersection_of: has_part GO:0000792 ! heterochromatin intersection_of: has_part GO:0042582 ! azurophil granule intersection_of: has_part GO:0070820 ! tertiary granule intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 intersection_of: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III intersection_of: has_plasma_membrane_part PR:000001892 ! CD33 molecule intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part PR:000002031 ! aminopeptidase N relationship: develops_from CL:0000612 ! eosinophilic myelocyte relationship: has_part CP:0000027 ! acidophilic cytoplasm relationship: has_part CP:0000040 ! reniform nucleus relationship: has_part GO:0000792 ! heterochromatin relationship: has_part GO:0042582 ! azurophil granule relationship: has_part GO:0070820 ! tertiary granule relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 relationship: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: has_plasma_membrane_part PR:000001892 ! CD33 molecule relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000002031 ! aminopeptidase N [Term] id: CL:0000774 name: band form eosinophil namespace: cell def: "A late eosinophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature basophil." [GOC:add, GOC:tfm, http://www.cap.org, ISBN:0721601464, PMID:19622087] is_a: CL:0000772 ! immature eosinophil is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000772 ! immature eosinophil intersection_of: has_part CP:0000039 ! banded nucleus relationship: develops_from CL:0000773 ! eosinophilic metamyelocyte relationship: has_part CP:0000039 ! banded nucleus [Term] id: CL:0000775 name: neutrophil namespace: cell def: "Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes." [GOC:add, GOC:amm, GOC:tfm, ISBN:0721601464] synonym: "neutrocyte" EXACT [] synonym: "neutrophil leucocyte" EXACT [] synonym: "neutrophil leukocyte" EXACT [] synonym: "neutrophilic leucocyte" EXACT [] synonym: "neutrophilic leukocyte" EXACT [] synonym: "PMN" BROAD [] synonym: "poly" BROAD [] synonym: "polymorphonuclear leucocyte" BROAD [] synonym: "polymorphonuclear leukocyte" BROAD [] synonym: "polymorphonuclear neutrophil" BROAD [] synonym: "polynuclear neutrophilic leucocyte" BROAD [] synonym: "polynuclear neutrophilic leukocyte" BROAD [] xref: BTO:0000130 xref: FMA:62860 is_a: CL:0000094 ! granulocyte intersection_of: CL:0000094 ! granulocyte intersection_of: has_plasma_membrane_part PR:000001479 ! low affinity immunoglobulin gamma Fc region receptor II intersection_of: has_plasma_membrane_part PR:000001879 ! leukosialin relationship: has_plasma_membrane_part PR:000001479 ! low affinity immunoglobulin gamma Fc region receptor II relationship: has_plasma_membrane_part PR:000001879 ! leukosialin [Term] id: CL:0000776 name: immature neutrophil namespace: cell def: "Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking." [GOC:add, ISBN:0721601464] synonym: "immatuer neutrophilic leukocyte" EXACT [] synonym: "immature neutrocyte" EXACT [] synonym: "immature neutrophil leucocyte" EXACT [] synonym: "immature neutrophil leukocyte" EXACT [] synonym: "immature neutrophilic leucocyte" EXACT [] is_a: CL:0000775 ! neutrophil intersection_of: CL:0000775 ! neutrophil intersection_of: lacks_part CP:0000025 ! lobed nucleus relationship: develops_from CL:0000564 ! neutrophilic promyelocyte relationship: lacks_part CP:0000025 ! lobed nucleus [Term] id: CL:0000777 name: mesangial phagocyte namespace: cell def: "A tissue-resident macrophage of the renal glomerular mesangium involved in the disposal and degradation of filtration residues, presentation of antigen to T cells and in tissue remodeling." [GOC:add, GOC:tfm, ISBN:0702022918, ISBN:3540536663, PMID:1600140, PMID:16146841] synonym: "mesangial cell" BROAD [] is_a: CL:0000864 ! tissue-resident macrophage is_a: CL:0002681 ! kidney cortical cell is_a: CL:1000500 ! kidney interstitial cell intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0019882 ! antigen processing and presentation intersection_of: capable_of GO:0048771 ! tissue remodeling intersection_of: part_of UBERON:0002320 ! glomerular mesangium relationship: capable_of GO:0019882 ! antigen processing and presentation relationship: capable_of GO:0048771 ! tissue remodeling relationship: part_of UBERON:0002320 ! glomerular mesangium [Term] id: CL:0000778 name: mononuclear osteoclast namespace: cell def: "A specialized mononuclear osteoclast associated with the absorption and removal of bone, precursor of multinuclear osteoclasts." [GOC:add, GOC:tfm, PMID:12713016, PMID:15055519, PMID:17380158, PMID:9415452] comment: Morphology: mononuclear, highly vesicular. is_a: CL:0000092 ! osteoclast is_a: CL:0000226 ! single nucleate cell intersection_of: CL:0000092 ! osteoclast intersection_of: has_quality PATO:0001407 ! mononucleate relationship: has_quality PATO:0001407 ! mononucleate [Term] id: CL:0000779 name: multinuclear osteoclast namespace: cell def: "A specialized multinuclear osteoclast associated with the absorption and removal of bone." [GOC:add, PMID:12713016, PMID:9415452] comment: Morphology: multinucleated, highly vesicular. synonym: "multinucleated osteoclast" EXACT [] is_a: CL:0000092 ! osteoclast is_a: CL:0000228 ! multinucleate cell intersection_of: CL:0000092 ! osteoclast intersection_of: has_quality PATO:0001908 ! multinucleate relationship: develops_from CL:0000778 ! mononuclear osteoclast relationship: has_quality PATO:0001908 ! multinucleate [Term] id: CL:0000780 name: multinuclear odontoclast namespace: cell def: "A specialized multinuclear osteoclast associated with the absorption and removal of cementum." [GOC:add, PMID:9415452] comment: Morphology: multinucleated, highly vesicular; location: roots of deciduous (milk) teeth. synonym: "multinucleated odontoclast" EXACT [] is_a: CL:0000588 ! odontoclast is_a: CL:0000779 ! multinuclear osteoclast intersection_of: CL:0000588 ! odontoclast intersection_of: has_quality PATO:0001908 ! multinucleate relationship: develops_from CL:0000781 ! mononuclear odontoclast relationship: has_quality PATO:0001908 ! multinucleate [Term] id: CL:0000781 name: mononuclear odontoclast namespace: cell def: "A specialized mononuclear osteoclast associated with the absorption and removal of cementum." [GOC:add, PMID:9415452] comment: Morphology: Mononuclear, highly vesicular; location: roots of deciduous (milk) teeth. is_a: CL:0000588 ! odontoclast is_a: CL:0000778 ! mononuclear osteoclast intersection_of: CL:0000588 ! odontoclast intersection_of: has_quality PATO:0001407 ! mononucleate relationship: has_quality PATO:0001407 ! mononucleate [Term] id: CL:0000782 name: myeloid dendritic cell namespace: cell def: "A dendritic cell of the myeloid lineage." [GOC:add, PMID:10449155, PMID:17332250, PMID:9521319] comment: These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8). synonym: "CD11c+CD123- DC" EXACT [] synonym: "interdigitating cell" BROAD [] synonym: "mDC" EXACT [] synonym: "veiled cell" BROAD [] xref: BTO:0004721 is_a: CL:0000990 ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: develops_from CL:0000763 ! myeloid cell intersection_of: lacks_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain relationship: develops_from CL:0000576 ! monocyte relationship: develops_from CL:0000763 ! myeloid cell relationship: lacks_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain [Term] id: CL:0000783 name: multinucleated phagocyte namespace: cell def: "A phagocyte formed by the fusion of mononuclear phagocytes." [GOC:add, GOC:tfm] is_a: CL:0000228 ! multinucleate cell is_a: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: has_quality PATO:0001908 ! multinucleate relationship: has_quality PATO:0001908 ! multinucleate [Term] id: CL:0000784 name: plasmacytoid dendritic cell namespace: cell def: "A dendritic cell type of distinct morphology, localization, and surface marker expression (CD123-positive) from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection." [GOC:add, GOC:dsd, PMCID:PMC2118448, PMCID:PMC538703, PMID:15549123, PMID:17332250, PMID:17850486, PMID:20304825] synonym: "DC2" EXACT [] synonym: "interferon-producing cell" EXACT [] synonym: "IPC" EXACT [] synonym: "lymphoid dendritic cell" EXACT [] synonym: "pDC" EXACT [] synonym: "plasmacytoid monocyte" EXACT [] synonym: "plasmacytoid T cell" EXACT [] synonym: "T-associated plasma cell" EXACT [] synonym: "type 2 DC" EXACT [] xref: BTO:0004625 is_a: CL:0000451 ! dendritic cell intersection_of: CL:0000451 ! dendritic cell intersection_of: capable_of GO:0032606 ! type I interferon production relationship: capable_of GO:0032606 ! type I interferon production relationship: develops_from CL:0000037 ! hematopoietic stem cell [Term] id: CL:0000785 name: mature B cell namespace: cell def: "A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen." [GOC:add, GOC:dsd, ISBN:0781735149] comment: Mature B cells are also reportedly CD10-negative, CD19-positive, CD22-positive, CD34-negative, CD48-positive, CD79a-positive, CD84-positive, CD127-negative, CD352-positive, RAG-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Transcription factors expressed: Pax5-positive. synonym: "mature B lymphocyte" EXACT [] synonym: "mature B-cell" EXACT [] synonym: "mature B-lymphocyte" EXACT [] is_a: CL:0000236 ! B cell intersection_of: CL:0000236 ! B cell intersection_of: capable_of GO:0042113 ! B cell activation intersection_of: has_completed GO:0002335 ! mature B cell differentiation disjoint_from: CL:0000816 ! immature B cell disjoint_from: CL:0000817 ! precursor B cell disjoint_from: CL:0000818 ! transitional stage B cell relationship: capable_of GO:0042113 ! B cell activation relationship: develops_from CL:0000818 ! transitional stage B cell relationship: has_completed GO:0002335 ! mature B cell differentiation [Term] id: CL:0000786 name: plasma cell namespace: cell def: "A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin." [GO_REF:0000031, GOC:add, GOC:dsd, http://en.wikipedia.org/wiki/Plasma_cell, ISBN:0721601464, ISBN:0781735149, PMID:19447676, PMID:20081059, PMID:20839338, PMID:20951740] comment: Plasma cells develop in the spleen and migrate to the bone marrow. Plasma cells are also reportedly CD5-negative, CD10-negative, CD19-positive, CD20-negative, CD21-negative, CD22-negative, CD23-negative, CD24-negative, CD25-negative, CD27-positive, CD34-negative, CD38-positive, CD40-positive, CD43-positive, CD45-positive, CD48-positive, CD53-low, CD80-negative, CD81-positive, CD86-positive, CD95-positive, CD196-negative, CD229-positive, CD270-positive, CD352-positive, CD361-positive, and IgD-negative. Transcription factors: BLIMP1-positive, IRF4-positive, PAX5-negative, SpiB-negative, Ets1-negative, and XBP1-positive. synonym: "effector B cell" RELATED [] synonym: "effector B-cell" RELATED [] synonym: "plasma B cell" EXACT [] synonym: "plasma B-cell" EXACT [] synonym: "plasmacyte" EXACT [] synonym: "plasmocyte" EXACT [] xref: BTO:0000392 xref: FMA:70574 is_a: CL:0000946 ! antibody secreting cell intersection_of: CL:0000946 ! antibody secreting cell intersection_of: has_part CP:0000043 ! cartwheel heterochromatin intersection_of: has_part GO:0005794 ! Golgi apparatus intersection_of: has_plasma_membrane_part PR:000001935 ! syndecan-1 intersection_of: lacks_plasma_membrane_part GO:0019814 ! immunoglobulin complex intersection_of: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: develops_from CL:0000980 ! plasmablast relationship: has_part CP:0000043 ! cartwheel heterochromatin relationship: has_part GO:0005794 ! Golgi apparatus relationship: has_plasma_membrane_part PR:000001935 ! syndecan-1 relationship: lacks_plasma_membrane_part GO:0019814 ! immunoglobulin complex relationship: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex [Term] id: CL:0000787 name: memory B cell namespace: cell def: "A memory B cell is a mature B cell that is long-lived, readily activated upon re-encounter of its antigenic determinant, and has been selected for expression of higher affinity immunoglobulin. This cell type has the phenotype CD19-positive, CD20-positive, MHC Class II-positive, and CD138-negative." [GO_REF:0000031, GOC:add, GOC:dsd, GOC:rhs, http://en.wikipedia.org/wiki/Memory_B_cell, ISBN:0781735149, PMID:20081059, PMID:20839338] comment: Memory B-cells are also reportedly CD5-negative, CD10-negative, CD21-positive, CD22-positive, CD23-negative, CD24-positive, CD25-positive, CD27-positive, CD34-negative, CD38-negative, CD40-positive, CD43-negative, CD44-positive, CD45-positive, CD53-positive, CD80-negative, CD81-negative, CD86-positive, and CD196/CCR6-positive. synonym: "memory B lymphocyte" EXACT [] synonym: "memory B-cell" EXACT [] synonym: "memory B-lymphocyte" EXACT [] is_a: CL:0000785 ! mature B cell intersection_of: CL:0000785 ! mature B cell intersection_of: has_completed GO:0002344 ! B cell affinity maturation intersection_of: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex intersection_of: has_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001935 ! syndecan-1 relationship: has_completed GO:0002344 ! B cell affinity maturation relationship: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: has_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001935 ! syndecan-1 [Term] id: CL:0000788 name: naive B cell namespace: cell def: "A naive B cell is a mature B cell that has the phenotype surface IgD-positive, surface IgM-positive, CD27-negative and that has not yet been activated by antigen in the periphery." [GO_REF:0000031, GOC:add, GOC:dsd, GOC:rhs, ISBN:0781765196, PMID:19447676, PMID:20081059, PMID:20839338, PMID:20933013] comment: Naïve B-cells are also reportedly CD10-negative, CD19-positive, CD20-positive, CD21-positive, CD22-positive, CD25-negative, CD27-negative, CD34-negative, CD40-positive, CD43-negative, CD45-positive, CD48-positive, CD53-positive, CD80-negative, CD81-positive, CD84-positive, CD86-negative, CD95-negative, CD138-negative, CD150-positive, CD184/CXCR4-positive, CD185/CXCR5-positive, CD196/CCR6-positive, CD200-positive, CD229-positive, CD243-positive, CD289-positive, CD290-positive, CD352-positive, MHCII/HLA-DR-positive, cadherin 9-positive, and sIgH-positive, Transcription factors: Pax5-positive, ETS1-positive, FOXO1A-positive, KLF4-positive, KLF9-positive, MiTF-positive, OBF1-positive, PLZF-positive, and SpiB-positive. synonym: "naive B lymphocyte" EXACT [] synonym: "naive B-cell" EXACT [] synonym: "naive B-lymphocyte" EXACT [] is_a: CL:0000785 ! mature B cell intersection_of: CL:0000785 ! mature B cell intersection_of: has_not_completed GO:0002344 ! B cell affinity maturation intersection_of: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex intersection_of: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex intersection_of: lacks_plasma_membrane_part PR:000001963 ! CD27 molecule relationship: develops_from CL:0000818 ! transitional stage B cell relationship: has_not_completed GO:0002344 ! B cell affinity maturation relationship: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex relationship: lacks_plasma_membrane_part PR:000001963 ! CD27 molecule [Term] id: CL:0000789 name: alpha-beta T cell namespace: cell def: "A T cell that expresses an alpha-beta T cell receptor complex." [GOC:add, GOC:tfm, ISBN:0781735149] synonym: "alpha-beta T lymphocyte" EXACT [] synonym: "alpha-beta T-cell" EXACT [] synonym: "alpha-beta T-lymphocyte" EXACT [] is_a: CL:0000084 ! T cell intersection_of: CL:0000084 ! T cell intersection_of: has_plasma_membrane_part GO:0042105 ! alpha-beta T cell receptor complex disjoint_from: CL:0000798 ! gamma-delta T cell relationship: has_plasma_membrane_part GO:0042105 ! alpha-beta T cell receptor complex [Term] id: CL:0000790 name: immature alpha-beta T cell namespace: cell def: "An alpha-beta T cell that has an immature phenotype and has not completed T cell selection." [GOC:add, GOC:tfm, ISBN:0781735149] synonym: "immature alpha-beta T lymphocyte" EXACT [] synonym: "immature alpha-beta T-cell" EXACT [] synonym: "immature alpha-beta T-lymphocyte" EXACT [] is_a: CL:0000789 ! alpha-beta T cell is_a: CL:0002420 ! immature T cell intersection_of: CL:0000789 ! alpha-beta T cell intersection_of: has_not_completed GO:0045058 ! T cell selection relationship: has_not_completed GO:0045058 ! T cell selection [Term] id: CL:0000791 name: mature alpha-beta T cell namespace: cell def: "A alpha-beta T cell that has a mature phenotype." [GOC:add, GOC:tfm, ISBN:0781735149] synonym: "mature alpha-beta T lymphocyte" EXACT [] synonym: "mature alpha-beta T-cell" EXACT [] synonym: "mature alpha-beta T-lymphocyte" EXACT [] is_a: CL:0000789 ! alpha-beta T cell is_a: CL:0002419 ! mature T cell intersection_of: CL:0000789 ! alpha-beta T cell intersection_of: has_completed GO:0045058 ! T cell selection relationship: develops_from CL:0000790 ! immature alpha-beta T cell relationship: has_completed GO:0045058 ! T cell selection [Term] id: CL:0000792 name: CD4-positive, CD25-positive, alpha-beta regulatory T cell namespace: cell def: "A CD4-positive, CD25-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release." [GOC:add, GOC:tfm, ISBN:0781735149, PMID:19464985] synonym: "CD4-positive, CD25-positive, alpha-beta regulatory T lymphocyte" EXACT [] synonym: "CD4-positive, CD25-positive, alpha-beta regulatory T-cell" EXACT [] synonym: "CD4-positive, CD25-positive, alpha-beta regulatory T-lymphocyte" EXACT [] synonym: "suppressor T cell" BROAD [] synonym: "suppressor T lymphocyte" BROAD [] synonym: "suppressor T-cell" BROAD [] synonym: "suppressor T-lymphocyte" BROAD [] xref: FMA:84070 is_a: CL:0000624 ! CD4-positive, alpha-beta T cell is_a: CL:0000815 ! regulatory T cell intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: capable_of GO:0050777 ! negative regulation of immune response intersection_of: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: capable_of GO:0050777 ! negative regulation of immune response relationship: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha [Term] id: CL:0000793 name: CD4-positive, alpha-beta intraepithelial T cell namespace: cell def: "A CD4-positive, alpha-beta T cell that is found in the columnar epithelium of the gastrointestinal tract." [GOC:add, GOC:tfm, ISBN:0781735149] synonym: "CD4-positive, alpha-beta intraepithelial T lymphocyte" EXACT [] synonym: "CD4-positive, alpha-beta intraepithelial T-cell" EXACT [] synonym: "CD4-positive, alpha-beta intraepithelial T-lymphocyte" EXACT [] synonym: "IEL" BROAD [] synonym: "intraepithelial lymphocyte" BROAD [] is_a: CL:0000624 ! CD4-positive, alpha-beta T cell is_a: CL:0000797 ! alpha-beta intraepithelial T cell intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: capable_of GO:0002385 ! mucosal immune response intersection_of: part_of UBERON:0001277 ! intestinal epithelium relationship: capable_of GO:0002385 ! mucosal immune response relationship: develops_from CL:0000810 ! CD4-positive, alpha-beta thymocyte relationship: part_of UBERON:0001277 ! intestinal epithelium [Term] id: CL:0000794 name: CD8-positive, alpha-beta cytotoxic T cell namespace: cell def: "A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, ISBN:0781735149] comment: Note that while T cells of this subset are loosely referred to 'cytotoxic T cells,' as many other T cell types, including CD4-positive, alpha-beta T cells and gamma-delta T cells exhibit cytotoxicity in vitro and in vivo. synonym: "CD8-positive, alpha-beta cytotoxic T lymphocyte" EXACT [] synonym: "CD8-positive, alpha-beta cytotoxic T-cell" EXACT [] synonym: "CD8-positive, alpha-beta cytotoxic T-lymphocyte" EXACT [] synonym: "cytotoxic T cell" BROAD [] synonym: "cytotoxic T lymphocyte" BROAD [] synonym: "cytotoxic T-cell" BROAD [] synonym: "cytotoxic T-lymphocyte" BROAD [] synonym: "killer T cell" BROAD [] synonym: "killer T lymphocyte" BROAD [] synonym: "killer T-cell" BROAD [] synonym: "killer T-lymphocyte" BROAD [] xref: FMA:70573 is_a: CL:0000625 ! CD8-positive, alpha-beta T cell is_a: CL:0000910 ! cytotoxic T cell intersection_of: CL:0000625 ! CD8-positive, alpha-beta T cell intersection_of: capable_of GO:0001913 ! T cell mediated cytotoxicity intersection_of: capable_of GO:0033380 ! granzyme B localization to T cell secretory granule intersection_of: has_completed GO:0030217 ! T cell differentiation intersection_of: has_part PR:000003466 ! perforin-1 intersection_of: has_part PR:000003499 ! granzyme B relationship: capable_of GO:0001913 ! T cell mediated cytotoxicity relationship: capable_of GO:0033380 ! granzyme B localization to T cell secretory granule relationship: develops_from CL:0000906 ! activated CD8-positive, alpha-beta T cell relationship: has_completed GO:0030217 ! T cell differentiation relationship: has_part PR:000003466 ! perforin-1 relationship: has_part PR:000003499 ! granzyme B [Term] id: CL:0000795 name: CD8-positive, alpha-beta regulatory T cell namespace: cell def: "A CD8-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release." [GOC:add, GOC:tfm, ISBN:0781735149] synonym: "CD8+ regulatory T cell" EXACT [] synonym: "CD8+ T(reg)" EXACT [] synonym: "CD8+ Treg" EXACT [] synonym: "CD8-positive T(reg)" EXACT [] synonym: "CD8-positive Treg" EXACT [] synonym: "CD8-positive, alpha-beta regulatory T lymphocyte" EXACT [] synonym: "CD8-positive, alpha-beta regulatory T-cell" EXACT [] synonym: "CD8-positive, alpha-beta regulatory T-lymphocyte" EXACT [] synonym: "CD8-positive, alpha-beta Treg" EXACT [] synonym: "suppressor T cell" BROAD [] synonym: "suppressor T lymphocyte" BROAD [] synonym: "suppressor T-cell" BROAD [] synonym: "suppressor T-lymphocyte" BROAD [] xref: FMA:84070 is_a: CL:0000625 ! CD8-positive, alpha-beta T cell is_a: CL:0000815 ! regulatory T cell intersection_of: CL:0000625 ! CD8-positive, alpha-beta T cell intersection_of: capable_of GO:0050777 ! negative regulation of immune response relationship: capable_of GO:0050777 ! negative regulation of immune response [Term] id: CL:0000796 name: CD8-alpha-beta-positive, alpha-beta intraepithelial T cell namespace: cell def: "A alpha-beta intraepithelial T cell found in the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements." [GOC:add, ISBN:0781735149] synonym: "CD8-positive, alpha-beta intraepithelial T lymphocyte" EXACT [] synonym: "CD8-positive, alpha-beta intraepithelial T-cell" EXACT [] synonym: "CD8-positive, alpha-beta intraepithelial T-lymphocyte" EXACT [] synonym: "IEL" BROAD [] synonym: "intraepithelial lymphocyte" BROAD [] is_a: CL:0000625 ! CD8-positive, alpha-beta T cell is_a: CL:0000797 ! alpha-beta intraepithelial T cell intersection_of: CL:0000797 ! alpha-beta intraepithelial T cell intersection_of: has_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 relationship: has_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 [Term] id: CL:0000797 name: alpha-beta intraepithelial T cell namespace: cell def: "A mature alpha-beta T cell of the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements." [GOC:add, GOC:tfm, ISBN:0781735149] synonym: "alpha-beta intraepithelial T lymphocyte" EXACT [] synonym: "alpha-beta intraepithelial T-cell" EXACT [] synonym: "alpha-beta intraepithelial T-lymphocyte" EXACT [] synonym: "IEL" BROAD [] synonym: "intraepithelial lymphocyte" BROAD [] is_a: CL:0000791 ! mature alpha-beta T cell is_a: CL:0002496 ! intraepithelial lymphocyte intersection_of: CL:0000791 ! mature alpha-beta T cell intersection_of: capable_of GO:0002385 ! mucosal immune response intersection_of: part_of UBERON:0001277 ! intestinal epithelium relationship: capable_of GO:0002385 ! mucosal immune response relationship: part_of UBERON:0001277 ! intestinal epithelium [Term] id: CL:0000798 name: gamma-delta T cell namespace: cell def: "A T cell that expresses a gamma-delta T cell receptor complex." [GOC:add, GOC:tfm, ISBN:0781735149] comment: Note that gamma-delta T cells have both thymic and extrathymic differentiation pathways. synonym: "gamma-delta T lymphocyte" EXACT [] synonym: "gamma-delta T-cell" EXACT [] synonym: "gamma-delta T-lymphocyte" EXACT [] synonym: "gammadelta T cell" EXACT [] synonym: "gd T cell" RELATED [] is_a: CL:0000084 ! T cell intersection_of: CL:0000084 ! T cell intersection_of: has_plasma_membrane_part GO:0042106 ! gamma-delta T cell receptor complex relationship: has_plasma_membrane_part GO:0042106 ! gamma-delta T cell receptor complex [Term] id: CL:0000799 name: immature gamma-delta T cell namespace: cell def: "A gamma-delta T cell that has an immature phenotype." [GOC:add, ISBN:0781735149] comment: Note that gamma-delta T cells have both thymic and extrathymic differentiation pathways. synonym: "immature gamma-delta T lymphocyte" EXACT [] synonym: "immature gamma-delta T-cell" EXACT [] synonym: "immature gamma-delta T-lymphocyte" EXACT [] is_a: CL:0000798 ! gamma-delta T cell is_a: CL:0002420 ! immature T cell intersection_of: CL:0000798 ! gamma-delta T cell intersection_of: has_not_completed GO:0042492 ! gamma-delta T cell differentiation intersection_of: has_not_completed GO:0045058 ! T cell selection relationship: develops_from CL:0000807 ! DN3 thymocyte relationship: has_not_completed GO:0042492 ! gamma-delta T cell differentiation relationship: has_not_completed GO:0045058 ! T cell selection [Term] id: CL:0000800 name: mature gamma-delta T cell namespace: cell def: "A gamma-delta T cell that has a mature phenotype. These cells can be found in tissues and circulation where they express unique TCR repertoire depending on their location." [GOC:add, GOC:tfm, ISBN:0781735149] synonym: "mature gamma-delta T lymphocyte" EXACT [] synonym: "mature gamma-delta T-cell" EXACT [] synonym: "mature gamma-delta T-lymphocyte" EXACT [] is_a: CL:0000798 ! gamma-delta T cell is_a: CL:0002419 ! mature T cell intersection_of: CL:0000798 ! gamma-delta T cell intersection_of: has_completed GO:0045058 ! T cell selection relationship: develops_from CL:0000799 ! immature gamma-delta T cell relationship: has_completed GO:0045058 ! T cell selection [Term] id: CL:0000801 name: gamma-delta intraepithelial T cell namespace: cell def: "A mature gamma-delta T cell that is found in the columnar epithelium of the gastrointestinal tract. These cells participate in mucosal immune responses." [GOC:add, GOC:tfm, ISBN:0781735149] synonym: "gamma-delta intraepithelial T lymphocyte" EXACT [] synonym: "gamma-delta intraepithelial T-cell" EXACT [] synonym: "gamma-delta intraepithelial T-lymphocyte" EXACT [] synonym: "IEL" BROAD [] synonym: "intraepithelial lymphocyte" BROAD [] is_a: CL:0000800 ! mature gamma-delta T cell is_a: CL:0002496 ! intraepithelial lymphocyte intersection_of: CL:0000800 ! mature gamma-delta T cell intersection_of: capable_of GO:0002385 ! mucosal immune response intersection_of: part_of UBERON:0001277 ! intestinal epithelium relationship: capable_of GO:0002385 ! mucosal immune response relationship: part_of UBERON:0001277 ! intestinal epithelium [Term] id: CL:0000802 name: CD8-alpha alpha positive, gamma-delta intraepithelial T cell namespace: cell def: "A gamma-delta intraepithelial T cell that has the phenotype CD8-alpha alpha-positive." [GOC:add, GOC:tfm, ISBN:0781735149] synonym: "CD8-positive, gamma-delta intraepithelial T lymphocyte" EXACT [] synonym: "CD8-positive, gamma-delta intraepithelial T-cell" EXACT [] synonym: "CD8-positive, gamma-delta intraepithelial T-lymphocyte" EXACT [] synonym: "IEL" BROAD [] synonym: "intraepithelial lymphocyte" BROAD [] is_a: CL:0000801 ! gamma-delta intraepithelial T cell intersection_of: CL:0000801 ! gamma-delta intraepithelial T cell intersection_of: has_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: has_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain [Term] id: CL:0000803 name: CD4-negative CD8-negative gamma-delta intraepithelial T cell namespace: cell def: "A gamma-delta intraepithelial T cell that has the phenotype CD4-negative and CD8-negative." [GOC:add, GOC:tfm, ISBN:0781735149] synonym: "CD4-positive, gamma-delta intraepithelial T lymphocyte" EXACT [] synonym: "CD4-positive, gamma-delta intraepithelial T-cell" EXACT [] synonym: "CD4-positive, gamma-delta intraepithelial T-lymphocyte" EXACT [] synonym: "IEL" BROAD [] synonym: "intraepithelial lymphocyte" BROAD [] is_a: CL:0000801 ! gamma-delta intraepithelial T cell intersection_of: CL:0000801 ! gamma-delta intraepithelial T cell intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain [Term] id: CL:0000805 name: immature single positive thymocyte namespace: cell def: "A thymocyte that has the phenotype CD4-negative, CD8-positive, CD44-negative, CD25-negative, and pre-TCR-positive." [GO_REF:0000031, GOC:add, GOC:tfm, http://www.immgen.org/index_content.html, ISBN:0781735149] comment: Note that this type of thymocyte has passed the beta-selection checkpoint and is rapidly proliferating and rearranging the T cell receptor alpha chain and expressing the CD8 coreceptor. This stage comes between the DN4 and DP stages. synonym: "immature single positive T cell" EXACT [] synonym: "immature single positive T lymphocyte" EXACT [] synonym: "immature single positive T-lymphocyte" EXACT [] synonym: "ISP" EXACT [] synonym: "T.ISP.th" EXACT [] is_a: CL:0000893 ! thymocyte intersection_of: CL:0000893 ! thymocyte intersection_of: has_high_plasma_membrane_amount PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part GO:0043384 ! pre-T cell receptor complex intersection_of: has_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001307 ! CD44 molecule intersection_of: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: develops_from CL:0000808 ! DN4 thymocyte relationship: has_high_plasma_membrane_amount PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part GO:0043384 ! pre-T cell receptor complex relationship: has_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001307 ! CD44 molecule relationship: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha [Term] id: CL:0000806 name: DN2 thymocyte namespace: cell def: "A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-positive." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149] comment: Note that this type of thymocyte is at the earliest stage of T cell receptor rearrangement of the beta, gamma, and delta T cell receptor chains. synonym: "DN2 alpha-beta immature T lymphocyte" EXACT [] synonym: "DN2 alpha-beta immature T-cell" EXACT [] synonym: "DN2 alpha-beta immature T-lymphocyte" EXACT [] synonym: "DN2 cell" EXACT [] synonym: "DN2 immature T cell" EXACT [] synonym: "double negative 2" EXACT [] synonym: "preT.DN2.Th" EXACT [] synonym: "TN2 cell" EXACT [] synonym: "TN2 thymocyte" EXACT [] is_a: CL:0002489 ! double negative thymocyte intersection_of: CL:0000893 ! thymocyte intersection_of: has_plasma_membrane_part PR:000001307 ! CD44 molecule intersection_of: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 relationship: develops_from CL:0000894 ! DN1 thymic pro-T cell relationship: has_plasma_membrane_part PR:000001307 ! CD44 molecule relationship: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 [Term] id: CL:0000807 name: DN3 thymocyte namespace: cell def: "A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, and CD25-positive and expressing the T cell receptor beta-chain in complex with the pre-T cell receptor alpha chain." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149] synonym: "DN3 alpha-beta immature T lymphocyte" EXACT [] synonym: "DN3 alpha-beta immature T-cell" EXACT [] synonym: "DN3 alpha-beta immature T-lymphocyte" EXACT [] synonym: "DN3 cell" EXACT [] synonym: "DN3 immature T cell" EXACT [] synonym: "double negative 3" EXACT [] synonym: "preT.DN3.Th" EXACT [] synonym: "TN3 cell" EXACT [] synonym: "TN3 thymocyte" EXACT [] is_a: CL:0002489 ! double negative thymocyte intersection_of: CL:0000893 ! thymocyte intersection_of: has_plasma_membrane_part GO:0043384 ! pre-T cell receptor complex intersection_of: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001307 ! CD44 molecule intersection_of: lacks_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 relationship: develops_from CL:0000806 ! DN2 thymocyte relationship: has_plasma_membrane_part GO:0043384 ! pre-T cell receptor complex relationship: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001307 ! CD44 molecule relationship: lacks_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 [Term] id: CL:0000808 name: DN4 thymocyte namespace: cell def: "A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, CD25-negative, and pre-TCR-positive." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149] comment: Note that this type of thymocyte has passed the beta-selection checkpoint and is rapidly proliferating and beginning to rearrange the T cell receptor alpha chain. synonym: "DN4 alpha-beta immature T lymphocyte" EXACT [] synonym: "DN4 alpha-beta immature T-lymphocyte" EXACT [] synonym: "DN4 cell" EXACT [] synonym: "DN4 immature T cell" EXACT [] synonym: "DN4 immature T-cell" EXACT [] synonym: "double negative 4" EXACT [] synonym: "T.DN4.th" EXACT [] is_a: CL:0002489 ! double negative thymocyte intersection_of: CL:0000893 ! thymocyte intersection_of: has_plasma_membrane_part GO:0043384 ! pre-T cell receptor complex intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001307 ! CD44 molecule intersection_of: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 relationship: develops_from CL:0000807 ! DN3 thymocyte relationship: has_plasma_membrane_part GO:0043384 ! pre-T cell receptor complex relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001307 ! CD44 molecule relationship: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 [Term] id: CL:0000809 name: double-positive, alpha-beta thymocyte namespace: cell def: "A thymocyte expressing the alpha-beta T cell receptor complex as well as both the CD4 and CD8 coreceptors." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149] comment: Thymocytes of this stage are undergoing positive and negative selection. synonym: "double-positive, alpha-beta immature T lymphocyte" EXACT [] synonym: "DP cell" EXACT [] synonym: "DP thymocyte" EXACT [] is_a: CL:0000790 ! immature alpha-beta T cell is_a: CL:0000893 ! thymocyte intersection_of: CL:0000790 ! immature alpha-beta T cell intersection_of: has_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: has_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 intersection_of: part_of UBERON:0002370 ! thymus relationship: develops_from CL:0000805 ! immature single positive thymocyte relationship: has_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: has_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 relationship: part_of UBERON:0002370 ! thymus [Term] id: CL:0000810 name: CD4-positive, alpha-beta thymocyte namespace: cell def: "An immature alpha-beta T cell that is located in the thymus and is CD4-positive and CD8-negative." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149] synonym: "CD4-positive, alpha-beta immature T lymphocyte" EXACT [] synonym: "CD4-positive, alpha-beta immature T-cell" EXACT [] synonym: "CD4-positive, alpha-beta immature T-lymphocyte" EXACT [] synonym: "SP CD4 cell" EXACT [] is_a: CL:0000790 ! immature alpha-beta T cell is_a: CL:0000893 ! thymocyte intersection_of: CL:0000790 ! immature alpha-beta T cell intersection_of: has_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: part_of UBERON:0002370 ! thymus relationship: develops_from CL:0000809 ! double-positive, alpha-beta thymocyte relationship: has_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: part_of UBERON:0002370 ! thymus [Term] id: CL:0000811 name: CD8-positive, alpha-beta thymocyte namespace: cell def: "An immature alpha-beta T cell that is located in the thymus and is CD8-positive and CD4-negative." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149] synonym: "CD8-positive, alpha-beta immature T cell" RELATED [] synonym: "CD8-positive, alpha-beta immature T lymphocyte" EXACT [] synonym: "CD8-positive, alpha-beta immature T-cell" EXACT [] synonym: "CD8-positive, alpha-beta immature T-lymphocyte" EXACT [] synonym: "SP CD8 cell" EXACT [] is_a: CL:0000790 ! immature alpha-beta T cell is_a: CL:0000893 ! thymocyte intersection_of: CL:0000790 ! immature alpha-beta T cell intersection_of: has_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: part_of UBERON:0002370 ! thymus relationship: develops_from CL:0000809 ! double-positive, alpha-beta thymocyte relationship: has_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: part_of UBERON:0002370 ! thymus [Term] id: CL:0000813 name: memory T cell namespace: cell def: "A distinctly differentiated long-lived T cell that has the phenotype CD45RO-positive and CD127-positive." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, ISBN:0781735149] synonym: "memory T lymphocyte" EXACT [] synonym: "memory T-cell" EXACT [] synonym: "memory T-lymphocyte" EXACT [] xref: BTO:0003435 is_a: CL:0002419 ! mature T cell intersection_of: CL:0002419 ! mature T cell intersection_of: has_plasma_membrane_part PR:000001017 ! receptor-type tyrosine-protein phosphatase C isoform CD45RO intersection_of: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha disjoint_from: CL:0000898 ! naive T cell relationship: has_plasma_membrane_part PR:000001017 ! receptor-type tyrosine-protein phosphatase C isoform CD45RO relationship: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha [Term] id: CL:0000814 name: mature NK T cell namespace: cell def: "A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response." [GOC:add, ISBN:0781735149] synonym: "mature natural killer T cell" EXACT [] synonym: "mature natural killer T lymphocyte" EXACT [] synonym: "mature natural killer T-cell" EXACT [] synonym: "mature natural killer T-lymphocyte" EXACT [] synonym: "mature NK T lymphocyte" EXACT [] synonym: "mature NK T-cell" EXACT [] synonym: "mature NK T-lymphocyte" EXACT [] synonym: "mature NKT cell" EXACT [] is_a: CL:0000791 ! mature alpha-beta T cell is_a: CL:0002127 ! innate effector T cell intersection_of: CL:0000791 ! mature alpha-beta T cell intersection_of: capable_of GO:0032394 ! MHC class Ib receptor activity intersection_of: capable_of GO:0045087 ! innate immune response intersection_of: has_completed GO:0030217 ! T cell differentiation intersection_of: has_plasma_membrane_part PR:000001874 ! KLRB1-like protein relationship: capable_of GO:0032394 ! MHC class Ib receptor activity relationship: capable_of GO:0045087 ! innate immune response relationship: develops_from CL:0002042 ! immature NK T cell stage IV relationship: has_completed GO:0030217 ! T cell differentiation relationship: has_plasma_membrane_part PR:000001874 ! KLRB1-like protein [Term] id: CL:0000815 name: regulatory T cell namespace: cell def: "A T cell which regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release." [GO_REF:0000031, GOC:add] comment: This cell type may express FoxP3 and CD25 and secretes IL-10 and TGF-beta. synonym: "regulatory T lymphocyte" EXACT [] synonym: "regulatory T-cell" EXACT [] synonym: "regulatory T-lymphocyte" EXACT [] synonym: "suppressor T cell" BROAD [] synonym: "suppressor T lymphocyte" BROAD [] synonym: "suppressor T-cell" BROAD [] synonym: "suppressor T-lymphocyte" BROAD [] xref: BTO:0004520 xref: FMA:84070 is_a: CL:0002419 ! mature T cell intersection_of: CL:0002419 ! mature T cell intersection_of: capable_of GO:0050777 ! negative regulation of immune response relationship: capable_of GO:0050777 ! negative regulation of immune response [Term] id: CL:0000816 name: immature B cell namespace: cell def: "An immature B cell is a precursor B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation." [GO_REF:0000031, GOC:add, GOC:dsd, GOC:rhs, GOC:tfm, ISBN:0781735149, PMID:20081059, PMID:20839338] comment: Immature B cells are also reportedly CD5-positive, CD10-positive, CD19-positive, CD20-positive, CD21-positive, CD22-positive, CD24-positive, CD25-negative, CD27-negative, CD34-negative, CD38-positive, CD40-positive, CD43-negative, CD45-positive, CD48-positive, CD53-positive, CD79a-positive, CD80-negative, CD81-positive, CD86-negative, CD95-negative, CD127-negative, CD138-negative, CD185-positive, CD196-positive, MHCII/HLA-DR-positive, RAG-positive, TdT-negative, Vpre-B-negative, and preBCR-negative. Transcription factors expressed: Pax5-positive. synonym: "immature B lymphocyte" EXACT [] synonym: "immature B-cell" EXACT [] synonym: "immature B-lymphocyte" EXACT [] synonym: "newly formed B cell" EXACT [ISBN:781735149] is_a: CL:0000817 ! precursor B cell intersection_of: CL:0000236 ! B cell intersection_of: has_not_completed GO:0045190 ! isotype switching intersection_of: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex intersection_of: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: develops_from CL:0000954 ! small pre-B-II cell relationship: has_not_completed GO:0045190 ! isotype switching relationship: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex relationship: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex [Term] id: CL:0000817 name: precursor B cell namespace: cell def: "A precursor B cell is a B cell with the phenotype CD10-positive." [GO_REF:0000031, GOC:rhs, GOC:tfm] synonym: "pre-B cell" EXACT [] xref: BTO:0001133 is_a: CL:0000236 ! B cell intersection_of: CL:0000236 ! B cell intersection_of: has_plasma_membrane_part PR:000001898 ! neprilysin disjoint_from: CL:0000826 ! pro-B cell relationship: has_plasma_membrane_part PR:000001898 ! neprilysin [Term] id: CL:0000818 name: transitional stage B cell namespace: cell def: "An immature B cell of an intermediate stage between the pre-B cell stage and the mature naive stage with the phenotype surface IgM-positive and CD19-positive, and are subject to the process of B cell selection. A transitional B cell migrates from the bone marrow into the peripheral circulation, and then to the spleen." [GO_REF:0000031, GOC:add, ISBN:0781735149, PMID:12810111] synonym: "T1 B cell" NARROW [] synonym: "T2 B cell" NARROW [] synonym: "T3 B cell" NARROW [] synonym: "transitional stage B lymphocyte" EXACT [] synonym: "transitional stage B-cell" EXACT [] synonym: "transitional stage B-lymphocyte" EXACT [] is_a: CL:0000236 ! B cell intersection_of: CL:0000236 ! B cell intersection_of: has_not_completed GO:0002335 ! mature B cell differentiation intersection_of: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex relationship: develops_from CL:0000816 ! immature B cell relationship: has_not_completed GO:0002335 ! mature B cell differentiation relationship: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex [Term] id: CL:0000819 name: B-1 B cell namespace: cell def: "A B cell of distinct lineage and surface marker expression. B-1 B cells are thought to be the primary source of natural IgM immunoglobulin, that is, IgM produced in large quantities without prior antigenic stimulation and generally reactive against various microorganisms, as well as the source of T-independent IgA immunoglobulin in the mucosal areas. These cells are CD43-positive." [GO_REF:0000031, GOC:add, GOC:dsd, http://en.wikipedia.org/wiki/B-1_cell, PMID:11861604, PMID:20933013, PMID:21220451] comment: There are small numbers of B-1 cells found in the lymph nodes and spleen, while larger numbers can be found in the peritoneal and pleural cavities. B-1 B cells are reportedly CD11b-positive, CD20-positive, CD21-positive, CD27-positive, CD44-positive, CD45RB-positive, CD48-positive, CD70-negative, CD150-positive, CD244-negative, CD352-positive, sIgM-positive, and sIgD-low. synonym: "B-1 B lymphocyte" EXACT [] synonym: "B-1 B-cell" EXACT [] synonym: "B-1 B-lymphocyte" EXACT [] synonym: "B-1 cell" EXACT [] synonym: "B1 B cell" EXACT [] synonym: "B1 B lymphocyte" EXACT [] synonym: "B1 B-cell" EXACT [] synonym: "B1 B-lymphocyte" EXACT [] synonym: "B1 cell" EXACT [] is_a: CL:0000785 ! mature B cell intersection_of: CL:0000785 ! mature B cell intersection_of: capable_of GO:0045087 ! innate immune response intersection_of: has_high_plasma_membrane_amount GO:0071753 ! IgM immunoglobulin complex intersection_of: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R intersection_of: has_plasma_membrane_part PR:000001879 ! leukosialin relationship: capable_of GO:0045087 ! innate immune response relationship: has_high_plasma_membrane_amount GO:0071753 ! IgM immunoglobulin complex relationship: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_plasma_membrane_part PR:000001879 ! leukosialin [Term] id: CL:0000820 name: B-1a B cell namespace: cell def: "A B-1 B cell that has the phenotype CD5-positive." [GOC:add, PMID:11861604] synonym: "B-1a B lymphocyte" EXACT [] synonym: "B-1a B-cell" EXACT [] synonym: "B-1a B-lymphocyte" EXACT [] synonym: "B1a B cell" EXACT [] synonym: "B1a B lymphocyte" EXACT [] synonym: "B1a B-cell" EXACT [] synonym: "B1a B-lymphocyte" EXACT [] synonym: "B1a cell" EXACT [] synonym: "CD5(+) B1 cell" EXACT [] synonym: "CD5+ B1 cell" EXACT [] synonym: "CD5-positive B1 cell" EXACT [] is_a: CL:0000819 ! B-1 B cell intersection_of: CL:0000819 ! B-1 B cell intersection_of: has_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: has_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 [Term] id: CL:0000821 name: B-1b B cell namespace: cell def: "A B-1 B cell that has the phenotype CD5-negative, but having other phenotypic attributes of a B-1 B cell." [GOC:add, PMID:11861604] synonym: "B-1b B lymphocyte" EXACT [] synonym: "B-1b B-cell" EXACT [] synonym: "B-1b B-lymphocyte" EXACT [] synonym: "B1b B cell" EXACT [] synonym: "B1b B lymphocyte" EXACT [] synonym: "B1b B-cell" EXACT [] synonym: "B1b B-lymphocyte" EXACT [] synonym: "B1b cell" EXACT [] is_a: CL:0000819 ! B-1 B cell intersection_of: CL:0000819 ! B-1 B cell intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 [Term] id: CL:0000822 name: B-2 B cell namespace: cell def: "A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative." [GOC:add, GOC:dsd, GOC:tfm, ISBN:0781735149, PMID:11861604, PMID:20933013] comment: B-2 B cells are reportedly CD48-positive, CD244-negative, and CD352-positive. synonym: "B-0 B cell" RELATED [] synonym: "B-2 B lymphocyte" EXACT [] synonym: "B-2 B-cell" EXACT [] synonym: "B-2 B-lymphocyte" EXACT [] synonym: "B2 B cell" EXACT [] synonym: "B2 B lymphocyte" EXACT [] synonym: "B2 B-cell" EXACT [] synonym: "B2 B-lymphocyte" EXACT [] synonym: "B2 cell" EXACT [] is_a: CL:0000785 ! mature B cell intersection_of: CL:0000785 ! mature B cell intersection_of: lacks_plasma_membrane_part PR:000001879 ! leukosialin relationship: lacks_plasma_membrane_part PR:000001879 ! leukosialin [Term] id: CL:0000823 name: immature natural killer cell namespace: cell def: "A natural killer cell that is developmentally immature and expresses natural killer cell receptors (NKR)." [GO_REF:0000031, GOC:add, ISBN:0781735149, PMID:12457618] comment: In mouse the NKR are Ly49 molecules and in human these cells express KIR molecules. synonym: "immature NK cell" EXACT [] synonym: "p-NK" RELATED [PMID:12457618] is_a: CL:0000623 ! natural killer cell intersection_of: CL:0000623 ! natural killer cell intersection_of: has_quality PATO:0001501 ! immature disjoint_from: CL:0000824 ! mature natural killer cell disjoint_from: CL:0000937 ! pre-natural killer cell relationship: develops_from CL:0000937 ! pre-natural killer cell relationship: has_quality PATO:0001501 ! immature [Term] id: CL:0000824 name: mature natural killer cell namespace: cell def: "A natural killer cell that is developmentally mature and expresses a variety of inhibitory and activating receptors that recognize MHC class I and other stress related molecules." [GO_REF:0000031, GOC:add, ISBN:0781735149, PMID:14685782] synonym: "LAK cell" BROAD [PMID:14685782] synonym: "lymphokine activated killer cell" BROAD [PMID:14685782] synonym: "mature NK cell" EXACT [] is_a: CL:0000623 ! natural killer cell disjoint_from: CL:0002338 ! CD56-positive, CD161-positive immature natural killer cell disjoint_from: CL:0002344 ! CD56-negative, CD161-positive immature natural killer cell relationship: develops_from CL:0000823 ! immature natural killer cell [Term] id: CL:0000825 name: pro-NK cell namespace: cell def: "A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative." [GO_REF:0000031, GOC:add, GOC:pam, PMID:11532393, PMID:12457618, PMID:15032583, PMID:15766674] comment: Most markers only described for human pro NK cells. synonym: "natural killer cell progenitor" EXACT [] synonym: "NKP" EXACT [PMID:12457618, PMID:15032583, PMID:15766674] synonym: "null cell" RELATED [PMID:11532393] synonym: "preNK cell" RELATED [PMID:11532393] synonym: "pro-natural killer cell" EXACT [] is_a: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: has_plasma_membrane_part PR:000001381 ! interleukin-2 receptor subunit beta intersection_of: has_plasma_membrane_part PR:000001898 ! neprilysin intersection_of: lacks_plasma_membrane_part PR:000001874 ! KLRB1-like protein intersection_of: lacks_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: has_plasma_membrane_part PR:000001381 ! interleukin-2 receptor subunit beta relationship: has_plasma_membrane_part PR:000001898 ! neprilysin relationship: lacks_plasma_membrane_part PR:000001874 ! KLRB1-like protein relationship: lacks_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor [Term] id: CL:0000826 name: pro-B cell namespace: cell def: "A progenitor cell of the B cell lineage, with some lineage specific activity such as early stages of recombination of B cell receptor genes, but not yet fully committed to the B cell lineage until the expression of PAX5 occurs." [GOC:add, GOC:dsd, ISBN:0781735149, PMID:12633665, PMID:16551251, PMID:18432934] comment: Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative. synonym: "pre-B cell (Philadelphia nomenclature)" RELATED [PMID:11244048] synonym: "pre-pro B cell" BROAD [PMID:17582343] synonym: "pro-B lymphocyte" EXACT [] synonym: "pro-B-cell" EXACT [] synonym: "pro-B-lymphocyte" EXACT [] synonym: "progenitor B cell" EXACT [] synonym: "progenitor B lymphocyte" EXACT [] synonym: "progenitor B-cell" EXACT [] synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 is_a: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase intersection_of: participates_in GO:0033152 ! immunoglobulin V(D)J recombination relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: has_part PR:000001903 ! paired box protein PAX-5 relationship: has_part PR:000006611 ! DNA nucleotidylexotransferase relationship: participates_in GO:0033152 ! immunoglobulin V(D)J recombination [Term] id: CL:0000827 name: pro-T cell namespace: cell def: "A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage." [GOC:add, ISBN:0781735149] synonym: "DN1 cell" NARROW [] synonym: "DN1 thymocyte" NARROW [] synonym: "pro-T lymphocyte" EXACT [] synonym: "progenitor T cell" EXACT [] synonym: "TN1 cell" NARROW [] is_a: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: capable_of GO:0030217 ! T cell differentiation relationship: capable_of GO:0030217 ! T cell differentiation relationship: develops_from CL:0000051 ! common lymphoid progenitor [Term] id: CL:0000828 name: thromboblast namespace: cell def: "A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates." [GOC:add, GOC:tfm, PMID:7758949] comment: Note that this is a non-mammalian cell type. is_a: CL:0000226 ! single nucleate cell is_a: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0002574 ! thrombocyte differentiation intersection_of: has_quality PATO:0001407 ! mononucleate relationship: capable_of GO:0002574 ! thrombocyte differentiation relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell relationship: has_quality PATO:0001407 ! mononucleate [Term] id: CL:0000829 name: basophilic myeloblast namespace: cell def: "A myeloblast committed to the basophil lineage." [GOC:add, ISBN:0721601464] is_a: CL:0000835 ! myeloblast intersection_of: CL:0000835 ! myeloblast intersection_of: capable_of GO:0030221 ! basophil differentiation relationship: capable_of GO:0030221 ! basophil differentiation relationship: develops_from CL:0000613 ! basophil progenitor cell [Term] id: CL:0000830 name: basophilic promyelocyte namespace: cell def: "A promyelocyte committed to the basophil lineage." [GOC:add, ISBN:0721601464] xref: FMA:84208 is_a: CL:0000836 ! promyelocyte intersection_of: CL:0000836 ! promyelocyte intersection_of: capable_of GO:0030221 ! basophil differentiation relationship: capable_of GO:0030221 ! basophil differentiation relationship: develops_from CL:0000829 ! basophilic myeloblast [Term] id: CL:0000831 name: mast cell progenitor namespace: cell def: "A progenitor cell of the mast cell lineage. Markers for this cell are FceRIa-low, CD117-positive, CD9-positive, T1/ST2-positive, SCA1-negative, and lineage-negative." [GOC:add, GOC:dsd, http://www.copewithcytokines.de, PMCID:PMC1183570, PMCID:PMC1312421, PMID:8629001, PMID:9354811] comment: MCP are CD16-positive, CD32-positive, CD34-positive, CD45-positive, integrin beta-7-positive, and lin-negative (CD2, CD3e, CD4, CD5, CD8a, CD14, CD19, CD20, CD27, integrin alpha-M, ly6c, ly6g, NCAM-1, and ter119). These cells also express the transcription factors GATA-1, GATA-2, and MITF, but not C/EBPa. synonym: "CFU-Mast " RELATED [] synonym: "CFU-MC" RELATED [] synonym: "colony forming unit mast cell" RELATED [] synonym: "MCP" EXACT [] is_a: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0060374 ! mast cell differentiation intersection_of: has_high_plasma_membrane_amount PR:000009143 ! integrin beta-7 intersection_of: has_low_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor intersection_of: has_low_plasma_membrane_amount PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha intersection_of: has_part PR:000007857 ! erythroid transcription factor intersection_of: has_part PR:000007858 ! endothelial transcription factor GATA-2 intersection_of: has_plasma_membrane_part PR:000005178 ! CD9 molecule intersection_of: has_plasma_membrane_part PR:000016401 ! transmembrane emp24 domain-containing protein 1 intersection_of: lacks_part PR:000005307 ! CCAAT/enhancer-binding protein alpha intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: lacks_plasma_membrane_part PR:000001963 ! CD27 molecule intersection_of: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G intersection_of: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 intersection_of: lacks_plasma_membrane_part PR:000002980 ! lymphocyte antigen 6C intersection_of: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 relationship: capable_of GO:0060374 ! mast cell differentiation relationship: develops_from CL:0002028 ! basophil mast progenitor cell relationship: has_high_plasma_membrane_amount PR:000009143 ! integrin beta-7 relationship: has_low_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor relationship: has_low_plasma_membrane_amount PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: has_plasma_membrane_part PR:000005178 ! CD9 molecule relationship: has_plasma_membrane_part PR:000016401 ! transmembrane emp24 domain-containing protein 1 relationship: lacks_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: lacks_plasma_membrane_part PR:000001963 ! CD27 molecule relationship: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G relationship: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: lacks_plasma_membrane_part PR:000002980 ! lymphocyte antigen 6C relationship: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 [Term] id: CL:0000832 name: eosinophilic myeloblast namespace: cell def: "A myeloblast committed to the eosinophil lineage." [GOC:add, ISBN:0721601464] is_a: CL:0000835 ! myeloblast intersection_of: CL:0000835 ! myeloblast intersection_of: capable_of GO:0030222 ! eosinophil differentiation relationship: capable_of GO:0030222 ! eosinophil differentiation relationship: develops_from CL:0000611 ! eosinophil progenitor cell [Term] id: CL:0000833 name: eosinophilic promyelocyte namespace: cell def: "A promyelocyte committed to the eosinophil lineage." [GOC:add, ISBN:0721601464] xref: FMA:84199 is_a: CL:0000836 ! promyelocyte intersection_of: CL:0000836 ! promyelocyte intersection_of: capable_of GO:0030222 ! eosinophil differentiation relationship: capable_of GO:0030222 ! eosinophil differentiation relationship: develops_from CL:0000832 ! eosinophilic myeloblast [Term] id: CL:0000834 name: neutrophil progenitor cell namespace: cell def: "A progenitor cell of the neutrophil lineage." [GOC:add, GOC:tfm, ISBN:0721601464] synonym: "neutrophil stem cell" RELATED [] is_a: CL:0002191 ! granulocytopoietic cell intersection_of: CL:0002191 ! granulocytopoietic cell intersection_of: capable_of GO:0030223 ! neutrophil differentiation relationship: capable_of GO:0030223 ! neutrophil differentiation relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell [Term] id: CL:0000835 name: myeloblast namespace: cell def: "The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow." [GOC:add, http://en.wikipedia.org/wiki/Myeloblast, http://www.cap.org, ISBN:0721601464] xref: BTO:0000187 xref: FMA:83524 is_a: CL:0002191 ! granulocytopoietic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0002191 ! granulocytopoietic cell intersection_of: has_part CP:0000028 ! basophilic cytoplasm intersection_of: has_part CP:0000037 ! increased nucleus size intersection_of: has_part GO:0000791 ! euchromatin intersection_of: lacks_part GO:0042582 ! azurophil granule relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell relationship: has_part CP:0000028 ! basophilic cytoplasm relationship: has_part CP:0000037 ! increased nucleus size relationship: has_part GO:0000791 ! euchromatin relationship: lacks_part GO:0042582 ! azurophil granule [Term] id: CL:0000836 name: promyelocyte namespace: cell def: "A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative." [GOC:add, GOC:amm, GOC:tfm, http://www.cap.org, ISBN:0721601464] xref: FMA:83530 is_a: CL:0002191 ! granulocytopoietic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: has_part CP:0000028 ! basophilic cytoplasm intersection_of: has_part CP:0000037 ! increased nucleus size intersection_of: has_part GO:0005730 ! nucleolus intersection_of: has_part GO:0042582 ! azurophil granule intersection_of: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 intersection_of: has_plasma_membrane_part PR:000001892 ! CD33 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III intersection_of: lacks_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: develops_from CL:0000835 ! myeloblast relationship: has_part CP:0000028 ! basophilic cytoplasm relationship: has_part CP:0000037 ! increased nucleus size relationship: has_part GO:0005730 ! nucleolus relationship: has_part GO:0042582 ! azurophil granule relationship: has_plasma_membrane_part PR:000001456 ! alpha-(1,3)-fucosyltransferase FUT4 relationship: has_plasma_membrane_part PR:000001892 ! CD33 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: lacks_plasma_membrane_part PR:000001932 ! signal transducer CD24 [Term] id: CL:0000837 name: hematopoietic multipotent progenitor cell namespace: cell def: "A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans." [GOC:add, GOC:tfm, PMID:19022770] comment: Markers differ between mouse and human. synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 is_a: CL:0000988 ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_quality PATO:0001402 ! multipotent intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G intersection_of: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: develops_from CL:0000037 ! hematopoietic stem cell relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_quality PATO:0001402 ! multipotent relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G relationship: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 [Term] id: CL:0000838 name: lymphoid lineage restricted progenitor cell namespace: cell def: "A progenitor cell restricted to the lymphoid lineage." [GOC:add, GOC:tfm] comment: Note that this is a class of cell types, not an identified single cell type. synonym: "lymphoid progenitor cell" BROAD [] xref: BTO:0004731 xref: FMA:70338 is_a: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: capable_of GO:0030098 ! lymphocyte differentiation disjoint_from: CL:0000839 ! myeloid lineage restricted progenitor cell relationship: capable_of GO:0030098 ! lymphocyte differentiation [Term] id: CL:0000839 name: myeloid lineage restricted progenitor cell namespace: cell def: "A progenitor cell restricted to the myeloid lineage." [GOC:add, GOC:tfm, PMID:19022770] comment: Note that this is a class of cell types, not an identified single cell type. synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: FMA:70339 is_a: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: capable_of GO:0030099 ! myeloid cell differentiation relationship: capable_of GO:0030099 ! myeloid cell differentiation [Term] id: CL:0000840 name: immature conventional dendritic cell namespace: cell def: "An immature cell of the conventional dendritic cell lineage, characterized by high levels of antigen uptake via endocytosis, macropinocytosis, and phagocytosis, and typically found resident in the tissues. Markers for this cell are CD80-low, CD86-low, and MHC-II-low." [GOC:add, GOC:tfm, PMID:9521319] synonym: "immature myeloid dendritic cell" NARROW [] is_a: CL:0000990 ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: develops_from CL:0001029 ! common dendritic progenitor relationship: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule [Term] id: CL:0000841 name: mature conventional dendritic cell namespace: cell def: "A mature cell of the conventional dendritic cell lineage, characterized by a high capacity for antigen presentation and typically found in a lymph node." [GOC:add, GOC:tfm, PMID:9521319] synonym: "mature myeloid dendritic cell" NARROW [] xref: FMA:83038 is_a: CL:0000990 ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule intersection_of: has_plasma_membrane_part PR:000001310 ! CD83 molecule relationship: develops_from CL:0000840 ! immature conventional dendritic cell relationship: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_plasma_membrane_part PR:000001310 ! CD83 molecule [Term] id: CL:0000842 name: mononuclear cell namespace: cell def: "A leukocyte with a single non-segmented nucleus in the mature form." [GOC:add] synonym: "peripheral blood mononuclear cell" NARROW [] xref: BTO:0000878 xref: FMA:86713 is_a: CL:0000226 ! single nucleate cell is_a: CL:0002087 ! nongranular leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: has_quality PATO:0001407 ! mononucleate intersection_of: lacks_part GO:0030141 ! secretory granule relationship: has_quality PATO:0001407 ! mononucleate relationship: lacks_part GO:0030141 ! secretory granule [Term] id: CL:0000843 name: follicular B cell namespace: cell def: "A resting mature B cell that has the phenotype IgM-positive, IgD-positive, CD23-positive and CD21-positive, and found in the B cell follicles of the white pulp of the spleen or the corticol areas of the peripheral lymph nodes. This cell type is also described as being CD19-positive, B220-positive, AA4-negative, CD43-negative, and CD5-negative." [GOC:add, GOC:dsd, http://en.wikipedia.org/wiki/Follicular_B_Cells, ISBN:0781735149, PMCID:PMC2193793, PMID:20933013] comment: Follicular B cells are also reportedly CD48-positive, CD84-positive, CD229-positive, and CD352-positive. synonym: "Fo B cell" EXACT [] synonym: "Fo B-cell" EXACT [] synonym: "follicular B lymphocyte" EXACT [] synonym: "follicular B-cell" EXACT [] synonym: "follicular B-lymphocyte" EXACT [] is_a: CL:0000822 ! B-2 B cell intersection_of: CL:0000785 ! mature B cell intersection_of: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex intersection_of: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex intersection_of: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R intersection_of: has_plasma_membrane_part PR:000001338 ! complement receptor type 2 intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001879 ! leukosialin intersection_of: lacks_plasma_membrane_part PR:000002037 ! complement component C1q receptor relationship: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex relationship: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_plasma_membrane_part PR:000001338 ! complement receptor type 2 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001879 ! leukosialin relationship: lacks_plasma_membrane_part PR:000002037 ! complement component C1q receptor [Term] id: CL:0000844 name: germinal center B cell namespace: cell def: "A rapidly cycling mature B cell that has distinct phenotypic characteristics and is involved in T-dependent immune responses and located typically in the germinal centers of lymph nodes. This cell type expresses Ly77 after activation." [GOC:add, GOC:dsd, GOC:tfm, ISBN:0781735149, PMID:19447676, PMID:20933013] comment: Germinal center B cells are also reportedly CD10-positive, CD19-positive, CD20-positive, CD38-positive, CD44-low, CD45-positive, CD48-positive, CD95-positive, CD352-positive, and HLA-DR-positive. Transcription factors: BCL6-positive, Ets1-positive, IRF8-positive, MTA3-positive, OBF1-positive, PAX5-positive, SpiB-positive, and STAT3-positive. synonym: "GC B cell" EXACT [] synonym: "GC B lymphocyte" EXACT [] synonym: "GC B-cell" EXACT [] synonym: "GC B-lymphocyte" EXACT [] synonym: "germinal center B lymphocyte" EXACT [] synonym: "germinal center B-cell" EXACT [] synonym: "germinal center B-lymphocyte" EXACT [] is_a: CL:0000785 ! mature B cell intersection_of: CL:0000785 ! mature B cell intersection_of: part_of UBERON:0001745 ! secondary nodular lymphoid tissue relationship: develops_from CL:0000843 ! follicular B cell relationship: part_of UBERON:0001745 ! secondary nodular lymphoid tissue [Term] id: CL:0000845 name: marginal zone B cell namespace: cell def: "A mature B cell that is located in the marginal zone of the spleen with the phenotype CD23-negative and CD21-positive and expressing a B cell receptor usually reactive to bacterial cell wall components or senescent self components such as oxidized-LDL. This cell type is also described as being CD19-positive, B220-positive, IgM-high, AA4-negative, CD35-high." [GOC:add, GOC:dsd, http://en.wikipedia.org/wiki/Marginal-zone_B_cell, ISBN:0781735149, PMID:10933592, PMID:20933013] comment: MZ B cells are reportedly CD1-positive (mice), CD20-positive, CD48-positive, CD84-positive, CD150-positive, CD229-positive, and CD352-positive. synonym: "marginal zone B lymphocyte" EXACT [] synonym: "marginal zone B-cell" EXACT [] synonym: "marginal zone B-lymphocyte" EXACT [] synonym: "MZ B cell" EXACT [] synonym: "MZ B lymphocyte" EXACT [] synonym: "MZ B-cell" EXACT [] synonym: "MZ B-lymphocyte" EXACT [] is_a: CL:0000785 ! mature B cell intersection_of: CL:0000785 ! mature B cell intersection_of: capable_of GO:0042742 ! defense response to bacterium intersection_of: has_high_plasma_membrane_amount GO:0071753 ! IgM immunoglobulin complex intersection_of: has_plasma_membrane_part PR:000001338 ! complement receptor type 2 intersection_of: lacks_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor intersection_of: lacks_plasma_membrane_part PR:000002037 ! complement component C1q receptor intersection_of: part_of UBERON:0001251 ! marginal zone of spleen relationship: capable_of GO:0042742 ! defense response to bacterium relationship: has_high_plasma_membrane_amount GO:0071753 ! IgM immunoglobulin complex relationship: has_plasma_membrane_part PR:000001338 ! complement receptor type 2 relationship: lacks_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor relationship: lacks_plasma_membrane_part PR:000002037 ! complement component C1q receptor relationship: part_of UBERON:0001251 ! marginal zone of spleen [Term] id: CL:0000846 name: vestibular dark cell namespace: cell def: "An epithelial cell of the vestibular sensory organ that is characterized by intense enzymatic activities and numerous basal membrane infoldings." [PMID:11223304] is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000847 name: ciliated olfactory receptor neuron namespace: cell def: "An olfactory receptor cell in which the apical ending of the dendrite is a pronounced ciliated olfactory knob." [PMID:16841163] synonym: "ciliated olfactory sensory neuron" EXACT [] synonym: "ciliated sensory neuron" EXACT [] is_a: CL:0000064 ! ciliated cell is_a: CL:0000207 ! olfactory receptor cell relationship: has_plasma_membrane_part GO:0005929 ! cilium [Term] id: CL:0000848 name: microvillous olfactory receptor neuron namespace: cell def: "An olfactory receptor cell in which the apical ending of the dendrite is a knob that bears numerous microvilli." [PMID:16841163] synonym: "microvillous olfactory sensory neuron" EXACT [] synonym: "microvillous sensory neuron" RELATED [] is_a: CL:0000207 ! olfactory receptor cell [Term] id: CL:0000849 name: crypt olfactory receptor neuron namespace: cell def: "An olfactory receptor cell with short cilia growing in an invagination bordered by microvilli." [PMID:16841163] synonym: "crypt cell" EXACT [] synonym: "crypt olfactory sensory neuron" EXACT [] synonym: "crypt sensory neuron" EXACT [] is_a: CL:0000207 ! olfactory receptor cell [Term] id: CL:0000850 name: serotonergic neuron namespace: cell alt_id: CL:0000403 def: "A neuron that releases serotonin as a neurotransmitter." [SANBI:mhl] synonym: "5-HT neuron" EXACT [] synonym: "5-hydroxytryptamine neuron" EXACT [] synonym: "serotinergic neuron" RELATED [] xref: FBbt:00005133 xref: WBbt:0006837 is_a: CL:0000540 ! neuron [Term] id: CL:0000851 name: neuromast mantle cell namespace: cell def: "Neuromast mantle cell is a non-sensory cell. Neuromast mantle cells surround the neuromast support cells and neuromast hair cells, separating the neuromast from the epidermis, and secrete cupula in which the ciliary bundles of all the hair cells are embedded." [ISBN:0125296509] is_a: CL:0000151 ! secretory cell [Term] id: CL:0000852 name: neuromast support cell namespace: cell def: "Neuromast support cell is a non-sensory cell of the neuromast that extend between the sensory hair cells from the basement membrane to the apical surface; neuromast support cells are surrounded by neuromast mantle cells." [ISBN:0125296509] is_a: CL:0000630 ! supportive cell [Term] id: CL:0000853 name: olfactory epithelial support cell namespace: cell def: "Olfactory epithelial support cell is a columnar cell that extends from the epithelial free margin to the basement membrane of the olfactory epithelium. This cell type has a large, vertically, elongate, euchromatic nucleus, along with other nuclei, forms a layer superficial to the cell body of the receptor cell; sends long somewhat irregular microvilli into the mucus layer; at the base, with expanded end-feet containing numerous lamellated dense bodies resembling lipofuscin of neurons." [GOC:tfm, ISBN:0517223651, SANBI:mhl] synonym: "olfactory sustentacular cell" EXACT [] synonym: "supporting cell of olfactory epithelium" EXACT [] synonym: "sustentaculocyte of olfactory epithelium" EXACT [] xref: FMA:62302 is_a: CL:0000630 ! supportive cell is_a: CL:0002167 ! olfactory epithelial cell [Term] id: CL:0000854 name: interneuromast cell namespace: cell def: "Interneuromast cell is a neuroectodermal cell deposited by the migrating lateral line primordium between the neuromasts. Interneuromast cells proliferate and migrate to form additional neuromasts." [SANBI:mhl] is_a: CL:0000133 ! neurectodermal cell relationship: develops_from CL:0000032 ! neuroplacodal cell [Term] id: CL:0000855 name: sensory hair cell namespace: cell def: "Hair cell is a mechanoreceptor cell that is sensitive to movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system." [SANBI:mhl] synonym: "hair cell" BROAD [] xref: BTO:0004744 is_a: CL:0000199 ! mechanoreceptor cell [Term] id: CL:0000856 name: neuromast hair cell namespace: cell def: "Neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface." [SANBI:mhl] is_a: CL:0000855 ! sensory hair cell [Term] id: CL:0000857 name: slow muscle myoblast namespace: cell def: "A skeletal muscle myoblast that differentiates into slow muscle fibers." [SANBI:mhl] is_a: CL:0000515 ! skeletal muscle myoblast [Term] id: CL:0000858 name: fast muscle myoblast namespace: cell def: "A skeletal muscle myoblast that differentiates into fast muscle fibers." [SANBI:mhl] is_a: CL:0000515 ! skeletal muscle myoblast [Term] id: CL:0000860 name: classical monocyte namespace: cell def: "A type of monocyte that responds rapidly to microbial stimuli by secreting cytokines and antimicrobial factors. This cell type is characterized by high expression of CCR2 in both rodents and humans, and of being larger size than non-classical monocytes." [GO_REF:0000031, PMID:16322748, PMID:18303997, PMID:20628149, PMID:20870168] comment: Markers: CCR2+CXCCR1 (human, mouse, rat). synonym: "inflammatory monocyte" EXACT [] is_a: CL:0000234 ! phagocyte is_a: CL:0000576 ! monocyte intersection_of: CL:0000576 ! monocyte intersection_of: capable_of GO:0002548 ! monocyte chemotaxis intersection_of: capable_of GO:0006909 ! phagocytosis intersection_of: capable_of GO:0006954 ! inflammatory response intersection_of: has_high_plasma_membrane_amount PR:000001199 ! C-C chemokine receptor type 2 intersection_of: has_low_plasma_membrane_amount PR:000001206 ! CX3C chemokine receptor 1 relationship: capable_of GO:0002548 ! monocyte chemotaxis relationship: capable_of GO:0006909 ! phagocytosis relationship: capable_of GO:0006954 ! inflammatory response relationship: has_high_plasma_membrane_amount PR:000001199 ! C-C chemokine receptor type 2 relationship: has_low_plasma_membrane_amount PR:000001206 ! CX3C chemokine receptor 1 [Term] id: CL:0000861 name: elicited macrophage namespace: cell def: "A macrophage which develops from an inflammatory monocyte and is recruited into the tissues in response to injury and infection as part of an inflammatory response. Markers include CD11b-positive, CD68-positive, and F4/80-positive." [GO_REF:0000031, GOC:add, GOC:ana, GOC:tfm, PMID:15771589] comment: Markers: CD11b+, CD68+; Mouse: F4/80+; role or process: immune, inflammation (inflammatory response). synonym: "free macrophage" EXACT [] synonym: "wandering histiocyte" EXACT [] xref: FMA:84643 xref: FMA:84645 is_a: CL:0000235 ! macrophage intersection_of: CL:0000235 ! macrophage intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 intersection_of: has_plasma_membrane_part PR:000002064 ! macrosialin intersection_of: participates_in GO:0006954 ! inflammatory response relationship: develops_from CL:0000860 ! classical monocyte relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 relationship: has_plasma_membrane_part PR:000002064 ! macrosialin relationship: participates_in GO:0006954 ! inflammatory response [Term] id: CL:0000862 name: suppressor macrophage namespace: cell def: "A macrophage that suppresses immune responses." [GOC:add, GOC:tfm, PMID:20402419] comment: Markers: May express: IL10, TGFbeta. is_a: CL:0000861 ! elicited macrophage intersection_of: CL:0000861 ! elicited macrophage intersection_of: capable_of GO:0050777 ! negative regulation of immune response relationship: capable_of GO:0050777 ! negative regulation of immune response [Term] id: CL:0000863 name: inflammatory macrophage namespace: cell def: "An elicited macrophage that is recruited into the tissues in response to injury and infection as part of an inflammatory response, expresses high levels of pro-inflammatory cytokines, ROS and NO, and shows potent microbicidal activity." [GO_REF:0000031, GOC:ana, PMID:19132917] comment: Markers: Express: TNFa, IL1b, IL6, iNOS, NADPH-oxidase; produce: reactive oxygen species, nitric oxide; role or process: immune, inflammation (inflammatory response). synonym: "classically activated macrophage" EXACT [] synonym: "M1 macrophage" RELATED [] is_a: CL:0000861 ! elicited macrophage intersection_of: CL:0000861 ! elicited macrophage intersection_of: capable_of GO:0032611 ! interleukin-1 beta production intersection_of: capable_of GO:0032635 ! interleukin-6 production intersection_of: capable_of GO:0032640 ! tumor necrosis factor production intersection_of: capable_of GO:0042554 ! superoxide anion generation intersection_of: capable_of GO:0042742 ! defense response to bacterium intersection_of: capable_of GO:0051768 ! nitric-oxide synthase 2 biosynthetic process relationship: capable_of GO:0032611 ! interleukin-1 beta production relationship: capable_of GO:0032635 ! interleukin-6 production relationship: capable_of GO:0032640 ! tumor necrosis factor production relationship: capable_of GO:0042554 ! superoxide anion generation relationship: capable_of GO:0042742 ! defense response to bacterium relationship: capable_of GO:0051768 ! nitric-oxide synthase 2 biosynthetic process [Term] id: CL:0000864 name: tissue-resident macrophage namespace: cell def: "A macrophage constitutively resident in a particular tissue under non-inflammatory conditions, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells." [GO_REF:0000031, GOC:ana, PMID:19770654] synonym: "fixed macrophage" EXACT [] synonym: "resting histiocyte" EXACT [] xref: FMA:84642 xref: FMA:84644 is_a: CL:0000235 ! macrophage intersection_of: CL:0000235 ! macrophage intersection_of: part_of UBERON:0000479 ! tissue relationship: part_of UBERON:0000479 ! tissue [Term] id: CL:0000865 name: gastrointestinal tract (lamina propria) macrophage namespace: cell def: "A gut-associated lymphoid tissue macrophage found in lamina propria of the gut." [GO_REF:0000031, GOC:ana, GOC:tfm] is_a: CL:0000885 ! gut-associated lymphoid tissue macrophage intersection_of: CL:0000885 ! gut-associated lymphoid tissue macrophage intersection_of: part_of UBERON:0001238 ! lamina propria of small intestine relationship: part_of UBERON:0001238 ! lamina propria of small intestine [Term] id: CL:0000866 name: thymic macrophage namespace: cell def: "A tissue-resident macrophage resident found in the thymus, involved in the clearance of apoptotic thymocytes." [GO_REF:0000031, GOC:ana, GOC:tfm, PMID:9048205] comment: Role or process: immune, clearance of apoptotic thymocytes, antigen-presentation. is_a: CL:0000864 ! tissue-resident macrophage intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0043277 ! apoptotic cell clearance intersection_of: part_of UBERON:0002370 ! thymus relationship: capable_of GO:0043277 ! apoptotic cell clearance relationship: part_of UBERON:0002370 ! thymus [Term] id: CL:0000867 name: secondary lymphoid organ macrophage namespace: cell def: "A tissue-resident macrophage found in a secondary lymphoid organ." [GO_REF:0000031, GOC:ana, GOC:tfm] is_a: CL:0000864 ! tissue-resident macrophage [Term] id: CL:0000868 name: lymph node macrophage namespace: cell def: "A secondary lymphoid organ macrophage found in a lymph node. This cell is CD169-high." [GO_REF:0000031, GOC:ana, GOC:tfm, PMID:11971865] comment: Marker was observed on rat cells. synonym: "MF.LN" EXACT [] is_a: CL:0000867 ! secondary lymphoid organ macrophage intersection_of: CL:0000867 ! secondary lymphoid organ macrophage intersection_of: has_high_plasma_membrane_amount PR:000001931 ! sialoadhesin intersection_of: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M intersection_of: has_low_plasma_membrane_amount PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 intersection_of: part_of UBERON:0000029 ! lymph node relationship: has_high_plasma_membrane_amount PR:000001931 ! sialoadhesin relationship: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: has_low_plasma_membrane_amount PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 relationship: part_of UBERON:0000029 ! lymph node [Term] id: CL:0000869 name: tonsillar macrophage namespace: cell def: "A gut-associated lymphoid tissue macrophage found in tonsils." [GO_REF:0000031, GOC:ana, PMID:16048540] is_a: CL:0000884 ! mucosa-associated lymphoid tissue macrophage intersection_of: CL:0000884 ! mucosa-associated lymphoid tissue macrophage intersection_of: capable_of GO:0002395 ! immune response in nasopharyngeal-associated lymphoid tissue intersection_of: part_of UBERON:0002372 ! tonsil relationship: capable_of GO:0002395 ! immune response in nasopharyngeal-associated lymphoid tissue relationship: part_of UBERON:0002372 ! tonsil [Term] id: CL:0000870 name: Peyer's patch macrophage namespace: cell def: "A gut-associated lymphoid tissue macrophage found in the Peyer's patches." [GO_REF:0000031, GOC:ana, GOC:tfm] is_a: CL:0000885 ! gut-associated lymphoid tissue macrophage intersection_of: CL:0000885 ! gut-associated lymphoid tissue macrophage intersection_of: part_of UBERON:0001211 ! Peyer's patch relationship: part_of UBERON:0001211 ! Peyer's patch [Term] id: CL:0000871 name: splenic macrophage namespace: cell def: "A secondary lymphoid organ macrophage found in the spleen." [GO_REF:0000031, PMID:15771589, PMID:16322748] comment: Role or process: immune, clearance of apoptotic and senescent cells. xref: FMA:83026 is_a: CL:0000867 ! secondary lymphoid organ macrophage intersection_of: CL:0000867 ! secondary lymphoid organ macrophage intersection_of: capable_of GO:0034102 ! erythrocyte clearance intersection_of: part_of UBERON:0002106 ! spleen relationship: capable_of GO:0034102 ! erythrocyte clearance relationship: part_of UBERON:0002106 ! spleen [Term] id: CL:0000872 name: splenic marginal zone macrophage namespace: cell def: "A splenic macrophage found in the marginal zone of the spleen, involved in recognition and clearance of particulate material from the splenic circulation. Markers include F4/80-negative, MARCO-positive, SR-A-positive, SIGN-R1-positive, and Dectin2-positive." [GO_REF:0000031, GOC:ana, PMID:16861066] comment: Markers: Mouse: F4/80-, MARCO+, SR-A+, SIGN-R1+, Dectin2+. is_a: CL:0000871 ! splenic macrophage intersection_of: CL:0000871 ! splenic macrophage intersection_of: has_plasma_membrane_part PR:000001806 ! C-type lectin domain family 6 member A intersection_of: has_plasma_membrane_part PR:000001884 ! macrophage receptor MARCO intersection_of: has_plasma_membrane_part PR:000001885 ! macrophage scavenger receptor types I and II intersection_of: has_plasma_membrane_part PR:000006172 ! CD209 molecule-like protein B intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: part_of UBERON:0001251 ! marginal zone of spleen relationship: has_plasma_membrane_part PR:000001806 ! C-type lectin domain family 6 member A relationship: has_plasma_membrane_part PR:000001884 ! macrophage receptor MARCO relationship: has_plasma_membrane_part PR:000001885 ! macrophage scavenger receptor types I and II relationship: has_plasma_membrane_part PR:000006172 ! CD209 molecule-like protein B relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: part_of UBERON:0001251 ! marginal zone of spleen [Term] id: CL:0000873 name: splenic metallophillic macrophage namespace: cell def: "A splenic macrophage found in the areas surrounding the white pulp of the spleen, adjacent to the marginal sinus. Markers include F4/80-negative, Dectin2-low, sialoadhesin-positive." [GO_REF:0000031, GOC:ana, PMID:20018690] comment: Markers: Mouse: F4/80-, Dectin2-low, sialoadhesin+. is_a: CL:0000871 ! splenic macrophage intersection_of: CL:0000871 ! splenic macrophage intersection_of: adjacent_to UBERON:0001959 ! white pulp of spleen intersection_of: has_low_plasma_membrane_amount PR:000001806 ! C-type lectin domain family 6 member A intersection_of: has_plasma_membrane_part PR:000001931 ! sialoadhesin intersection_of: lacks_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 intersection_of: part_of UBERON:0001251 ! marginal zone of spleen relationship: adjacent_to UBERON:0001959 ! white pulp of spleen relationship: has_low_plasma_membrane_amount PR:000001806 ! C-type lectin domain family 6 member A relationship: has_plasma_membrane_part PR:000001931 ! sialoadhesin relationship: lacks_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 relationship: part_of UBERON:0001251 ! marginal zone of spleen [Term] id: CL:0000874 name: splenic red pulp macrophage namespace: cell def: "A splenic macrophage found in the red-pulp of the spleen, and involved in immune responses to blood-borne pathogens and in the clearance of senescent erythrocytes. Markers include F4/80-positive, CD68-positive, MR-positive, Dectin2-positive, macrosialin-positive, and sialoadhesin-low." [GO_REF:0000031, GOC:ana, PMID:19644016] comment: Markers: Mouse: F4/80+, CD68+, MR+, Dectin2+, macrosialin+, sialoadhesin-low; role or process: immune, clearance of senescent erythrocytes. is_a: CL:0000871 ! splenic macrophage intersection_of: CL:0000871 ! splenic macrophage intersection_of: capable_of GO:0006955 ! immune response intersection_of: capable_of GO:0034102 ! erythrocyte clearance intersection_of: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M intersection_of: has_low_plasma_membrane_amount PR:000001931 ! sialoadhesin intersection_of: has_plasma_membrane_part PR:000001806 ! C-type lectin domain family 6 member A intersection_of: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 intersection_of: has_plasma_membrane_part PR:000002064 ! macrosialin intersection_of: has_plasma_membrane_part PR:000002972 ! macrophage mannose receptor 1 intersection_of: lacks_plasma_membrane_part PR:000001013 ! integrin alpha-X intersection_of: part_of UBERON:0001250 ! red pulp of spleen relationship: capable_of GO:0006955 ! immune response relationship: capable_of GO:0034102 ! erythrocyte clearance relationship: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: has_low_plasma_membrane_amount PR:000001931 ! sialoadhesin relationship: has_plasma_membrane_part PR:000001806 ! C-type lectin domain family 6 member A relationship: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 relationship: has_plasma_membrane_part PR:000002064 ! macrosialin relationship: has_plasma_membrane_part PR:000002972 ! macrophage mannose receptor 1 relationship: lacks_plasma_membrane_part PR:000001013 ! integrin alpha-X relationship: part_of UBERON:0001250 ! red pulp of spleen [Term] id: CL:0000875 name: non-classical monocyte namespace: cell def: "Subset of monocytes characterized by low expression of CCR2, low responsiveness to monocyte chemoattractant CCL2/MCP1, low phagocytic activity, but increased co-stimulatory activity. May also play a role in tissue repair." [GO_REF:0000031, PMID:16322748, PMID:18303997, PMID:20628149, PMID:20870168] comment: Markers: CCR2-CX3CCR1+ (human, mouse, rat); human: CD16+, CCR5+, CD32/FcgRII-high, MHCII+, CD86+; mouse: CD62L-Ly6C-. synonym: "patrolling monocyte" EXACT [] synonym: "resident monocyte" EXACT [] is_a: CL:0000576 ! monocyte intersection_of: CL:0000576 ! monocyte intersection_of: capable_of GO:0031294 ! lymphocyte costimulation intersection_of: has_high_plasma_membrane_amount PR:000001206 ! CX3C chemokine receptor 1 intersection_of: has_low_plasma_membrane_amount PR:000001199 ! C-C chemokine receptor type 2 relationship: capable_of GO:0031294 ! lymphocyte costimulation relationship: has_high_plasma_membrane_amount PR:000001206 ! CX3C chemokine receptor 1 relationship: has_low_plasma_membrane_amount PR:000001199 ! C-C chemokine receptor type 2 [Term] id: CL:0000876 name: splenic white pulp macrophage namespace: cell def: "A splenic macrophage found in the white pulp of the spleen. Markers include F4/80-negative, CD68-positive, and macrosialin-positive." [GO_REF:0000031, GOC:ana, PMID:11207597] comment: Markers: Mouse: F4/80-, CD68+, macrosialin+. is_a: CL:0000871 ! splenic macrophage intersection_of: CL:0000871 ! splenic macrophage intersection_of: has_plasma_membrane_part PR:000002064 ! macrosialin intersection_of: lacks_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 intersection_of: part_of UBERON:0001959 ! white pulp of spleen relationship: has_plasma_membrane_part PR:000002064 ! macrosialin relationship: lacks_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 relationship: part_of UBERON:0001959 ! white pulp of spleen [Term] id: CL:0000877 name: splenic tingible body macrophage namespace: cell def: "A splenic white pulp macrophage found in and around the germinal centers of the white pulp of the spleen that participates in phagocytosis of apoptotic B cells from the germinal centers. A marker for a cell of this type is Mertk-positive." [GO_REF:0000031, GOC:ana, GOC:tfm, PMID:19631584] is_a: CL:0000876 ! splenic white pulp macrophage intersection_of: CL:0000876 ! splenic white pulp macrophage intersection_of: capable_of GO:0043277 ! apoptotic cell clearance intersection_of: has_plasma_membrane_part PR:000010329 ! tyrosine-protein kinase Mer intersection_of: part_of UBERON:0001249 ! spleen lymphoid follicle relationship: capable_of GO:0043277 ! apoptotic cell clearance relationship: has_plasma_membrane_part PR:000010329 ! tyrosine-protein kinase Mer relationship: part_of UBERON:0001249 ! spleen lymphoid follicle [Term] id: CL:0000878 name: central nervous system macrophage namespace: cell def: "A tissue-resident macrophage found in the central nervous system." [GO_REF:0000031, PMID:16322748] synonym: "CNS macrophage" EXACT [] is_a: CL:0000864 ! tissue-resident macrophage intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: part_of UBERON:0001017 ! central nervous system relationship: part_of UBERON:0001017 ! central nervous system [Term] id: CL:0000879 name: meningeal macrophage namespace: cell def: "A central nervous system macrophage found in the meninges (the three membranes that surround the brain). This macrophage types is highly phagocytic and expresses scavenger receptors." [GO_REF:0000031, GOC:ana, PMID:11591794] is_a: CL:0000878 ! central nervous system macrophage intersection_of: CL:0000878 ! central nervous system macrophage intersection_of: capable_of GO:0005044 ! scavenger receptor activity intersection_of: part_of UBERON:0002360 ! meninx relationship: capable_of GO:0005044 ! scavenger receptor activity relationship: part_of UBERON:0002360 ! meninx [Term] id: CL:0000880 name: choroid-plexus macrophage namespace: cell def: "A central nervous system macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This cell expresses scavenger receptors." [GO_REF:0000031, GOC:ana, PMID:9550136] is_a: CL:0000878 ! central nervous system macrophage intersection_of: CL:0000878 ! central nervous system macrophage intersection_of: capable_of GO:0005044 ! scavenger receptor activity intersection_of: located_in UBERON:0001886 ! choroid plexus relationship: capable_of GO:0005044 ! scavenger receptor activity relationship: located_in UBERON:0001886 ! choroid plexus [Term] id: CL:0000881 name: perivascular macrophage namespace: cell def: "A central nervous system macrophage found in small blood vessels in the brain. Markers include CD14+CD16+CD163+." [GO_REF:0000031, GOC:tfm, PMID:16507898] comment: Markers: Human/monkey, mice: CD163. Human: CD14+CD16+CD163+. is_a: CL:0000878 ! central nervous system macrophage intersection_of: CL:0000878 ! central nervous system macrophage intersection_of: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III intersection_of: has_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: has_plasma_membrane_part PR:000001925 ! scavenger receptor cysteine-rich type 1 protein M130 intersection_of: part_of UBERON:0001981 ! blood vessel relationship: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: has_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: has_plasma_membrane_part PR:000001925 ! scavenger receptor cysteine-rich type 1 protein M130 relationship: part_of UBERON:0001981 ! blood vessel [Term] id: CL:0000882 name: thymic medullary macrophage namespace: cell def: "A thymic macrophage found in the thymic medulla." [GO_REF:0000031, GOC:ana, PMID:9048205] is_a: CL:0000866 ! thymic macrophage intersection_of: CL:0000866 ! thymic macrophage intersection_of: part_of UBERON:0002124 ! medulla of thymus relationship: part_of UBERON:0002124 ! medulla of thymus [Term] id: CL:0000883 name: thymic cortical macrophage namespace: cell def: "A thymic macrophage found in the thymic cortex." [GO_REF:0000031, GOC:ana, GOC:tfm, PMID:9048205] is_a: CL:0000866 ! thymic macrophage intersection_of: CL:0000866 ! thymic macrophage intersection_of: part_of UBERON:0002123 ! cortex of thymus relationship: part_of UBERON:0002123 ! cortex of thymus [Term] id: CL:0000884 name: mucosa-associated lymphoid tissue macrophage namespace: cell def: "A tissue-resident macrophage found in the mucosa associated lymphoid tissue." [GO_REF:0000031, GOC:ana, GOC:tfm, PMID:19906191] is_a: CL:0000867 ! secondary lymphoid organ macrophage intersection_of: CL:0000867 ! secondary lymphoid organ macrophage intersection_of: part_of UBERON:0001961 ! mucosa-associated lymphoid tissue relationship: part_of UBERON:0001961 ! mucosa-associated lymphoid tissue [Term] id: CL:0000885 name: gut-associated lymphoid tissue macrophage namespace: cell def: "A mucosa-associated lymphoid tissue macrophage found in the mucosa-associated lymphoid tissues of the gut." [GO_REF:0000031, GOC:ana, PMID:19906191] is_a: CL:0000884 ! mucosa-associated lymphoid tissue macrophage intersection_of: CL:0000884 ! mucosa-associated lymphoid tissue macrophage intersection_of: capable_of GO:0002387 ! immune response in gut-associated lymphoid tissue intersection_of: part_of UBERON:0001962 ! gut-associated lymphoid tissue relationship: capable_of GO:0002387 ! immune response in gut-associated lymphoid tissue relationship: part_of UBERON:0001962 ! gut-associated lymphoid tissue [Term] id: CL:0000886 name: nasal and broncial associated lymphoid tissue macrophage namespace: cell def: "A mucosa-associated lymphoid tissue macrophage found in the nasal and bronchial mucosa-associated lymphoid tissues." [GO_REF:0000031, GOC:ana, PMID:16048540] is_a: CL:0000884 ! mucosa-associated lymphoid tissue macrophage intersection_of: CL:0000884 ! mucosa-associated lymphoid tissue macrophage intersection_of: capable_of GO:0002395 ! immune response in nasopharyngeal-associated lymphoid tissue intersection_of: part_of UBERON:0001963 ! bronchial-associated lymphoid tissue relationship: capable_of GO:0002395 ! immune response in nasopharyngeal-associated lymphoid tissue relationship: part_of UBERON:0001963 ! bronchial-associated lymphoid tissue [Term] id: CL:0000887 name: lymph node subcapsular sinus macrophage namespace: cell def: "A lymph node macrophage found in the subcapsular sinus of lymph nodes that participates in sensing, clearance, and antigen presentation of lymph-borne particulate antigens. This macrophage is capable of activating invaraint NKT cells and is CD169-positive." [GO_REF:0000031, GOC:tfm, PMID:14668803, PMID:17934446, PMID:20228797] is_a: CL:0000868 ! lymph node macrophage intersection_of: CL:0000868 ! lymph node macrophage intersection_of: adjacent_to UBERON:0002194 ! capsule of lymph node intersection_of: capable_of GO:0032816 ! positive regulation of natural killer cell activation intersection_of: has_plasma_membrane_part PR:000001931 ! sialoadhesin relationship: adjacent_to UBERON:0002194 ! capsule of lymph node relationship: capable_of GO:0032816 ! positive regulation of natural killer cell activation relationship: has_plasma_membrane_part PR:000001931 ! sialoadhesin [Term] id: CL:0000888 name: lymph node tingible body macrophage namespace: cell def: "A lymph node macrophage found in the cortex of lymph nodes, in particular in and around the germinal centers, and that participates in phagocytosis of apoptotic B cells from the germinal centers." [GO_REF:0000031, GOC:ana, GOC:tfm, PMID:19631584] is_a: CL:0000868 ! lymph node macrophage intersection_of: CL:0000868 ! lymph node macrophage intersection_of: capable_of GO:0002905 ! regulation of mature B cell apoptotic process intersection_of: capable_of GO:0043277 ! apoptotic cell clearance intersection_of: part_of UBERON:0002006 ! cortex of lymph node relationship: capable_of GO:0002905 ! regulation of mature B cell apoptotic process relationship: capable_of GO:0043277 ! apoptotic cell clearance relationship: part_of UBERON:0002006 ! cortex of lymph node [Term] id: CL:0000889 name: myeloid suppressor cell namespace: cell def: "An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive." [GO_REF:0000031, GOC:add, GOC:ana, PMID:16168663, PMID:17016554, PMID:17016559] comment: Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis. is_a: CL:0000766 ! myeloid leukocyte intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0050777 ! negative regulation of immune response intersection_of: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_quality PATO:0001501 ! immature relationship: capable_of GO:0050777 ! negative regulation of immune response relationship: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_quality PATO:0001501 ! immature [Term] id: CL:0000890 name: alternatively activated macrophage namespace: cell def: "An elicited macrophage characterized by low production of pro-inflammatory and Th1 polarizing cytokines and high expression of arginase-1, and associated with tissue remodelling." [GO_REF:0000031, GOC:ana, GOC:tfm, PMID:20510870] comment: Role or process: tissue remodeling. synonym: "M2 macrophage" RELATED [] is_a: CL:0000861 ! elicited macrophage intersection_of: CL:0000861 ! elicited macrophage intersection_of: capable_of GO:0048771 ! tissue remodeling intersection_of: has_part PR:000001844 ! arginase-1 relationship: capable_of GO:0048771 ! tissue remodeling relationship: has_part PR:000001844 ! arginase-1 [Term] id: CL:0000891 name: foam cell namespace: cell def: "A type of cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions." [GOC:add] xref: BTO:0003872 xref: FMA:83586 is_a: CL:0000003 ! native cell [Term] id: CL:0000892 name: smooth muscle cell derived foam cell namespace: cell def: "A type of foam cell derived from a smooth muscle cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions." [GOC:add] is_a: CL:0000891 ! foam cell relationship: develops_from CL:0000192 ! smooth muscle cell [Term] id: CL:0000893 name: thymocyte namespace: cell def: "An immature T cell located in the thymus." [GO_REF:0000031, GOC:add, GOC:tfm, PMID:12415312] synonym: "immature T cell" BROAD [] synonym: "immature T lymphocyte" BROAD [] synonym: "immature T-cell" BROAD [] synonym: "immature T-lymphocyte" BROAD [] synonym: "thymic lymphocyte" EXACT [] xref: BTO:0001372 xref: FMA:72202 xref: XAO:0003159 is_a: CL:0002420 ! immature T cell intersection_of: CL:0000084 ! T cell intersection_of: has_not_completed GO:0045058 ! T cell selection intersection_of: part_of UBERON:0002370 ! thymus relationship: has_not_completed GO:0045058 ! T cell selection relationship: part_of UBERON:0002370 ! thymus [Term] id: CL:0000894 name: DN1 thymic pro-T cell namespace: cell def: "A pro-T cell that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-negative." [GO_REF:0000031, GOC:add, GOC:tfm] synonym: "DN1 thymic pro-T lymphocyte" EXACT [] synonym: "DN1 thymic pro-T-cell" EXACT [] synonym: "DN1 thymic pro-T-lymphocyte" EXACT [] synonym: "DN1 thymic progenitor T cell" EXACT [] synonym: "DN1 thymocyte" EXACT [] synonym: "double negative 1" EXACT [] synonym: "preT.DN1.Th" EXACT [] is_a: CL:0000827 ! pro-T cell intersection_of: CL:0000827 ! pro-T cell intersection_of: has_plasma_membrane_part PR:000001307 ! CD44 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha intersection_of: part_of UBERON:0002370 ! thymus relationship: develops_from CL:0002425 ! early T lineage precursor relationship: has_plasma_membrane_part PR:000001307 ! CD44 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: part_of UBERON:0002370 ! thymus [Term] id: CL:0000895 name: naive thymus-derived CD4-positive, alpha-beta T cell namespace: cell def: "An antigen inexperienced CD4-positive, alpha-beta T cell with the phenotype CCR7-positive, CD127-positive and CD62L-positive. This cell type develops in the thymus. This cell type is also described as being CD25-negative, CD62L-high, and CD44-low." [GO_REF:0000031, GOC:add, GOC:tfm, http://www.immgen.org/index_content.html, PMID:19100699] comment: These cells have not been exposed to antigen following thymic T-cell selection; found in blood and secondary lymphoid organs. synonym: "naive thymus-derived CD4-positive, alpha-beta T lymphocyte" EXACT [] synonym: "naive thymus-derived CD4-positive, alpha-beta T-cell" EXACT [] synonym: "naive thymus-derived CD4-positive, alpha-beta T-lymphocyte" EXACT [] synonym: "T.4Nve.Sp" EXACT [] synonym: "Th0" EXACT [GOC:tfm] is_a: CL:0000624 ! CD4-positive, alpha-beta T cell is_a: CL:0000898 ! naive T cell intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: has_high_plasma_membrane_amount PR:000001318 ! L-selectin intersection_of: has_low_plasma_membrane_amount PR:000001307 ! CD44 molecule intersection_of: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: has_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 intersection_of: has_plasma_membrane_part PR:000001318 ! L-selectin intersection_of: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: develops_from CL:0002436 ! mature CD4 single-positive thymocyte relationship: has_high_plasma_membrane_amount PR:000001318 ! L-selectin relationship: has_low_plasma_membrane_amount PR:000001307 ! CD44 molecule relationship: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: has_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 relationship: has_plasma_membrane_part PR:000001318 ! L-selectin relationship: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha [Term] id: CL:0000896 name: activated CD4-positive, alpha-beta T cell namespace: cell def: "A recently activated CD4-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive." [GO_REF:0000031, GOC:add, GOC:pam] synonym: "activated CD4-positive, alpha-beta T lymphocyte" EXACT [] synonym: "activated CD4-positive, alpha-beta T-cell" EXACT [] synonym: "activated CD4-positive, alpha-beta T-lymphocyte" EXACT [] is_a: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: has_plasma_membrane_part PR:000001343 ! CD69 molecule intersection_of: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000001318 ! L-selectin intersection_of: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: develops_from CL:0000895 ! naive thymus-derived CD4-positive, alpha-beta T cell relationship: has_plasma_membrane_part PR:000001343 ! CD69 molecule relationship: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000001318 ! L-selectin relationship: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha [Term] id: CL:0000897 name: CD4-positive, alpha-beta memory T cell namespace: cell def: "CD4-positive, alpha-beta long-lived T cell with the phenotype CD45RO-positive and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122- high." [GO_REF:0000031, GOC:add, GOC:tfm, http://www.immgen.org/index_content.html, ISBN:0781735149] synonym: "CD4-positive, alpha-beta memory T lymphocyte" EXACT [] synonym: "CD4-positive, alpha-beta memory T-cell" EXACT [] synonym: "CD4-positive, alpha-beta memory T-lymphocyte" EXACT [] synonym: "T4.Mem.Sp" RELATED [] is_a: CL:0000624 ! CD4-positive, alpha-beta T cell is_a: CL:0000813 ! memory T cell intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: has_high_plasma_membrane_amount PR:000001307 ! CD44 molecule intersection_of: has_high_plasma_membrane_amount PR:000001381 ! interleukin-2 receptor subunit beta intersection_of: has_plasma_membrane_part PR:000001017 ! receptor-type tyrosine-protein phosphatase C isoform CD45RO intersection_of: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell relationship: has_high_plasma_membrane_amount PR:000001307 ! CD44 molecule relationship: has_high_plasma_membrane_amount PR:000001381 ! interleukin-2 receptor subunit beta relationship: has_plasma_membrane_part PR:000001017 ! receptor-type tyrosine-protein phosphatase C isoform CD45RO relationship: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha [Term] id: CL:0000898 name: naive T cell namespace: cell def: "Mature T cell not yet exposed to antigen with the phenotype CCR7-positive, CD45RA-positive, and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19100699] synonym: "naive T lymphocyte" EXACT [] synonym: "naive T-cell" EXACT [] synonym: "naive T-lymphocyte" EXACT [] is_a: CL:0002419 ! mature T cell intersection_of: CL:0002419 ! mature T cell intersection_of: has_completed GO:0045058 ! T cell selection intersection_of: has_high_plasma_membrane_amount PR:000001318 ! L-selectin intersection_of: has_low_plasma_membrane_amount PR:000001307 ! CD44 molecule intersection_of: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: has_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 intersection_of: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: has_completed GO:0045058 ! T cell selection relationship: has_high_plasma_membrane_amount PR:000001318 ! L-selectin relationship: has_low_plasma_membrane_amount PR:000001307 ! CD44 molecule relationship: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: has_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 relationship: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha [Term] id: CL:0000899 name: T-helper 17 cell namespace: cell def: "CD4-positive, alpha-beta T cell with the phenotype RORgamma-t-positive that produces IL-17." [GO_REF:0000031, GOC:add, GOC:pam, PMID:20303875, PMID:20969597] synonym: "helper T cell type 17" EXACT [] synonym: "IL-17-producing CD4+ T helper" EXACT [] synonym: "T helper cells type 17" EXACT [] synonym: "T(H)-17 cell" EXACT [] synonym: "Th17 cell" EXACT [] synonym: "Th17 T cell" EXACT [] synonym: "Th17 T lymphocyte" EXACT [] synonym: "Th17 T-cell" EXACT [] synonym: "Th17 T-lymphocyte" EXACT [] is_a: CL:0000492 ! CD4-positive helper T cell intersection_of: CL:0000492 ! CD4-positive helper T cell intersection_of: capable_of GO:0032620 ! interleukin-17 production intersection_of: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 relationship: capable_of GO:0032620 ! interleukin-17 production relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell relationship: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 [Term] id: CL:0000900 name: naive thymus-derived CD8-positive, alpha-beta T cell namespace: cell def: "A CD8-positive, alpha-beta T cell that has not experienced activation via antigen contact and has the phenotype CD45RA-positive, CCR7-positive and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low." [GO_REF:0000031, GOC:add, GOC:tfm, http://www.immgen.org/index_content.html, ISBN:0781735149] comment: Additional markers in human are CD45RA. This cell traffics in secondary lymphoid organs and blood. synonym: "naive thymus-dervied CD8-positive, alpha-beta T lymphocyte" EXACT [] synonym: "naive thymus-dervied CD8-positive, alpha-beta T-cell" EXACT [] synonym: "naive thymus-dervied CD8-positive, alpha-beta T-lymphocyte" EXACT [] synonym: "T.8Nve.Sp" NARROW [] is_a: CL:0000625 ! CD8-positive, alpha-beta T cell is_a: CL:0000898 ! naive T cell intersection_of: CL:0000625 ! CD8-positive, alpha-beta T cell intersection_of: has_high_plasma_membrane_amount PR:000001318 ! L-selectin intersection_of: has_low_plasma_membrane_amount PR:000001307 ! CD44 molecule intersection_of: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: has_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 intersection_of: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: develops_from CL:0002437 ! mature CD8 single-positive thymocyte relationship: has_high_plasma_membrane_amount PR:000001318 ! L-selectin relationship: has_low_plasma_membrane_amount PR:000001307 ! CD44 molecule relationship: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: has_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 relationship: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha [Term] id: CL:0000901 name: Tr1 cell namespace: cell def: "CD4-positive alpha-beta T cell with regulatory function that produces IL-10." [GO_REF:0000031, GOC:add, GOC:pam, PMID:16903904] comment: These cells are reportedly induced by IL-10 and are capable of producing IFN-gamma, IL-5, IL-10, and TGF-beta.) synonym: "T-regulatory T cell type 1" EXACT [] synonym: "Tr1 T cell" EXACT [] synonym: "Tr1 T lymphocyte" EXACT [] synonym: "Tr1 T-cell" EXACT [] synonym: "Tr1 T-lymphocyte" EXACT [] is_a: CL:0000492 ! CD4-positive helper T cell is_a: CL:0000815 ! regulatory T cell intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: capable_of GO:0032613 ! interleukin-10 production intersection_of: capable_of GO:0050777 ! negative regulation of immune response relationship: capable_of GO:0032613 ! interleukin-10 production relationship: capable_of GO:0050777 ! negative regulation of immune response relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell [Term] id: CL:0000902 name: induced T-regulatory cell namespace: cell def: "CD4-positive alpha-beta T cell with the phenotype CD25-positive, CTLA-4-positive, and FoxP3-positive with regulatory function." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19464985] synonym: "adaptive Treg" RELATED [] synonym: "aTreg" RELATED [] synonym: "induced regulatory T cell" EXACT [] synonym: "induced regulatory T lymphocyte" EXACT [] synonym: "induced regulatory T-cell" EXACT [] synonym: "induced regulatory T-lymphocyte" EXACT [] synonym: "induced Treg" EXACT [] synonym: "iTreg" EXACT [] is_a: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell intersection_of: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell intersection_of: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell intersection_of: has_part PR:000001350 ! forkhead box protein P3 intersection_of: has_plasma_membrane_part PR:000001852 ! cytotoxic T-lymphocyte protein 4 relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell relationship: has_part PR:000001350 ! forkhead box protein P3 relationship: has_plasma_membrane_part PR:000001852 ! cytotoxic T-lymphocyte protein 4 [Term] id: CL:0000903 name: natural T-regulatory cell namespace: cell def: "CD4-positive alpha-beta T cell with the phenotype FoxP3-positive, CD25-positive, CD62L-positive, and CTLA-4 positive with regulatory function." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19464985] synonym: "natural regulatory T cell" EXACT [] synonym: "natural regulatory T lymphocyte" EXACT [] synonym: "natural regulatory T-cell" EXACT [] synonym: "natural regulatory T-lymphocyte" EXACT [] synonym: "natural Treg" EXACT [] synonym: "nTreg" EXACT [] is_a: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell intersection_of: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell intersection_of: develops_from CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: has_part PR:000001350 ! forkhead box protein P3 intersection_of: has_plasma_membrane_part PR:000001318 ! L-selectin intersection_of: has_plasma_membrane_part PR:000001852 ! cytotoxic T-lymphocyte protein 4 relationship: develops_from CL:0000809 ! double-positive, alpha-beta thymocyte relationship: has_part PR:000001350 ! forkhead box protein P3 relationship: has_plasma_membrane_part PR:000001318 ! L-selectin relationship: has_plasma_membrane_part PR:000001852 ! cytotoxic T-lymphocyte protein 4 [Term] id: CL:0000904 name: central memory CD4-positive, alpha-beta T cell namespace: cell def: "CD4-positive, alpha-beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RO-positive, and CD25-negative." [GO_REF:0000031, GOC:add, GOC:pam] synonym: "central CD4-positive, alpha-beta memory T cell" EXACT [] synonym: "central CD4-positive, alpha-beta memory T lymphocyte" EXACT [] synonym: "central CD4-positive, alpha-beta memory T-cell" EXACT [] synonym: "central CD4-positive, alpha-beta memory T-lymphocyte" EXACT [] synonym: "central memory CD4-positive, alpha-beta T lymphocyte" EXACT [] synonym: "central memory CD4-positive, alpha-beta T-cell" EXACT [] synonym: "central memory CD4-positive, alpha-beta T-lymphocyte" EXACT [] is_a: CL:0000897 ! CD4-positive, alpha-beta memory T cell intersection_of: CL:0000897 ! CD4-positive, alpha-beta memory T cell intersection_of: has_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 intersection_of: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: has_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 relationship: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha [Term] id: CL:0000905 name: effector memory CD4-positive, alpha-beta T cell namespace: cell def: "CD4-positive, alpha-beta memory T cell with the phenotype CCR7-negative, CD127-positive, CD45RO-positive, and CD25-negative." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm] synonym: "effector CD4-positive, alpha-beta memory T cell" EXACT [] synonym: "effector CD4-positive, alpha-beta memory T lymphocyte" EXACT [] synonym: "effector CD4-positive, alpha-beta memory T-cell" EXACT [] synonym: "effector CD4-positive, alpha-beta memory T-lymphocyte" EXACT [] synonym: "effector memory CD4-positive, alpha-beta T lymphocyte" EXACT [] synonym: "effector memory CD4-positive, alpha-beta T-cell" EXACT [] synonym: "effector memory CD4-positive, alpha-beta T-lymphocyte" EXACT [] is_a: CL:0000897 ! CD4-positive, alpha-beta memory T cell intersection_of: CL:0000897 ! CD4-positive, alpha-beta memory T cell intersection_of: lacks_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 intersection_of: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 relationship: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha [Term] id: CL:0000906 name: activated CD8-positive, alpha-beta T cell namespace: cell def: "A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, CD25-positive, and CCR7-negative." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm] synonym: "activated CD8-positive, alpha-beta T lymphocyte" EXACT [] synonym: "activated CD8-positive, alpha-beta T-cell" EXACT [] synonym: "activated CD8-positive, alpha-beta T-lymphocyte" EXACT [] is_a: CL:0000625 ! CD8-positive, alpha-beta T cell intersection_of: CL:0000625 ! CD8-positive, alpha-beta T cell intersection_of: has_plasma_membrane_part PR:000001343 ! CD69 molecule intersection_of: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 intersection_of: lacks_plasma_membrane_part PR:000001318 ! L-selectin intersection_of: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: develops_from CL:0000900 ! naive thymus-derived CD8-positive, alpha-beta T cell relationship: has_plasma_membrane_part PR:000001343 ! CD69 molecule relationship: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 relationship: lacks_plasma_membrane_part PR:000001318 ! L-selectin relationship: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha [Term] id: CL:0000907 name: central memory CD8 positive, alpha-beta T cell namespace: cell def: "A CD8-positive, alpha beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RO-positive, and CD25-negative." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:20146720] synonym: "central CD8-positive, alpha-beta memory T cell" EXACT [] synonym: "central CD8-positive, alpha-beta memory T lymphocyte" EXACT [] synonym: "central CD8-positive, alpha-beta memory T-cell" EXACT [] synonym: "central CD8-positive, alpha-beta memory T-lymphocyte" EXACT [] synonym: "central memory CD8-positive, alpha-beta T lymphocyte" EXACT [] synonym: "central memory CD8-positive, alpha-beta T-cell" EXACT [] synonym: "central memory CD8-positive, alpha-beta T-lymphocyte" EXACT [] is_a: CL:0000909 ! CD8-positive, alpha-beta memory T cell intersection_of: CL:0000909 ! CD8-positive, alpha-beta memory T cell intersection_of: has_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 intersection_of: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: has_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 relationship: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha [Term] id: CL:0000908 name: CD8-positive, alpha-beta cytokine secreting effector T cell namespace: cell def: "A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive, that secretes cytokines." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:20146720] synonym: "CD8-positive, alpha-beta cytokine secreting effector T lymphocyte" EXACT [] synonym: "CD8-positive, alpha-beta cytokine secreting effector T-cell" EXACT [] synonym: "CD8-positive, alpha-beta cytokine secreting effector T-lymphocyte" EXACT [] is_a: CL:0000625 ! CD8-positive, alpha-beta T cell is_a: CL:0000912 ! helper T cell intersection_of: CL:0000625 ! CD8-positive, alpha-beta T cell intersection_of: capable_of GO:0001816 ! cytokine production intersection_of: has_completed GO:0030217 ! T cell differentiation intersection_of: has_plasma_membrane_part PR:000001343 ! CD69 molecule intersection_of: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000001318 ! L-selectin intersection_of: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: capable_of GO:0001816 ! cytokine production relationship: develops_from CL:0000906 ! activated CD8-positive, alpha-beta T cell relationship: has_completed GO:0030217 ! T cell differentiation relationship: has_plasma_membrane_part PR:000001343 ! CD69 molecule relationship: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000001318 ! L-selectin relationship: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha [Term] id: CL:0000909 name: CD8-positive, alpha-beta memory T cell namespace: cell def: "A CD8-positive, alpha-beta T cell with memory phenotype indicated by being CD45RO and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122- high." [GO_REF:0000031, GOC:tfm, PMID:20146720] synonym: "CD8-positive, alpha-beta memory T lymphocyte" EXACT [] synonym: "CD8-positive, alpha-beta memory T-cell" EXACT [] synonym: "CD8-positive, alpha-beta memory T-lymphocyte" EXACT [] synonym: "T.8Mem.Sp" EXACT [] is_a: CL:0000625 ! CD8-positive, alpha-beta T cell is_a: CL:0000813 ! memory T cell intersection_of: CL:0000625 ! CD8-positive, alpha-beta T cell intersection_of: has_high_plasma_membrane_amount PR:000001307 ! CD44 molecule intersection_of: has_high_plasma_membrane_amount PR:000001381 ! interleukin-2 receptor subunit beta intersection_of: has_plasma_membrane_part PR:000001017 ! receptor-type tyrosine-protein phosphatase C isoform CD45RO intersection_of: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: develops_from CL:0000906 ! activated CD8-positive, alpha-beta T cell relationship: has_high_plasma_membrane_amount PR:000001307 ! CD44 molecule relationship: has_high_plasma_membrane_amount PR:000001381 ! interleukin-2 receptor subunit beta relationship: has_plasma_membrane_part PR:000001017 ! receptor-type tyrosine-protein phosphatase C isoform CD45RO relationship: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha [Term] id: CL:0000910 name: cytotoxic T cell namespace: cell def: "A mature T cell that differentiated and acquired cytotoxic function with the phenotype perforin-positive and granzyme-B positive." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:18395547] synonym: "cytotoxic T lymphocyte" EXACT [] synonym: "cytotoxic T-cell" EXACT [] synonym: "cytotoxic T-lymphocyte" EXACT [] xref: BTO:0000289 xref: FMA:70573 is_a: CL:0000911 ! effector T cell intersection_of: CL:0000911 ! effector T cell intersection_of: capable_of GO:0001913 ! T cell mediated cytotoxicity relationship: capable_of GO:0001913 ! T cell mediated cytotoxicity [Term] id: CL:0000911 name: effector T cell namespace: cell def: "A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response." [GOC:PAM-ADD, GOC:tfm, ISBN:0877799148, PMID:18395547] synonym: "effector T lymphocyte" EXACT [] synonym: "effector T-cell" EXACT [] synonym: "effector T-lymphocyte" EXACT [] is_a: CL:0002419 ! mature T cell intersection_of: CL:0002419 ! mature T cell intersection_of: has_completed GO:0030217 ! T cell differentiation intersection_of: has_completed GO:0045058 ! T cell selection relationship: has_completed GO:0030217 ! T cell differentiation relationship: has_completed GO:0045058 ! T cell selection [Term] id: CL:0000912 name: helper T cell namespace: cell def: "A effector T cell that provides help in the form of secreted cytokines to other immune cells." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:18395547] synonym: "helper T lymphocyte" EXACT [] synonym: "helper T-cell" EXACT [] synonym: "helper T-lymphocyte" EXACT [] synonym: "T-helper cell" EXACT [] xref: BTO:0002417 is_a: CL:0000911 ! effector T cell intersection_of: CL:0000911 ! effector T cell intersection_of: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0001816 ! cytokine production [Term] id: CL:0000913 name: effector memory CD8-positive, alpha-beta T cell namespace: cell def: "A CD8-positive, alpha beta memory T cell with the phenotype CCR7-negative, CD127-positive, CD45RO-positive, and CD25-negative." [GO_REF:0000031, GOC:add, GOC:pam, PMID:20146720] synonym: "effector CD8-positive, alpha-beta memory T cell" EXACT [] synonym: "effector CD8-positive, alpha-beta memory T lymphocyte" EXACT [] synonym: "effector CD8-positive, alpha-beta memory T-cell" EXACT [] synonym: "effector CD8-positive, alpha-beta memory T-lymphocyte" EXACT [] synonym: "effector memory CD8-positive, alpha-beta T lymphocyte" EXACT [] synonym: "effector memory CD8-positive, alpha-beta T-cell" EXACT [] synonym: "effector memory CD8-positive, alpha-beta T-lymphocyte" EXACT [] is_a: CL:0000909 ! CD8-positive, alpha-beta memory T cell intersection_of: CL:0000909 ! CD8-positive, alpha-beta memory T cell intersection_of: lacks_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 intersection_of: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 relationship: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha [Term] id: CL:0000914 name: immature NK T cell namespace: cell def: "An immature alpha-beta T-cell that express Egr2. These cells give rise to T cells expressing NK markers." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17589542, PMID:19169262] synonym: "immature NK T lymphocyte" EXACT [] synonym: "immature NK T-cell" EXACT [] synonym: "immature NK T-lymphocyte" EXACT [] synonym: "immature NKT cell" EXACT [] is_a: CL:0000790 ! immature alpha-beta T cell intersection_of: CL:0000790 ! immature alpha-beta T cell intersection_of: has_part PR:000003469 ! early growth response protein 2 relationship: develops_from CL:0000809 ! double-positive, alpha-beta thymocyte relationship: has_part PR:000003469 ! early growth response protein 2 [Term] id: CL:0000915 name: CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell namespace: cell def: "An alpha-beta intraepithelial T cell with the phenotype CD8-alpha-alpha-positive located in the columnar epithelium of the gastrointestinal tract. These cells have a memory phenotype of CD2-negative and CD5-negative." [GO_REF:0000031, GOC:add, GOC:pam, PMID:11685222] synonym: "CD8-alpha-alpha-positive, alpha-beta intraepithelial T lymphocyte" EXACT [] synonym: "CD8-alpha-alpha-positive, alpha-beta intraepithelial T-cell" EXACT [] synonym: "CD8-alpha-alpha-positive, alpha-beta intraepithelial T-lymphocyte" EXACT [] is_a: CL:0000797 ! alpha-beta intraepithelial T cell intersection_of: CL:0000797 ! alpha-beta intraepithelial T cell intersection_of: has_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: develops_from CL:0000811 ! CD8-positive, alpha-beta thymocyte relationship: has_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 [Term] id: CL:0000916 name: dendritic epidermal T cell namespace: cell def: "A mature gamma-delta T cell located in the epidermis that regulates wound healing." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:11976459] comment: In mice, DETC have an invariant T cell receptor. synonym: "dendritic epidermal T lymphocyte" EXACT [] synonym: "dendritic epidermal T-cell" EXACT [] synonym: "dendritic epidermal T-lymphocyte" EXACT [] synonym: "DETC" EXACT [] is_a: CL:0000800 ! mature gamma-delta T cell intersection_of: CL:0000800 ! mature gamma-delta T cell intersection_of: capable_of GO:0060054 ! positive regulation of epithelial cell proliferation involved in wound healing intersection_of: part_of UBERON:0001003 ! epidermis relationship: capable_of GO:0060054 ! positive regulation of epithelial cell proliferation involved in wound healing relationship: develops_from CL:0002401 ! mature dendritic epithelial T cell precursor relationship: part_of UBERON:0001003 ! epidermis [Term] id: CL:0000917 name: Tc1 cell namespace: cell def: "A CD8-positive, alpha-beta positive T cell expressing T-bet and eomesodermin and secreting interferon-gamma." [GO_REF:0000031, GOC:add, GOC:pam, PMID:9914231] synonym: "T-cytotoxic T cell type 1" EXACT [] synonym: "Tc1 T cell" EXACT [] synonym: "Tc1 T lymphocyte" EXACT [] synonym: "Tc1 T-cell" EXACT [] synonym: "Tc1 T-lymphocyte" EXACT [] xref: BTO:0004793 xref: BTO:0004888 xref: FMA:84793 is_a: CL:0000908 ! CD8-positive, alpha-beta cytokine secreting effector T cell intersection_of: CL:0000908 ! CD8-positive, alpha-beta cytokine secreting effector T cell intersection_of: capable_of GO:0032609 ! interferon-gamma production intersection_of: has_part PR:000001835 ! T-box transcription factor TBX21 intersection_of: has_part PR:000003463 ! eomesodermin relationship: capable_of GO:0032609 ! interferon-gamma production relationship: has_part PR:000001835 ! T-box transcription factor TBX21 relationship: has_part PR:000003463 ! eomesodermin [Term] id: CL:0000918 name: Tc2 cell namespace: cell def: "A CD8-positive, alpha-beta positive T cell expressing GATA-3 and secreting IL-4." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:9914231] synonym: "T-cytotoxic T cell type 2" EXACT [] synonym: "Tc2 T cell" EXACT [] synonym: "Tc2 T lymphocyte" EXACT [] synonym: "Tc2 T-cell" EXACT [] synonym: "Tc2 T-lymphocyte" EXACT [] xref: BTO:0004794 xref: FMA:84794 is_a: CL:0000908 ! CD8-positive, alpha-beta cytokine secreting effector T cell intersection_of: CL:0000908 ! CD8-positive, alpha-beta cytokine secreting effector T cell intersection_of: capable_of GO:0032633 ! interleukin-4 production intersection_of: has_part PR:000001941 ! trans-acting T-cell-specific transcription factor GATA-3 relationship: capable_of GO:0032633 ! interleukin-4 production relationship: has_part PR:000001941 ! trans-acting T-cell-specific transcription factor GATA-3 [Term] id: CL:0000919 name: CD8-positive, CD25-positive, alpha-beta regulatory T cell namespace: cell def: "A CD8-positive alpha beta-positive T cell with the phenotype FoxP3-positive and having suppressor function." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19118505] synonym: "CD8+CD25+ T cell" EXACT [] synonym: "CD8+CD25+ T lymphocyte" EXACT [] synonym: "CD8+CD25+ T(reg)" EXACT [] synonym: "CD8+CD25+ T-cell" EXACT [] synonym: "CD8+CD25+ T-lymphocyte " EXACT [] synonym: "CD8+CD25+ Treg" EXACT [] synonym: "CD8-positive, CD25-positive Treg" EXACT [] synonym: "CD8-positive, CD25-positive, alpha-beta regulatory T lymphocyte" EXACT [] synonym: "CD8-positive, CD25-positive, alpha-beta regulatory T-cell" EXACT [] synonym: "CD8-positive, CD25-positive, alpha-beta regulatory T-lymphocyte" EXACT [] is_a: CL:0000795 ! CD8-positive, alpha-beta regulatory T cell intersection_of: CL:0000795 ! CD8-positive, alpha-beta regulatory T cell intersection_of: has_part PR:000001350 ! forkhead box protein P3 intersection_of: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: develops_from CL:0000906 ! activated CD8-positive, alpha-beta T cell relationship: has_part PR:000001350 ! forkhead box protein P3 relationship: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha [Term] id: CL:0000920 name: CD8-positive, CD28-negative, alpha-beta regulatory T cell namespace: cell def: "CD8-positive, alpha-beta positive regulatory T cell with the phenotype CD28-negative and FoxP3-positive." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19118505] synonym: "CD8+CD28- T cell" EXACT [] synonym: "CD8+CD28- T lymphocyte" EXACT [] synonym: "CD8+CD28- T(reg)" EXACT [] synonym: "CD8+CD28- T-cell" EXACT [] synonym: "CD8+CD28- T-lymphocyte " EXACT [] synonym: "CD8+CD28- Treg" EXACT [] synonym: "CD8-positive, CD28-negative T(reg)" EXACT [] synonym: "CD8-positive, CD28-negative Treg" EXACT [] synonym: "CD8-positive, CD28-negative, alpha-beta regulatory T lymphocyte" EXACT [] synonym: "CD8-positive, CD28-negative, alpha-beta regulatory T-cell" EXACT [] synonym: "CD8-positive, CD28-negative, alpha-beta regulatory T-lymphocyte" EXACT [] is_a: CL:0000795 ! CD8-positive, alpha-beta regulatory T cell intersection_of: CL:0000795 ! CD8-positive, alpha-beta regulatory T cell intersection_of: has_part PR:000001350 ! forkhead box protein P3 intersection_of: lacks_plasma_membrane_part PR:000001841 ! T-cell-specific surface glycoprotein CD28 relationship: develops_from CL:0000906 ! activated CD8-positive, alpha-beta T cell relationship: has_part PR:000001350 ! forkhead box protein P3 relationship: lacks_plasma_membrane_part PR:000001841 ! T-cell-specific surface glycoprotein CD28 [Term] id: CL:0000921 name: type I NK T cell namespace: cell def: "An alpha-beta T cell expressing NK cell markers that is CD1d restricted and expresses specific V-alpha chains. NK T cells of this type recognize the glycolipid alpha-galactosylceramide in the context of CD1d." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:15039760] comment: In mouse the canonical TCR is V-alpha-14, and in humans it is V-alpha 24. synonym: "classical NK T cell" EXACT [] synonym: "invariant NK T cell" RELATED [] synonym: "type I NK T lymphocyte" EXACT [] synonym: "type I NK T-cell" EXACT [] synonym: "type I NK T-lymphocyte" EXACT [] synonym: "type I NKT cell" EXACT [] is_a: CL:0000814 ! mature NK T cell intersection_of: CL:0000814 ! mature NK T cell intersection_of: capable_of GO:0043208 ! glycosphingolipid binding relationship: capable_of GO:0043208 ! glycosphingolipid binding [Term] id: CL:0000922 name: type II NK T cell namespace: cell def: "An alpha-beta T cell expressing NK call markers that is CD1d restricted and expresses a diverse TCR repertoire. Type II NKT cells do not become activated by alpha-galactosylceramide when presented by CD1d." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:15039760] synonym: "type II NK T lymphocyte" EXACT [] synonym: "type II NK T-cell" EXACT [] synonym: "type II NK T-lymphocyte" EXACT [] synonym: "type II NKT cell" EXACT [] is_a: CL:0000814 ! mature NK T cell intersection_of: CL:0000814 ! mature NK T cell intersection_of: capable_of GO:0002288 ! NK T cell activation involved in immune response relationship: capable_of GO:0002288 ! NK T cell activation involved in immune response [Term] id: CL:0000923 name: CD4-positive type I NK T cell namespace: cell def: "A type I NK T cell that has the phenotype CD4-positive." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17303398] synonym: "CD4-positive type I NK T lymphocyte" EXACT [] synonym: "CD4-positive type I NK T-cell" EXACT [] synonym: "CD4-positive type I NK T-lymphocyte" EXACT [] synonym: "CD4-positive type I NKT cell" EXACT [] synonym: "NKT.4+.SP" NARROW [] is_a: CL:0000624 ! CD4-positive, alpha-beta T cell is_a: CL:0000921 ! type I NK T cell intersection_of: CL:0000921 ! type I NK T cell intersection_of: has_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: has_plasma_membrane_part PR:000001004 ! CD4 molecule [Term] id: CL:0000924 name: CD4-negative, CD8-negative type I NK T cell namespace: cell def: "A type I NK T cell that has the phenotype CD4-negative and CD8-negative." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:18997862] synonym: "CD4-negative, CD8-negative type I NK T lymphocyte" EXACT [] synonym: "CD4-negative, CD8-negative type I NK T-cell" EXACT [] synonym: "CD4-negative, CD8-negative type I NK T-lymphocyte" EXACT [] synonym: "CD4-negative, CD8-negative type I NKT cell" EXACT [] synonym: "NKT.4-.Sp" NARROW [] is_a: CL:0000921 ! type I NK T cell intersection_of: CL:0000921 ! type I NK T cell intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain [Term] id: CL:0000925 name: activated CD4-positive type I NK T cell namespace: cell def: "A type I NK T cell that has been recently activated, secretes interferon-gamma and IL-4, and has the phenotype CD4-positive, CD69-positive, and downregulated NK markers." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17303398] synonym: "activated CD4-positive type I NK T lymphocyte" EXACT [] synonym: "activated CD4-positive type I NK T-cell" EXACT [] synonym: "activated CD4-positive type I NK T-lymphocyte" EXACT [] synonym: "activated CD4-positive type I NKT cell" EXACT [] is_a: CL:0000492 ! CD4-positive helper T cell is_a: CL:0000923 ! CD4-positive type I NK T cell intersection_of: CL:0000921 ! type I NK T cell intersection_of: capable_of GO:0032609 ! interferon-gamma production intersection_of: capable_of GO:0032633 ! interleukin-4 production intersection_of: has_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: has_plasma_membrane_part PR:000001343 ! CD69 molecule relationship: capable_of GO:0032609 ! interferon-gamma production relationship: capable_of GO:0032633 ! interleukin-4 production relationship: develops_from CL:0000923 ! CD4-positive type I NK T cell relationship: has_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: has_plasma_membrane_part PR:000001343 ! CD69 molecule [Term] id: CL:0000926 name: CD4-positive type I NK T cell secreting interferon-gamma namespace: cell def: "A mature NK T cell that secretes interferon-gamma and enhances type 1 immune responses." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17303398] synonym: "CD4-positive type I NK T cell secreting IFN-gamma" EXACT [] synonym: "CD4-positive type I NK T lymphocyte secreting interferon-gamma" EXACT [] synonym: "CD4-positive type I NK T-cell secreting interferon-gamma" EXACT [] synonym: "CD4-positive type I NK T-lymphocyte secreting interferon-gamma" EXACT [] synonym: "CD4-positive type I NKT cell secreting interferon-gamma" EXACT [] is_a: CL:0000492 ! CD4-positive helper T cell is_a: CL:0000923 ! CD4-positive type I NK T cell intersection_of: CL:0000921 ! type I NK T cell intersection_of: capable_of GO:0002827 ! positive regulation of T-helper 1 type immune response intersection_of: capable_of GO:0032609 ! interferon-gamma production intersection_of: has_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: capable_of GO:0002827 ! positive regulation of T-helper 1 type immune response relationship: capable_of GO:0032609 ! interferon-gamma production relationship: develops_from CL:0000925 ! activated CD4-positive type I NK T cell relationship: has_plasma_membrane_part PR:000001004 ! CD4 molecule [Term] id: CL:0000927 name: CD4-positive type I NK T cell secreting interleukin-4 namespace: cell def: "A mature NK T cell that predominantly secretes type 2 cytokines such as interleukin-4 and interleukin-13 and enhances type 2 immune responses." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm] synonym: "CD4-positive type I NK T cell secreting IL-4" EXACT [] synonym: "CD4-positive type I NK T lymphocyte secreting interleukin-4" EXACT [] synonym: "CD4-positive type I NK T-cell secreting interleukin-4" EXACT [] synonym: "CD4-positive type I NK T-lymphocyte secreting interleukin-4" EXACT [] synonym: "CD4-positive type I NKT cell secreting interleukin-4" EXACT [] is_a: CL:0000492 ! CD4-positive helper T cell is_a: CL:0000923 ! CD4-positive type I NK T cell intersection_of: CL:0000921 ! type I NK T cell intersection_of: capable_of GO:0002830 ! positive regulation of type 2 immune response intersection_of: capable_of GO:0032616 ! interleukin-13 production intersection_of: capable_of GO:0032633 ! interleukin-4 production intersection_of: has_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: capable_of GO:0002830 ! positive regulation of type 2 immune response relationship: capable_of GO:0032616 ! interleukin-13 production relationship: capable_of GO:0032633 ! interleukin-4 production relationship: develops_from CL:0000925 ! activated CD4-positive type I NK T cell relationship: has_plasma_membrane_part PR:000001004 ! CD4 molecule [Term] id: CL:0000928 name: activated CD4-negative, CD8-negative type I NK T cell namespace: cell def: "A type I NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has phenotype CD4-negative, CD8-negative, CD69-positive, and downregulated NK markers." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17303398] synonym: "activated CD4-negative, CD8-negative type I NK T lymphocyte" EXACT [] synonym: "activated CD4-negative, CD8-negative type I NK T-cell" EXACT [] synonym: "activated CD4-negative, CD8-negative type I NK T-lymphocyte" EXACT [] synonym: "activated CD4-negative, CD8-negative type I NKT cell" EXACT [] is_a: CL:0000912 ! helper T cell is_a: CL:0000924 ! CD4-negative, CD8-negative type I NK T cell intersection_of: CL:0000921 ! type I NK T cell intersection_of: capable_of GO:0002369 ! T cell cytokine production intersection_of: has_plasma_membrane_part PR:000001343 ! CD69 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: capable_of GO:0002369 ! T cell cytokine production relationship: develops_from CL:0000924 ! CD4-negative, CD8-negative type I NK T cell relationship: has_plasma_membrane_part PR:000001343 ! CD69 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain [Term] id: CL:0000929 name: CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma namespace: cell def: "A mature NK T cell that secretes interferon-gamma and enhances Th1 immune responses." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17303398] synonym: "CD4-negative, CD8-negative type I NK T cell secreting IFN-gamma" EXACT [] synonym: "CD4-negative, CD8-negative type I NK T lymphocyte secreting interferon-gamma" EXACT [] synonym: "CD4-negative, CD8-negative type I NK T-cell secreting interferon-gamma" EXACT [] synonym: "CD4-negative, CD8-negative type I NK T-lymphocyte secreting interferon-gamma" EXACT [] synonym: "CD4-negative, CD8-negative type I NKT cell secreting interferon-gamma" EXACT [] is_a: CL:0000912 ! helper T cell is_a: CL:0000924 ! CD4-negative, CD8-negative type I NK T cell intersection_of: CL:0000921 ! type I NK T cell intersection_of: capable_of GO:0002827 ! positive regulation of T-helper 1 type immune response intersection_of: capable_of GO:0032609 ! interferon-gamma production intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: capable_of GO:0002827 ! positive regulation of T-helper 1 type immune response relationship: capable_of GO:0032609 ! interferon-gamma production relationship: develops_from CL:0000928 ! activated CD4-negative, CD8-negative type I NK T cell relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain [Term] id: CL:0000930 name: CD4-negative, CD8-negative type I NK T cell secreting interleukin-4 namespace: cell def: "A mature NK T cell that secretes interleukin-4 and enhances Th2 immune responses." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17303398] synonym: "CD4-negative, CD8-negative type I NK T cell secreting IL-4" EXACT [] synonym: "CD4-negative, CD8-negative type I NK T lymphocyte secreting interleukin-4" EXACT [] synonym: "CD4-negative, CD8-negative type I NK T-cell secreting interleukin-4" EXACT [] synonym: "CD4-negative, CD8-negative type I NK T-lymphocyte secreting interleukin-4" EXACT [] synonym: "CD4-negative, CD8-negative type I NKT cell secreting interleukin-4" EXACT [] is_a: CL:0000912 ! helper T cell is_a: CL:0000924 ! CD4-negative, CD8-negative type I NK T cell intersection_of: CL:0000921 ! type I NK T cell intersection_of: capable_of GO:0002830 ! positive regulation of type 2 immune response intersection_of: capable_of GO:0032633 ! interleukin-4 production intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: capable_of GO:0002830 ! positive regulation of type 2 immune response relationship: capable_of GO:0032633 ! interleukin-4 production relationship: develops_from CL:0000928 ! activated CD4-negative, CD8-negative type I NK T cell relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain [Term] id: CL:0000931 name: activated type II NK T cell namespace: cell def: "A type II NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has the phenotype CD69-positive and downregulated NK markers." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17964217] synonym: "activated type II NK T lymphocyte" EXACT [] synonym: "activated type II NK T-cell" EXACT [] synonym: "activated type II NK T-lymphocyte" EXACT [] synonym: "activated type II NKT cell" EXACT [] is_a: CL:0000912 ! helper T cell is_a: CL:0000922 ! type II NK T cell intersection_of: CL:0000922 ! type II NK T cell intersection_of: capable_of GO:0002369 ! T cell cytokine production intersection_of: has_plasma_membrane_part PR:000001343 ! CD69 molecule relationship: capable_of GO:0002369 ! T cell cytokine production relationship: has_plasma_membrane_part PR:000001343 ! CD69 molecule [Term] id: CL:0000932 name: type II NK T cell secreting interferon-gamma namespace: cell def: "A type II NK T cell that has been recently activated, secretes interferon-gamma, and has the phenotype CD69-positive and downregulated NK markers." [GO_REF:0000031, GOC:add, GOC:pam, PMID:17964217] synonym: "type II NK T cell secreting IFN-gamma" EXACT [] synonym: "type II NK T lymphocyte secreting interferon-gamma" EXACT [] synonym: "type II NK T-cell secreting interferon-gamma" EXACT [] synonym: "type II NK T-lymphocyte secreting interferon-gamma" EXACT [] synonym: "type II NKT cell secreting interferon-gamma" EXACT [] is_a: CL:0000912 ! helper T cell is_a: CL:0000922 ! type II NK T cell intersection_of: CL:0000922 ! type II NK T cell intersection_of: capable_of GO:0032609 ! interferon-gamma production intersection_of: has_plasma_membrane_part PR:000001343 ! CD69 molecule relationship: capable_of GO:0032609 ! interferon-gamma production relationship: develops_from CL:0000931 ! activated type II NK T cell relationship: has_plasma_membrane_part PR:000001343 ! CD69 molecule [Term] id: CL:0000933 name: type II NK T cell secreting interleukin-4 namespace: cell def: "A type II NK T cell that has been recently activated, secretes interleukin-4, and has the phenotype CD69-positive and downregulated NK markers." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:17964217] synonym: "type II NK T cell secreting IL-4" EXACT [] synonym: "type II NK T lymphocyte secreting interleukin-4" EXACT [] synonym: "type II NK T-cell secreting interleukin-4" EXACT [] synonym: "type II NK T-lymphocyte secreting interleukin-4" EXACT [] synonym: "type II NKT cell secreting interleukin-4" EXACT [] is_a: CL:0000912 ! helper T cell is_a: CL:0000922 ! type II NK T cell intersection_of: CL:0000922 ! type II NK T cell intersection_of: capable_of GO:0032633 ! interleukin-4 production intersection_of: has_plasma_membrane_part PR:000001343 ! CD69 molecule relationship: capable_of GO:0032633 ! interleukin-4 production relationship: develops_from CL:0000931 ! activated type II NK T cell relationship: has_plasma_membrane_part PR:000001343 ! CD69 molecule [Term] id: CL:0000934 name: CD4-positive, alpha-beta cytotoxic T cell namespace: cell def: "A CD4-positive, alpha-beta T cell that has cytotoxic function." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:18440213] synonym: "CD4-positive, alpha-beta cytotoxic T lymphocyte" EXACT [] synonym: "CD4-positive, alpha-beta cytotoxic T-cell" EXACT [] synonym: "CD4-positive, alpha-beta cytotoxic T-lymphocyte" EXACT [] is_a: CL:0000624 ! CD4-positive, alpha-beta T cell is_a: CL:0000910 ! cytotoxic T cell intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: capable_of GO:0001913 ! T cell mediated cytotoxicity intersection_of: has_completed GO:0030217 ! T cell differentiation relationship: capable_of GO:0001913 ! T cell mediated cytotoxicity relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell relationship: has_completed GO:0030217 ! T cell differentiation [Term] id: CL:0000935 name: CD4-negative, CD8-negative, alpha-beta intraepithelial T cell namespace: cell def: "A CD4-negative, CD8-negative, alpha-beta intraepithelial T cell that is found in the columnar epithelium of the gastrointestinal tract." [GO_REF:0000031, GOC:add, GOC:pam, PMID:11685222] synonym: "CD4-negative, CD8-negative, alpha-beta intraepithelial T lymphocyte" EXACT [] synonym: "CD4-negative, CD8-negative, alpha-beta intraepithelial T-cell" EXACT [] synonym: "CD4-negative, CD8-negative, alpha-beta intraepithelial T-lymphocyte" EXACT [] is_a: CL:0000797 ! alpha-beta intraepithelial T cell intersection_of: CL:0000797 ! alpha-beta intraepithelial T cell intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000025403 ! T-cell surface glycoprotein CD8 alpha chain isoform 1 relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000025403 ! T-cell surface glycoprotein CD8 alpha chain isoform 1 [Term] id: CL:0000936 name: early lymphoid progenitor namespace: cell def: "A lymphoid progenitor cell that is found in bone marrow, gives rise to B cells, T cells, natural killer cells and dendritic cells, and has the phenotype Lin-negative, Kit-positive, Sca-1-positive, FLT3-positive, CD34-positive, CD150 negative, and GlyA-negative." [GO_REF:0000031, GOC:add, GOC:dsd, GOC:pam, GOC:tfm, PMID:19022770] comment: Markers are associated with mouse cells. ELP transcription factors include E2A-positive, Ikaros-positive, EBF-negative, Pax5-negative, PU.1-negative. synonym: "ELP" EXACT [] synonym: "GMLP" RELATED [PMID:18371378] synonym: "LMPP" EXACT [] synonym: "lymphoid-primed multipotent progenitor" EXACT [] is_a: CL:0000837 ! hematopoietic multipotent progenitor cell intersection_of: CL:0000837 ! hematopoietic multipotent progenitor cell intersection_of: capable_of GO:0030098 ! lymphocyte differentiation intersection_of: has_plasma_membrane_part PR:000002001 ! FL cytokine receptor intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: has_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001460 ! glycophorin-A relationship: capable_of GO:0030098 ! lymphocyte differentiation relationship: develops_from CL:0002035 ! Slamf1-negative multipotent progenitor cell relationship: has_plasma_membrane_part PR:000002001 ! FL cytokine receptor relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: has_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001460 ! glycophorin-A [Term] id: CL:0000937 name: pre-natural killer cell namespace: cell def: "Cell committed to natural killer cell lineage that has the phenotype CD122-positive, CD34-positive, and CD117-positive. This cell type lacks expression of natural killer receptor proteins." [GO_REF:0000031, GOC:add, GOC:dsd, GOC:pam, GOC:tfm, PMID:16551251, PMID:17100874] comment: These cells are also reportedly CD7-low, CD10-negative, CD45RA-positive, alpha-4-beta-7 integrin-high. synonym: "pre-NK cell" EXACT [] is_a: CL:0000623 ! natural killer cell intersection_of: CL:0000623 ! natural killer cell intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000001381 ! interleukin-2 receptor subunit beta intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor disjoint_from: CL:0002338 ! CD56-positive, CD161-positive immature natural killer cell disjoint_from: CL:0002344 ! CD56-negative, CD161-positive immature natural killer cell relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000001381 ! interleukin-2 receptor subunit beta relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor [Term] id: CL:0000938 name: CD56-bright cytokine secreting natural killer cell namespace: cell def: "NK cell that has the phenotype CD56-bright, CD16-negative, and CD84-positive with the function to secrete interferon-gamma but is not cytotoxic." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19796267] comment: Markers are associated with human cell types. synonym: "CD56-bright cytokine secreting NK cell" EXACT [] is_a: CL:0000824 ! mature natural killer cell intersection_of: CL:0000824 ! mature natural killer cell intersection_of: capable_of GO:0032609 ! interferon-gamma production intersection_of: has_high_plasma_membrane_amount PR:000001024 ! neural cell adhesion molecule 1 intersection_of: has_plasma_membrane_part PR:000001319 ! SLAM family member 5 intersection_of: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III disjoint_from: CL:0000939 ! cytotoxic CD56-dim natural killer cell relationship: capable_of GO:0032609 ! interferon-gamma production relationship: has_high_plasma_membrane_amount PR:000001024 ! neural cell adhesion molecule 1 relationship: has_plasma_membrane_part PR:000001319 ! SLAM family member 5 relationship: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III [Term] id: CL:0000939 name: cytotoxic CD56-dim natural killer cell namespace: cell def: "A mature natural killer cell that has the phenotype CD56-low and CD16-positive and is capable of cytotoxic function and cytokine production." [GO_REF:0000031, GOC:add, GOC:pam, PMID:19796267] comment: This population is mainly found in human. synonym: "cytotoxic CD56-dim NK cell" EXACT [] is_a: CL:0000824 ! mature natural killer cell intersection_of: CL:0000824 ! mature natural killer cell intersection_of: capable_of GO:0001816 ! cytokine production intersection_of: capable_of GO:0042267 ! natural killer cell mediated cytotoxicity intersection_of: has_low_plasma_membrane_amount PR:000001024 ! neural cell adhesion molecule 1 intersection_of: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0042267 ! natural killer cell mediated cytotoxicity relationship: has_low_plasma_membrane_amount PR:000001024 ! neural cell adhesion molecule 1 relationship: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III [Term] id: CL:0000940 name: mucosal invariant T cell namespace: cell def: "An alpha-beta T cell that is found in the lamina propria of mucosal tissues and is restricted by the MR-1 molecule." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19416870] synonym: "mucosal invariant T lymphocyte" EXACT [] synonym: "mucosal invariant T-cell" EXACT [] synonym: "mucosal invariant T-lymphocyte" EXACT [] is_a: CL:0000791 ! mature alpha-beta T cell is_a: CL:0002127 ! innate effector T cell intersection_of: CL:0000791 ! mature alpha-beta T cell intersection_of: capable_of GO:0002227 ! innate immune response in mucosa intersection_of: capable_of GO:0032394 ! MHC class Ib receptor activity intersection_of: has_completed GO:0030217 ! T cell differentiation relationship: capable_of GO:0002227 ! innate immune response in mucosa relationship: capable_of GO:0032394 ! MHC class Ib receptor activity relationship: has_completed GO:0030217 ! T cell differentiation [Term] id: CL:0000941 name: thymic conventional dendritic cell namespace: cell def: "A dendritic cell arising in thymus that has the phenotype CD11c-positive, CD11b-negative, and CD45RA-negative." [GO_REF:0000031, GOC:add, GOC:pam, PMID:19273629] comment: In the mouse this cell expresses CD8-alpha-alpha. is_a: CL:0000990 ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: has_plasma_membrane_part PR:000001013 ! integrin alpha-X intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: part_of UBERON:0002370 ! thymus relationship: develops_from CL:0000894 ! DN1 thymic pro-T cell relationship: has_plasma_membrane_part PR:000001013 ! integrin alpha-X relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: part_of UBERON:0002370 ! thymus [Term] id: CL:0000942 name: thymic plasmacytoid dendritic cell namespace: cell def: "A plasmacytoid dendritic cell developing in the thymus with phenotype CD11c-negative or low, CD45RA-positive, CD11b-negative, and CD123-positive." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19941119] is_a: CL:0000784 ! plasmacytoid dendritic cell intersection_of: CL:0000784 ! plasmacytoid dendritic cell intersection_of: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: has_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: develops_from CL:0000894 ! DN1 thymic pro-T cell relationship: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: has_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M [Term] id: CL:0000943 name: Be1 Cell namespace: cell def: "A Be cell that facilitates development of T-helper 1 (Th1) phenotype in CD4-positive T cells, and secretes high levels of interleukin-2, tumor necrosis factor-alpha and interferon-gamma." [GO_REF:0000031, GOC:dsd, GOC:msz, GOC:tfm, PMID:11101868, PMID:20224569] comment: Be1 cells are also reportedly capable of secreting IL-6, IL-10, and IL-12. They are also reportedly CD11b-negative and B220-positive. synonym: "B effector 1 cell" EXACT [PMID:11101868, PMID:20224569] synonym: "B effector cell type 1" RELATED [] is_a: CL:0000968 ! Be cell intersection_of: CL:0000968 ! Be cell intersection_of: capable_of GO:0032609 ! interferon-gamma production intersection_of: capable_of GO:0032623 ! interleukin-2 production intersection_of: capable_of GO:0032640 ! tumor necrosis factor production intersection_of: capable_of GO:0045627 ! positive regulation of T-helper 1 cell differentiation relationship: capable_of GO:0032609 ! interferon-gamma production relationship: capable_of GO:0032623 ! interleukin-2 production relationship: capable_of GO:0032640 ! tumor necrosis factor production relationship: capable_of GO:0045627 ! positive regulation of T-helper 1 cell differentiation [Term] id: CL:0000944 name: Be2 cell namespace: cell def: "A Be cell that facilitates development of T-helper 2 (Th2) phenotype T cells, and secretes high levels of interleukin-2, interleukin-10, interleukin-4, and interleukin-6." [GO_REF:0000031, GOC:dsd, GOC:msz, GOC:tfm, PMID:11101868, PMID:20224569] comment: Be2 cells are also reportedly capable of secreting IL-13 and TNF. They are also reportedly CD11b-negative and B220-positive. synonym: "B effector 2 cell" EXACT [PMID:11101868, PMID:20224569] synonym: "B effector cell type 2" RELATED [] is_a: CL:0000968 ! Be cell intersection_of: CL:0000968 ! Be cell intersection_of: capable_of GO:0032613 ! interleukin-10 production intersection_of: capable_of GO:0032623 ! interleukin-2 production intersection_of: capable_of GO:0032633 ! interleukin-4 production intersection_of: capable_of GO:0032635 ! interleukin-6 production intersection_of: capable_of GO:0045630 ! positive regulation of T-helper 2 cell differentiation relationship: capable_of GO:0032613 ! interleukin-10 production relationship: capable_of GO:0032623 ! interleukin-2 production relationship: capable_of GO:0032633 ! interleukin-4 production relationship: capable_of GO:0032635 ! interleukin-6 production relationship: capable_of GO:0045630 ! positive regulation of T-helper 2 cell differentiation [Term] id: CL:0000945 name: lymphocyte of B lineage namespace: cell def: "A lymphocyte of B lineage is a lymphocyte that expresses CD19 on the cell surface. An additional defining characteristic is the commitment to express an immunoglobulin complex." [GO_REF:0000031, GOC:add, GOC:rhs, GOC:tfm, ISBN:0781735149] comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: has_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: develops_from CL:0000826 ! pro-B cell relationship: has_plasma_membrane_part PR:000001002 ! CD19 molecule [Term] id: CL:0000946 name: antibody secreting cell namespace: cell def: "A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0721601464, ISBN:0781735149] is_a: CL:0000945 ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: secretes GO:0042571 ! immunoglobulin complex, circulating relationship: secretes GO:0042571 ! immunoglobulin complex, circulating [Term] id: CL:0000947 name: IgE plasma cell namespace: cell def: "A long lived plasma cell that secretes IgE." [GO_REF:0000031, GOC:msz, ISBN:781735149] is_a: CL:0000974 ! long lived plasma cell intersection_of: CL:0000974 ! long lived plasma cell intersection_of: secretes GO:0071743 ! IgE immunoglobulin complex, circulating relationship: secretes GO:0071743 ! IgE immunoglobulin complex, circulating [Term] id: CL:0000948 name: IgE memory B cell namespace: cell def: "A class switched memory B cell that expresses IgE on the cell surface." [GO_REF:0000031, GOC:rhs, ISBN:0781765196] synonym: "IgE memory B lymphocyte" EXACT [] synonym: "IgE memory B-cell" EXACT [] synonym: "IgE memory B-lymphocyte" EXACT [] synonym: "memory IgE B cell" EXACT [] synonym: "memory IgE B lymphocyte" EXACT [] synonym: "memory IgE B-cell" EXACT [] synonym: "memory IgE B-lymphocyte" EXACT [] is_a: CL:0000972 ! class switched memory B cell intersection_of: CL:0000972 ! class switched memory B cell intersection_of: has_plasma_membrane_part GO:0071742 ! IgE immunoglobulin complex relationship: has_plasma_membrane_part GO:0071742 ! IgE immunoglobulin complex [Term] id: CL:0000949 name: IgD plasmablast namespace: cell def: "A plasmablast that secretes IgD, and which occur in a small proportion of B cells in the adult." [GO_REF:0000031, GOC:msz] is_a: CL:0000980 ! plasmablast intersection_of: CL:0000980 ! plasmablast intersection_of: secretes GO:0071739 ! IgD immunoglobulin complex, circulating relationship: secretes GO:0071739 ! IgD immunoglobulin complex, circulating [Term] id: CL:0000950 name: IgE plasmablast namespace: cell def: "A plasmablast that secretes IgE." [GO_REF:0000031, GOC:msz] is_a: CL:0000980 ! plasmablast intersection_of: CL:0000980 ! plasmablast intersection_of: secretes GO:0071743 ! IgE immunoglobulin complex, circulating relationship: secretes GO:0071743 ! IgE immunoglobulin complex, circulating [Term] id: CL:0000951 name: IgE short lived plasma cell namespace: cell def: "A short lived plasma cell that secretes IgE." [GO_REF:0000031, GOC:msz, ISBN:781735149] is_a: CL:0000975 ! short lived plasma cell intersection_of: CL:0000975 ! short lived plasma cell intersection_of: secretes GO:0071743 ! IgE immunoglobulin complex, circulating relationship: secretes GO:0071743 ! IgE immunoglobulin complex, circulating [Term] id: CL:0000952 name: preBCR-positive large pre-B-II cell namespace: cell def: "An preBRC-positive large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-positive, composed of surrogate light chain protein (SL), which is composed of VpreB , Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu) on the cell surface." [GO_REF:0000031, GOC:rhs, GOC:tfm, PMID:9785673] is_a: CL:0000957 ! large pre-B-II cell intersection_of: CL:0000957 ! large pre-B-II cell intersection_of: has_not_completed GO:0071708 ! immunoglobulin light chain V-J recombination intersection_of: has_plasma_membrane_part GO:0035369 ! pre-B cell receptor complex intersection_of: has_plasma_membrane_part PR:000001858 ! immunoglobulin iota chain intersection_of: has_plasma_membrane_part PR:000001859 ! immunoglobulin lambda-like polypeptide 1 relationship: has_not_completed GO:0071708 ! immunoglobulin light chain V-J recombination relationship: has_plasma_membrane_part GO:0035369 ! pre-B cell receptor complex relationship: has_plasma_membrane_part PR:000001858 ! immunoglobulin iota chain relationship: has_plasma_membrane_part PR:000001859 ! immunoglobulin lambda-like polypeptide 1 [Term] id: CL:0000953 name: preBCR-negative large pre-B-II cell namespace: cell def: "A pre-BCR-negative large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-negative, composed of surrogate light chain protein (SL), which is composed of VpreB and Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu), on the cell surface, and lack a DNA rearrangement of immunoglobulin light chain genes." [GO_REF:0000031, GOC:rhs, GOC:tfm, PMID:9785673] is_a: CL:0000957 ! large pre-B-II cell intersection_of: CL:0000957 ! large pre-B-II cell intersection_of: has_not_completed GO:0071708 ! immunoglobulin light chain V-J recombination intersection_of: lacks_plasma_membrane_part GO:0035369 ! pre-B cell receptor complex intersection_of: lacks_plasma_membrane_part PR:000001858 ! immunoglobulin iota chain intersection_of: lacks_plasma_membrane_part PR:000001859 ! immunoglobulin lambda-like polypeptide 1 relationship: has_not_completed GO:0071708 ! immunoglobulin light chain V-J recombination relationship: lacks_plasma_membrane_part GO:0035369 ! pre-B cell receptor complex relationship: lacks_plasma_membrane_part PR:000001858 ! immunoglobulin iota chain relationship: lacks_plasma_membrane_part PR:000001859 ! immunoglobulin lambda-like polypeptide 1 [Term] id: CL:0000954 name: small pre-B-II cell namespace: cell def: "A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes." [GO_REF:0000031, GOC:dsd, GOC:rhs, GOC:tfm, PMID:16551251, PMID:18432934, PMID:9785673] comment: Small pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-negative, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. synonym: "small pre-BII cell" EXACT [] is_a: CL:0000955 ! pre-B-II cell intersection_of: CL:0000955 ! pre-B-II cell intersection_of: has_part PR:000003457 ! V(D)J recombination-activating protein 1 intersection_of: has_part PR:000003460 ! V(D)J recombination-activating protein 2 intersection_of: lacks_plasma_membrane_part GO:0019815 ! B cell receptor complex intersection_of: lacks_plasma_membrane_part GO:0035369 ! pre-B cell receptor complex intersection_of: participates_in GO:0071708 ! immunoglobulin light chain V-J recombination relationship: has_part PR:000003457 ! V(D)J recombination-activating protein 1 relationship: has_part PR:000003460 ! V(D)J recombination-activating protein 2 relationship: lacks_plasma_membrane_part GO:0019815 ! B cell receptor complex relationship: lacks_plasma_membrane_part GO:0035369 ! pre-B cell receptor complex relationship: participates_in GO:0071708 ! immunoglobulin light chain V-J recombination [Term] id: CL:0000955 name: pre-B-II cell namespace: cell def: "A pre-B-II cell is a precursor B cell that expresses immunoglobulin mu heavy chain (IgHmu+), and lack expression of CD34, TdT, immunoglobulin kappa light chain and immunoglobulin lambda light chain." [GO_REF:0000031, GOC:dsd, GOC:rhs, GOC:tfm, PMID:9785673] comment: pre-B-II cell are also reportedly CD19-positive, CD22-positive, CD38-positive, CD45-positive, and CD48-positive. synonym: "pre-B-lymphocyte" EXACT [] synonym: "pre-BII cell" EXACT [] xref: BTO:0001133 is_a: CL:0000817 ! precursor B cell intersection_of: CL:0000817 ! precursor B cell intersection_of: has_completed GO:0071707 ! immunoglobulin heavy chain V-D-J recombination intersection_of: lacks_part PR:000006611 ! DNA nucleotidylexotransferase intersection_of: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule disjoint_from: CL:0000956 ! pre-B-I cell relationship: develops_from CL:0000826 ! pro-B cell relationship: has_completed GO:0071707 ! immunoglobulin heavy chain V-D-J recombination relationship: lacks_part PR:000006611 ! DNA nucleotidylexotransferase relationship: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule [Term] id: CL:0000956 name: pre-B-I cell namespace: cell def: "A pre-B-I cell is a precursor B cell that expresses CD34 and surrogate immunoglobulin light chain (VpreB , Lambda 5 (mouse)/14.1 (human)) on the cell surface, and TdT, Rag1,and Rag2 intracellularly. Cell type carries a D-JH DNA rearrangement, and lacks expression of immunglobulin heavy chain protein." [GO_REF:0000031, GOC:dsd, GOC:rhs, GOC:tfm, PMID:16551251, PMID:18432934, PMID:20839338, PMID:9785673] comment: Human pre-B-I cells are reportedly CD10-positive, CD19-positive, CD22-positive, CD38-positive, CD45-low, CD79a-positive, CD127-negative, pre-BCR-negative, IgM-negative, IgD-negative, and Tdt-positive. Transcription factors expressed: Pax5-positive. synonym: "pre-BI cell" EXACT [] synonym: "pro-B cell (Philadelphia nomenclature)" RELATED [PMID:11244048] is_a: CL:0000817 ! precursor B cell intersection_of: CL:0000817 ! precursor B cell intersection_of: has_part PR:000003457 ! V(D)J recombination-activating protein 1 intersection_of: has_part PR:000003460 ! V(D)J recombination-activating protein 2 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000001858 ! immunoglobulin iota chain intersection_of: has_plasma_membrane_part PR:000001859 ! immunoglobulin lambda-like polypeptide 1 intersection_of: participates_in GO:0071707 ! immunoglobulin heavy chain V-D-J recombination relationship: develops_from CL:0000826 ! pro-B cell relationship: has_part PR:000003457 ! V(D)J recombination-activating protein 1 relationship: has_part PR:000003460 ! V(D)J recombination-activating protein 2 relationship: has_part PR:000006611 ! DNA nucleotidylexotransferase relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000001858 ! immunoglobulin iota chain relationship: has_plasma_membrane_part PR:000001859 ! immunoglobulin lambda-like polypeptide 1 relationship: participates_in GO:0071707 ! immunoglobulin heavy chain V-D-J recombination [Term] id: CL:0000957 name: large pre-B-II cell namespace: cell def: "A large pre-B-II cell is a pre-B-II cell that is proliferating and is Rag1-negative and Rag2-negative." [GO_REF:0000031, GOC:dsd, GOC:rhs, PMID:16551251, PMID:18432934, PMID:9785673] comment: Large pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-positive, pre-BCR-positive, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. synonym: "large pre-B cell" BROAD [PMID:11244048] synonym: "large pre-BII cell" EXACT [] is_a: CL:0000955 ! pre-B-II cell intersection_of: CL:0000955 ! pre-B-II cell intersection_of: lacks_part PR:000003457 ! V(D)J recombination-activating protein 1 intersection_of: lacks_part PR:000003460 ! V(D)J recombination-activating protein 2 intersection_of: participates_in GO:0046651 ! lymphocyte proliferation relationship: lacks_part PR:000003457 ! V(D)J recombination-activating protein 1 relationship: lacks_part PR:000003460 ! V(D)J recombination-activating protein 2 relationship: participates_in GO:0046651 ! lymphocyte proliferation [Term] id: CL:0000958 name: T1 B cell namespace: cell def: "A transitional stage B cell that migrates from the bone marrow into the peripheral circulation, and finally to the spleen. This cell type has the phenotype surface IgM-positive, surface IgD-negative, CD21-negative, CD23-negative, and CD62L-negative, and CD93-positive. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-negative." [GO_REF:0000031, GOC:dsd, GOC:msz, GOC:tfm, PMCID:PMC2193793, PMID:12810111] comment: T1 B cells are also reportedly CD10-negative/positive??, CD20-positive, CD24-positive, CD38-positive, CD48-positive, CD84-positive, CD150-positive, CD244-negative, and CD352-positive. synonym: "T1 B lymphocyte" EXACT [] synonym: "T1 B-cell" EXACT [] synonym: "T1 B-lymphocyte" EXACT [] synonym: "transitional stage 1 B cell" EXACT [] is_a: CL:0000818 ! transitional stage B cell intersection_of: CL:0000818 ! transitional stage B cell intersection_of: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor intersection_of: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex intersection_of: lacks_plasma_membrane_part PR:000001318 ! L-selectin intersection_of: lacks_plasma_membrane_part PR:000001338 ! complement receptor type 2 intersection_of: lacks_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor relationship: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor relationship: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: lacks_plasma_membrane_part PR:000001318 ! L-selectin relationship: lacks_plasma_membrane_part PR:000001338 ! complement receptor type 2 relationship: lacks_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor [Term] id: CL:0000959 name: T2 B cell namespace: cell def: "A transitional stage B cell that has the phenotype surface IgM-positive, surface IgD-postive, CD21-positive, CD23-positive, CD62L-negative, CD93-positive and is located in the splenic B follicles. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-positive." [GO_REF:0000031, GOC:dsd, GOC:msz, GOC:tfm, PMCID:PMC2193793, PMID:12810111] comment: T2 B cells are also reportedly CD20-positive, CD24-positive, CD38-positive, CD48-positive, CD84-positive, CD150-positive, CD244-negative, and CD352-positive. synonym: "T2 B lymphocyte" EXACT [] synonym: "T2 B-cell" EXACT [] synonym: "T2 B-lymphocyte" EXACT [] synonym: "transitional stage 2 B cell" EXACT [] is_a: CL:0000818 ! transitional stage B cell intersection_of: CL:0000818 ! transitional stage B cell intersection_of: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex intersection_of: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex intersection_of: has_plasma_membrane_part PR:000001338 ! complement receptor type 2 intersection_of: has_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor intersection_of: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor intersection_of: lacks_plasma_membrane_part PR:000001318 ! L-selectin relationship: develops_from CL:0000958 ! T1 B cell relationship: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex relationship: has_plasma_membrane_part PR:000001338 ! complement receptor type 2 relationship: has_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor relationship: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor relationship: lacks_plasma_membrane_part PR:000001318 ! L-selectin [Term] id: CL:0000960 name: T3 B cell namespace: cell def: "A transitional stage B cell that expresses surface IgM and IgD, and CD62L. This cell type appears to be an anergic B cell that does not proliferate upon BCR signaling, is found in the spleen and lymph nodes, and has the phenotype surface IgM-positive, surface IgD-positive, CD21-positive, CD23-positive, CD62L-positive, and CD93-positive. This cell type has also been described as IgM-low, CD19-positive, B220-positive, AA4-positive, and CD23-positive (i.e. this cell-type is distinguished from T2 cells by surface expression of IgM)." [GO_REF:0000031, GOC:msz, GOC:tfm, http://www.immgen.org/index_content.html, PMID:12810111, PMID:17174121] synonym: "An1 B cell" EXACT [PMID:17174121] synonym: "T3 B lymphocyte" EXACT [] synonym: "T3 B-cell" EXACT [] synonym: "T3 B-lymphocyte" EXACT [] synonym: "transitional stage 3 B cell" EXACT [] is_a: CL:0000818 ! transitional stage B cell intersection_of: CL:0000818 ! transitional stage B cell intersection_of: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex intersection_of: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex intersection_of: has_plasma_membrane_part PR:000001318 ! L-selectin intersection_of: has_plasma_membrane_part PR:000001338 ! complement receptor type 2 intersection_of: has_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor intersection_of: participates_in GO:0002515 ! B cell anergy relationship: develops_from CL:0000959 ! T2 B cell relationship: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex relationship: has_plasma_membrane_part PR:000001318 ! L-selectin relationship: has_plasma_membrane_part PR:000001338 ! complement receptor type 2 relationship: has_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor relationship: participates_in GO:0002515 ! B cell anergy [Term] id: CL:0000961 name: Bm1 B cell namespace: cell def: "A follicular B cell that is IgD-positive, CD23-negative, and CD38-negative. This naive cell type is activated in the extrafollicular areas through interaction with interdigitating dendritic cells and antigen-specific CD4-positive T cells." [GO_REF:0000031, GOC:dsd, GOC:msz, PMID:17992590, PMID:18432934, PMID:8006591] comment: These cells are also reportedly CD10-negative, CD39-positive, CD44-positive, CD71-negative, CD77-negative, IgM-positive, IgG-negative, IgA-negative, and IgE-negative. synonym: "Bm1 B lymphocyte" EXACT [] synonym: "Bm1 B-cell" EXACT [] synonym: "Bm1 B-lymphocyte" EXACT [] is_a: CL:0000843 ! follicular B cell is_a: CL:0002056 ! Fraction F mature B cell intersection_of: CL:0000843 ! follicular B cell intersection_of: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex intersection_of: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: lacks_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor relationship: develops_from CL:0000818 ! transitional stage B cell relationship: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: lacks_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor [Term] id: CL:0000962 name: Bm2 B cell namespace: cell def: "A follicular B cell that is IgD-positive and CD23-positive and CD38-positive. This naive cell type is activated in the extrafollicular areas via interaction with dendritic cells and antigen specific T cells." [GO_REF:0000031, GOC:dsd, GOC:msz, PMID:17992590, PMID:18432934, PMID:8006591] comment: These cells are also CD10-negative, CD39-positive, CD44-positive, CD71-negative, CD77-negative, IgM-positive, IgG-negative, IgA-negative, and IgE-negative. synonym: "Bm2 B lymphocyte" EXACT [] synonym: "Bm2 B-cell" EXACT [] synonym: "Bm2 B-lymphocyte" EXACT [] is_a: CL:0000843 ! follicular B cell intersection_of: CL:0000843 ! follicular B cell intersection_of: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: has_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor relationship: develops_from CL:0000961 ! Bm1 B cell relationship: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: has_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor [Term] id: CL:0000963 name: Bm3-delta B cell namespace: cell def: "A germinal center B cell that develops from a Bm3 B cell. This cell has the phenotype IgM-negative, IgD-positive, and CD38-positive." [GO_REF:0000031, GOC:add, GOC:msz, GOC:tfm, PMID:9280752] synonym: "Bm3-delta B lymphocyte" EXACT [] synonym: "Bm3-delta B-cell" EXACT [] synonym: "Bm3-delta B-lymphocyte" EXACT [] is_a: CL:0000844 ! germinal center B cell intersection_of: CL:0000844 ! germinal center B cell intersection_of: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: lacks_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex relationship: develops_from CL:0000965 ! Bm3 B cell relationship: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: lacks_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex [Term] id: CL:0000964 name: Bm2' B cell namespace: cell def: "A germinal center B cell that founds a germinal center, and has the phenotype IgD-positive, CD38-positive, and CD23-negative." [GO_REF:0000031, GOC:dsd, GOC:msz, GOC:tfm, PMID:17992590, PMID:18432934, PMID:8006591] comment: Bm2' B cells are also reportedly CD10-positive, CD39-negative, CD44-negative, CD71-positive, CD77-negative, IgM-positive, IgG-negative, IgA-negative, and IgE-negative. synonym: "Bm2' B lymphocyte" EXACT [] synonym: "Bm2' B-cell" EXACT [] synonym: "Bm2' B-lymphocyte" EXACT [] synonym: "Bm2-prime B cell" EXACT [] synonym: "Bm2-prime B lymphocyte " EXACT [] synonym: "Bm2-prime B-cell " EXACT [] synonym: "Bm2-prime B-lymphocyte " EXACT [] synonym: "germinal center founder cell" RELATED [] is_a: CL:0000844 ! germinal center B cell intersection_of: CL:0000844 ! germinal center B cell intersection_of: capable_of GO:0002634 ! regulation of germinal center formation intersection_of: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: lacks_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor relationship: capable_of GO:0002634 ! regulation of germinal center formation relationship: develops_from CL:0000962 ! Bm2 B cell relationship: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: lacks_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor [Term] id: CL:0000965 name: Bm3 B cell namespace: cell def: "A germinal center B cell that is rapidly dividing and has the phenotype IgD-negative, CD38-positive, and CD77-positive. Somatic hypermutation of the immunoglobulin V gene region can occur during proliferation of this cell type." [GO_REF:0000031, GOC:dsd, GOC:msz, PMID:18432934, PMID:8006591] comment: Bm3 B cells are also reportedly CD10-positive, CD23-negative, CD39-negative, CD44-negative, CD71-positive, and CD77-positive. synonym: "Bm3 B lymphocyte" EXACT [] synonym: "Bm3 B-cell" EXACT [] synonym: "Bm3 B-lymphocyte" EXACT [] synonym: "centroblast" RELATED [PMID:8006591] is_a: CL:0000844 ! germinal center B cell intersection_of: CL:0000844 ! germinal center B cell intersection_of: capable_of GO:0016446 ! somatic hypermutation of immunoglobulin genes intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: has_plasma_membrane_part PR:000003516 ! lactosylceramide 4-alpha-galactosyltransferase intersection_of: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: capable_of GO:0016446 ! somatic hypermutation of immunoglobulin genes relationship: develops_from CL:0000964 ! Bm2' B cell relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: has_plasma_membrane_part PR:000003516 ! lactosylceramide 4-alpha-galactosyltransferase relationship: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex [Term] id: CL:0000966 name: Bm4 B cell namespace: cell def: "A germinal center B cell that has the phenotype CD77-negative, IgD-negative, and CD38-positive. These cells have undergone somatic mutation of the B cell receptor." [GO_REF:0000031, GOC:dsd, GOC:msz, PMID:18432934, PMID:8006591] comment: Bm4 B cells are also reportedly CD10-positive, CD23-negative, CD39-negative, CD44-positive, and CD71-positive. synonym: "Bm4 B lymphocyte" EXACT [] synonym: "Bm4 B-cell" EXACT [] synonym: "Bm4 B-lymphocyte" EXACT [] synonym: "centrocyte" RELATED [PMID:17992590] is_a: CL:0000844 ! germinal center B cell intersection_of: CL:0000844 ! germinal center B cell intersection_of: has_completed GO:0016446 ! somatic hypermutation of immunoglobulin genes intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex intersection_of: lacks_plasma_membrane_part PR:000003516 ! lactosylceramide 4-alpha-galactosyltransferase relationship: develops_from CL:0000963 ! Bm3-delta B cell relationship: has_completed GO:0016446 ! somatic hypermutation of immunoglobulin genes relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: lacks_plasma_membrane_part PR:000003516 ! lactosylceramide 4-alpha-galactosyltransferase [Term] id: CL:0000967 name: Bm5 B cell namespace: cell def: "A memory B cell arising in the germinal center that is IgD-negative and has undergone somatic mutation of the variable region of the immunoglobulin heavy and light chain genes." [GO_REF:0000031, GOC:dsd, GOC:msz, GOC:tfm, PMID:18432934, PMID:8006591] comment: Bm5 B cells are also reportedly CD10-positive, CD23-negative, CD38-negative, CD39-positive, CD44-positive, CD71-positive, and CD77-negative. synonym: "Bm5 B lymphocyte" EXACT [] synonym: "Bm5 B-cell" EXACT [] synonym: "Bm5 B-lymphocyte" EXACT [] is_a: CL:0000787 ! memory B cell intersection_of: CL:0000787 ! memory B cell intersection_of: has_completed GO:0002314 ! germinal center B cell differentiation intersection_of: has_completed GO:0016446 ! somatic hypermutation of immunoglobulin genes intersection_of: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: develops_from CL:0000966 ! Bm4 B cell relationship: has_completed GO:0002314 ! germinal center B cell differentiation relationship: has_completed GO:0016446 ! somatic hypermutation of immunoglobulin genes relationship: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex [Term] id: CL:0000968 name: Be cell namespace: cell def: "A mature B cell that produces cytokines that can influence CD4 T cell differentiation." [GO_REF:0000031, GOC:msz, GOC:tfm, PMID:11101868, PMID:20224569] synonym: "B effector cell" EXACT [] synonym: "effector B cell" EXACT [] synonym: "effector B lymphocyte" EXACT [] synonym: "effector B-cell" EXACT [] synonym: "effector B-lymphocyte" EXACT [] is_a: CL:0000785 ! mature B cell intersection_of: CL:0000785 ! mature B cell intersection_of: capable_of GO:0001816 ! cytokine production intersection_of: capable_of GO:0043370 ! regulation of CD4-positive, alpha-beta T cell differentiation relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0043370 ! regulation of CD4-positive, alpha-beta T cell differentiation [Term] id: CL:0000969 name: regulatory B cell namespace: cell def: "A mature B cell that has the phenotype CD1d-positive and expresses interleukin-10. This cell type has been associated with suppression of chronic inflammatory responses and T cell responses." [GO_REF:0000031, GOC:dsd, GOC:msz, GOC:tfm, MESH:D060151, PMID:11869683, PMID:18482568, PMID:20224569, PMID:20809522] comment: Regulatory B cells reportedly represent 1-2% of the spleen and 7-8% of the peritoneal B220-positive cells in mice. They are also found in the bone marrow, lymph node, and blood of mice. These cells are also reportedly capable of secreting IL-10 and are reportedly CD5-positive, CD21-positive, CD24-positive, CD93-negative, B220-positive, IgM-positive, and IgD-positive. synonym: "B(reg)" EXACT [] synonym: "B10 cell" EXACT [] synonym: "Breg" EXACT [] synonym: "regulatory B lymphocyte" EXACT [] synonym: "regulatory B-cell" EXACT [] synonym: "regulatory B-lymphocyte" EXACT [] is_a: CL:0000785 ! mature B cell intersection_of: CL:0000785 ! mature B cell intersection_of: capable_of GO:0032613 ! interleukin-10 production intersection_of: capable_of GO:0050777 ! negative regulation of immune response intersection_of: has_plasma_membrane_part PR:000002028 ! T-cell surface glycoprotein CD1d relationship: capable_of GO:0032613 ! interleukin-10 production relationship: capable_of GO:0050777 ! negative regulation of immune response relationship: has_plasma_membrane_part PR:000002028 ! T-cell surface glycoprotein CD1d [Term] id: CL:0000970 name: unswitched memory B cell namespace: cell def: "An unswitched memory B cell is a memory B cell that has the phenotype IgM-positive and/or IgD-positive, CD27-positive, CD138-negative, IgG-negative, IgE-negative, and IgA-negative." [GO_REF:0000031, GOC:dsd, GOC:rhs, ISBN:0781765196, PMID:20933013] comment: Unswitched memory B cells are also reportedly CD48-positive, CD84-positive, CD229-positive, and CD352-positive. synonym: "unswitched memory B lymphocyte" EXACT [] synonym: "unswitched memory B-cell" EXACT [] synonym: "unswitched memory B-lymphocyte" EXACT [] is_a: CL:0000787 ! memory B cell intersection_of: CL:0000787 ! memory B cell intersection_of: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex intersection_of: has_plasma_membrane_part PR:000001963 ! CD27 molecule intersection_of: lacks_plasma_membrane_part GO:0071735 ! IgG immunoglobulin complex intersection_of: lacks_plasma_membrane_part GO:0071742 ! IgE immunoglobulin complex intersection_of: lacks_plasma_membrane_part GO:0071745 ! IgA immunoglobulin complex intersection_of: lacks_plasma_membrane_part PR:000001935 ! syndecan-1 relationship: develops_from CL:0000980 ! plasmablast relationship: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex relationship: has_plasma_membrane_part PR:000001963 ! CD27 molecule relationship: lacks_plasma_membrane_part GO:0071735 ! IgG immunoglobulin complex relationship: lacks_plasma_membrane_part GO:0071742 ! IgE immunoglobulin complex relationship: lacks_plasma_membrane_part GO:0071745 ! IgA immunoglobulin complex relationship: lacks_plasma_membrane_part PR:000001935 ! syndecan-1 [Term] id: CL:0000971 name: IgM memory B cell namespace: cell def: "An IgM memory B cell is an unswitched memory B cell with the phenotype IgM-positive and IgD-negative." [GO_REF:0000031, GOC:dsd, GOC:rhs, ISBN:0781765196, PMID:19447676] comment: IgM memory B cells are also reportedly CD1c-positive, CD95-positive, CD80-positive, CD84-positive, CD86-positive, CD150-negative, CD229-positive, CD289-positive, and CD290-positive. Transcription factors: Notch2-positive, PAX5-positive, SpiB-positive, Ets1-positive, and OBF1-positive. synonym: "IgM memory B lymphocyte" EXACT [] synonym: "IgM memory B-cell" EXACT [] synonym: "IgM memory B-lymphocyte" EXACT [] synonym: "memory IgM B cell" EXACT [] synonym: "memory IgM B lymphocyte" EXACT [] synonym: "memory IgM B-cell" EXACT [] synonym: "memory IgM B-lymphocyte" EXACT [] is_a: CL:0000970 ! unswitched memory B cell intersection_of: CL:0000970 ! unswitched memory B cell intersection_of: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex [Term] id: CL:0000972 name: class switched memory B cell namespace: cell def: "A class switched memory B cell is a memory B cell that has undergone Ig class switching and therefore is IgM-negative on the cell surface. These cells are usually CD27-positive and have either IgG, IgE, or IgA on the cell surface." [GO_REF:0000031, GOC:dsd, GOC:rhs, ISBN:0781765196, PMID:20933013] comment: Class switched memory B cells are also reportedly CD48-positive, CD229-positive, and CD352-positive. synonym: "class switched memory B lymphocyte" EXACT [] synonym: "class switched memory B-cell" EXACT [] synonym: "class switched memory B-lymphocyte" EXACT [] is_a: CL:0000787 ! memory B cell intersection_of: CL:0000787 ! memory B cell intersection_of: has_completed GO:0045190 ! isotype switching intersection_of: has_plasma_membrane_part PR:000001963 ! CD27 molecule intersection_of: lacks_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex relationship: develops_from CL:0000970 ! unswitched memory B cell relationship: has_completed GO:0045190 ! isotype switching relationship: has_plasma_membrane_part PR:000001963 ! CD27 molecule relationship: lacks_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex [Term] id: CL:0000973 name: IgA memory B cell namespace: cell def: "A class switched memory B cell that expresses IgA." [GO_REF:0000031, GOC:dsd, GOC:msz, ISBN:0781765196] comment: IgA memory B cell are also reportedly RORalpha-positive. synonym: "IgA memory B lymphocyte" EXACT [] synonym: "IgA memory B-cell" EXACT [] synonym: "IgA memory B-lymphocyte" EXACT [] synonym: "memory IgA B cell" EXACT [] synonym: "memory IgA B lymphocyte" EXACT [] synonym: "memory IgA B-cell" EXACT [] synonym: "memory IgA B-lymphocyte" EXACT [] is_a: CL:0000972 ! class switched memory B cell intersection_of: CL:0000972 ! class switched memory B cell intersection_of: has_plasma_membrane_part GO:0071745 ! IgA immunoglobulin complex relationship: has_plasma_membrane_part GO:0071745 ! IgA immunoglobulin complex [Term] id: CL:0000974 name: long lived plasma cell namespace: cell def: "A fully differentiated plasma cell that lives for years, as opposed to months, secretes immunoglobulin, and has the phenotype weakly CD19-positive, CD20-negative, CD38-negative, strongly CD138-positive, MHC Class II-negative, surface immunoglobulin-negative, IgD-negative, and strongly CXCR4-positive. The majority of these cells of this type reside in the bone marrow." [GO_REF:0000031, GOC:msz, GOC:tfm, ISBN:9780781765190, PMID:16014527] is_a: CL:0000786 ! plasma cell intersection_of: CL:0000786 ! plasma cell intersection_of: has_high_plasma_membrane_amount PR:000001208 ! C-X-C chemokine receptor type 4 intersection_of: has_high_plasma_membrane_amount PR:000001935 ! syndecan-1 intersection_of: has_low_plasma_membrane_amount PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part GO:0019814 ! immunoglobulin complex intersection_of: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex intersection_of: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: develops_from CL:0000975 ! short lived plasma cell relationship: has_high_plasma_membrane_amount PR:000001208 ! C-X-C chemokine receptor type 4 relationship: has_high_plasma_membrane_amount PR:000001935 ! syndecan-1 relationship: has_low_plasma_membrane_amount PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part GO:0019814 ! immunoglobulin complex relationship: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 [Term] id: CL:0000975 name: short lived plasma cell namespace: cell def: "A fully differentiated plasma cell that lives for months." [GO_REF:0000031, GOC:msz, PMID:16014527] is_a: CL:0000786 ! plasma cell intersection_of: CL:0000786 ! plasma cell intersection_of: has_quality PATO:0001604 ! decreased life span relationship: develops_from CL:0000980 ! plasmablast relationship: has_quality PATO:0001604 ! decreased life span [Term] id: CL:0000976 name: IgA short lived plasma cell namespace: cell def: "A short lived plasma cell that secretes IgA. These cells may be found in the bone marrow as well as in the mucosal immune system." [GO_REF:0000031, GOC:msz, ISBN:781735149] is_a: CL:0000975 ! short lived plasma cell intersection_of: CL:0000975 ! short lived plasma cell intersection_of: secretes GO:0071746 ! IgA immunoglobulin complex, circulating relationship: secretes GO:0071746 ! IgA immunoglobulin complex, circulating [Term] id: CL:0000977 name: IgG short lived plasma cell namespace: cell def: "A short lived plasma cell that secretes IgG." [GO_REF:0000031, GOC:msz, ISBN:781735149] is_a: CL:0000975 ! short lived plasma cell intersection_of: CL:0000975 ! short lived plasma cell intersection_of: secretes GO:0071736 ! IgG immunoglobulin complex, circulating relationship: secretes GO:0071736 ! IgG immunoglobulin complex, circulating [Term] id: CL:0000978 name: IgM short lived plasma cell namespace: cell def: "A short lived plasma cell that secretes IgM." [GO_REF:0000031, GOC:msz, ISBN:781735149] is_a: CL:0000975 ! short lived plasma cell intersection_of: CL:0000975 ! short lived plasma cell intersection_of: secretes GO:0071754 ! IgM immunoglobulin complex, circulating relationship: secretes GO:0071754 ! IgM immunoglobulin complex, circulating [Term] id: CL:0000979 name: IgG memory B cell namespace: cell def: "An IgG memory B cell is a class switched memory B cell that is class switched and expresses IgG on the cell surface." [GO_REF:0000031, GOC:rhs, ISBN:0781765196] synonym: "IgG memory B lymphocyte" EXACT [] synonym: "IgG memory B-cell" EXACT [] synonym: "IgG memory B-lymphocyte" EXACT [] synonym: "memory IgG B cell" EXACT [] synonym: "memory IgG B lymphocyte" EXACT [] synonym: "memory IgG B-cell" EXACT [] synonym: "memory IgG B-lymphocyte" EXACT [] is_a: CL:0000972 ! class switched memory B cell intersection_of: CL:0000972 ! class switched memory B cell intersection_of: has_plasma_membrane_part GO:0071735 ! IgG immunoglobulin complex relationship: has_plasma_membrane_part GO:0071735 ! IgG immunoglobulin complex [Term] id: CL:0000980 name: plasmablast namespace: cell def: "An activated mature (naive or memory) B cell that is secreting immunoglobulin, typified by being CD27-positive, CD38-positive, CD138-negative." [GO_REF:0000031, GOC:dsd, GOC:msz, GOC:tfm, PMCID:PMC2673126] comment: Plasmablasts are also reportedly CD48-positive, CD63-positive, CD229-positive, CD270-positive, CD319-positive, CD352-positive, CD361-positive, and IgD-negative. xref: FMA:84371 is_a: CL:0000785 ! mature B cell is_a: CL:0000946 ! antibody secreting cell intersection_of: CL:0000785 ! mature B cell intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: has_plasma_membrane_part PR:000001963 ! CD27 molecule intersection_of: lacks_plasma_membrane_part PR:000001935 ! syndecan-1 intersection_of: secretes GO:0042571 ! immunoglobulin complex, circulating relationship: develops_from CL:0000785 ! mature B cell relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: has_plasma_membrane_part PR:000001963 ! CD27 molecule relationship: lacks_plasma_membrane_part PR:000001935 ! syndecan-1 relationship: secretes GO:0042571 ! immunoglobulin complex, circulating [Term] id: CL:0000981 name: double negative memory B cell namespace: cell def: "A memory B cell with the phenotype IgD-negative and CD27-negative." [GO_REF:0000031, GOC:msz, GOC:tfm] synonym: "dn memory B cell" EXACT [] synonym: "dn memory B lymphocyte" EXACT [] synonym: "dn memory B-cell" EXACT [] synonym: "dn memory B-lymphocyte" EXACT [] synonym: "double negative memory B lymphocyte" EXACT [] synonym: "double negative memory B-cell" EXACT [] synonym: "double negative memory B-lymphocyte" EXACT [] is_a: CL:0000787 ! memory B cell intersection_of: CL:0000787 ! memory B cell intersection_of: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex intersection_of: lacks_plasma_membrane_part PR:000001963 ! CD27 molecule relationship: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: lacks_plasma_membrane_part PR:000001963 ! CD27 molecule [Term] id: CL:0000982 name: IgG plasmablast namespace: cell def: "A plasmablast that secretes IgG." [GO_REF:0000031, GOC:msz] is_a: CL:0000980 ! plasmablast intersection_of: CL:0000980 ! plasmablast intersection_of: secretes GO:0071736 ! IgG immunoglobulin complex, circulating relationship: secretes GO:0071736 ! IgG immunoglobulin complex, circulating [Term] id: CL:0000983 name: IgM plasmablast namespace: cell def: "A plasmablast that secretes IgM." [GO_REF:0000031, GOC:msz] is_a: CL:0000980 ! plasmablast intersection_of: CL:0000980 ! plasmablast intersection_of: secretes GO:0071754 ! IgM immunoglobulin complex, circulating relationship: secretes GO:0071754 ! IgM immunoglobulin complex, circulating [Term] id: CL:0000984 name: IgA plasmablast namespace: cell def: "A plasmablast that secretes IgA." [GO_REF:0000031, GOC:msz] is_a: CL:0000980 ! plasmablast intersection_of: CL:0000980 ! plasmablast intersection_of: secretes GO:0071746 ! IgA immunoglobulin complex, circulating relationship: secretes GO:0071746 ! IgA immunoglobulin complex, circulating [Term] id: CL:0000985 name: IgG plasma cell namespace: cell def: "A fully differentiated plasma cell that secretes IgG." [GO_REF:0000031, GOC:msz, ISBN:781735149] is_a: CL:0000974 ! long lived plasma cell intersection_of: CL:0000974 ! long lived plasma cell intersection_of: secretes GO:0071736 ! IgG immunoglobulin complex, circulating relationship: secretes GO:0071736 ! IgG immunoglobulin complex, circulating [Term] id: CL:0000986 name: IgM plasma cell namespace: cell def: "A fully differentiated plasma cell that secretes IgM." [GO_REF:0000031, GOC:msz, ISBN:781735149] is_a: CL:0000974 ! long lived plasma cell intersection_of: CL:0000974 ! long lived plasma cell intersection_of: secretes GO:0071754 ! IgM immunoglobulin complex, circulating relationship: secretes GO:0071754 ! IgM immunoglobulin complex, circulating [Term] id: CL:0000987 name: IgA plasma cell namespace: cell def: "A fully differentiated plasma cell that secretes IgA." [GO_REF:0000031, GOC:msz, ISBN:781735149] is_a: CL:0000974 ! long lived plasma cell intersection_of: CL:0000974 ! long lived plasma cell intersection_of: secretes GO:0071746 ! IgA immunoglobulin complex, circulating relationship: secretes GO:0071746 ! IgA immunoglobulin complex, circulating [Term] id: CL:0000988 name: hematopoietic cell namespace: cell def: "A cell of a hematopoietic lineage." [GO_REF:0000031, GOC:add] synonym: "haematopoietic cell" EXACT [] synonym: "haemopoietic cell" EXACT [] synonym: "hemopoietic cell" EXACT [] xref: BTO:0000574 xref: FMA:70366 xref: FMA:83598 is_a: CL:0000548 ! animal cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0000989 name: CD11c-low plasmacytoid dendritic cell namespace: cell def: "CD11c-low plasmacytoid dendritic cell is a leukocyte that is CD11c-low, CD45R-positive, GR1-positive and CD11b-negative." [GO_REF:0000031, GOC:amm, GOC:dsd, PMID:15771572, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000001)(PMID:19243617). These cells are CD281-positive (TLR1), CD282-positive (TLR2), CD285-positive (TLR5), CD286-positive (TLR6), and CD288-positive (TLR8). is_a: CL:0000784 ! plasmacytoid dendritic cell intersection_of: CL:0000784 ! plasmacytoid dendritic cell intersection_of: has_low_plasma_membrane_amount PR:000001013 ! integrin alpha-X intersection_of: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R intersection_of: has_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_low_plasma_membrane_amount PR:000001013 ! integrin alpha-X relationship: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M [Term] id: CL:0000990 name: conventional dendritic cell namespace: cell def: "Conventional dendritic cell is a dendritic cell that is CD11c-high." [GO_REF:0000031, GOC:amm, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000003)(PMID:19243617) These cells are also CD20-negative, MHCII-positive. synonym: "cDC" EXACT [] synonym: "DC1" EXACT [] synonym: "dendritic reticular cell" EXACT [] synonym: "interdigitating cell" BROAD [] synonym: "type 1 DC" EXACT [] synonym: "veiled cell" BROAD [] xref: FMA:84191 is_a: CL:0000451 ! dendritic cell intersection_of: CL:0000451 ! dendritic cell intersection_of: has_high_plasma_membrane_amount PR:000001013 ! integrin alpha-X relationship: has_high_plasma_membrane_amount PR:000001013 ! integrin alpha-X [Term] id: CL:0000991 name: CD11c-negative plasmacytoid dendritic cell namespace: cell def: "CD11c-negative plasmacytoid dendritic cell is a leukocyte is CD11c-negative, CD45RA-positive, CD85g-positive(ILT7), CD123-positive, CD303-positive." [GO_REF:0000031, GOC:amm, PMID:15771572, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000004)(PMID:19243617). These cells are CD281-positive (TLR1), CD286-positive (TLR6), and CD290-positive (TLR10). synonym: "CD303-positive dendritic cell" EXACT [] is_a: CL:0000784 ! plasmacytoid dendritic cell intersection_of: CL:0000784 ! plasmacytoid dendritic cell intersection_of: capable_of GO:0001816 ! cytokine production intersection_of: capable_of GO:0032606 ! type I interferon production intersection_of: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R intersection_of: has_plasma_membrane_part PR:000001292 ! C-type lectin domain family 4 member C intersection_of: has_plasma_membrane_part PR:000001398 ! leukocyte immunoglobulin-like receptor subfamily A member 4 intersection_of: has_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0032606 ! type I interferon production relationship: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_plasma_membrane_part PR:000001292 ! C-type lectin domain family 4 member C relationship: has_plasma_membrane_part PR:000001398 ! leukocyte immunoglobulin-like receptor subfamily A member 4 relationship: has_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain [Term] id: CL:0000992 name: immature CD11c-low plasmacytoid dendritic cell namespace: cell def: "Immature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD80-low and CD86-low." [GO_REF:0000031, GOC:amm, PMID:15771572, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000006)(PMID:19243617). is_a: CL:0000989 ! CD11c-low plasmacytoid dendritic cell intersection_of: CL:0000989 ! CD11c-low plasmacytoid dendritic cell intersection_of: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: develops_from CL:0001029 ! common dendritic progenitor relationship: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule [Term] id: CL:0000993 name: mature CD11c-low plasmacytoid dendritic cell namespace: cell def: "Mature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD83-high and is CD80-positive, CD86-positive, and MHCII-positive." [GO_REF:0000031, GOC:amm, PMID:15771572, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000007)(PMID:19243617). is_a: CL:0000989 ! CD11c-low plasmacytoid dendritic cell intersection_of: CL:0000989 ! CD11c-low plasmacytoid dendritic cell intersection_of: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule intersection_of: has_plasma_membrane_part PR:000001310 ! CD83 molecule relationship: develops_from CL:0000992 ! immature CD11c-low plasmacytoid dendritic cell relationship: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_plasma_membrane_part PR:000001310 ! CD83 molecule [Term] id: CL:0000994 name: immature CD11c-negative plasmacytoid dendritic cell namespace: cell def: "Immature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-negative, CD86-low and MHCII-low." [GO_REF:0000031, GOC:amm, PMID:15771572, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000008)(PMID:19243617). is_a: CL:0000991 ! CD11c-negative plasmacytoid dendritic cell intersection_of: CL:0000991 ! CD11c-negative plasmacytoid dendritic cell intersection_of: capable_of GO:0019882 ! antigen processing and presentation intersection_of: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: lacks_plasma_membrane_part PR:000001438 ! CD80 molecule relationship: capable_of GO:0019882 ! antigen processing and presentation relationship: develops_from CL:0000995 ! CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor relationship: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: lacks_plasma_membrane_part PR:000001438 ! CD80 molecule [Term] id: CL:0000995 name: CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor namespace: cell comment: Originally described in the dendritic cell ontology (DC_CL:1100000)(PMID:19243617). synonym: "CD71-positive common myeloid precursor OR CD7-negative lymphoid precursor OR CD7-positive lymphoid" BROAD [] is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell union_of: CL:0001021 ! CD34-positive, CD38-positive common lymphoid progenitor union_of: CL:0001026 ! CD34-positive, CD38-positive common myeloid progenitor [Term] id: CL:0000996 name: mature CD11c-negative plasmacytoid dendritic cell namespace: cell def: "Mature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, PMID:15771572, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000009)(PMID:19243617). is_a: CL:0000991 ! CD11c-negative plasmacytoid dendritic cell intersection_of: CL:0000991 ! CD11c-negative plasmacytoid dendritic cell intersection_of: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule intersection_of: has_plasma_membrane_part PR:000001310 ! CD83 molecule relationship: develops_from CL:0000994 ! immature CD11c-negative plasmacytoid dendritic cell relationship: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_plasma_membrane_part PR:000001310 ! CD83 molecule [Term] id: CL:0000997 name: immature CD8_alpha-negative CD11b-positive dendritic cell namespace: cell def: "Immature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] comment: Originally described in the dendritic cell ontology (DC_CL:0000010)(PMID:19243617). is_a: CL:0000840 ! immature conventional dendritic cell is_a: CL:0000999 ! CD4-positive CD11b-positive dendritic cell intersection_of: CL:0000999 ! CD4-positive CD11b-positive dendritic cell intersection_of: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: develops_from CL:0002010 ! pre-conventional dendritic cell relationship: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule [Term] id: CL:0000998 name: CD8_alpha-negative CD11b-negative dendritic cell namespace: cell def: "CD8_alpha-negative CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative CD8_alpha-negative and is CD205-positive. This cell is able to cross- present antigen to CD8-alpha-positive T cells." [GO_REF:0000031, GOC:amm, http:www.immgen.org/index_content.html, PMCID:PMC2346585] comment: These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000011)(PMID:19243617). synonym: "DC.8-4-11b-" EXACT [] synonym: "triple negative dendritic cell" EXACT [] is_a: CL:0000990 ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: capable_of GO:0002474 ! antigen processing and presentation of peptide antigen via MHC class I intersection_of: has_plasma_membrane_part PR:000001026 ! lymphocyte antigen 75 intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: capable_of GO:0002474 ! antigen processing and presentation of peptide antigen via MHC class I relationship: develops_from CL:0002010 ! pre-conventional dendritic cell relationship: has_plasma_membrane_part PR:000001026 ! lymphocyte antigen 75 relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain [Term] id: CL:0000999 name: CD4-positive CD11b-positive dendritic cell namespace: cell def: "CD8_alpha-negative CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-positive and is CD205-negative and CD8_alpha-negative." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] comment: Defined as having a disposition to secreting anti-inflammatory cytokines. These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000012)(PMID:19243617). synonym: "DC.4+" EXACT [] is_a: CL:0002465 ! CD11b-positive dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: capable_of GO:0001816 ! cytokine production intersection_of: capable_of GO:0050728 ! negative regulation of inflammatory response intersection_of: has_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001026 ! lymphocyte antigen 75 intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0050728 ! negative regulation of inflammatory response relationship: develops_from CL:0002010 ! pre-conventional dendritic cell relationship: has_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001026 ! lymphocyte antigen 75 relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain [Term] id: CL:0001000 name: CD8_alpha-positive CD11b-negative dendritic cell namespace: cell def: "CD8_alpha-positive CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative and is CD205-positive and CD8_alpha-positive." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] comment: Cells are defined as having a disposition to secreting inflammatory cytokines. Originally described in the dendritic cell ontology (DC_CL:0000013)(PMID:19243617). synonym: "DC.8+" EXACT [] is_a: CL:0000990 ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: capable_of GO:0001816 ! cytokine production intersection_of: capable_of GO:0042590 ! antigen processing and presentation of exogenous peptide antigen via MHC class I intersection_of: capable_of GO:0050729 ! positive regulation of inflammatory response intersection_of: has_plasma_membrane_part PR:000001026 ! lymphocyte antigen 75 intersection_of: has_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0042590 ! antigen processing and presentation of exogenous peptide antigen via MHC class I relationship: capable_of GO:0050729 ! positive regulation of inflammatory response relationship: develops_from CL:0002010 ! pre-conventional dendritic cell relationship: has_plasma_membrane_part PR:000001026 ! lymphocyte antigen 75 relationship: has_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M [Term] id: CL:0001001 name: immature CD8_alpha-negative CD11b-negative dendritic cell namespace: cell def: "Immature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] comment: These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000014)(PMID:19243617). is_a: CL:0000840 ! immature conventional dendritic cell is_a: CL:0000998 ! CD8_alpha-negative CD11b-negative dendritic cell intersection_of: CL:0000998 ! CD8_alpha-negative CD11b-negative dendritic cell intersection_of: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: develops_from CL:0002010 ! pre-conventional dendritic cell relationship: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule [Term] id: CL:0001002 name: mature CD8_alpha-negative CD11b-negative dendritic cell namespace: cell def: "Mature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] comment: These markers are associated with mouse cells. Defined as having a disposition to secretion of anti-inflammatory cytokines. Originally described in the dendritic cell ontology (DC_CL:0000015)(PMID:19243617). is_a: CL:0000841 ! mature conventional dendritic cell is_a: CL:0000998 ! CD8_alpha-negative CD11b-negative dendritic cell intersection_of: CL:0000998 ! CD8_alpha-negative CD11b-negative dendritic cell intersection_of: capable_of GO:0001816 ! cytokine production intersection_of: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule intersection_of: has_plasma_membrane_part PR:000001310 ! CD83 molecule relationship: capable_of GO:0001816 ! cytokine production relationship: develops_from CL:0001001 ! immature CD8_alpha-negative CD11b-negative dendritic cell relationship: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_plasma_membrane_part PR:000001310 ! CD83 molecule [Term] id: CL:0001003 name: mature CD8_alpha-negative CD11b-positive dendritic cell namespace: cell def: "Mature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] comment: Originally described in the dendritic cell ontology (DC_CL:0000016)(PMID:19243617). is_a: CL:0000841 ! mature conventional dendritic cell is_a: CL:0000999 ! CD4-positive CD11b-positive dendritic cell intersection_of: CL:0000999 ! CD4-positive CD11b-positive dendritic cell intersection_of: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule intersection_of: has_plasma_membrane_part PR:000001310 ! CD83 molecule relationship: develops_from CL:0000997 ! immature CD8_alpha-negative CD11b-positive dendritic cell relationship: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_plasma_membrane_part PR:000001310 ! CD83 molecule [Term] id: CL:0001004 name: immature CD8_alpha-positive CD11b-negative dendritic cell namespace: cell def: "Immature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] comment: Originally described in the dendritic cell ontology (DC_CL:0000017)(PMID:19243617). is_a: CL:0000840 ! immature conventional dendritic cell is_a: CL:0001000 ! CD8_alpha-positive CD11b-negative dendritic cell intersection_of: CL:0001000 ! CD8_alpha-positive CD11b-negative dendritic cell intersection_of: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: develops_from CL:0002010 ! pre-conventional dendritic cell relationship: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule [Term] id: CL:0001005 name: mature CD8_alpha-positive CD11b-negative dendritic cell namespace: cell def: "Mature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] comment: Originally described in the dendritic cell ontology (DC_CL:0000018)(PMID:19243617). is_a: CL:0000841 ! mature conventional dendritic cell is_a: CL:0001000 ! CD8_alpha-positive CD11b-negative dendritic cell intersection_of: CL:0001000 ! CD8_alpha-positive CD11b-negative dendritic cell intersection_of: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule intersection_of: has_plasma_membrane_part PR:000001310 ! CD83 molecule relationship: develops_from CL:0001004 ! immature CD8_alpha-positive CD11b-negative dendritic cell relationship: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_plasma_membrane_part PR:000001310 ! CD83 molecule [Term] id: CL:0001006 name: dermal dendritic cell namespace: cell def: "Dermal dendritic cell is a conventional dendritic cell that is CD11b-positive, CD205-positive and CD8 alpha-negative." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] comment: Originally described in the dendritic cell ontology (DC_CL:0000019)(PMID:19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD285-positive (TLR5), CD288-positive (TLR8), and CD289-positive (TLR9). xref: BTO:0004812 is_a: CL:0002465 ! CD11b-positive dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001026 ! lymphocyte antigen 75 intersection_of: has_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: part_of UBERON:0002067 ! dermis relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001026 ! lymphocyte antigen 75 relationship: has_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: part_of UBERON:0002067 ! dermis [Term] id: CL:0001007 name: interstitial dendritic cell namespace: cell def: "Interstitial dendritic cell is a conventional dendritic cell that is CD11b-positive, CD1a-positive, CD206-positive, CD209-positive, and CD36-positive." [GO_REF:0000031, GOC:amm, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000020)(PMID:19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD286-positive (TLR6), CD288-positive (TLR8), and CD290-positive (TLR10). is_a: CL:0002465 ! CD11b-positive dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001300 ! CD209 molecule intersection_of: has_plasma_membrane_part PR:000001905 ! platelet glycoprotein 4 intersection_of: has_plasma_membrane_part PR:000002025 ! T-cell surface glycoprotein CD1a intersection_of: has_plasma_membrane_part PR:000002972 ! macrophage mannose receptor 1 relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001300 ! CD209 molecule relationship: has_plasma_membrane_part PR:000001905 ! platelet glycoprotein 4 relationship: has_plasma_membrane_part PR:000002025 ! T-cell surface glycoprotein CD1a relationship: has_plasma_membrane_part PR:000002972 ! macrophage mannose receptor 1 [Term] id: CL:0001008 name: Kit and Sca1-positive hematopoietic stem cell namespace: cell def: "A hematopoietic stem cell that has plasma membrane part Kit-positive, SCA-1-positive, CD150-positive and CD34-negative." [GO_REF:0000031, GOC:add, GOC:amm, GOC:tfm, PMID:17952047, PMID:19022770] comment: Cell markers are associated with mouse hematopoietic stem cell. Originally described in the dendritic cell ontology (DC_CL:0000043)(PMID:19243617). synonym: "LSK stem cell" EXACT [] synonym: "Sca1-positive hematopoietic stem cell" EXACT [] is_a: CL:0000037 ! hematopoietic stem cell intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: has_plasma_membrane_part PR:000001833 ! SLAM family member 1 intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: has_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 intersection_of: lacks_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001308 ! CD48 molecule intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000001896 ! natural killer cell receptor 2B4 intersection_of: lacks_plasma_membrane_part PR:000002977 ! killer cell lectin-like receptor subfamily B member 1C intersection_of: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 disjoint_from: CL:0001024 ! CD34-positive, CD38-negative hematopoietic stem cell relationship: has_plasma_membrane_part PR:000001833 ! SLAM family member 1 relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: has_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: lacks_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001308 ! CD48 molecule relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000001896 ! natural killer cell receptor 2B4 relationship: lacks_plasma_membrane_part PR:000002977 ! killer cell lectin-like receptor subfamily B member 1C relationship: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 [Term] id: CL:0001009 name: immature dermal dendritic cell namespace: cell def: "Immature dermal dendritic cell is a dermal dendritic cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] comment: Originally described in the dendritic cell ontology (DC_CL:0000022)(PMID:19243617). is_a: CL:0000840 ! immature conventional dendritic cell is_a: CL:0001006 ! dermal dendritic cell intersection_of: CL:0001006 ! dermal dendritic cell intersection_of: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: develops_from CL:0001029 ! common dendritic progenitor relationship: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule [Term] id: CL:0001010 name: mature dermal dendritic cell namespace: cell def: "Mature dermal dendritic cell is a dermal dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] comment: Originally described in the dendritic cell ontology (DC_CL:0000023)(PMID:19243617). is_a: CL:0000841 ! mature conventional dendritic cell is_a: CL:0001006 ! dermal dendritic cell intersection_of: CL:0001006 ! dermal dendritic cell intersection_of: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule intersection_of: has_plasma_membrane_part PR:000001310 ! CD83 molecule relationship: develops_from CL:0001009 ! immature dermal dendritic cell relationship: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_plasma_membrane_part PR:000001310 ! CD83 molecule [Term] id: CL:0001011 name: immature interstitial dendritic cell namespace: cell def: "Immature interstitial dendritic cell is a interstitial dendritic cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, GOC:tfm, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000024)(PMID:19243617). is_a: CL:0000840 ! immature conventional dendritic cell is_a: CL:0001007 ! interstitial dendritic cell intersection_of: CL:0001007 ! interstitial dendritic cell intersection_of: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: develops_from CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor relationship: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule [Term] id: CL:0001012 name: CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor namespace: cell comment: Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617). is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell union_of: CL:0000557 ! granulocyte monocyte progenitor cell union_of: CL:0001027 ! CD7-negative lymphoid progenitor cell [Term] id: CL:0001013 name: mature interstitial dendritic cell namespace: cell def: "Mature interstitial dendritic cell is a interstitial dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, GOC:tfm, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000025)(PMID:19243617). is_a: CL:0000841 ! mature conventional dendritic cell is_a: CL:0001007 ! interstitial dendritic cell intersection_of: CL:0001007 ! interstitial dendritic cell intersection_of: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule intersection_of: has_plasma_membrane_part PR:000001310 ! CD83 molecule relationship: develops_from CL:0001011 ! immature interstitial dendritic cell relationship: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_plasma_membrane_part PR:000001310 ! CD83 molecule [Term] id: CL:0001014 name: CD1a-positive Langerhans cell namespace: cell def: "CD1a-positive Langerhans cell is a Langerhans_cell that is CD1a-positive and CD324-positive." [GO_REF:0000031, GOC:amm, PMID:17850486] comment: These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000026)(PMID:19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD284-positive (TLR4), CD286-positive (TLR6), CD287-positive (TLR7), and CD290-positive (TLR10). When activated, these cells are capable of producing IL-6, IL-8, and IL-15. synonym: "CD1a-LC" EXACT [] is_a: CL:0000453 ! Langerhans cell intersection_of: CL:0000453 ! Langerhans cell intersection_of: has_plasma_membrane_part PR:000001447 ! epithelial cadherin intersection_of: has_plasma_membrane_part PR:000002025 ! T-cell surface glycoprotein CD1a relationship: has_plasma_membrane_part PR:000001447 ! epithelial cadherin relationship: has_plasma_membrane_part PR:000002025 ! T-cell surface glycoprotein CD1a [Term] id: CL:0001015 name: CD8_alpha-low Langerhans cell namespace: cell def: "CD8_alpha-low Langerhans cell is a Langerhans cell that is CD205-high and is CD8_alpha-low." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] comment: These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000027)(PMID:19243617). They are also CD205-high, CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD285-positive (TLR5), CD286-positive (TLR6), and CD289-positive (TLR9). is_a: CL:0000453 ! Langerhans cell intersection_of: CL:0000453 ! Langerhans cell intersection_of: has_high_plasma_membrane_amount PR:000001026 ! lymphocyte antigen 75 intersection_of: has_low_plasma_membrane_amount PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: has_high_plasma_membrane_amount PR:000001026 ! lymphocyte antigen 75 relationship: has_low_plasma_membrane_amount PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain [Term] id: CL:0001016 name: immature CD1a-positive Langerhans cell namespace: cell def: "Immature CD1a-positive Langerhans cell is a CD1a-positive Langerhans cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, GOC:tfm, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000028)(PMID:19243617). is_a: CL:0000840 ! immature conventional dendritic cell is_a: CL:0001014 ! CD1a-positive Langerhans cell intersection_of: CL:0001014 ! CD1a-positive Langerhans cell intersection_of: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule [Term] id: CL:0001017 name: mature CD1a-positive Langerhans cell namespace: cell def: "Mature CD1a-positive Langerhans cell is a CD1a-positive Langerhans cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, GOC:tfm, PMID:17850486] comment: Originally described in the dendritic cell ontology (DC_CL:0000029)(PMID:19243617). When activated, these cells produce IL-6, IL-8, and IL-15. is_a: CL:0000841 ! mature conventional dendritic cell is_a: CL:0001014 ! CD1a-positive Langerhans cell intersection_of: CL:0001014 ! CD1a-positive Langerhans cell intersection_of: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule intersection_of: has_plasma_membrane_part PR:000001310 ! CD83 molecule relationship: develops_from CL:0001016 ! immature CD1a-positive Langerhans cell relationship: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_plasma_membrane_part PR:000001310 ! CD83 molecule [Term] id: CL:0001018 name: immature CD8_alpha-low Langerhans cell namespace: cell def: "Immature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that is CD80-low, CD86-low, and MHCII-low." [GO_REF:0000031, GOC:amm, GOC:tfm, PMCID:PMC2346585] comment: These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000030)(PMID:19243617). is_a: CL:0000840 ! immature conventional dendritic cell is_a: CL:0001015 ! CD8_alpha-low Langerhans cell intersection_of: CL:0001015 ! CD8_alpha-low Langerhans cell intersection_of: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: develops_from CL:0001019 ! CD115-positive monocyte OR common dendritic progenitor relationship: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule [Term] id: CL:0001019 name: CD115-positive monocyte OR common dendritic progenitor namespace: cell comment: Originally described in the dendritic cell ontology (DC_CL:1111000)(PMID:19243617). is_a: CL:0002031 ! hematopoietic lineage restricted progenitor cell union_of: CL:0001022 ! CD115-positive monocyte union_of: CL:0001029 ! common dendritic progenitor [Term] id: CL:0001020 name: mature CD8_alpha-low Langerhans cell namespace: cell def: "Mature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that that is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GO_REF:0000031, GOC:amm, PMCID:PMC2346585] comment: These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000031)(PMID:19243617). is_a: CL:0000841 ! mature conventional dendritic cell is_a: CL:0001015 ! CD8_alpha-low Langerhans cell intersection_of: CL:0001015 ! CD8_alpha-low Langerhans cell intersection_of: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule intersection_of: has_plasma_membrane_part PR:000001310 ! CD83 molecule relationship: develops_from CL:0001018 ! immature CD8_alpha-low Langerhans cell relationship: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_plasma_membrane_part PR:000001310 ! CD83 molecule [Term] id: CL:0001021 name: CD34-positive, CD38-positive common lymphoid progenitor namespace: cell def: "A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive." [GO_REF:0000031, GOC:add, GOC:amm, GOC:tfm, PMCID:PMC2346585, PMID:19022770] comment: These markers are associated with human common lymphoid progenitors. Originally described in the dendritic cell ontology (DC_CL:0000032)(PMID:19243617). synonym: "CD10-positive common lymphocyte precursor" EXACT [] synonym: "CD10-positive common lymphocyte progenitor" EXACT [] synonym: "CD10-positive common lymphoid precursor" EXACT [] is_a: CL:0000051 ! common lymphoid progenitor intersection_of: CL:0000051 ! common lymphoid progenitor intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: has_plasma_membrane_part PR:000001898 ! neprilysin disjoint_from: CL:0001025 ! Kit-positive, Sca1-positive common lymphoid progenitor relationship: develops_from CL:0002043 ! CD34-positive, CD38-negative multipotent progenitor cell relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: has_plasma_membrane_part PR:000001898 ! neprilysin [Term] id: CL:0001022 name: CD115-positive monocyte namespace: cell def: "CD115-positive monocyte is a monocyte that is CD115-positive and CD11b-positive." [GO_REF:0000031, GOC:add, GOC:amm, PMID:17952047] comment: These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000033)(PMID:19243617). is_a: CL:0000576 ! monocyte intersection_of: CL:0000576 ! monocyte intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor relationship: develops_from CL:0002001 ! CD34-positive, CD38-positive granulocyte monocyte progenitor relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor [Term] id: CL:0001023 name: Kit-positive, CD34-positive common myeloid progenitor namespace: cell def: "A common myeloid progenitor that is Kit-positive and CD34-positive, Il7ra-negative, and is SCA1-low and Fcgr2-low and Fcgr3-low." [GO_REF:0000031, GOC:add, GOC:amm, GOC:tfm, http://www.immgen.org/index_content.html, PMID:1261582, PMID:17952047] comment: Markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000034)(PMID:19243617). synonym: "CD117-positive common myeloid precursor" BROAD [] is_a: CL:0000049 ! common myeloid progenitor intersection_of: CL:0000049 ! common myeloid progenitor intersection_of: has_low_plasma_membrane_amount GO:0033001 ! Fc-gamma receptor III complex intersection_of: has_low_plasma_membrane_amount PR:000001481 ! low affinity immunoglobulin gamma Fc region receptor II-b intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 disjoint_from: CL:0001026 ! CD34-positive, CD38-positive common myeloid progenitor relationship: develops_from CL:0002035 ! Slamf1-negative multipotent progenitor cell relationship: has_low_plasma_membrane_amount GO:0033001 ! Fc-gamma receptor III complex relationship: has_low_plasma_membrane_amount PR:000001481 ! low affinity immunoglobulin gamma Fc region receptor II-b relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 [Term] id: CL:0001024 name: CD34-positive, CD38-negative hematopoietic stem cell namespace: cell def: "CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive." [GO_REF:0000031, GOC:add, GOC:amm, GOC:tfm, PMID:10430905, PMID:11750107, PMID:16551251, PMID:20024907, PMID:9389721] comment: Cell markers are associated with human hematopoietic stem cells. Originally described in the dendritic cell ontology (DC_CL:0000035)(PMID:19243617). synonym: "CD133-positive hematopoietic stem cell" EXACT [PMID:16140871] xref: FMA:86475 is_a: CL:0000037 ! hematopoietic stem cell intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000001786 ! prominin-1 intersection_of: has_plasma_membrane_part PR:000001809 ! CD59-like glycoprotein intersection_of: has_plasma_membrane_part PR:000001843 ! Thy-1 membrane glycoprotein intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III intersection_of: lacks_plasma_membrane_part PR:000001892 ! CD33 molecule intersection_of: lacks_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000001786 ! prominin-1 relationship: has_plasma_membrane_part PR:000001809 ! CD59-like glycoprotein relationship: has_plasma_membrane_part PR:000001843 ! Thy-1 membrane glycoprotein relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: lacks_plasma_membrane_part PR:000001892 ! CD33 molecule relationship: lacks_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 [Term] id: CL:0001025 name: Kit-positive, Sca1-positive common lymphoid progenitor namespace: cell def: "A common lymphoid progenitor that is Kit-low, FLT3-positive, IL7ralpha-positive, and SCA1-low." [GO_REF:0000031, GOC:add, GOC:amm, GOC:tfm, http://www.immgen.org/index_content.html, PMID:17952047] comment: Markers are associated with mouse cells. synonym: "CD217-positive common lymphocyte precursor" EXACT [] synonym: "CD217-positive common lymphocyte progenitor" EXACT [] synonym: "CD217-positive common lymphoid precursor" EXACT [] is_a: CL:0000051 ! common lymphoid progenitor intersection_of: CL:0000051 ! common lymphoid progenitor intersection_of: has_low_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor intersection_of: has_low_plasma_membrane_amount PR:000002979 ! lymphocyte antigen 6A-2/6E-1 intersection_of: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: has_plasma_membrane_part PR:000001963 ! CD27 molecule intersection_of: has_plasma_membrane_part PR:000002001 ! FL cytokine receptor intersection_of: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor intersection_of: lacks_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: develops_from CL:0000936 ! early lymphoid progenitor relationship: has_low_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor relationship: has_low_plasma_membrane_amount PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: has_plasma_membrane_part PR:000001963 ! CD27 molecule relationship: has_plasma_membrane_part PR:000002001 ! FL cytokine receptor relationship: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor relationship: lacks_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R [Term] id: CL:0001026 name: CD34-positive, CD38-positive common myeloid progenitor namespace: cell def: "A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative." [GO_REF:0000031, GOC:add, GOC:amm, PMCID:PMC2626675, PMID:16551251] comment: Markers are associated with human cell type. Originally described in the dendritic cell ontology (DC_CL:0000038)(PMID:19243617). synonym: "CD71-positive common myeloid precursor" NARROW [] is_a: CL:0000049 ! common myeloid progenitor intersection_of: CL:0000049 ! common myeloid progenitor intersection_of: has_low_plasma_membrane_amount PR:000001865 ! interleukin-3 receptor class 2 alpha chain intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: lacks_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: lacks_plasma_membrane_part PR:000001836 ! CD7 molecule intersection_of: lacks_plasma_membrane_part PR:000001867 ! interleukin-5 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000001898 ! neprilysin relationship: develops_from CL:0002043 ! CD34-positive, CD38-negative multipotent progenitor cell relationship: has_low_plasma_membrane_amount PR:000001865 ! interleukin-3 receptor class 2 alpha chain relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: lacks_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: lacks_plasma_membrane_part PR:000001836 ! CD7 molecule relationship: lacks_plasma_membrane_part PR:000001867 ! interleukin-5 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000001898 ! neprilysin [Term] id: CL:0001027 name: CD7-negative lymphoid progenitor cell namespace: cell def: "CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative." [GO_REF:0000031, GOC:amm, PMID:16551251] comment: These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000039)(PMID:19243617). synonym: "CD7-negative lymphoid precursor" EXACT [] is_a: CL:0000051 ! common lymphoid progenitor intersection_of: CL:0000051 ! common lymphoid progenitor intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: lacks_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: lacks_plasma_membrane_part PR:000001836 ! CD7 molecule relationship: develops_from CL:0001021 ! CD34-positive, CD38-positive common lymphoid progenitor relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: lacks_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: lacks_plasma_membrane_part PR:000001836 ! CD7 molecule [Term] id: CL:0001028 name: CD7-positive lymphoid progenitor cell namespace: cell def: "CD7-positive lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-positive and is CD45RA-negative." [GO_REF:0000031, GOC:amm, GOC:tfm, PMID:16551251, PMID:19491395] comment: These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000040)(PMID:19243617). synonym: "CD7-positive lymphoid precursor" EXACT [] is_a: CL:0000051 ! common lymphoid progenitor intersection_of: CL:0000051 ! common lymphoid progenitor intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000001836 ! CD7 molecule intersection_of: lacks_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: develops_from CL:0001027 ! CD7-negative lymphoid progenitor cell relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000001836 ! CD7 molecule relationship: lacks_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA [Term] id: CL:0001029 name: common dendritic progenitor namespace: cell def: "Common dendritic precursor is a hematopoietic progenitor cell that is CD117-low, CD135-positive, CD115-positive and lacks plasma membrane parts for hematopoietic lineage markers." [GO_REF:0000031, GOC:amm, GOC:tfm, PMID:16551251, PMID:17922016, PMID:19286519] comment: Surface markers are for mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000041) CDP are reportedly CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD11c-positive, CD14-negative, CD19-negative, CD20-negative, CD56-negative, B220-negative, Ly6g-negative, MHCII-positive, and Ter119-negative. (PMID:19243617). synonym: "CDP" EXACT [PMID:21219184] synonym: "common dendritic precursor" EXACT [] synonym: "pro-DCs" EXACT [PMID:21219184] is_a: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: has_low_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor intersection_of: has_plasma_membrane_part PR:000002001 ! FL cytokine receptor intersection_of: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G intersection_of: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 relationship: develops_from CL:0002009 ! macrophage dendritic cell progenitor relationship: has_low_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor relationship: has_plasma_membrane_part PR:000002001 ! FL cytokine receptor relationship: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G relationship: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 [Term] id: CL:0001030 name: CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor namespace: cell comment: Originally described in the dendritic cell ontology (DC_CL:1111100)(PMID:19243617). is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell union_of: CL:0001023 ! Kit-positive, CD34-positive common myeloid progenitor union_of: CL:0001025 ! Kit-positive, Sca1-positive common lymphoid progenitor [Term] id: CL:0001031 name: cerebellar granule cell namespace: cell def: "Granule cell that is part of the cerebellum." [GOC:mah] xref: BTO:0004278 is_a: CL:0000120 ! granule cell intersection_of: CL:0000120 ! granule cell intersection_of: part_of UBERON:0002037 ! cerebellum relationship: part_of UBERON:0002037 ! cerebellum [Term] id: CL:0001032 name: cortical granule cell namespace: cell def: "Granule cell that is part of the cerebral cortex." [GOC:mah] is_a: CL:0000120 ! granule cell is_a: CL:0002609 ! neuron of cerebral cortex intersection_of: CL:0000120 ! granule cell intersection_of: part_of UBERON:0000956 ! cerebral cortex relationship: part_of UBERON:0000956 ! cerebral cortex [Term] id: CL:0001033 name: hippocampal granule cell namespace: cell def: "Granule cell that is part of the hippocampus." [GOC:mah] is_a: CL:0001032 ! cortical granule cell is_a: CL:0002608 ! hippocampal neuron intersection_of: CL:0000120 ! granule cell intersection_of: part_of UBERON:0001954 ! Ammon's horn relationship: part_of UBERON:0001954 ! Ammon's horn [Term] id: CL:0001034 name: cell in vitro namespace: cell def: "A cell that has been removed from a natural environment, and placed in a controlled artificial environment for use in some investigation. Includes multicellular organism cells removed from an organism, and unicellular organisms removed from a natural environment." [ReO:mhb] comment: 'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. This term is intended to contrast with 'native', which refers to cells or other biological entities that are found in a natural setting. is_a: CL:0000000 ! cell created_by: haendel creation_date: 2012-01-12T09:58:38Z [Term] id: CL:0001035 name: bone cell namespace: cell def: "A connective tissue cell found in bone." [GO_REF:0000034, GOC:add] is_a: CL:0000548 ! animal cell intersection_of: CL:0000548 ! animal cell intersection_of: part_of UBERON:0001474 ! bone relationship: part_of UBERON:0001474 ! bone created_by: adiehl creation_date: 2011-11-16T04:28:16Z [Term] id: CL:0001039 name: terminally differentiated osteoblast def: "Osteoblast that is terminally differentiated, located adjacent to acellular or cellular bone tissue within periosteum, and is capable of mineralizing the matrix." [VSAO:curator] xref: VSAO:0000116 is_a: CL:0000062 ! osteoblast [Term] id: CL:0001040 name: non-terminally differentiated osteoblast def: "Osteoblast that is non-terminally differentiated and located in cellular bone tissue or under the periosteum in acellular bone." [VSAO:curator] comment: VSAO relationship simplified OBO_REL:integral_part_of VSAO:0000118 xref: VSAO:0000117 is_a: CL:0000062 ! osteoblast is_a: CL:0001035 ! bone cell relationship: part_of UBERON:0002481 ! bone tissue [Term] id: CL:0001041 name: CD8-positive, CXCR3-positive, alpha-beta regulatory T cell namespace: cell def: "A CD8-positive alpha-beta-positive T cell with the phenotype CXCR3-positive and having suppressor function. They are capable of producing IL-10, suppressing proliferation, and suppressing IFN-gamma production." [GOC:dsd, PMID:19609979] comment: These cells may be the human equivalent of murine CD8-positive, CD122-positive alpha-beta regulatory T cell. They are also found in the CD45RA-negative and CD62L-positive fraction. synonym: "CD8+CXCR3+ T cell" EXACT [] synonym: "CD8+CXCR3+ T lymphocyte" EXACT [] synonym: "CD8+CXCR3+ T(reg)" EXACT [] synonym: "CD8+CXCR3+ T-cell" EXACT [] synonym: "CD8+CXCR3+ T-lymphocyte " EXACT [] synonym: "CD8+CXCR3+ Treg" EXACT [] synonym: "CD8-positive, CXCR3-positive, alpha-beta regulatory T lymphocyte" EXACT [] synonym: "CD8-positive, CXCR3-positive, alpha-beta regulatory T-cell" EXACT [] synonym: "CD8-positive, CXCR3-positive, alpha-beta regulatory T-lymphocyte" EXACT [] synonym: "CD8-positive, CXCR3-positive, T(reg)" EXACT [] synonym: "CD8-positive, CXCR3-positive, Treg" EXACT [] is_a: CL:0000795 ! CD8-positive, alpha-beta regulatory T cell intersection_of: CL:0000795 ! CD8-positive, alpha-beta regulatory T cell intersection_of: capable_of GO:0032613 ! interleukin-10 production intersection_of: capable_of GO:0032689 ! negative regulation of interferon-gamma production intersection_of: capable_of GO:0042130 ! negative regulation of T cell proliferation intersection_of: has_part PR:000001207 ! C-X-C chemokine receptor type 3 relationship: capable_of GO:0032613 ! interleukin-10 production relationship: capable_of GO:0032689 ! negative regulation of interferon-gamma production relationship: capable_of GO:0042130 ! negative regulation of T cell proliferation relationship: has_part PR:000001207 ! C-X-C chemokine receptor type 3 [Term] id: CL:0001042 name: T-helper 22 cell namespace: cell def: "CD4-positive, alpha-beta T cell that produces IL-22." [GOC:dsd, PMID:19578368, PMID:19578369] comment: TH22 cells are also reportedly CCR4-positive, CCR6-positive, CCR10-positive, CXCR3-negative. TH22 cells are reportedly capable of secreting IL-13. synonym: "helper T cell type 22" EXACT [] synonym: "T(H)-22 cell" EXACT [] synonym: "Th22 cell" EXACT [] synonym: "Th22 T cell" EXACT [] synonym: "Th22 T lymphocyte" EXACT [] synonym: "Th22 T-cell" EXACT [] synonym: "Th22 T-lymphocyte" EXACT [] is_a: CL:0000492 ! CD4-positive helper T cell intersection_of: CL:0000492 ! CD4-positive helper T cell intersection_of: capable_of GO:0032626 ! interleukin-22 production relationship: capable_of GO:0032626 ! interleukin-22 production relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell [Term] id: CL:0001658 name: visual pigment cell (sensu Nematoda and Protostomia) namespace: cell xref: FBbt:00004230 is_a: CL:0000149 ! visual pigment cell is_a: CL:0000341 ! pigment cell (sensu Nematoda and Protostomia) [Term] id: CL:0002000 name: Kit-positive erythroid progenitor cell namespace: cell def: "An erythroid progenitor cell is Kit-positive, Ly6A-negative, CD41-negative, CD127-negative, and CD123-negative. This cell type is also described as being lin-negative, Kit-positive, CD150-negative, CD41-negative, CD105-positive, and FcgR-negative." [GOC:ak, GOC:tfm, http://www.immgen.org/index_content.html, PMID:19805084] comment: Markers found on mouse cells. is_a: CL:0000038 ! erythroid progenitor cell intersection_of: CL:0000038 ! erythroid progenitor cell intersection_of: has_plasma_membrane_part PR:000001345 ! endoglin intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part GO:0033001 ! Fc-gamma receptor III complex intersection_of: lacks_plasma_membrane_part PR:000001833 ! SLAM family member 1 intersection_of: lacks_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 intersection_of: lacks_plasma_membrane_part PR:000009127 ! integrin alpha-IIb relationship: develops_from CL:0002006 ! Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell relationship: has_plasma_membrane_part PR:000001345 ! endoglin relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part GO:0033001 ! Fc-gamma receptor III complex relationship: lacks_plasma_membrane_part PR:000001833 ! SLAM family member 1 relationship: lacks_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain relationship: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: lacks_plasma_membrane_part PR:000009127 ! integrin alpha-IIb created_by: tmeehan creation_date: 2010-04-26T10:14:16Z [Term] id: CL:0002001 name: CD34-positive, CD38-positive granulocyte monocyte progenitor namespace: cell def: "A granulocyte monocyte progenitor is CD34-positive, CD38-positive, IL-3receptor-alpha-positive and is CD45RA-negative." [GOC:tfm, PMID:12615892, PMID:19022770] comment: Markers are for human cells. According to different research groups, CD45RA is present or absent on this cell population. is_a: CL:0000557 ! granulocyte monocyte progenitor cell intersection_of: CL:0000557 ! granulocyte monocyte progenitor cell intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: has_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain relationship: develops_from CL:0001026 ! CD34-positive, CD38-positive common myeloid progenitor relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: has_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain created_by: tmeehan creation_date: 2010-01-13T03:19:22Z [Term] id: CL:0002002 name: Kit-positive granulocyte monocyte progenitor namespace: cell def: "A granulocyte monocyte progenitor that is Kit-positive, CD34-positive, Fc-gamma receptor II/II-positive, and is Sca-1-negative, Il7ra-negative, Cxc3r1-negative, and CD90-negative." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:12615892, PMID:16322423, PMID:19022770, PMID:19273628] comment: Markers are found on mouse cells. is_a: CL:0000557 ! granulocyte monocyte progenitor cell intersection_of: CL:0000557 ! granulocyte monocyte progenitor cell intersection_of: has_high_plasma_membrane_amount GO:0033001 ! Fc-gamma receptor III complex intersection_of: has_high_plasma_membrane_amount PR:000001479 ! low affinity immunoglobulin gamma Fc region receptor II intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part PR:000001206 ! CX3C chemokine receptor 1 intersection_of: lacks_plasma_membrane_part PR:000001843 ! Thy-1 membrane glycoprotein intersection_of: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: develops_from CL:0001023 ! Kit-positive, CD34-positive common myeloid progenitor relationship: has_high_plasma_membrane_amount GO:0033001 ! Fc-gamma receptor III complex relationship: has_high_plasma_membrane_amount PR:000001479 ! low affinity immunoglobulin gamma Fc region receptor II relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part PR:000001206 ! CX3C chemokine receptor 1 relationship: lacks_plasma_membrane_part PR:000001843 ! Thy-1 membrane glycoprotein relationship: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 created_by: tmeehan creation_date: 2010-01-13T03:19:28Z [Term] id: CL:0002003 name: CD34-positive, GlyA-negative erythroid progenitor cell namespace: cell def: "An erythroid progenitor cell that is CD34-positive and is GlyA-negative." [GOC:ak, GOC:tfm, PMID:19621348] comment: Cell markers associated with human cells. xref: FMA:83517 is_a: CL:0000038 ! erythroid progenitor cell intersection_of: CL:0000038 ! erythroid progenitor cell intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: lacks_plasma_membrane_part PR:000001460 ! glycophorin-A relationship: develops_from CL:0002005 ! CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: lacks_plasma_membrane_part PR:000001460 ! glycophorin-A created_by: tmeehan creation_date: 2010-04-26T10:14:30Z [Term] id: CL:0002004 name: CD34-negative, GlyA-negative proerythroblast namespace: cell def: "A proerythoblast that is CD34-negative and GlyA-negative." [GOC:ak, GOC:tfm, PMID:19621348] comment: Cell surface markers are associated with human cells. is_a: CL:0000547 ! proerythroblast intersection_of: CL:0000547 ! proerythroblast intersection_of: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: lacks_plasma_membrane_part PR:000001460 ! glycophorin-A relationship: develops_from CL:0002003 ! CD34-positive, GlyA-negative erythroid progenitor cell relationship: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: lacks_plasma_membrane_part PR:000001460 ! glycophorin-A created_by: tmeehan creation_date: 2010-04-26T10:31:50Z [Term] id: CL:0002005 name: CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell namespace: cell def: "A megakaryocyte erythroid progenitor cell is CD34-positive, CD38-positive and is IL3-receptor alpha-negative and CD45RA-negative." [GOC:tfm, PMID:12615892, PMID:190227700] comment: Markers are associated with human cell type. is_a: CL:0000050 ! megakaryocyte-erythroid progenitor cell intersection_of: CL:0000050 ! megakaryocyte-erythroid progenitor cell intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: lacks_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: lacks_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: lacks_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: lacks_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain created_by: tmeehan creation_date: 2010-01-13T03:43:10Z [Term] id: CL:0002006 name: Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell namespace: cell def: "A megakaryocyte erythroid progenitor cell that is Kit-positive and is Sca1-negative, CD34-negative, CD90-negative, IL7r-alpha-negative and Fcgr II/III-low." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:12615892, PMID:19022770] comment: Markers are associated with mouse cells. is_a: CL:0000050 ! megakaryocyte-erythroid progenitor cell intersection_of: CL:0000050 ! megakaryocyte-erythroid progenitor cell intersection_of: has_low_plasma_membrane_amount GO:0033001 ! Fc-gamma receptor III complex intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: lacks_plasma_membrane_part PR:000001479 ! low affinity immunoglobulin gamma Fc region receptor II intersection_of: lacks_plasma_membrane_part PR:000001843 ! Thy-1 membrane glycoprotein intersection_of: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: has_low_plasma_membrane_amount GO:0033001 ! Fc-gamma receptor III complex relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: lacks_plasma_membrane_part PR:000001479 ! low affinity immunoglobulin gamma Fc region receptor II relationship: lacks_plasma_membrane_part PR:000001843 ! Thy-1 membrane glycoprotein relationship: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 created_by: tmeehan creation_date: 2010-01-13T03:43:12Z [Term] id: CL:0002007 name: Kit-low, CD34-positive eosinophil progenitor cell namespace: cell def: "A lineage marker-negative, CD34-positive, IL5r-alpha-positive, and Sca1-negative eosinophil progenitor cell." [GOC:tfm, PMID:17582345] comment: Markers are found on mouse cells. is_a: CL:0000611 ! eosinophil progenitor cell intersection_of: CL:0000611 ! eosinophil progenitor cell intersection_of: has_low_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000001867 ! interleukin-5 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: develops_from CL:0002002 ! Kit-positive granulocyte monocyte progenitor relationship: has_low_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000001867 ! interleukin-5 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 created_by: tmeehan creation_date: 2010-01-14T03:25:15Z [Term] id: CL:0002008 name: CD34-positive, CD38-positive eosinophil progenitor cell namespace: cell def: "A lineage marker-negative, CD34-positive, CD38-positive, IL3r-alpha-positive, IL5r-alpha-positive, and CD45RA-negative eosinophil progenitor cell." [GOC:tfm, PMCID:PMC2626675] comment: Markers are associated with human cells. is_a: CL:0000611 ! eosinophil progenitor cell intersection_of: CL:0000611 ! eosinophil progenitor cell intersection_of: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: has_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain relationship: develops_from CL:0002001 ! CD34-positive, CD38-positive granulocyte monocyte progenitor relationship: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: has_plasma_membrane_part PR:000001865 ! interleukin-3 receptor class 2 alpha chain created_by: tmeehan creation_date: 2010-01-14T03:25:17Z [Term] id: CL:0002009 name: macrophage dendritic cell progenitor namespace: cell def: "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages." [GOC:tfm, PMID:19273628] synonym: "MDP" EXACT [] is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell created_by: tmeehan creation_date: 2010-01-19T02:51:58Z [Term] id: CL:0002010 name: pre-conventional dendritic cell namespace: cell def: "A lin-negative, MHC-II-negative, CD11c-positive, FLT3-positive cell with intermediate expression of SIRP-alpha." [GOC:tfm] is_a: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: has_plasma_membrane_part PR:000001013 ! integrin alpha-X intersection_of: has_plasma_membrane_part PR:000001968 ! tyrosine-protein phosphatase non-receptor type substrate 1 intersection_of: has_plasma_membrane_part PR:000002001 ! FL cytokine receptor intersection_of: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G intersection_of: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 relationship: develops_from CL:0001029 ! common dendritic progenitor relationship: has_plasma_membrane_part PR:000001013 ! integrin alpha-X relationship: has_plasma_membrane_part PR:000001968 ! tyrosine-protein phosphatase non-receptor type substrate 1 relationship: has_plasma_membrane_part PR:000002001 ! FL cytokine receptor relationship: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G relationship: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 created_by: tmeehan creation_date: 2010-01-19T03:39:30Z [Term] id: CL:0002011 name: Kit-positive macrophage dendritic cell progenitor namespace: cell def: "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. Marker for this cell is Kit-high, CD115-positive, CD135-positive, Cx3cr1-positive, and is Il7ra-negative." [GOC:tfm, PMID:19273628] comment: Markers are associated with mouse cells. synonym: "murine MDP" EXACT [] is_a: CL:0002009 ! macrophage dendritic cell progenitor intersection_of: CL:0002009 ! macrophage dendritic cell progenitor intersection_of: has_high_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor intersection_of: has_plasma_membrane_part PR:000001206 ! CX3C chemokine receptor 1 intersection_of: has_plasma_membrane_part PR:000002001 ! FL cytokine receptor intersection_of: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor relationship: develops_from CL:0002002 ! Kit-positive granulocyte monocyte progenitor relationship: has_high_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor relationship: has_plasma_membrane_part PR:000001206 ! CX3C chemokine receptor 1 relationship: has_plasma_membrane_part PR:000002001 ! FL cytokine receptor relationship: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor created_by: tmeehan creation_date: 2010-01-26T02:43:40Z [Term] id: CL:0002012 name: Kit-low proerythroblast namespace: cell def: "A proerythoblast that is Kit-low, Lyg76-positive, and CD71-positive." [GOC:ak, GOC:tfm, PMID:19805084] comment: Markers are associated with mouse cells. is_a: CL:0000547 ! proerythroblast intersection_of: CL:0000547 ! proerythroblast intersection_of: has_high_plasma_membrane_amount PR:000001945 ! transferrin receptor protein 1 intersection_of: has_low_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor intersection_of: has_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 intersection_of: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: develops_from CL:0002000 ! Kit-positive erythroid progenitor cell relationship: has_high_plasma_membrane_amount PR:000001945 ! transferrin receptor protein 1 relationship: has_low_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor relationship: has_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 relationship: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 created_by: tmeehan creation_date: 2010-04-26T10:31:56Z [Term] id: CL:0002013 name: GlyA-positive basophillic erythroblast namespace: cell def: "A basophilic erythroblast that is GlyA-positive." [GOC:ak, GOC:tfm, PMID:1638021] comment: Markers are associated with human cells. is_a: CL:0000549 ! basophilic erythroblast intersection_of: CL:0000549 ! basophilic erythroblast intersection_of: has_plasma_membrane_part PR:000001460 ! glycophorin-A intersection_of: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: develops_from CL:0002004 ! CD34-negative, GlyA-negative proerythroblast relationship: has_plasma_membrane_part PR:000001460 ! glycophorin-A relationship: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule created_by: tmeehan creation_date: 2010-04-26T10:41:15Z [Term] id: CL:0002014 name: Kit-negative, Ly-76 high basophilic erythroblast namespace: cell def: "A basophilic erythroblast that is Lyg 76-high and is Kit-negative." [GOC:ak, GOC:tfm, PMID:19805084] comment: Cell surface markers are associated with mouse cells. is_a: CL:0000549 ! basophilic erythroblast intersection_of: CL:0000549 ! basophilic erythroblast intersection_of: has_high_plasma_membrane_amount PR:000002981 ! lymphocyte antigen 76 intersection_of: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: develops_from CL:0002012 ! Kit-low proerythroblast relationship: has_high_plasma_membrane_amount PR:000002981 ! lymphocyte antigen 76 relationship: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 created_by: tmeehan creation_date: 2010-04-26T10:41:22Z [Term] id: CL:0002015 name: Kit-negative, Ly-76 high polychromatophilic erythroblast namespace: cell def: "A polychromatophilic erythroblast that is Lyg 76-high and is Kit-negative." [GOC:ak, GOC:tfm, PMID:19805084] synonym: "late basophilic and polychromatophilic erythroblast" BROAD [] is_a: CL:0000550 ! polychromatophilic erythroblast intersection_of: CL:0000550 ! polychromatophilic erythroblast intersection_of: has_high_plasma_membrane_amount PR:000002981 ! lymphocyte antigen 76 intersection_of: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: develops_from CL:0002014 ! Kit-negative, Ly-76 high basophilic erythroblast relationship: has_high_plasma_membrane_amount PR:000002981 ! lymphocyte antigen 76 relationship: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 created_by: tmeehan creation_date: 2010-04-26T10:53:11Z [Term] id: CL:0002016 name: CD71-low, GlyA-positive polychromatic erythroblast namespace: cell def: "A polychromatiic erythroblast that is Gly-A-positive and CD71-low." [GOC:ak, GOC:tfm, PMID:1638021] comment: Cell surface markers are associated with human cells. is_a: CL:0000550 ! polychromatophilic erythroblast intersection_of: CL:0000550 ! polychromatophilic erythroblast intersection_of: has_low_plasma_membrane_amount PR:000001945 ! transferrin receptor protein 1 intersection_of: has_plasma_membrane_part PR:000001460 ! glycophorin-A relationship: develops_from CL:0002013 ! GlyA-positive basophillic erythroblast relationship: has_low_plasma_membrane_amount PR:000001945 ! transferrin receptor protein 1 relationship: has_plasma_membrane_part PR:000001460 ! glycophorin-A created_by: tmeehan creation_date: 2010-04-26T10:53:16Z [Term] id: CL:0002017 name: Kit-negative, Ly-76 high orthochromatophilic erythroblasts namespace: cell def: "An orthochromatophilic erythroblast that is ter119-high, CD71-low, and Kit-negative." [GOC:ak, GOC:tfm, PMID:19805084] comment: Cell surface markers associated with mouse cells. is_a: CL:0000552 ! orthochromatic erythroblast intersection_of: CL:0000552 ! orthochromatic erythroblast intersection_of: has_high_plasma_membrane_amount PR:000002981 ! lymphocyte antigen 76 intersection_of: has_low_plasma_membrane_amount PR:000001945 ! transferrin receptor protein 1 intersection_of: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: develops_from CL:0002015 ! Kit-negative, Ly-76 high polychromatophilic erythroblast relationship: has_high_plasma_membrane_amount PR:000002981 ! lymphocyte antigen 76 relationship: has_low_plasma_membrane_amount PR:000001945 ! transferrin receptor protein 1 relationship: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 created_by: tmeehan creation_date: 2010-04-26T11:04:15Z [Term] id: CL:0002018 name: CD71-negative, GlyA-positive orthochromatic erythroblast namespace: cell def: "An erythroblast that is GlyA-positive and CD71-negative." [GOC:ak, GOC:tfm, PMID:1638021] comment: Markers associated with human cells. is_a: CL:0000552 ! orthochromatic erythroblast intersection_of: CL:0000552 ! orthochromatic erythroblast intersection_of: has_plasma_membrane_part PR:000001460 ! glycophorin-A intersection_of: lacks_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 relationship: develops_from CL:0002016 ! CD71-low, GlyA-positive polychromatic erythroblast relationship: has_plasma_membrane_part PR:000001460 ! glycophorin-A relationship: lacks_plasma_membrane_part PR:000001945 ! transferrin receptor protein 1 created_by: tmeehan creation_date: 2010-04-26T11:04:21Z [Term] id: CL:0002019 name: Ly-76 high reticulocyte namespace: cell def: "A reticulocyte that is Ly76-high and is Kit-negative." [GOC:ak, GOC:tfm, PMID:18539294] comment: Marker associated with mouse cells. is_a: CL:0002422 ! enucleated reticulocyte intersection_of: CL:0002422 ! enucleated reticulocyte intersection_of: has_high_plasma_membrane_amount PR:000002981 ! lymphocyte antigen 76 relationship: develops_from CL:0002017 ! Kit-negative, Ly-76 high orthochromatophilic erythroblasts relationship: has_high_plasma_membrane_amount PR:000002981 ! lymphocyte antigen 76 created_by: tmeehan creation_date: 2010-04-26T11:37:00Z [Term] id: CL:0002020 name: GlyA-positive reticulocytes namespace: cell def: "A reticulocyte that is GlyA-positive." [GOC:ak, GOC:tfm, PMID:1638021] comment: Markers is associated with human cells. is_a: CL:0002422 ! enucleated reticulocyte intersection_of: CL:0002422 ! enucleated reticulocyte intersection_of: has_plasma_membrane_part PR:000001460 ! glycophorin-A relationship: develops_from CL:0002018 ! CD71-negative, GlyA-positive orthochromatic erythroblast relationship: has_plasma_membrane_part PR:000001460 ! glycophorin-A created_by: tmeehan creation_date: 2010-04-26T11:48:25Z [Term] id: CL:0002021 name: GlyA-positive erythrocyte namespace: cell def: "An enucleate erythrocyte that is GlyA-positive." [GOC:ak, GOC:tfm, PMID:20134094] comment: Marker is associated with human cell types. is_a: CL:0000595 ! enucleate erythrocyte intersection_of: CL:0000595 ! enucleate erythrocyte intersection_of: has_plasma_membrane_part PR:000001460 ! glycophorin-A relationship: develops_from CL:0002020 ! GlyA-positive reticulocytes relationship: has_plasma_membrane_part PR:000001460 ! glycophorin-A created_by: tmeehan creation_date: 2010-04-26T11:51:22Z [Term] id: CL:0002022 name: Ly-76 high positive erythrocyte namespace: cell def: "An enucleate erythrocyte that is Lyg-76-high." [GOC:ak, GOC:tfm, PMID:19805084] comment: Marker is associated with mouse cell types. is_a: CL:0000595 ! enucleate erythrocyte intersection_of: CL:0000595 ! enucleate erythrocyte intersection_of: has_high_plasma_membrane_amount PR:000002981 ! lymphocyte antigen 76 relationship: develops_from CL:0002019 ! Ly-76 high reticulocyte relationship: has_high_plasma_membrane_amount PR:000002981 ! lymphocyte antigen 76 created_by: tmeehan creation_date: 2010-04-26T11:51:27Z [Term] id: CL:0002023 name: CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell namespace: cell def: "A megakaroycotye progenitor cell that is CD34-positive, CD41-positive and CD42-positive on the cell surface." [GOC:ak, GOC:tfm, PMID:15232614] comment: Markers are associated with human cell type. is_a: CL:0000553 ! megakaryocyte progenitor cell intersection_of: CL:0000553 ! megakaryocyte progenitor cell intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000001907 ! platelet glycoprotein Ib alpha chain intersection_of: has_plasma_membrane_part PR:000009127 ! integrin alpha-IIb relationship: develops_from CL:0002025 ! CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000001907 ! platelet glycoprotein Ib alpha chain relationship: has_plasma_membrane_part PR:000009127 ! integrin alpha-IIb created_by: tmeehan creation_date: 2010-04-26T02:39:09Z [Term] id: CL:0002024 name: Kit-positive megakaryocyte progenitor cell namespace: cell def: "A megakaryocyte progenitor cell that is Kit-positive, CD41-positive, CD9-positive, Sca-1-negative, IL7ralpha-negative, CD150-negative, and Fcgamma receptor II/III-low." [GOC:ak, GOC:tfm, PMID:16951553] comment: Markers are associated with mouse cells. is_a: CL:0000553 ! megakaryocyte progenitor cell intersection_of: CL:0000553 ! megakaryocyte progenitor cell intersection_of: has_low_plasma_membrane_amount PR:000001479 ! low affinity immunoglobulin gamma Fc region receptor II intersection_of: has_low_plasma_membrane_amount PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: has_plasma_membrane_part PR:000005178 ! CD9 molecule intersection_of: lacks_plasma_membrane_part PR:000001833 ! SLAM family member 1 intersection_of: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: develops_from CL:0002006 ! Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell relationship: has_low_plasma_membrane_amount PR:000001479 ! low affinity immunoglobulin gamma Fc region receptor II relationship: has_low_plasma_membrane_amount PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: has_plasma_membrane_part PR:000005178 ! CD9 molecule relationship: lacks_plasma_membrane_part PR:000001833 ! SLAM family member 1 relationship: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 created_by: tmeehan creation_date: 2010-04-26T02:39:15Z [Term] id: CL:0002025 name: CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell namespace: cell def: "A megakaryocyte progenitor cell that is CD34-positive, CD41-positive, and CD42-negative." [GOC:ak, GOC:tfm, PMID:15232614] comment: Markers are commonly associated with human cells. is_a: CL:0000553 ! megakaryocyte progenitor cell intersection_of: CL:0000553 ! megakaryocyte progenitor cell intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000009127 ! integrin alpha-IIb intersection_of: lacks_plasma_membrane_part PR:000001907 ! platelet glycoprotein Ib alpha chain relationship: develops_from CL:0002005 ! CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000009127 ! integrin alpha-IIb relationship: lacks_plasma_membrane_part PR:000001907 ! platelet glycoprotein Ib alpha chain created_by: tmeehan creation_date: 2010-04-26T03:52:47Z [Term] id: CL:0002026 name: CD34-negative, CD41-positive, CD42-positive megakaryocyte cell namespace: cell def: "A megakaryocyte progenitor cell that is CD34-negative, CD41-positive and CD42-positive." [GOC:ak, GOC:tfm, PMID:15232614] comment: Markers are commonly associated with human cells. is_a: CL:0000556 ! megakaryocyte intersection_of: CL:0000556 ! megakaryocyte intersection_of: has_plasma_membrane_part PR:000001907 ! platelet glycoprotein Ib alpha chain intersection_of: has_plasma_membrane_part PR:000009127 ! integrin alpha-IIb intersection_of: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: develops_from CL:0002023 ! CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell relationship: has_plasma_membrane_part PR:000001907 ! platelet glycoprotein Ib alpha chain relationship: has_plasma_membrane_part PR:000009127 ! integrin alpha-IIb relationship: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule created_by: tmeehan creation_date: 2010-04-26T03:59:22Z [Term] id: CL:0002027 name: CD9-positive, CD41-positive megakaryocyte cell namespace: cell def: "A megakaryocyte cell with is CD9-positive and CD41-positive." [GOC:tfm] comment: Markers are commonly associated with mouse cells. is_a: CL:0000556 ! megakaryocyte intersection_of: CL:0000556 ! megakaryocyte intersection_of: has_plasma_membrane_part PR:000005178 ! CD9 molecule intersection_of: has_plasma_membrane_part PR:000009127 ! integrin alpha-IIb relationship: develops_from CL:0002024 ! Kit-positive megakaryocyte progenitor cell relationship: has_plasma_membrane_part PR:000005178 ! CD9 molecule relationship: has_plasma_membrane_part PR:000009127 ! integrin alpha-IIb created_by: tmeehan creation_date: 2010-04-27T10:39:07Z [Term] id: CL:0002028 name: basophil mast progenitor cell namespace: cell def: "A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa" [GOC:ak, GOC:dsd, GOC:tfm, PMCID:PMC1312421] comment: There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low. synonym: "BMCP" EXACT [] is_a: CL:0002191 ! granulocytopoietic cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030221 ! basophil differentiation intersection_of: capable_of GO:0060374 ! mast cell differentiation intersection_of: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha intersection_of: has_part PR:000007857 ! erythroid transcription factor intersection_of: has_part PR:000007858 ! endothelial transcription factor GATA-2 intersection_of: has_plasma_membrane_part PR:000001867 ! interleukin-5 receptor subunit alpha intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000016401 ! transmembrane emp24 domain-containing protein 1 relationship: capable_of GO:0030221 ! basophil differentiation relationship: capable_of GO:0060374 ! mast cell differentiation relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: has_plasma_membrane_part PR:000001867 ! interleukin-5 receptor subunit alpha relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000016401 ! transmembrane emp24 domain-containing protein 1 created_by: tmeehan creation_date: 2010-04-27T12:46:33Z [Term] id: CL:0002029 name: Fc-epsilon RIalpha-low mast cell progenitor namespace: cell def: "A lineage-negative, Kit-positive, CD45-positive mast cell progenitor that is Fc-epsilon RIalpha-low." [GOC:tfm, PMCID:PMC1312421] is_a: CL:0000831 ! mast cell progenitor intersection_of: CL:0000831 ! mast cell progenitor intersection_of: has_low_plasma_membrane_amount PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha intersection_of: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: has_plasma_membrane_part PR:000009143 ! integrin beta-7 intersection_of: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: develops_from CL:0002044 ! Kit-positive, integrin beta7-high basophil mast progenitor cell relationship: has_low_plasma_membrane_amount PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha relationship: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: has_plasma_membrane_part PR:000009143 ! integrin beta-7 relationship: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 created_by: tmeehan creation_date: 2010-04-27T01:22:19Z [Term] id: CL:0002030 name: Fc-epsilon RIalpha-high basophil progenitor cell namespace: cell def: "A lineage negative, Sca1-negative basophil progenitor cell that is Fc epsilon RIalpha-high." [GOC:tfm, PMCID:PMC1312421] comment: Markers are associated with mouse cells. is_a: CL:0000613 ! basophil progenitor cell intersection_of: CL:0000613 ! basophil progenitor cell intersection_of: has_high_plasma_membrane_amount PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: lacks_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: develops_from CL:0002044 ! Kit-positive, integrin beta7-high basophil mast progenitor cell relationship: has_high_plasma_membrane_amount PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: lacks_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 created_by: tmeehan creation_date: 2010-04-27T01:22:32Z [Term] id: CL:0002031 name: hematopoietic lineage restricted progenitor cell namespace: cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] is_a: CL:0000988 ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: has_quality PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: develops_from CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: has_quality PATO:0001400 ! unipotent created_by: tmeehan creation_date: 2010-01-06T03:43:20Z [Term] id: CL:0002032 name: hematopoietic oligopotent progenitor cell namespace: cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers." [GOC:tfm, PMID:19022770] is_a: CL:0000988 ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: has_quality PATO:0001401 ! oligopotent intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G intersection_of: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 relationship: develops_from CL:0000837 ! hematopoietic multipotent progenitor cell relationship: has_quality PATO:0001401 ! oligopotent relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001083 ! CD2 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: lacks_plasma_membrane_part PR:000002978 ! lymphocyte antigen 6G relationship: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 created_by: tmeehan creation_date: 2010-01-06T03:43:27Z [Term] id: CL:0002033 name: short term hematopoietic stem cell namespace: cell def: "A hematopoietic stem cell capable of rapid replenishment of myeloerythroid progenitors and limited self renewal capability. This cell is Kit-positive, Sca1-positive, CD34-positive, CD150-positive, and is Flt3-negative." [GOC:tfm, PMID:15572596, PMID:19022770] comment: Markers are associated with mouse cells. These cells are also reportedly CD11b-low and CD90-low. synonym: "ST stem cell" EXACT [] synonym: "ST-HSC" EXACT [] is_a: CL:0001008 ! Kit and Sca1-positive hematopoietic stem cell intersection_of: CL:0001008 ! Kit and Sca1-positive hematopoietic stem cell intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000001833 ! SLAM family member 1 intersection_of: lacks_plasma_membrane_part PR:000002001 ! FL cytokine receptor relationship: develops_from CL:0002034 ! long term hematopoietic stem cell relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000001833 ! SLAM family member 1 relationship: lacks_plasma_membrane_part PR:000002001 ! FL cytokine receptor created_by: tmeehan creation_date: 2010-01-08T09:19:25Z [Term] id: CL:0002034 name: long term hematopoietic stem cell namespace: cell def: "A hematopoietic stem cell with long term self renewal capability. This cell is Kit-positive, Sca1-positive, CD150-positive, CD90-low, CD34-negative and Flt3-negative." [GOC:tfm, PMID:15572596, PMID:17582345] comment: Markers are associated with mouse cells. synonym: "LT stem cell" EXACT [] synonym: "LT-HSC" EXACT [] is_a: CL:0001008 ! Kit and Sca1-positive hematopoietic stem cell intersection_of: CL:0001008 ! Kit and Sca1-positive hematopoietic stem cell intersection_of: has_low_plasma_membrane_amount PR:000001843 ! Thy-1 membrane glycoprotein intersection_of: has_plasma_membrane_part PR:000001833 ! SLAM family member 1 intersection_of: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: lacks_plasma_membrane_part PR:000002001 ! FL cytokine receptor relationship: has_low_plasma_membrane_amount PR:000001843 ! Thy-1 membrane glycoprotein relationship: has_plasma_membrane_part PR:000001833 ! SLAM family member 1 relationship: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: lacks_plasma_membrane_part PR:000002001 ! FL cytokine receptor created_by: tmeehan creation_date: 2010-01-08T09:19:28Z [Term] id: CL:0002035 name: Slamf1-negative multipotent progenitor cell namespace: cell def: "A hematopoietic progenitor that has restricted self-renewal capability. Cell is Kit-positive, Ly6-positive, CD150-negative and Flt3-negative." [GOC:tfm, PMID:19022770] comment: Markers are associated with mouse cells. is_a: CL:0000837 ! hematopoietic multipotent progenitor cell intersection_of: CL:0000837 ! hematopoietic multipotent progenitor cell intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: has_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 intersection_of: lacks_plasma_membrane_part PR:000001833 ! SLAM family member 1 intersection_of: lacks_plasma_membrane_part PR:000002001 ! FL cytokine receptor relationship: develops_from CL:0002036 ! Slamf1-positive multipotent progenitor cell relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: has_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: lacks_plasma_membrane_part PR:000001833 ! SLAM family member 1 relationship: lacks_plasma_membrane_part PR:000002001 ! FL cytokine receptor created_by: tmeehan creation_date: 2010-01-08T11:16:33Z [Term] id: CL:0002036 name: Slamf1-positive multipotent progenitor cell namespace: cell def: "A hematopoietic progenitor that has some limited self-renewal capability. Cells are lin-negative, Kit-positive, CD34-positive, and Slamf1-positive." [GOC:tfm, PMID:19022770] comment: Markers are associated with mouse cells. synonym: "KSL cell" EXACT [] is_a: CL:0000837 ! hematopoietic multipotent progenitor cell intersection_of: CL:0000837 ! hematopoietic multipotent progenitor cell intersection_of: has_plasma_membrane_part PR:000001833 ! SLAM family member 1 intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: has_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 disjoint_from: CL:0002043 ! CD34-positive, CD38-negative multipotent progenitor cell relationship: develops_from CL:0002033 ! short term hematopoietic stem cell relationship: has_plasma_membrane_part PR:000001833 ! SLAM family member 1 relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: has_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 created_by: tmeehan creation_date: 2010-01-08T11:16:35Z [Term] id: CL:0002037 name: CD2-positive, CD5-positive, CD44-positive alpha-beta intraepithelial T cell namespace: cell def: "Intraepithelial T cells with a memory phenotype of CD2-positive, CD5-positive, and CD44-positive." [GOC:tfm, PMID:16048545] synonym: "memory alpha beta IEL" EXACT [PMID:16048545] is_a: CL:0000793 ! CD4-positive, alpha-beta intraepithelial T cell intersection_of: CL:0000793 ! CD4-positive, alpha-beta intraepithelial T cell intersection_of: has_plasma_membrane_part PR:000001083 ! CD2 molecule intersection_of: has_plasma_membrane_part PR:000001307 ! CD44 molecule intersection_of: has_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: has_plasma_membrane_part PR:000001083 ! CD2 molecule relationship: has_plasma_membrane_part PR:000001307 ! CD44 molecule relationship: has_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 created_by: tmeehan creation_date: 2009-10-20T02:20:43Z [Term] id: CL:0002038 name: T follicular helper cell namespace: cell def: "A CD4-positive, CXCR5-positive, CCR7-negative alpha-beta T cell located in follicles of secondary lymph nodes that expresses is BCL6-high, ICOS-high and PD1-high, and stimulates follicular B cells to undergo class-switching and antibody production." [GOC:tfm, PMID:19855402, PMID:20107805, PMID:22043829] synonym: "follicular B helper T cell" RELATED [PMID:22043829] synonym: "follicular helper T cell" RELATED [PMID:22649468] synonym: "follicular helper T-cell" RELATED [PMID:22508770] synonym: "follicular T cell" RELATED [PMID:20107805, PMID:21914188] synonym: "follicular T-cell" RELATED [] synonym: "follicular T-helper cell" RELATED [PMID:22552227] synonym: "T(FH)" EXACT [PMID:20207847] synonym: "Tfh" EXACT [PMID:20107805, PMID:20383172] is_a: CL:0000492 ! CD4-positive helper T cell intersection_of: CL:0000492 ! CD4-positive helper T cell intersection_of: capable_of GO:0045830 ! positive regulation of isotype switching intersection_of: capable_of GO:0051024 ! positive regulation of immunoglobulin secretion intersection_of: has_part PR:000003450 ! B-cell lymphoma 6 protein intersection_of: has_plasma_membrane_part PR:000001209 ! C-X-C chemokine receptor type 5 intersection_of: has_plasma_membrane_part PR:000001860 ! inducible T-cell costimulator intersection_of: has_plasma_membrane_part PR:000001919 ! programmed cell death protein 1 intersection_of: lacks_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 relationship: capable_of GO:0045830 ! positive regulation of isotype switching relationship: capable_of GO:0051024 ! positive regulation of immunoglobulin secretion relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell relationship: has_part PR:000003450 ! B-cell lymphoma 6 protein relationship: has_plasma_membrane_part PR:000001209 ! C-X-C chemokine receptor type 5 relationship: has_plasma_membrane_part PR:000001860 ! inducible T-cell costimulator relationship: has_plasma_membrane_part PR:000001919 ! programmed cell death protein 1 relationship: lacks_plasma_membrane_part PR:000001203 ! C-C chemokine receptor type 7 created_by: tmeehan creation_date: 2009-10-29T04:01:27Z [Term] id: CL:0002039 name: immature NK T cell stage I namespace: cell def: "A CD24-high, CD4-low, CD8-low, CD44-negative, NK1.1-negative NK T cell." [GOC:tfm, PMID:17589542] is_a: CL:0000914 ! immature NK T cell intersection_of: CL:0000914 ! immature NK T cell intersection_of: has_high_plasma_membrane_amount PR:000001932 ! signal transducer CD24 intersection_of: has_low_plasma_membrane_amount PR:000001004 ! CD4 molecule intersection_of: has_low_plasma_membrane_amount PR:000025402 ! T cell receptor co-receptor CD8 intersection_of: lacks_plasma_membrane_part PR:000001307 ! CD44 molecule intersection_of: lacks_plasma_membrane_part PR:000001874 ! KLRB1-like protein relationship: develops_from CL:0000809 ! double-positive, alpha-beta thymocyte relationship: has_high_plasma_membrane_amount PR:000001932 ! signal transducer CD24 relationship: has_low_plasma_membrane_amount PR:000001004 ! CD4 molecule relationship: has_low_plasma_membrane_amount PR:000025402 ! T cell receptor co-receptor CD8 relationship: lacks_plasma_membrane_part PR:000001307 ! CD44 molecule relationship: lacks_plasma_membrane_part PR:000001874 ! KLRB1-like protein created_by: tmeehan creation_date: 2009-10-29T04:09:16Z [Term] id: CL:0002040 name: immature NK T cell stage II namespace: cell def: "A CD24-low, CD44-negative, NK1.1-negative NK T cell." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:17589542] comment: NKT.44-NK1.1-.Th was assigned as an exact synonym based on sorting strategy displayed at immgene.org. synonym: "NKT.44-NK1.1-.Th" EXACT [] is_a: CL:0000914 ! immature NK T cell intersection_of: CL:0000914 ! immature NK T cell intersection_of: has_low_plasma_membrane_amount PR:000001932 ! signal transducer CD24 intersection_of: lacks_plasma_membrane_part PR:000001307 ! CD44 molecule intersection_of: lacks_plasma_membrane_part PR:000001874 ! KLRB1-like protein relationship: develops_from CL:0002039 ! immature NK T cell stage I relationship: has_low_plasma_membrane_amount PR:000001932 ! signal transducer CD24 relationship: lacks_plasma_membrane_part PR:000001307 ! CD44 molecule relationship: lacks_plasma_membrane_part PR:000001874 ! KLRB1-like protein created_by: tmeehan creation_date: 2009-10-29T04:13:43Z [Term] id: CL:0002041 name: immature NK T cell stage III namespace: cell def: "A CD24-low, CD44-positive, DX5-low, NK1.1-negative NK T cell." [PMID:17589542] synonym: "NKT.44+.NK1.1-.Th" BROAD [] is_a: CL:0000914 ! immature NK T cell intersection_of: CL:0000914 ! immature NK T cell intersection_of: has_low_plasma_membrane_amount PR:000001008 ! integrin alpha-2 intersection_of: has_low_plasma_membrane_amount PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part PR:000001307 ! CD44 molecule intersection_of: lacks_plasma_membrane_part PR:000001874 ! KLRB1-like protein relationship: develops_from CL:0002040 ! immature NK T cell stage II relationship: has_low_plasma_membrane_amount PR:000001008 ! integrin alpha-2 relationship: has_low_plasma_membrane_amount PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000001307 ! CD44 molecule relationship: lacks_plasma_membrane_part PR:000001874 ! KLRB1-like protein created_by: tmeehan creation_date: 2009-10-29T04:14:48Z [Term] id: CL:0002042 name: immature NK T cell stage IV namespace: cell def: "A CD24-low, CD44-positive, DX5-high, NK1.1-negative NK T cell." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:17589542] synonym: "NKT.44+.NK1.1-.Th" BROAD [] is_a: CL:0000914 ! immature NK T cell intersection_of: CL:0000914 ! immature NK T cell intersection_of: has_high_plasma_membrane_amount PR:000001008 ! integrin alpha-2 intersection_of: has_low_plasma_membrane_amount PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part PR:000001307 ! CD44 molecule intersection_of: lacks_plasma_membrane_part PR:000001874 ! KLRB1-like protein relationship: develops_from CL:0002041 ! immature NK T cell stage III relationship: has_high_plasma_membrane_amount PR:000001008 ! integrin alpha-2 relationship: has_low_plasma_membrane_amount PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000001307 ! CD44 molecule relationship: lacks_plasma_membrane_part PR:000001874 ! KLRB1-like protein created_by: tmeehan creation_date: 2009-10-29T04:17:38Z [Term] id: CL:0002043 name: CD34-positive, CD38-negative multipotent progenitor cell namespace: cell def: "A hematopoietic multipotent progenitor cell that is CD34-positive, CD38-negative, CD45RA-negative, and CD90-negative." [GOC:tfm, PMID:18371405, PMID:19022770] comment: Cell markers are associated with human hematopoietic multipotent progenitor cells. is_a: CL:0000837 ! hematopoietic multipotent progenitor cell intersection_of: CL:0000837 ! hematopoietic multipotent progenitor cell intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: lacks_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: lacks_plasma_membrane_part PR:000001843 ! Thy-1 membrane glycoprotein relationship: develops_from CL:0001024 ! CD34-positive, CD38-negative hematopoietic stem cell relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: lacks_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: lacks_plasma_membrane_part PR:000001843 ! Thy-1 membrane glycoprotein created_by: tmeehan creation_date: 2010-01-12T11:14:15Z [Term] id: CL:0002044 name: Kit-positive, integrin beta7-high basophil mast progenitor cell namespace: cell def: "A basophil mast progenitor cell that is Beta-7 integrin-high, Kit-positive FcRgammaII/III-positive and Sca1-negative." [GOC:ak, GOC:tfm] comment: Markers are associated with mouse cells. is_a: CL:0002028 ! basophil mast progenitor cell intersection_of: CL:0002028 ! basophil mast progenitor cell intersection_of: has_high_plasma_membrane_amount PR:000009143 ! integrin beta-7 intersection_of: has_plasma_membrane_part PR:000001479 ! low affinity immunoglobulin gamma Fc region receptor II intersection_of: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III intersection_of: lacks_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: has_high_plasma_membrane_amount PR:000009143 ! integrin beta-7 relationship: has_plasma_membrane_part PR:000001479 ! low affinity immunoglobulin gamma Fc region receptor II relationship: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: lacks_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 created_by: tmeehan creation_date: 2010-04-27T01:22:38Z [Term] id: CL:0002045 name: Fraction A pre-pro B cell namespace: cell def: "A pro-B cell that CD45R/B220-positive, CD43-positive, HSA-low, BP-1-negative and Ly6c-negative. This cell type is also described as being lin-negative, AA4-positive, Kit-positive, IL7Ra-positive and CD45R-positive." [GOC:ak, GOC:tfm, http://www.immgen.org/index_content.html, PMID:12633665, PMID:17582343] comment: Markers associated with mouse cells. synonym: "fraction A" EXACT [] synonym: "pre pro B cell" RELATED [] is_a: CL:0000826 ! pro-B cell intersection_of: CL:0000826 ! pro-B cell intersection_of: has_low_plasma_membrane_amount PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: has_plasma_membrane_part PR:000001879 ! leukosialin intersection_of: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part PR:000002039 ! glutamyl aminopeptidase intersection_of: lacks_plasma_membrane_part PR:000002980 ! lymphocyte antigen 6C relationship: has_low_plasma_membrane_amount PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: has_plasma_membrane_part PR:000001879 ! leukosialin relationship: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part PR:000002039 ! glutamyl aminopeptidase relationship: lacks_plasma_membrane_part PR:000002980 ! lymphocyte antigen 6C created_by: tmeehan creation_date: 2010-04-28T10:50:07Z [Term] id: CL:0002046 name: early pro-B cell namespace: cell def: "A pro-B cell that is CD22-positive, CD34-positive, CD38-positive and TdT-positive (has TdT activity). Pre-BCR is expressed on the cell surface. Cell is CD19-negative, CD20-negative, complement receptor type 2-negative and CD10-low. D-to-J recombination of the heavy chain occurs at this stage." [GOC:dsd, GOC:tfm, PMID:18432934] comment: Markers are commonly associated with human cells. These cells are also reportedly CD21-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. is_a: CL:0000826 ! pro-B cell intersection_of: CL:0000826 ! pro-B cell intersection_of: has_low_plasma_membrane_amount PR:000001898 ! neprilysin intersection_of: has_plasma_membrane_part GO:0035369 ! pre-B cell receptor complex intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000001288 ! B-cell receptor CD22 intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 intersection_of: lacks_plasma_membrane_part PR:000001338 ! complement receptor type 2 intersection_of: participates_in GO:0071707 ! immunoglobulin heavy chain V-D-J recombination relationship: has_low_plasma_membrane_amount PR:000001898 ! neprilysin relationship: has_plasma_membrane_part GO:0035369 ! pre-B cell receptor complex relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000001288 ! B-cell receptor CD22 relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 relationship: lacks_plasma_membrane_part PR:000001338 ! complement receptor type 2 relationship: participates_in GO:0071707 ! immunoglobulin heavy chain V-D-J recombination created_by: tmeehan creation_date: 2010-04-28T11:19:11Z [Term] id: CL:0002047 name: Fraction B precursor B cell namespace: cell def: "A precursor B cell that is CD45RA-positive, CD43-positive, CD24-positive and BP-1-negative." [GOC:ak, GOC:tfm, PMID:18432934] comment: Markers are commonly associated with mouse cells. These cells are also reportedly RAG1-positive and RAG2-positive. synonym: "Fr. B" EXACT [] synonym: "Fraction B" EXACT [] is_a: CL:0002400 ! Fraction B/C precursor B cell intersection_of: CL:0002400 ! Fraction B/C precursor B cell intersection_of: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 intersection_of: lacks_plasma_membrane_part PR:000002039 ! glutamyl aminopeptidase relationship: develops_from CL:0002045 ! Fraction A pre-pro B cell relationship: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: lacks_plasma_membrane_part PR:000002039 ! glutamyl aminopeptidase created_by: tmeehan creation_date: 2010-04-28T11:56:21Z [Term] id: CL:0002048 name: late pro-B cell namespace: cell def: "A pre-B cell precursor is CD19-low, CD22-positive , CD34-positive, CD38-positive." [GOC:dsd, GOC:tfm, PMID:18432934] comment: Late pro-B cells are also reportedly CD10-positive, CD20-negative, CD21-negative, and TdT-positive. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. is_a: CL:0000817 ! precursor B cell intersection_of: CL:0000817 ! precursor B cell intersection_of: has_low_plasma_membrane_amount PR:000001002 ! CD19 molecule intersection_of: has_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: has_plasma_membrane_part PR:000001288 ! B-cell receptor CD22 intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: develops_from CL:0002046 ! early pro-B cell relationship: has_low_plasma_membrane_amount PR:000001002 ! CD19 molecule relationship: has_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: has_plasma_membrane_part PR:000001288 ! B-cell receptor CD22 relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 created_by: tmeehan creation_date: 2010-04-28T12:06:06Z [Term] id: CL:0002049 name: Fraction C precursor B cell namespace: cell def: "A precursor B cell is CD45R-positive, CD43-positive, CD24-positive, and BP-positive. Intracellularly expression of surrogate light chain, Rag1 and Rag2, TdT, occurs while there is no expression of mu heavy chain." [GOC:tfm, PMID:17582343] synonym: "Fraction C" RELATED [] is_a: CL:0002400 ! Fraction B/C precursor B cell intersection_of: CL:0002400 ! Fraction B/C precursor B cell intersection_of: has_not_completed GO:0071707 ! immunoglobulin heavy chain V-D-J recombination intersection_of: has_part PR:000001858 ! immunoglobulin iota chain intersection_of: has_part PR:000001859 ! immunoglobulin lambda-like polypeptide 1 intersection_of: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part PR:000002039 ! glutamyl aminopeptidase intersection_of: has_plasma_membrane_part PR:000003457 ! V(D)J recombination-activating protein 1 intersection_of: has_plasma_membrane_part PR:000003460 ! V(D)J recombination-activating protein 2 relationship: develops_from CL:0002047 ! Fraction B precursor B cell relationship: has_not_completed GO:0071707 ! immunoglobulin heavy chain V-D-J recombination relationship: has_part PR:000001858 ! immunoglobulin iota chain relationship: has_part PR:000001859 ! immunoglobulin lambda-like polypeptide 1 relationship: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000002039 ! glutamyl aminopeptidase relationship: has_plasma_membrane_part PR:000003457 ! V(D)J recombination-activating protein 1 relationship: has_plasma_membrane_part PR:000003460 ! V(D)J recombination-activating protein 2 created_by: tmeehan creation_date: 2010-04-28T02:04:01Z [Term] id: CL:0002050 name: Fraction C' precursor B cell namespace: cell def: "A pre-BCR-positive precursor B cell that is CD24-high, CD25-positive, CD43-positive, CD45R-positive and BP-positive." [GOC:tfm, PMID:17582343] synonym: "Fr. C'" EXACT [] synonym: "Fraction C-prime" EXACT [] is_a: CL:0000817 ! precursor B cell intersection_of: CL:0000817 ! precursor B cell intersection_of: has_high_plasma_membrane_amount PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part GO:0035369 ! pre-B cell receptor complex intersection_of: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R intersection_of: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha intersection_of: has_plasma_membrane_part PR:000001879 ! leukosialin intersection_of: has_plasma_membrane_part PR:000002039 ! glutamyl aminopeptidase relationship: develops_from CL:0002049 ! Fraction C precursor B cell relationship: has_high_plasma_membrane_amount PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part GO:0035369 ! pre-B cell receptor complex relationship: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: has_plasma_membrane_part PR:000001879 ! leukosialin relationship: has_plasma_membrane_part PR:000002039 ! glutamyl aminopeptidase created_by: tmeehan creation_date: 2010-04-28T02:13:46Z [Term] id: CL:0002051 name: CD38-high pre-BCR positive cell namespace: cell def: "A pre-BCR positive T cell that is CD38-high." [GOC:tfm, PMID:18432934] comment: Markers are associated with human cells. synonym: "large pre-B cell type I" RELATED [] is_a: CL:0000952 ! preBCR-positive large pre-B-II cell intersection_of: CL:0000952 ! preBCR-positive large pre-B-II cell intersection_of: has_high_plasma_membrane_amount PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: has_plasma_membrane_part PR:000001288 ! B-cell receptor CD22 relationship: develops_from CL:0002048 ! late pro-B cell relationship: has_high_plasma_membrane_amount PR:000001408 ! ADP-ribosyl cyclase 1 relationship: has_plasma_membrane_part PR:000001288 ! B-cell receptor CD22 created_by: tmeehan creation_date: 2010-04-28T02:27:47Z [Term] id: CL:0002052 name: Fraction D precursor B cell namespace: cell def: "A pre-B cell that is pre-BCR-negative, and the kappa- and lambda- light immunoglobulin light chain-negative, CD43-low, and is BP-1-positive, CD45R-positive and CD25-positive. This cell type is also described as being AA4-positive, IgM-negative, CD19-positive, CD43-low/negative, and HSA-positive." [GOC:ak, GOC:dsd, GOC:tfm, http://www.immgen.org/index_content.html, PMID:17582343, PMID:18432934] comment: Fraction D precursor B cells are also reportedly CD24-positive and sIgD-negative. synonym: "Fr. D" EXACT [] synonym: "Fraction D pre-B cell" EXACT [GOC:tfm] is_a: CL:0000817 ! precursor B cell intersection_of: CL:0000817 ! precursor B cell intersection_of: has_low_plasma_membrane_amount PR:000001879 ! leukosialin intersection_of: has_not_completed GO:0071708 ! immunoglobulin light chain V-J recombination intersection_of: has_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R intersection_of: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor intersection_of: has_plasma_membrane_part PR:000002039 ! glutamyl aminopeptidase intersection_of: lacks_plasma_membrane_part GO:0035369 ! pre-B cell receptor complex relationship: develops_from CL:0002050 ! Fraction C' precursor B cell relationship: has_low_plasma_membrane_amount PR:000001879 ! leukosialin relationship: has_not_completed GO:0071708 ! immunoglobulin light chain V-J recombination relationship: has_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor relationship: has_plasma_membrane_part PR:000002039 ! glutamyl aminopeptidase relationship: lacks_plasma_membrane_part GO:0035369 ! pre-B cell receptor complex created_by: tmeehan creation_date: 2010-04-28T02:55:16Z [Term] id: CL:0002053 name: CD22-positive, CD38-low small pre-B cell namespace: cell def: "A small pre-B cell that is CD22-positive and CD38-low." [GOC:tfm, PMID:18432934] comment: Markers are associated with human cell. RAG expression maybe diminishing. synonym: "small pre-B cell" EXACT [] is_a: CL:0000954 ! small pre-B-II cell intersection_of: CL:0000954 ! small pre-B-II cell intersection_of: has_low_plasma_membrane_amount PR:000001408 ! ADP-ribosyl cyclase 1 intersection_of: has_plasma_membrane_part PR:000001288 ! B-cell receptor CD22 relationship: develops_from CL:0002051 ! CD38-high pre-BCR positive cell relationship: has_low_plasma_membrane_amount PR:000001408 ! ADP-ribosyl cyclase 1 relationship: has_plasma_membrane_part PR:000001288 ! B-cell receptor CD22 created_by: tmeehan creation_date: 2010-04-28T03:04:48Z [Term] id: CL:0002054 name: Fraction E immature B cell namespace: cell def: "An immature B cell that is IgM-positive, CD45R-positive, CD43-low, CD25-negative, and CD127-negative. This cell type has also been described as being AA4-positive, IgM-positive, CD19-positive, CD43-low/negative, and HSA-positive." [GOC:ak, GOC:dsd, GOC:tfm, PMID:17582343, PMID:18432934] comment: Markers associated with mouse cells. These cells are also reportedly sIgD-negative. is_a: CL:0000816 ! immature B cell intersection_of: CL:0000816 ! immature B cell intersection_of: has_low_plasma_membrane_amount PR:000001879 ! leukosialin intersection_of: has_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor intersection_of: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha intersection_of: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: develops_from CL:0002052 ! Fraction D precursor B cell relationship: has_low_plasma_membrane_amount PR:000001879 ! leukosialin relationship: has_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor relationship: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: lacks_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha created_by: tmeehan creation_date: 2010-04-28T03:13:47Z [Term] id: CL:0002055 name: CD38-negative immature B cell namespace: cell def: "An immature B cell that is CD38-negative, CD10-low, CD21-low, and CD22-high." [GOC:tfm, PMID:18432934] comment: Markers are associated with human cell type. is_a: CL:0000816 ! immature B cell intersection_of: CL:0000816 ! immature B cell intersection_of: has_high_plasma_membrane_amount PR:000001288 ! B-cell receptor CD22 intersection_of: has_low_plasma_membrane_amount PR:000001338 ! complement receptor type 2 intersection_of: has_low_plasma_membrane_amount PR:000001898 ! neprilysin intersection_of: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: develops_from CL:0002053 ! CD22-positive, CD38-low small pre-B cell relationship: has_high_plasma_membrane_amount PR:000001288 ! B-cell receptor CD22 relationship: has_low_plasma_membrane_amount PR:000001338 ! complement receptor type 2 relationship: has_low_plasma_membrane_amount PR:000001898 ! neprilysin relationship: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 created_by: tmeehan creation_date: 2010-04-28T03:19:14Z [Term] id: CL:0002056 name: Fraction F mature B cell namespace: cell def: "A mature B cell subset originally defined as having being CD45R-positive, IgM-positive, IgD-positive and CD43-negative. Subsequent research demonstrated being CD21-positive and CD23-negative and CD93 negative." [GOC:tfm, PMID:17582343] is_a: CL:0000822 ! B-2 B cell intersection_of: CL:0000785 ! mature B cell intersection_of: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex intersection_of: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex intersection_of: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R intersection_of: has_plasma_membrane_part PR:000001338 ! complement receptor type 2 intersection_of: lacks_plasma_membrane_part PR:000001879 ! leukosialin intersection_of: lacks_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor intersection_of: lacks_plasma_membrane_part PR:000002037 ! complement component C1q receptor relationship: develops_from CL:0002054 ! Fraction E immature B cell relationship: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex relationship: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_plasma_membrane_part PR:000001338 ! complement receptor type 2 relationship: lacks_plasma_membrane_part PR:000001879 ! leukosialin relationship: lacks_plasma_membrane_part PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor relationship: lacks_plasma_membrane_part PR:000002037 ! complement component C1q receptor created_by: tmeehan creation_date: 2010-04-30T03:01:48Z [Term] id: CL:0002057 name: CD14-positive, CD16-negative classical monocyte namespace: cell def: "A monocyte that is CD14-positive, CD16-negative, CD64-positive, CD163-positive," [GOC:tfm, PMID:15615263, PMID:1706877, PMID:19689341] comment: Markers are associated with human monocytes. is_a: CL:0000860 ! classical monocyte intersection_of: CL:0000860 ! classical monocyte intersection_of: has_plasma_membrane_part PR:000001465 ! high affinity immunoglobulin gamma Fc receptor I intersection_of: has_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: has_plasma_membrane_part PR:000001925 ! scavenger receptor cysteine-rich type 1 protein M130 relationship: has_plasma_membrane_part PR:000001465 ! high affinity immunoglobulin gamma Fc receptor I relationship: has_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: has_plasma_membrane_part PR:000001925 ! scavenger receptor cysteine-rich type 1 protein M130 created_by: tmeehan creation_date: 2010-06-05T08:25:41Z [Term] id: CL:0002058 name: Gr1-low non-classical monocyte namespace: cell def: "A resident monocyte that is Gr-1 low, CD43-positive, and CX3CR1-positive." [GOC:tfm, PMID:8890901] comment: Markers are associated with mice. The Gr epitope is used to describe this cell type is found on both Ly6c and Ly6g. However, its the Ly6c that is considered the specific marker, and thus used in the cross-product. Also, this cell-type is sometimes described as being Gr1-negative. is_a: CL:0000875 ! non-classical monocyte is_a: CL:0001022 ! CD115-positive monocyte intersection_of: CL:0000875 ! non-classical monocyte intersection_of: has_low_plasma_membrane_amount PR:000001199 ! C-C chemokine receptor type 2 intersection_of: has_low_plasma_membrane_amount PR:000002980 ! lymphocyte antigen 6C intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001206 ! CX3C chemokine receptor 1 intersection_of: has_plasma_membrane_part PR:000001879 ! leukosialin intersection_of: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor intersection_of: lacks_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: develops_from CL:0002398 ! Gr1-positive, CD43-positive monocyte relationship: has_low_plasma_membrane_amount PR:000001199 ! C-C chemokine receptor type 2 relationship: has_low_plasma_membrane_amount PR:000002980 ! lymphocyte antigen 6C relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001206 ! CX3C chemokine receptor 1 relationship: has_plasma_membrane_part PR:000001879 ! leukosialin relationship: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor relationship: lacks_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R created_by: tmeehan creation_date: 2010-06-05T08:25:44Z [Term] id: CL:0002059 name: CD8alpha-positive thymic conventional dendritic cell namespace: cell def: "A conventional thymic dendritic cell that is CD8alpha-positive." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:19273629] synonym: "CD8alpha-alpha-positive thymic conventional dendritic cell" EXACT [] synonym: "DC.8+.Th" EXACT [] is_a: CL:0000941 ! thymic conventional dendritic cell intersection_of: CL:0000941 ! thymic conventional dendritic cell intersection_of: has_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: has_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain created_by: tmeehan creation_date: 2010-06-07T02:48:36Z [Term] id: CL:0002060 name: melanophage namespace: cell def: "A melanin-containing macrophage that obtains the pigment by phagocytosis of melanosomes." [GOC:tfm, PMID:20479296, PMID:2943821] is_a: CL:0000864 ! tissue-resident macrophage intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: has_part CHEBI:25179 ! melanin intersection_of: part_of UBERON:0002097 ! skin of body relationship: has_part CHEBI:25179 ! melanin relationship: part_of UBERON:0002097 ! skin of body created_by: tmeehan creation_date: 2010-06-22T10:46:12Z [Term] id: CL:0002061 name: T-helper 9 cell namespace: cell def: "A T-helper cell that is characterized by secreting interleukin 9 and responding to helminth infections. This cell-type can derives from Th2 cells in the presence of TGF-beta and IL-4. Th2 cytokine production is surpressed." [GOC:tfm, PMID:18931678, PMID:19604299, PMID:20154671] synonym: "T helper cells type 9" EXACT [] synonym: "T(H)-9 cell" EXACT [] synonym: "Th9" EXACT [PMID:18931678] is_a: CL:0000492 ! CD4-positive helper T cell intersection_of: CL:0000492 ! CD4-positive helper T cell intersection_of: capable_of GO:0002215 ! defense response to nematode intersection_of: capable_of GO:0032638 ! interleukin-9 production intersection_of: has_plasma_membrane_part PR:000008982 ! interleukin-17 receptor B relationship: capable_of GO:0002215 ! defense response to nematode relationship: capable_of GO:0032638 ! interleukin-9 production relationship: has_plasma_membrane_part PR:000008982 ! interleukin-17 receptor B created_by: tmeehan creation_date: 2010-06-22T11:18:44Z [Term] id: CL:0002062 name: type I pneumocyte namespace: cell def: "A type I pneumocyte is a flattened, branched pneumocyte that covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange." [GOC:tfm, http://www.copewithcytokines.de, PMID:20054144] synonym: "AT1" EXACT [] synonym: "ATI" EXACT [] synonym: "lung type 1 cells" EXACT [] synonym: "membranous pneumocytes" EXACT [] synonym: "pulmonary alveolar type I cell" EXACT [] synonym: "small alveolar cells" EXACT [] synonym: "squamous alveolar cell" EXACT [] synonym: "squamous alveolar lining cell" EXACT [] synonym: "type 1 alveolar epithelial cells" EXACT [] synonym: "type 1 pneumocyte" EXACT [] synonym: "type I alveolar cells" EXACT [] synonym: "type I alveolar epithelial cells" EXACT [] xref: BTO:0000780 xref: FMA:62500 is_a: CL:0000322 ! pneumocyte intersection_of: CL:0000322 ! pneumocyte intersection_of: capable_of GO:0007585 ! respiratory gaseous exchange relationship: capable_of GO:0007585 ! respiratory gaseous exchange created_by: tmeehan creation_date: 2010-06-23T04:37:54Z [Term] id: CL:0002063 name: type II pneumocyte namespace: cell def: "A type II pneumocyte is a pneumocyte that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a type I pneumocyte. Thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli." [GOC:tfm, http://www.copewithcytokines.de, ISBN:0412046911, PMID:8540632] synonym: "AT2" EXACT [] synonym: "ATII" EXACT [] synonym: "cuboidal type II cell" EXACT [] synonym: "granular pneumocyte" EXACT [] synonym: "great alveolar cell" EXACT [] synonym: "lung type 2 cell" EXACT [] synonym: "lung type II cell" RELATED [] synonym: "TII" EXACT [] synonym: "type 2 alveolar epithelial cell" EXACT [] synonym: "type 2 alveolocyte" EXACT [] synonym: "type 2 pneumocyte" EXACT [] synonym: "type II alveolar cell" EXACT [] synonym: "type II alveolar epithelial cell" EXACT [] synonym: "type II alveolocyte" EXACT [] xref: BTO:0000538 xref: FMA:62501 is_a: CL:0000157 ! surfactant secreting cell is_a: CL:0000322 ! pneumocyte intersection_of: CL:0000322 ! pneumocyte intersection_of: capable_of GO:0032940 ! secretion by cell intersection_of: capable_of GO:0043129 ! surfactant homeostasis relationship: capable_of GO:0032940 ! secretion by cell relationship: capable_of GO:0043129 ! surfactant homeostasis created_by: tmeehan creation_date: 2010-06-24T12:04:13Z [Term] id: CL:0002064 name: pancreatic acinar cell namespace: cell def: "A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules." [GOC:tfm, http://www.copewithcytokines.de/cope.cgi?key=pancreatic%20acinar%20cells, ISBN:0517223651, PMID:20395539] synonym: "acinar cell of pancreas" EXACT [] xref: BTO:0000028 xref: CALOHA:TS-0737 xref: FMA:63032 is_a: CL:0000622 ! acinar cell is_a: CL:1001433 ! epithelial cell of exocrine pancreas intersection_of: CL:0000622 ! acinar cell intersection_of: part_of UBERON:0001263 ! pancreatic acinus relationship: has_part GO:0042589 ! zymogen granule membrane relationship: part_of UBERON:0001263 ! pancreatic acinus created_by: tmeehan creation_date: 2010-06-24T03:16:29Z [Term] id: CL:0002066 name: Feyrter cell namespace: cell def: "A neuroendocrine cell found in the epithelium of the lungs and respiratory tract. This cell type is rounded or elliptical in shape, situated mainly in the basal part of the epithelium; regulates bronchial secretion, smooth muscle contraction, lobular growth, ciliary activity and chemoreception. Cell has an electron-lucent cytoplasm, contains numerous dense-cored vesicles with a clear halo between the core and the limiting membrane." [GOC:tfm, ISBN:0412046911, ISBN:0517223651] synonym: "bronchiolar Kulchitsky cell" EXACT [] synonym: "Kultschitzky cell of bronchiole" EXACT [] synonym: "P cell" BROAD [] synonym: "respiratory enterochromaffin cell " EXACT [] xref: FMA:14118 is_a: CL:0000165 ! neuroendocrine cell created_by: tmeehan creation_date: 2010-06-28T08:24:30Z [Term] id: CL:0002067 name: type A enterocrine cell namespace: cell def: "An enterocrine cell that produces glucagon." [GOC:tfm, ISBN:0412046911] xref: FMA:62939 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000170 ! glucagon secreting cell created_by: tmeehan creation_date: 2010-09-10T10:48:54Z [Term] id: CL:0002068 name: Purkinje myocyte namespace: cell def: "Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter." [FMA:0412046911, GOC:tfm, PMID:19939742] synonym: "myocytus conducens cardiacus" EXACT [] synonym: "Purkinje cell fiber" EXACT [] synonym: "Purkinje muscle cell" EXACT [] xref: BTO:0001032 xref: FMA:14146 is_a: CL:0002086 ! specialized cardiac myocyte created_by: tmeehan creation_date: 2010-06-28T08:36:15Z [Term] id: CL:0002069 name: type II vestibular sensory cell namespace: cell def: "Mostly cylindrical, resemble Type 1 in their contents and the presence of a kinocilium and stereocilium apically; much greater variation in size, some almost span the entire thickness of the sensory epithelium, while others are smaller than Type 1; receive multiple efferent nerve boutons around their bases as well as afferent endings, which are small expansions rather than chalices." [GOC:tfm, ISBN:0517223651] synonym: "type 2 vestibular hair cell" EXACT [] synonym: "type 2 vestibular sensory cell" EXACT [] synonym: "type II hair cell" EXACT [] xref: FMA:67909 is_a: CL:0000609 ! vestibular hair cell created_by: tmeehan creation_date: 2010-06-29T09:58:13Z [Term] id: CL:0002070 name: type I vestibular sensory cell namespace: cell def: "Bottle-shaped with narrow neck; broad, rounded basal portion where nucleus is located; stereocilia and a single kinocilium is present apically; receive nerve bouton at their base from an afferent cup-shaped (chalice or calyx) nerve ending." [GOC:tfm, ISBN:0517223651] synonym: "type 1 vestibular hair cell" EXACT [] synonym: "type 1 vestibular sensory cell" EXACT [] synonym: "type I hair cell" EXACT [] xref: FMA:62352 is_a: CL:0000609 ! vestibular hair cell created_by: tmeehan creation_date: 2010-06-29T09:58:19Z [Term] id: CL:0002071 name: enterocyte of epithelium of large intestine namespace: cell def: "Columnar cell which populate the epithelium of large intestine and absorb water. This cell is the most numerous of the epithelial cell types in the large intestine; bear apical microvilli, contain secretory granules in their apical cytoplasm; secretion appears to be largely mucins, but is also rich in antibodies of the IgA type." [GOC:tfm, ISBN:0517223651] synonym: "columnar cell" EXACT [] synonym: "columnar cell of the colon" EXACT [] synonym: "vacuolar absorptive cell" EXACT [] xref: BTO:0002484 xref: FMA:63638 xref: FMA:66771 is_a: CL:0000584 ! enterocyte is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:0001278 ! epithelium of large intestine relationship: part_of UBERON:0001278 ! epithelium of large intestine created_by: tmeehan creation_date: 2010-06-29T11:07:25Z [Term] id: CL:0002072 name: nodal myocyte namespace: cell def: "A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery." [FMA:67101, GOC:tfm] synonym: "cardiac pacemaker cell" EXACT [GOC:pr] synonym: "myocytus nodalis" EXACT [] synonym: "P cell" EXACT [] synonym: "pacemaker cell" BROAD [] xref: BTO:0004190 xref: FMA:67101 is_a: CL:0002086 ! specialized cardiac myocyte created_by: tmeehan creation_date: 2010-06-29T11:41:37Z [Term] id: CL:0002073 name: transitional myocyte namespace: cell def: "Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes." [FMA:67142, GOC:tfm] xref: FMA:67142 is_a: CL:0002086 ! specialized cardiac myocyte created_by: tmeehan creation_date: 2010-06-29T02:39:32Z [Term] id: CL:0002074 name: myocardial endocrine cell namespace: cell def: "The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides)." [FMA:67111, GOC:tfm] xref: FMA:67111 is_a: CL:0000163 ! endocrine cell is_a: CL:0002086 ! specialized cardiac myocyte created_by: tmeehan creation_date: 2010-06-29T11:50:47Z [Term] id: CL:0002075 name: brush cell of trachebronchial tree namespace: cell def: "Infrequent type of columnar epithelial cell. This cell is characterized by the presence of a tuft of blunt, squat microvilli (approximately 120-140/cell) on the cell surface. The microvilli contain filaments that stretch into the underlying cytoplasm. They have a distinctive pear shape with a wide base and a narrow microvillous apex. Function not known." [GOC:tfm, ISBN:0517223651, PMID:15817800] synonym: "pulmonary brush cell" RELATED [] is_a: CL:0002202 ! epithelial cell of tracheobronchial tree is_a: CL:0002204 ! brush cell intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0007196 ! tracheobronchial tree relationship: part_of UBERON:0007196 ! tracheobronchial tree created_by: tmeehan creation_date: 2010-06-29T03:22:46Z [Term] id: CL:0002076 name: endo-epithelial cell namespace: cell def: "An epithelial cell derived from endoderm." [FMA:69075, GOC:tfm] xref: FMA:69075 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell relationship: develops_from CL:0000223 ! endodermal cell created_by: tmeehan creation_date: 2010-06-29T03:38:14Z [Term] id: CL:0002077 name: ecto-epithelial cell namespace: cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell relationship: develops_from CL:0000221 ! ectodermal cell created_by: tmeehan creation_date: 2010-06-29T03:38:22Z [Term] id: CL:0002078 name: meso-epithelial cell namespace: cell def: "Epithelial cell derived from mesoderm or mesenchyme." [FMA:69076, GOC:tfm] synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell relationship: develops_from CL:0000222 ! mesodermal cell created_by: tmeehan creation_date: 2010-06-29T03:49:14Z [Term] id: CL:0002079 name: pancreatic ductal cell namespace: cell def: "Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH." [FMA:63099, GOC:tfm, PMID:14740223] xref: FMA:63099 is_a: CL:1000488 ! cholangiocyte is_a: CL:1001433 ! epithelial cell of exocrine pancreas intersection_of: CL:0000083 ! epithelial cell of pancreas intersection_of: capable_of GO:0015106 ! bicarbonate transmembrane transporter activity intersection_of: part_of UBERON:0001064 ! ventral pancreatic duct relationship: capable_of GO:0015106 ! bicarbonate transmembrane transporter activity relationship: part_of UBERON:0001064 ! ventral pancreatic duct created_by: tmeehan creation_date: 2010-06-30T08:49:43Z [Term] id: CL:0002080 name: pancreatic centro-acinar cell namespace: cell def: "A cubodial epithelial cell that is continuous with the lining of intercalated ducts that drain the acinus. This cell type secretes a high pH solution to aid in activation of zymogens, and can differentiate into endocrine and exocrine pancreatic cell types." [GOC:tfm, PMID:12142741, PMID:20018761, PMID:8185160] synonym: "centroacinar cell of Langerhans" EXACT [] synonym: "pancreatic centroacinar cell" EXACT [] xref: FMA:62455 is_a: CL:1001433 ! epithelial cell of exocrine pancreas intersection_of: CL:0000083 ! epithelial cell of pancreas intersection_of: capable_of GO:0015106 ! bicarbonate transmembrane transporter activity intersection_of: part_of UBERON:0001263 ! pancreatic acinus relationship: capable_of GO:0015106 ! bicarbonate transmembrane transporter activity relationship: part_of UBERON:0001263 ! pancreatic acinus created_by: tmeehan creation_date: 2010-06-30T08:49:52Z [Term] id: CL:0002081 name: type II cell of carotid body namespace: cell def: "This cell resembles a glia cell, express the glial marker S100 and act as a supporting cell to type I cell. This cell is located in a small cluster of type I and type II cells near the fork of the carotid artery." [GOC:tfm, http://en.wikipedia.org/wiki/Carotid_body, PMID:7938227] synonym: "sheath cell of carotid body" EXACT [] xref: FMA:84187 is_a: CL:0000703 ! sustentacular cell is_a: CL:0002256 ! supporting cell of carotid body created_by: tmeehan creation_date: 2010-06-30T04:23:42Z [Term] id: CL:0002082 name: type II cell of adrenal medulla namespace: cell def: "A chromaffin cell of the adrenal medulla that produces epinephrine." [GOC:tfm] synonym: "adremergic chromaffin cell" EXACT [] synonym: "adrenal secreting cell of the adrenal medulla" EXACT [] synonym: "epiniphrine secreting cell of the adrenal medulla" EXACT [] xref: FMA:69322 is_a: CL:0000336 ! adrenal medulla chromaffin cell is_a: CL:0000454 ! epinephrine secreting cell created_by: tmeehan creation_date: 2010-07-14T09:41:42Z [Term] id: CL:0002083 name: type I cell of adrenal medulla namespace: cell def: "A chromaffin cell of the adrenal medulla that produces norepinephrine." [GOC:tfm, ISBN:068340007X] synonym: "noradrenergic chromaffin cell" EXACT [] xref: FMA:69321 is_a: CL:0000336 ! adrenal medulla chromaffin cell is_a: CL:0000459 ! norepinephrin secreting cell intersection_of: CL:0000336 ! adrenal medulla chromaffin cell intersection_of: capable_of GO:0048243 ! norepinephrine secretion intersection_of: part_of UBERON:0001236 ! adrenal medulla relationship: capable_of GO:0048243 ! norepinephrine secretion relationship: part_of UBERON:0001236 ! adrenal medulla created_by: tmeehan creation_date: 2010-07-14T10:12:24Z [Term] id: CL:0002084 name: Boettcher cell namespace: cell def: "A Boettcher cell is a polyhedral cells on the basilar membrane of the cochlea, and is located beneath Claudius cells. A Boettcher cell is considered a supporting cell for the organ of Corti, and is present only in the lower turn of the cochlea. These cells interweave with each other, and project microvilli into the intercellular space. Because of their structural specialization, a Boettcher cell is believed to play a significant role in the function of the cochlea. They demonstrate high levels of calmodulin, and may be involved in mediating Ca(2+) regulation and ion transport." [GOC:tfm, http://en.wikipedia.org/wiki/Boettcher_cell] synonym: "Boettcher's cell" EXACT [] synonym: "Bottcher cell" EXACT [] synonym: "Bottcher's cell" EXACT [] is_a: CL:0002315 ! supporting cell of cochlea created_by: tmeehan creation_date: 2010-07-14T03:22:02Z [Term] id: CL:0002085 name: tanycyte namespace: cell alt_id: CL:0000643 def: "Specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. Resemble spongioblasts seen in developing brain. Found in the adult brain in the third ventricle, cerebral aqueduct, spinal canal and floor of the fourth ventricle." [GOC:tfm, http://neurolex.org/wiki/Category\:Tanycyte] synonym: "stretch cell" EXACT [] xref: BTO:0001953 xref: FMA:54560 is_a: CL:0000683 ! ependymoglial cell created_by: tmeehan creation_date: 2010-07-15T11:21:11Z [Term] id: CL:0002086 name: specialized cardiac myocyte namespace: cell def: "A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart." [FMA:67968, GOC:tfm] xref: FMA:67968 is_a: CL:0000746 ! cardiac muscle cell created_by: tmeehan creation_date: 2010-07-21T01:33:38Z [Term] id: CL:0002087 name: nongranular leukocyte namespace: cell def: "A leukocyte that lacks granules." [GOC:tfm] synonym: "agranular leukocyte" EXACT [] xref: FMA:62855 is_a: CL:0000738 ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: lacks_part GO:0030141 ! secretory granule relationship: lacks_part GO:0030141 ! secretory granule created_by: tmeehan creation_date: 2010-07-22T11:30:33Z [Term] id: CL:0002088 name: interstitial cell of Cajal namespace: cell def: "This is a cell found in the gastrointestinal tract of mammals and serves as a pacemaker that triggers gut contraction. ICCs mediate inputs from the enteric nervous system to smooth muscle cells and are thought to be the cells from which gastrointestinal stromal tumors (GISTs) arise." [GOC:tfm, PMID:16460275, PMID:19520112] comment: Some argue this cell type is of mesenchymal origin. synonym: "ICC" EXACT [] synonym: "intestinal pacemaker cell" EXACT [GOC:pr] xref: BTO:0003914 xref: FMA:86573 is_a: CL:0000710 ! neurecto-epithelial cell intersection_of: CL:0000710 ! neurecto-epithelial cell intersection_of: capable_of GO:0043134 ! regulation of hindgut contraction relationship: capable_of GO:0043134 ! regulation of hindgut contraction created_by: tmeehan creation_date: 2010-07-22T03:26:00Z [Term] id: CL:0002089 name: nuocyte namespace: cell def: "A leukocyte cell capable of secreting IL-13 in response to a helminth infection. This cell is lineage-negative, ICOS-positive, IL1RL1-positive, IL7Ralpha-positive, and IL17Br-positive." [GOC:tfm, PMID:20200518] is_a: CL:0000738 ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: capable_of GO:0002830 ! positive regulation of type 2 immune response intersection_of: capable_of GO:0032616 ! interleukin-13 production intersection_of: has_plasma_membrane_part PR:000001860 ! inducible T-cell costimulator intersection_of: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: has_plasma_membrane_part PR:000008982 ! interleukin-17 receptor B intersection_of: has_plasma_membrane_part PR:000008994 ! interleukin-1 receptor-like 1 intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001008 ! integrin alpha-2 intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001326 ! bone marrow stromal antigen 2 intersection_of: lacks_plasma_membrane_part PR:000001893 ! natural cytotoxicity triggering receptor 1 intersection_of: lacks_plasma_membrane_part PR:000001927 ! sialic acid-binding Ig-like lectin 5 intersection_of: lacks_plasma_membrane_part PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha relationship: capable_of GO:0002830 ! positive regulation of type 2 immune response relationship: capable_of GO:0032616 ! interleukin-13 production relationship: has_plasma_membrane_part PR:000001860 ! inducible T-cell costimulator relationship: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: has_plasma_membrane_part PR:000008982 ! interleukin-17 receptor B relationship: has_plasma_membrane_part PR:000008994 ! interleukin-1 receptor-like 1 relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001008 ! integrin alpha-2 relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001326 ! bone marrow stromal antigen 2 relationship: lacks_plasma_membrane_part PR:000001893 ! natural cytotoxicity triggering receptor 1 relationship: lacks_plasma_membrane_part PR:000001927 ! sialic acid-binding Ig-like lectin 5 relationship: lacks_plasma_membrane_part PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha created_by: tmeehan creation_date: 2010-08-12T02:22:19Z [Term] id: CL:0002090 name: polar body namespace: cell def: "One of two small cells formed by the first and second meiotic division of oocytes." [GOC:tfm, http://en.wikipedia.org/wiki/Polar_body, ISBN:068340007X] xref: EHDAA2:0004716 xref: FMA:85543 xref: WBbt:0008429 xref: XAO:0000262 is_a: CL:0000021 ! female germ cell created_by: tmeehan creation_date: 2010-08-23T09:49:53Z [Term] id: CL:0002091 name: primary polar body namespace: cell def: "A small cell formed by the first meiotic division of oocytes." [GOC:tfm, ISBN:068340007X] synonym: "first polar body" EXACT [EHDAA2:0000541] synonym: "polocytus primarius" EXACT [FMA:18650] xref: EHDAA2:0000541 xref: EMAPA:16032 xref: FMA:18650 xref: VHOG:0000464 is_a: CL:0002090 ! polar body created_by: tmeehan creation_date: 2010-08-23T09:49:58Z [Term] id: CL:0002092 name: bone marrow cell namespace: cell def: "A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells." [GOC:tfm, ISBN:0618947256] comment: MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. xref: BTO:0004850 xref: FMA:83621 is_a: CL:0001035 ! bone cell intersection_of: CL:0001035 ! bone cell intersection_of: part_of UBERON:0002371 ! bone marrow relationship: part_of UBERON:0002371 ! bone marrow created_by: tmeehan creation_date: 2010-07-22T04:48:15Z [Term] id: CL:0002093 name: secondary polar body namespace: cell def: "A small cell formed by the second meiotic division of oocytes. In mammals, the second polar body may fail to form unless the ovum has been penetrated by a sperm cell." [GOC:tfm, ISBN:068340007X] synonym: "polocytus secundarius" EXACT [FMA:18651] synonym: "second polar body" EXACT [EHDAA2:0001820] xref: EHDAA2:0001820 xref: EMAPA:16034 xref: EMAPA:16045 xref: FMA:18651 is_a: CL:0002090 ! polar body created_by: tmeehan creation_date: 2010-08-23T09:50:01Z [Term] id: CL:0002094 name: interstitial cell of ovary namespace: cell def: "A cell that makes up the loose connective tissue of the ovary." [GOC:tfm] xref: FMA:18709 is_a: CL:0002132 ! stromal cell of ovary created_by: tmeehan creation_date: 2010-08-23T11:11:34Z [Term] id: CL:0002095 name: hilus cell of ovary namespace: cell def: "A cell in the hilum of the ovary that produces androgens." [GOC:tfm, ISBN:068340007X] synonym: "hilar cell of ovary" EXACT [] xref: FMA:18710 is_a: CL:0000593 ! androgen secreting cell is_a: CL:0002132 ! stromal cell of ovary created_by: tmeehan creation_date: 2010-08-23T11:18:18Z [Term] id: CL:0002096 name: internodal tract myocyte namespace: cell def: "A specialised myocyte that lies between the sinoatrial node and the atrioventricular node and is involved in the conduction of electrical signals." [GOC:tfm, ISBN:0781729300] xref: FMA:223275 is_a: CL:0002086 ! specialized cardiac myocyte created_by: tmeehan creation_date: 2010-08-23T11:24:11Z [Term] id: CL:0002097 name: cortical cell of adrenal gland namespace: cell def: "A cell of the adrenal cortex. Cell types include those that synthesize and secrete chemical derivatives (steroids) of cholesterol." [GOC:tfm] synonym: "adrenal cortex cell" EXACT [] synonym: "adrenocortical cell" EXACT [] xref: FMA:69545 is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000174 ! steroid hormone secreting cell is_a: CL:0002078 ! meso-epithelial cell intersection_of: CL:0002078 ! meso-epithelial cell intersection_of: part_of UBERON:0001235 ! adrenal cortex relationship: part_of UBERON:0001235 ! adrenal cortex created_by: tmeehan creation_date: 2010-08-24T01:37:44Z [Term] id: CL:0002098 name: regular cardiac myocyte namespace: cell def: "A cardiac myocyte that is connected together by transverse intercalated discs at a regular interval." [GOC:tfm] synonym: "regular cardiac muscle cell" EXACT [] synonym: "regular cardiac muscle fiber" EXACT [] xref: FMA:67967 is_a: CL:0000746 ! cardiac muscle cell created_by: tmeehan creation_date: 2010-08-23T11:33:10Z [Term] id: CL:0002099 name: type I cell of adrenal cortex namespace: cell alt_id: CL:1000423 def: "A small, polyhedral, cell found in rounded groups or curved columns with deeply staining nuclei, scanty basophilic cytoplasm and a few lipid droplets. This cell in the zona glomerulosa produces mineralocorticoids." [GOC:tfm, ISBN:0517223651] synonym: "epithelial cell of zona glomerulosa of adrenal gland" EXACT [] xref: FMA:69273 is_a: CL:0000456 ! mineralocorticoid secreting cell is_a: CL:0002097 ! cortical cell of adrenal gland intersection_of: CL:0002097 ! cortical cell of adrenal gland intersection_of: part_of UBERON:0002053 ! zona glomerulosa of adrenal gland relationship: part_of UBERON:0002053 ! zona glomerulosa of adrenal gland created_by: tmeehan creation_date: 2010-08-24T01:42:02Z [Term] id: CL:0002100 name: regular interventricular cardiac myocyte namespace: cell def: "A regular cardiac myocyte of the interventricular region of the heart." [GOC:tfm] xref: FMA:228792 is_a: CL:0002098 ! regular cardiac myocyte created_by: tmeehan creation_date: 2010-08-23T11:40:52Z [Term] id: CL:0002101 name: CD38-positive naive B cell namespace: cell def: "A CD38-positive naive B cell is a mature B cell that has the phenotype CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] synonym: "CD38+ naive B cell" EXACT [] synonym: "CD38+ naive B lymphocyte" EXACT [] synonym: "CD38+ naive B-cell" EXACT [] synonym: "CD38+ naive B-lymphocyte" EXACT [] synonym: "CD38-positive naive B lymphocyte" EXACT [] synonym: "CD38-positive naive B-cell" EXACT [] synonym: "CD38-positive naive B-lymphocyte" EXACT [] is_a: CL:0000788 ! naive B cell intersection_of: CL:0000788 ! naive B cell intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 [Term] id: CL:0002102 name: CD38-negative naive B cell namespace: cell def: "A CD38-negative naive B cell is a mature B cell that has the phenotype CD38-negative, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] synonym: "CD38- naive B cell" EXACT [] synonym: "CD38- naive B lymphocyte" EXACT [] synonym: "CD38- naive B-cell" EXACT [] synonym: "CD38- naive B-lymphocyte" EXACT [] synonym: "CD38-negative naive B lymphocyte" EXACT [] synonym: "CD38-negative naive B-cell" EXACT [] synonym: "CD38-negative naive B-lymphocyte" EXACT [] is_a: CL:0000788 ! naive B cell intersection_of: CL:0000788 ! naive B cell intersection_of: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 [Term] id: CL:0002103 name: IgG-positive double negative memory B cell namespace: cell def: "An IgG-positive double negative memory B cell is a double negative memory B cell with the phenotype IgG-positive, IgD-negative, and CD27-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] synonym: "IgG+ dn memory B cell" EXACT [] synonym: "IgG+ dn memory B lymphocyte" EXACT [] synonym: "IgG+ dn memory B-cell" EXACT [] synonym: "IgG+ dn memory B-lymphocyte" EXACT [] synonym: "IgG+ double negative memory B cell" EXACT [] synonym: "IgG+ double negative memory B lymphocyte" EXACT [] synonym: "IgG+ double negative memory B-cell" EXACT [] synonym: "IgG+ double negative memory B-lymphocyte" EXACT [] synonym: "IgG-positive dn memory B cell" EXACT [] synonym: "IgG-positive dn memory B lymphocyte" EXACT [] synonym: "IgG-positive dn memory B-cell" EXACT [] synonym: "IgG-positive dn memory B-lymphocyte" EXACT [] synonym: "IgG-positive double negative memory B lymphocyte" EXACT [] synonym: "IgG-positive double negative memory B-cell" EXACT [] synonym: "IgG-positive double negative memory B-lymphocyte" EXACT [] is_a: CL:0000981 ! double negative memory B cell intersection_of: CL:0000981 ! double negative memory B cell intersection_of: has_plasma_membrane_part GO:0071735 ! IgG immunoglobulin complex relationship: has_plasma_membrane_part GO:0071735 ! IgG immunoglobulin complex [Term] id: CL:0002104 name: IgG-negative double negative memory B cell namespace: cell def: "An IgG-negative double negative memory B cell is a double negative memory B cell with the phenotype IgG-negative, IgD-negative, and CD27-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] synonym: "IgG- dn memory B cell" EXACT [] synonym: "IgG- dn memory B lymphocyte" EXACT [] synonym: "IgG- dn memory B-cell" EXACT [] synonym: "IgG- dn memory B-lymphocyte" EXACT [] synonym: "IgG- double negative memory B cell" EXACT [] synonym: "IgG- double negative memory B lymphocyte" EXACT [] synonym: "IgG- double negative memory B-cell" EXACT [] synonym: "IgG- double negative memory B-lymphocyte" EXACT [] synonym: "IgG-negative dn memory B cell" EXACT [] synonym: "IgG-negative dn memory B lymphocyte" EXACT [] synonym: "IgG-negative dn memory B-cell" EXACT [] synonym: "IgG-negative dn memory B-lymphocyte" EXACT [] synonym: "IgG-negative double negative memory B lymphocyte" EXACT [] synonym: "IgG-negative double negative memory B-cell" EXACT [] synonym: "IgG-negative double negative memory B-lymphocyte" EXACT [] is_a: CL:0000981 ! double negative memory B cell intersection_of: CL:0000981 ! double negative memory B cell intersection_of: lacks_plasma_membrane_part GO:0071735 ! IgG immunoglobulin complex relationship: lacks_plasma_membrane_part GO:0071735 ! IgG immunoglobulin complex [Term] id: CL:0002105 name: CD38-positive IgG memory B cell namespace: cell def: "A CD38-positive IgG memory B cell is a class switched memory B cell that expresses IgG on the cell surface with the phenotype CD38-positive and IgG-positive." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] synonym: "CD38+ IgG memory B cell" EXACT [] synonym: "CD38+ IgG memory B lymphocyte" EXACT [] synonym: "CD38+ IgG memory B-cell" EXACT [] synonym: "CD38+ IgG memory B-lymphocyte" EXACT [] synonym: "CD38-positive IgG memory B lymphocyte" EXACT [] synonym: "CD38-positive IgG memory B-cell" EXACT [] synonym: "CD38-positive IgG memory B-lymphocyte" EXACT [] is_a: CL:0000979 ! IgG memory B cell intersection_of: CL:0000979 ! IgG memory B cell intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 [Term] id: CL:0002106 name: IgD-positive CD38-positive IgG memory B cell namespace: cell def: "An IgD-positive CD38-positive IgG memory B cell is a CD38-positive IgG-positive class switched memory B cell that has class switched and expresses IgD on the cell surface with the phenotype IgD-positive, CD38-positive, and IgG-positive." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] is_a: CL:0002105 ! CD38-positive IgG memory B cell intersection_of: CL:0002105 ! CD38-positive IgG memory B cell intersection_of: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: has_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex [Term] id: CL:0002107 name: IgD-negative CD38-positive IgG memory B cell namespace: cell def: "An IgD-negative CD38-positive IgG memory B cell is a CD38-positive IgG-positive that has class switched and lacks expression of IgD on the cell surface with the phenotype IgD-negative, CD38-positive, and IgG-positive." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] is_a: CL:0002105 ! CD38-positive IgG memory B cell intersection_of: CL:0002105 ! CD38-positive IgG memory B cell intersection_of: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex [Term] id: CL:0002108 name: CD38-negative IgG memory B cell namespace: cell def: "A CD38-negative IgG memory B cell is a IgG-positive class switched memory B cell that has class switched and expresses IgG on the cell surface with the phenotype CD38-negative, IgD-negative, and IgG-positive." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] is_a: CL:0000979 ! IgG memory B cell intersection_of: CL:0000979 ! IgG memory B cell intersection_of: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex intersection_of: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: lacks_plasma_membrane_part GO:0071738 ! IgD immunoglobulin complex relationship: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 [Term] id: CL:0002109 name: B220-positive CD38-positive naive B cell namespace: cell def: "A B220-positive CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-positive, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] synonym: "B220+CD38+ naive B cell" EXACT [] synonym: "B220+CD38+ naive B lymphocyte" EXACT [] synonym: "B220+CD38+ naive B-cell" EXACT [] synonym: "B220+CD38+ naive B-lymphocyte" EXACT [] synonym: "B220-positive CD38-positive naive B lymphocyte" EXACT [] synonym: "B220-positive CD38-positive naive B-cell" EXACT [] synonym: "B220-positive CD38-positive naive B-lymphocyte" EXACT [] synonym: "CD38+B220+ naive B cell" EXACT [] synonym: "CD38+B220+ naive B lymphocyte" EXACT [] synonym: "CD38+B220+ naive B-cell" EXACT [] synonym: "CD38+B220+ naive B-lymphocyte" EXACT [] is_a: CL:0002101 ! CD38-positive naive B cell intersection_of: CL:0002101 ! CD38-positive naive B cell intersection_of: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R [Term] id: CL:0002110 name: B220-low CD38-positive naive B cell namespace: cell def: "A B220-low CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-low, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] is_a: CL:0002101 ! CD38-positive naive B cell intersection_of: CL:0002101 ! CD38-positive naive B cell intersection_of: has_low_plasma_membrane_amount PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_low_plasma_membrane_amount PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R [Term] id: CL:0002111 name: CD38-negative unswitched memory B cell namespace: cell def: "An CD38-negative unswitched memory B cell is an unswitched memory B cell that has the phenotype CD38-negative, IgD-positive, CD138-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] synonym: "CD38- unswitched memory B cell" EXACT [] synonym: "CD38- unswitched memory B lymphocyte" EXACT [] synonym: "CD38- unswitched memory B-cell" EXACT [] synonym: "CD38- unswitched memory B-lymphocyte" EXACT [] synonym: "CD38-negative unswitched memory B lymphocyte" EXACT [] synonym: "CD38-negative unswitched memory B-cell" EXACT [] synonym: "CD38-negative unswitched memory B-lymphocyte" EXACT [] is_a: CL:0000970 ! unswitched memory B cell intersection_of: CL:0000970 ! unswitched memory B cell intersection_of: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 [Term] id: CL:0002112 name: B220-positive CD38-negative unswitched memory B cell namespace: cell def: "A B220-positive CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-positive, CD38-negative, IgD-positive, CD138-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] is_a: CL:0002111 ! CD38-negative unswitched memory B cell intersection_of: CL:0002111 ! CD38-negative unswitched memory B cell intersection_of: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R [Term] id: CL:0002113 name: B220-low CD38-negative unswitched memory B cell namespace: cell def: "A B220-low CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-low, CD38-negative, IgD-positive, CD138-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] is_a: CL:0002111 ! CD38-negative unswitched memory B cell intersection_of: CL:0002111 ! CD38-negative unswitched memory B cell intersection_of: has_low_plasma_membrane_amount PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_low_plasma_membrane_amount PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R [Term] id: CL:0002114 name: CD38-positive unswitched memory B cell namespace: cell def: "A CD38-positive unswitched memory B cell is an unswitched memory B cell that has the phenotype CD38-positive, IgD-positive, CD138-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] synonym: "CD38+ unswitched memory B cell" EXACT [] synonym: "CD38+ unswitched memory B lymphocyte" EXACT [] synonym: "CD38+ unswitched memory B-cell" EXACT [] synonym: "CD38+ unswitched memory B-lymphocyte" EXACT [] synonym: "CD38-positive unswitched memory B lymphocyte" EXACT [] synonym: "CD38-positive unswitched memory B-cell" EXACT [] synonym: "CD38-positive unswitched memory B-lymphocyte" EXACT [] is_a: CL:0000970 ! unswitched memory B cell intersection_of: CL:0000970 ! unswitched memory B cell intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 [Term] id: CL:0002115 name: B220-positive CD38-positive unswitched memory B cell namespace: cell def: "A B220-positive CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-positive, CD38-positive, IgD-positive, CD138-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] is_a: CL:0002114 ! CD38-positive unswitched memory B cell intersection_of: CL:0002114 ! CD38-positive unswitched memory B cell intersection_of: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R [Term] id: CL:0002116 name: B220-low CD38-positive unswitched memory B cell namespace: cell def: "A B220-low CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-low, CD38-positive, IgD-positive, CD138-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] is_a: CL:0002114 ! CD38-positive unswitched memory B cell intersection_of: CL:0002114 ! CD38-positive unswitched memory B cell intersection_of: has_low_plasma_membrane_amount PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_low_plasma_membrane_amount PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R [Term] id: CL:0002117 name: IgG-negative class switched memory B cell namespace: cell def: "A class switched memory B cell that lacks IgG on the cell surface." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] synonym: "IgG- class switched memory B cell" EXACT [] synonym: "IgG- class switched memory B lymphocyte" EXACT [] synonym: "IgG- class switched memory B-cell" EXACT [] synonym: "IgG- class switched memory B-lymphocyte" EXACT [] synonym: "IgG-negative class switched memory B lymphocyte" EXACT [] synonym: "IgG-negative class switched memory B-cell" EXACT [] synonym: "IgG-negative class switched memory B-lymphocyte" EXACT [] is_a: CL:0000972 ! class switched memory B cell intersection_of: CL:0000972 ! class switched memory B cell intersection_of: lacks_plasma_membrane_part GO:0071735 ! IgG immunoglobulin complex relationship: lacks_plasma_membrane_part GO:0071735 ! IgG immunoglobulin complex [Term] id: CL:0002118 name: CD38-negative IgG-negative class switched memory B cell namespace: cell def: "A CD38-negative IgG-negative memory B cell is a IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-negative and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] is_a: CL:0002117 ! IgG-negative class switched memory B cell intersection_of: CL:0002117 ! IgG-negative class switched memory B cell intersection_of: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: lacks_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 [Term] id: CL:0002119 name: CD38-positive IgG-negative class switched memory B cell namespace: cell def: "A CD38-positive IgG-negative memory B cell is an IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-positive and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] is_a: CL:0002117 ! IgG-negative class switched memory B cell intersection_of: CL:0002117 ! IgG-negative class switched memory B cell intersection_of: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 relationship: has_plasma_membrane_part PR:000001408 ! ADP-ribosyl cyclase 1 [Term] id: CL:0002120 name: CD24-positive CD38-negative IgG-negative class switched memory B cell namespace: cell def: "An CD24-positive CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-positive, CD38-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] is_a: CL:0002118 ! CD38-negative IgG-negative class switched memory B cell intersection_of: CL:0002118 ! CD38-negative IgG-negative class switched memory B cell intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 [Term] id: CL:0002121 name: CD24-negative CD38-negative IgG-negative class switched memory B cell namespace: cell def: "A CD24-negative CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-negative, CD38-negative, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] is_a: CL:0002118 ! CD38-negative IgG-negative class switched memory B cell intersection_of: CL:0002118 ! CD38-negative IgG-negative class switched memory B cell intersection_of: lacks_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: lacks_plasma_membrane_part PR:000001932 ! signal transducer CD24 [Term] id: CL:0002122 name: B220-positive CD38-positive IgG-negative class switched memory B cell namespace: cell def: "A B220-positive CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-positive, CD38-positive, and IgG-negative." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] is_a: CL:0002119 ! CD38-positive IgG-negative class switched memory B cell intersection_of: CL:0002119 ! CD38-positive IgG-negative class switched memory B cell intersection_of: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R [Term] id: CL:0002123 name: B220-low CD38-positive IgG-negative class switched memory B cell namespace: cell def: "A B220-low CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-low, CD38-positive, and IgG-positive." [GOC:dsd, GOC:rhs, GOC:tfm, PMID:20123131] is_a: CL:0002119 ! CD38-positive IgG-negative class switched memory B cell intersection_of: CL:0002119 ! CD38-positive IgG-negative class switched memory B cell intersection_of: has_low_plasma_membrane_amount PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_low_plasma_membrane_amount PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R [Term] id: CL:0002124 name: CD27-positive gamma-delta T cell namespace: cell def: "A circulating gamma-delta T cell that is CD27-positive and capable of producing IFN-gamma." [GOC:dsd, GOC:tfm, PMID:19270712] synonym: "gammadelta27-positive" EXACT [] synonym: "gd27-positive" EXACT [] is_a: CL:0000800 ! mature gamma-delta T cell is_a: CL:0000912 ! helper T cell intersection_of: CL:0000800 ! mature gamma-delta T cell intersection_of: capable_of GO:0032609 ! interferon-gamma production intersection_of: has_completed GO:0030217 ! T cell differentiation intersection_of: has_plasma_membrane_part PR:000001963 ! CD27 molecule relationship: capable_of GO:0032609 ! interferon-gamma production relationship: develops_from CL:0002126 ! CD25-positive, CD27-positive immature gamma-delta T cell relationship: has_completed GO:0030217 ! T cell differentiation relationship: has_plasma_membrane_part PR:000001963 ! CD27 molecule created_by: tmeehan creation_date: 2010-08-18T09:57:19Z [Term] id: CL:0002125 name: CD27-negative gamma-delta T cell namespace: cell def: "A circulating gamma-delta T cell that expresses RORgamma(t), is CD27-negative and is capable of IL-17 secretion." [GOC:dsd, GOC:tfm, PMID:19270712] synonym: "gammadelta-17 cells" EXACT [PMID:21976777] is_a: CL:0000800 ! mature gamma-delta T cell is_a: CL:0000912 ! helper T cell intersection_of: CL:0000800 ! mature gamma-delta T cell intersection_of: capable_of GO:0032620 ! interleukin-17 production intersection_of: has_completed GO:0030217 ! T cell differentiation intersection_of: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 intersection_of: lacks_plasma_membrane_part PR:000001963 ! CD27 molecule relationship: capable_of GO:0032620 ! interleukin-17 production relationship: develops_from CL:0002126 ! CD25-positive, CD27-positive immature gamma-delta T cell relationship: has_completed GO:0030217 ! T cell differentiation relationship: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 relationship: lacks_plasma_membrane_part PR:000001963 ! CD27 molecule created_by: tmeehan creation_date: 2010-08-18T09:57:29Z [Term] id: CL:0002126 name: CD25-positive, CD27-positive immature gamma-delta T cell namespace: cell def: "A CD25-positive, CD27-positive immature gamma-delta T cell found in the thymus that has an immature phenotype (i.e. CD24-high, CD25-high, CD62L-high, CD44-high, CD2-low, CD5-low)." [GOC:tfm, PMID:19270712] is_a: CL:0000799 ! immature gamma-delta T cell is_a: CL:0000893 ! thymocyte intersection_of: CL:0000799 ! immature gamma-delta T cell intersection_of: has_high_plasma_membrane_amount PR:000001307 ! CD44 molecule intersection_of: has_high_plasma_membrane_amount PR:000001318 ! L-selectin intersection_of: has_high_plasma_membrane_amount PR:000001932 ! signal transducer CD24 intersection_of: has_low_plasma_membrane_amount PR:000001083 ! CD2 molecule intersection_of: has_low_plasma_membrane_amount PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha intersection_of: has_plasma_membrane_part PR:000001919 ! programmed cell death protein 1 intersection_of: part_of UBERON:0002370 ! thymus relationship: has_high_plasma_membrane_amount PR:000001307 ! CD44 molecule relationship: has_high_plasma_membrane_amount PR:000001318 ! L-selectin relationship: has_high_plasma_membrane_amount PR:000001932 ! signal transducer CD24 relationship: has_low_plasma_membrane_amount PR:000001083 ! CD2 molecule relationship: has_low_plasma_membrane_amount PR:000001839 ! T-cell surface glycoprotein CD5 relationship: has_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: has_plasma_membrane_part PR:000001919 ! programmed cell death protein 1 relationship: part_of UBERON:0002370 ! thymus created_by: tmeehan creation_date: 2010-08-18T10:35:37Z [Term] id: CL:0002127 name: innate effector T cell namespace: cell def: "A T cell with a receptor of limited diversity that is capable of immediate effector functions upon stimulation." [GOC:tfm, PMID:20581831] is_a: CL:0000911 ! effector T cell intersection_of: CL:0000911 ! effector T cell intersection_of: capable_of GO:0045087 ! innate immune response relationship: capable_of GO:0045087 ! innate immune response created_by: tmeehan creation_date: 2010-08-20T02:14:25Z [Term] id: CL:0002128 name: Tc17 cell namespace: cell def: "A CD8-positive, alpha-beta positive T cell with the phenotype CCR6-positive, CCR5-high, CD45RA-negative, and secreting IL-17 and some IFNg." [GOC:dsd, GOC:tfm, PMID:19201830] comment: Found in the CD27-positive CD28-positive or CD27-negative CD28-positive fractions with the phenotype CCR4-negative and CCR7-negative. synonym: "Tc17 T cell" EXACT [] synonym: "Tc17 T lymphocyte" EXACT [] synonym: "Tc17 T-cell" EXACT [] synonym: "Tc17 T-lymphocyte" EXACT [] is_a: CL:0000908 ! CD8-positive, alpha-beta cytokine secreting effector T cell intersection_of: CL:0000908 ! CD8-positive, alpha-beta cytokine secreting effector T cell intersection_of: capable_of GO:0032620 ! interleukin-17 production intersection_of: has_high_plasma_membrane_amount PR:000001201 ! C-C chemokine receptor type 5 intersection_of: has_plasma_membrane_part PR:000001202 ! C-C chemokine receptor type 6 intersection_of: lacks_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: capable_of GO:0032620 ! interleukin-17 production relationship: has_high_plasma_membrane_amount PR:000001201 ! C-C chemokine receptor type 5 relationship: has_plasma_membrane_part PR:000001202 ! C-C chemokine receptor type 6 relationship: lacks_plasma_membrane_part PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA [Term] id: CL:0002129 name: regular atrial cardiac myocyte namespace: cell def: "Regular cardiac myocyte of a cardiac atrium." [GOC:tfm] synonym: "atrial cardiac muscle cell" EXACT [GOC:pr] synonym: "atrial myocyte" EXACT [] synonym: "regular atrial cardiac muscle fiber" EXACT [] synonym: "regular cardiac muscle cell of atrium" EXACT [] xref: FMA:83108 is_a: CL:0002098 ! regular cardiac myocyte created_by: tmeehan creation_date: 2010-08-23T11:41:03Z [Term] id: CL:0002130 name: regular interatrial cardiac myocyte namespace: cell def: "A cardiac myocyte of the interatrial region of the heart." [GOC:tfm] xref: FMA:228790 is_a: CL:0002098 ! regular cardiac myocyte created_by: tmeehan creation_date: 2010-08-23T11:41:09Z [Term] id: CL:0002131 name: regular ventricular cardiac myocyte namespace: cell def: "Regular cardiac myocyte of a cardiac ventricle." [GOC:tfm] synonym: "regular cardiac muscle cell of ventricle" EXACT [] synonym: "regular ventricular cardiac muscle fiber" EXACT [] synonym: "ventricular cardiac muscle cell" BROAD [GOC:pr] synonym: "ventricular myocyte" EXACT [] xref: FMA:83109 is_a: CL:0002098 ! regular cardiac myocyte created_by: tmeehan creation_date: 2010-08-23T11:41:13Z [Term] id: CL:0002132 name: stromal cell of ovary namespace: cell def: "A stomal cell of the ovary" [GOC:tfm] synonym: "ovarian stromal cell" EXACT [GOC:cjm] xref: FMA:72299 is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0000992 ! female gonad relationship: part_of UBERON:0000992 ! female gonad created_by: tmeehan creation_date: 2010-08-23T12:10:31Z [Term] id: CL:0002133 name: stromal cell of ovorain cortex namespace: cell def: "A stromal cell of the ovarian cortex." [GOC:tfm] xref: FMA:256169 is_a: CL:0002132 ! stromal cell of ovary created_by: tmeehan creation_date: 2010-08-23T12:12:15Z [Term] id: CL:0002134 name: stromal cell of ovarian medulla namespace: cell def: "A stromal cell of the ovarian medulla." [GOC:tfm] xref: FMA:256171 is_a: CL:0002132 ! stromal cell of ovary created_by: tmeehan creation_date: 2010-08-23T12:12:17Z [Term] id: CL:0002135 name: nonkeratinized cell of epidermis namespace: cell def: "Epidermal cells that do not contain keratin. Cell type is usually associated with moist epidermal tissues." [GO:tfm, PMID:1987287] xref: FMA:62880 is_a: CL:0000362 ! epidermal cell created_by: tmeehan creation_date: 2010-08-24T08:43:27Z [Term] id: CL:0002136 name: type II cell of adrenal cortex namespace: cell def: "A cell in the zona fasciculata that produce glucocorticoids, e.g cortisol." [GOC:tfm, ISBN:0517223651] synonym: "type II cortical cell of adrenal gland" EXACT [] xref: FMA:69547 is_a: CL:0000460 ! glucocorticoid secreting cell is_a: CL:0002097 ! cortical cell of adrenal gland created_by: tmeehan creation_date: 2010-08-24T01:50:42Z [Term] id: CL:0002137 name: type III cell of adrenal cortex namespace: cell def: "A cell in the zona reticularis that produce sex hormones." [GOC:tfm, ISBN:0517223651] xref: FMA:69564 is_a: CL:0000593 ! androgen secreting cell is_a: CL:0002097 ! cortical cell of adrenal gland created_by: tmeehan creation_date: 2010-08-24T01:50:44Z [Term] id: CL:0002138 name: endothelial cell of lymphatic vessel namespace: cell alt_id: CL:1000421 def: "A endothelial cell of a lymphatic vessel. The border of the oak leaf-shaped endothelial cell of initial lymphatics are joined by specialized buttons. The discontinuous feature of buttons distinguishes them from zippers in collecting lymphatics, but both types of junctions are composed of proteins typical of adherens junctions and tight junctions found in the endothelium of blood vessels. Buttons seal the sides of flaps of the oak leaf-shaped endothelial cell, leaving open the tips of flaps as routes for fluid entry without disassembly and reformation of intercellular junctions." [GOC:tfm, PMID:17846148] synonym: "LEC" EXACT [] synonym: "lymphatic endothelial cell" EXACT [] xref: BTO:0004167 xref: FMA:68458 is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0002139 ! endothelial cell of vascular tree intersection_of: develops_from CL:0005022 ! vascular lymphangioblast intersection_of: part_of UBERON:0001473 ! lymphatic vessel relationship: develops_from CL:0005022 ! vascular lymphangioblast relationship: part_of UBERON:0001473 ! lymphatic vessel created_by: tmeehan creation_date: 2010-08-24T02:05:28Z [Term] id: CL:0002139 name: endothelial cell of vascular tree namespace: cell def: "An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels." [GOC:dsd, GOC:tfm, PMID:12768659] comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. synonym: "cubodial endothelial cell of vascular tree" NARROW [] synonym: "vascular endothelial cell" EXACT [] xref: BTO:0001854 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell created_by: tmeehan creation_date: 2010-08-24T02:06:40Z [Term] id: CL:0002140 name: acinar cell of sebaceous gland namespace: cell alt_id: CL:0002587 def: "A sebum secreting cell of the skin that secretes sebum into the hair follicles." [GOC:tfm] synonym: "sebocyte" EXACT [] xref: BTO:0004613 xref: FMA:70953 is_a: CL:0000317 ! sebum secreting cell is_a: CL:0000622 ! acinar cell is_a: CL:1000448 ! epithelial cell of sweat gland intersection_of: CL:0000317 ! sebum secreting cell intersection_of: part_of UBERON:0003487 ! skin sebaceous gland relationship: part_of UBERON:0003487 ! skin sebaceous gland created_by: tmeehan creation_date: 2010-08-24T09:27:52Z [Term] id: CL:0002141 name: active chief cell of parathyroid gland namespace: cell def: "A parathyroid chief cell that is actively secreting hormone. Have large Golgi complexes with numerous vesicles and small membrane-bound granules; secretory granules are rare, cytoplasmic glycogen sparse, much of the cytoplasm being occupied by flat sacs of granular endoplasmic reticulum in parallel arrays; in normal humans, inactive chief cells outnumber active chief cells in a ratio of 3-5:1" [FMA:0517223651, GOC:tfm] xref: FMA:69082 is_a: CL:0000446 ! chief cell of parathyroid gland created_by: tmeehan creation_date: 2010-08-24T09:30:15Z [Term] id: CL:0002142 name: dark cell of eccrine sweat gland namespace: cell def: "A cell pyramidal in shape, with their broad ends facing and forming the greater extent of the lining of the main lumen. Secretes glycoproteins associated with mucus." [ISBN:0517223651] xref: FMA:70659 is_a: CL:0000318 ! sweat secreting cell is_a: CL:0000434 ! eccrine cell created_by: tmeehan creation_date: 2010-08-24T02:15:16Z [Term] id: CL:0002143 name: dark chief cell of parathyroid cell namespace: cell def: "A chief cell that is smaller than light chief cells and has a smaller and darker nucleus and a finely granular cytoplasm with many granules." [GOC:tfm, ISBN:0721662544] xref: FMA:69080 is_a: CL:0000446 ! chief cell of parathyroid gland created_by: tmeehan creation_date: 2010-08-24T02:18:36Z [Term] id: CL:0002144 name: capillary endothelial cell namespace: cell def: "An endothelial cell found in capillaries." [GOC:tfm] xref: BTO:0004956 xref: FMA:67756 is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0001915 ! endothelium of capillary relationship: part_of UBERON:0001915 ! endothelium of capillary created_by: tmeehan creation_date: 2010-08-24T10:15:00Z [Term] id: CL:0002145 name: ciliated columnar cell of tracheobronchial tree namespace: cell def: "A ciliated columnar cell found in the trachea and bronchus. Vary from low to tall columnar; possesses up to 300 cilia at its surface, interspersed with long irregular microvilli with the cilia varying in length from about 6um in the trachea to about 4um in the terminal bronchioles; driving force of the ciliary current in the bronchial tree." [GOC:tfm, ISBN:0517223651] xref: FMA:70542 is_a: CL:0002202 ! epithelial cell of tracheobronchial tree is_a: CL:0005012 ! multi-ciliated epithelial cell relationship: develops_from CL:0002209 ! intermediate epitheliocyte created_by: tmeehan creation_date: 2010-08-24T03:38:29Z [Term] id: CL:0002146 name: clear cell of eccrine sweat gland namespace: cell def: "A sweat producing cell of eccrine sweat glands. Pyramidal in shape, with its base resting on the basal lamina or myoepitheliocytes, and its microvillus-covered apical plasma membrane line up the intercellular canaliculi. Cell is not stained by hematoxylin or eosin." [GOC:tfm, ISBN:0517223651] xref: FMA:70658 is_a: CL:0000318 ! sweat secreting cell is_a: CL:0000434 ! eccrine cell created_by: tmeehan creation_date: 2010-08-24T10:33:02Z [Term] id: CL:0002147 name: clear chief cell of parathyroid cell namespace: cell def: "A chief cell of parathyroid glands that does not stain with hematoxylin or eosin. This cell is larger, has a larger nucleus and fewer secretory granules than dark chief cells." [GOC:tfm, ISBN:0618947256] xref: FMA:69081 is_a: CL:0000446 ! chief cell of parathyroid gland created_by: tmeehan creation_date: 2010-08-24T10:39:42Z [Term] id: CL:0002148 name: dental pulp cell namespace: cell def: "A cell found within the dental pulp." [GOC:tfm, PMID:11087820] xref: BTO:0000339 xref: FMA:87170 is_a: CL:0002159 ! general ecto-epithelial cell is_a: CL:0002320 ! connective tissue cell relationship: part_of UBERON:0001754 ! dental pulp created_by: tmeehan creation_date: 2010-08-24T02:52:09Z [Term] id: CL:0002149 name: epithelial cell of uterus namespace: cell alt_id: CL:1000294 def: "An epithelial cell of the uterus." [GOC:tfm] xref: FMA:256161 is_a: CL:0002076 ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0000995 ! uterus relationship: part_of UBERON:0000995 ! uterus created_by: tmeehan creation_date: 2010-08-24T10:45:54Z [Term] id: CL:0002150 name: epithelioid macrophage namespace: cell def: "Epithelioid macrophage is an activated macrophage that resembles an epithelial cell with finely granular, pale eosinophilic cytoplasm and central, ovoid nucleus (oval or elongate). This cell type is able to merge into one another to form aggregates. The presence of such aggregates may characterize some pathologic conditions, mainly granulomatous inflammation." [MESH:A11.329.372.300, PMID:12673090] synonym: "epithelioid cell" BROAD [] synonym: "epithelioid histocyte" EXACT [MESH:A11.329.372.300, PMID:12673090] synonym: "epitheloid macrophage" EXACT [] xref: FMA:83514 is_a: CL:0000235 ! macrophage relationship: develops_from CL:0000861 ! elicited macrophage created_by: tmeehan creation_date: 2010-08-24T03:48:30Z [Term] id: CL:0002151 name: late promyelocyte namespace: cell def: "A promyelocyte that is considerably smaller, with more condensed chromatin, and nucleoli are no longer conspicuous." [ISBN:0412046911] xref: FMA:83534 is_a: CL:0000836 ! promyelocyte created_by: tmeehan creation_date: 2010-08-24T03:07:50Z [Term] id: CL:0002152 name: columnar cell of endocervix namespace: cell def: "A columnar cell of the cervix uteri." [GOC:tfm, ISBN:0721662544] xref: FMA:86486 is_a: CL:0002149 ! epithelial cell of uterus relationship: part_of UBERON:0000458 ! endocervix created_by: tmeehan creation_date: 2010-08-24T10:47:47Z [Term] id: CL:0002153 name: corneocyte namespace: cell def: "The dead keratin-filled squamous cell of the stratum corneum. This cell type lacks a nucleus." [GOC:tfm, ISBN:068340007X] xref: BTO:0001943 xref: FMA:68650 is_a: CL:0000225 ! anucleate cell is_a: CL:0000311 ! keratin accumulating cell relationship: develops_from CL:0000312 ! keratinocyte relationship: part_of UBERON:0002027 ! stratum corneum of epidermis created_by: tmeehan creation_date: 2010-08-24T10:53:03Z [Term] id: CL:0002154 name: early promyelocyte namespace: cell def: "A promyelocyte with a nucleus that is indented and contains more marginated heterochromatin compared to its precursor cell (myeloblast); cytoplasm is deeply basophilic and contains numerous mitochondria and meandering cysternae of endoplasmic reticulum; largest of the granulocyte lineages." [FMA:0412046911, GOC:tfm] xref: FMA:83533 is_a: CL:0000836 ! promyelocyte created_by: tmeehan creation_date: 2010-08-24T03:07:53Z [Term] id: CL:0002155 name: echinocyte namespace: cell def: "A crenated erythrocyte with 30+ crenations, bumps or spurs that are the result of damage due to age or disease." [GOC:tfm] synonym: "burr cell" EXACT [] xref: FMA:81099 is_a: CL:0000595 ! enucleate erythrocyte created_by: tmeehan creation_date: 2010-08-24T03:15:21Z [Term] id: CL:0002157 name: endosteal cell namespace: cell def: "A cell type that makes up the highly vascular membrane lining the marrow cavity of long bones." [FMA:0618947256, GOC:tfm] xref: FMA:86495 is_a: CL:0001035 ! bone cell is_a: CL:0002078 ! meso-epithelial cell relationship: part_of UBERON:0009859 ! endosteum created_by: tmeehan creation_date: 2010-08-24T03:33:58Z [Term] id: CL:0002158 name: external epithelial cell of tympanic membrane namespace: cell def: "Epithelial cell found on the external side of the tympanic membrane" [GOC:tfm, PMID:5686391] xref: FMA:70558 is_a: CL:0002159 ! general ecto-epithelial cell created_by: tmeehan creation_date: 2010-08-25T10:25:31Z [Term] id: CL:0002159 name: general ecto-epithelial cell namespace: cell def: "Epithelial cells derived from general body ectoderm and ectoderm placodes." [GOC:tfm] xref: FMA:70556 is_a: CL:0002077 ! ecto-epithelial cell created_by: tmeehan creation_date: 2010-08-26T08:31:08Z [Term] id: CL:0002160 name: basal external epithelial cell of tympanic membrane namespace: cell def: "A cell type found in the basal epithelial layer on the external side of the tympanic membrane. Cell type is flattened with intracellular spaces of variable dimensions." [PMID:5686391] is_a: CL:0002158 ! external epithelial cell of tympanic membrane created_by: tmeehan creation_date: 2010-08-25T10:28:44Z [Term] id: CL:0002161 name: superficial external epithelial cell of tympanic membrane namespace: cell def: "A cell type found on the superficial layer of the external side of the tympanic membrane. This cell-type lacks a nucleus." [PMID:5686391] is_a: CL:0002158 ! external epithelial cell of tympanic membrane created_by: tmeehan creation_date: 2010-08-25T10:28:48Z [Term] id: CL:0002162 name: internal epithelial cell of tympanic membrane namespace: cell def: "An extremely flattened cell type found on the inner side of the tympanic membrane. The surface of this cell type carries sparse pleomorphic microvilli that are more common near the junctional zones." [FMA:5686391, GOC:tfm] xref: FMA:70626 is_a: CL:0002076 ! endo-epithelial cell relationship: part_of UBERON:0002364 ! tympanic membrane created_by: tmeehan creation_date: 2010-08-25T10:49:46Z [Term] id: CL:0002163 name: internal pillar cell of cochlea namespace: cell def: "A rod-shpaed cell that forms a single row adjacent to and supporting the inner hair cells." [GOC:tfm, http://www.theodora.com/anatomy/the_internal_ear_or_labyrinth.html] xref: FMA:75722 xref: FMA:75726 is_a: CL:1000191 ! pillar cell created_by: tmeehan creation_date: 2010-08-25T11:05:21Z [Term] id: CL:0002164 name: external pillar cell of cochlea namespace: cell def: "A rod-shaped cell found in 3 or 4 rows that lie adjacent to and support the outer hair cells." [GOC:tfm, http://www.theodora.com/anatomy/the_internal_ear_or_labyrinth.html] xref: FMA:75727 is_a: CL:1000191 ! pillar cell created_by: tmeehan creation_date: 2010-08-25T11:05:23Z [Term] id: CL:0002165 name: phalangeal cell namespace: cell def: "A supporting cell that is attached to the basement membrane and forms rows that support the hair cells." [GOC:tfm, ISBN:0618947256] xref: FMA:79800 is_a: CL:0002490 ! organ of Corti supporting cell created_by: tmeehan creation_date: 2010-08-25T01:29:07Z [Term] id: CL:0002166 name: epithelial cell of Malassez namespace: cell def: "An epithelial cell that remains from the disintegration of the epithelial root sheath involved in the development of teeth." [GOC:tfm, ISBN:0517223651, ISBN:0815129521] synonym: "epithelial cell rests of Malassez " EXACT [] synonym: "epithelial debris of Malassez" EXACT [] xref: FMA:62987 is_a: CL:0002159 ! general ecto-epithelial cell is_a: CL:0002251 ! epithelial cell of alimentary canal intersection_of: CL:0002159 ! general ecto-epithelial cell intersection_of: part_of UBERON:0001708 ! jaw skeleton relationship: part_of UBERON:0001708 ! jaw skeleton created_by: tmeehan creation_date: 2010-08-26T08:51:27Z [Term] id: CL:0002167 name: olfactory epithelial cell namespace: cell def: "A specialized cell involved in sensory perception of smell." [GOC:tfm, PMID:7143026] xref: FMA:67870 is_a: CL:0000098 ! sensory epithelial cell is_a: CL:0000710 ! neurecto-epithelial cell created_by: tmeehan creation_date: 2010-08-26T01:47:13Z [Term] id: CL:0002168 name: border cell of cochlea namespace: cell def: "A border cell is a slender columnar cell on the medial portion of the basilar membrane." [FMA:0412046911, GOC:tfm] xref: FMA:79798 is_a: CL:0002315 ! supporting cell of cochlea created_by: tmeehan creation_date: 2010-08-25T01:47:12Z [Term] id: CL:0002169 name: basal cell of olfactory epithelium namespace: cell alt_id: CL:1000395 def: "An epithelial cell located on the basal lamina of the olfactory epithelium." [GOC:tfm, PMID:7143026] xref: FMA:62303 is_a: CL:0002167 ! olfactory epithelial cell intersection_of: CL:0002167 ! olfactory epithelial cell intersection_of: part_of UBERON:0001997 ! olfactory epithelium relationship: part_of UBERON:0001997 ! olfactory epithelium created_by: tmeehan creation_date: 2010-08-26T01:58:54Z [Term] id: CL:0002170 name: keratinized cell of the oral mucosa namespace: cell def: "A keratinized cell located in the hard palate or gingiva." [GOC:tfm, PMID:12014572] is_a: CL:0000237 ! keratinizing barrier epithelial cell is_a: CL:0002251 ! epithelial cell of alimentary canal is_a: CL:0002336 ! buccal mucosa cell relationship: part_of UBERON:0003729 ! mouth mucosa created_by: tmeehan creation_date: 2010-08-26T02:51:30Z [Term] id: CL:0002171 name: globose cell of olfactory epithelium namespace: cell def: "A rounded or elliptical epithelial cell, with pale-staining open face nucleus and pale cytoplasm rich in free ribosomes and clusters of centrioles; form a distinct basal zone spaced slightly from the basal surface of the epithelium." [GOC:tfm, PMID:17468753] synonym: "blastema cell of olfactory epithelium" EXACT [] xref: FMA:67874 is_a: CL:0002169 ! basal cell of olfactory epithelium created_by: tmeehan creation_date: 2010-08-26T01:59:18Z [Term] id: CL:0002172 name: interdental cell of cochlea namespace: cell def: "A long, spindle-shaped supporting cells arranged in parallel rows that secretes components of the tectorial membrane and potassium ions into the endolymph." [GOC:tfm, MP:0004482, PMID:2111803] synonym: "interdental cell" EXACT [] xref: FMA:79797 is_a: CL:0001035 ! bone cell is_a: CL:0002315 ! supporting cell of cochlea relationship: part_of UBERON:0002276 ! lamina of spiral limbus created_by: tmeehan creation_date: 2010-08-25T02:02:48Z [Term] id: CL:0002173 name: extraglomerular mesangial cell namespace: cell def: "A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells." [GOC:tfm, http:/www.copewithcytokines.de/cope.cgi?key=Lacis%20cells, ISBN:0412046911] synonym: "Goormaghtigh cell" EXACT [] synonym: "lacis cell" RELATED [] synonym: "polar cushion cells" EXACT [] xref: FMA:84143 xref: KUPO:0001033 is_a: CL:0000650 ! mesangial cell is_a: CL:1000500 ! kidney interstitial cell is_a: CL:1000618 ! juxtaglomerular complex cell is_a: CL:1001318 ! renal interstitial pericyte intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0002321 ! extraglomerular mesangium relationship: part_of UBERON:0002321 ! extraglomerular mesangium created_by: tmeehan creation_date: 2010-08-25T02:20:55Z [Term] id: CL:0002174 name: follicular cell of ovary namespace: cell def: "A cell within the follicle of an ovary." [GOC:tfm] xref: EMAPA:31247 xref: FMA:70589 is_a: CL:0002078 ! meso-epithelial cell created_by: tmeehan creation_date: 2010-08-25T03:01:27Z [Term] id: CL:0002175 name: primary follicular cell of ovary namespace: cell def: "A cell within the primary follicle of the ovary." [GOC:tfm] xref: FMA:70590 is_a: CL:0002174 ! follicular cell of ovary created_by: tmeehan creation_date: 2010-08-25T03:03:42Z [Term] id: CL:0002176 name: secondary follicular cell of ovary namespace: cell def: "A cell of a secondary follicile within the ovary." [GOC:tfm] xref: FMA:70591 is_a: CL:0002174 ! follicular cell of ovary created_by: tmeehan creation_date: 2010-08-25T03:03:48Z [Term] id: CL:0002177 name: folliculostellate cell of pars distalis of adenohypophysis namespace: cell def: "A supporting cell of the anterior pituitary gland involved in trophic and catabolic processes; expresses a broad spectrum of cytokeratins indicative of their epithelial nature." [GOC:tfm] synonym: "folliculostellate cell of pars anterior of adenohypophysis" EXACT [] xref: FMA:83102 is_a: CL:0000642 ! folliculostellate cell is_a: CL:0000710 ! neurecto-epithelial cell created_by: tmeehan creation_date: 2010-08-25T03:10:10Z [Term] id: CL:0002178 name: epithelial cell of stomach namespace: cell alt_id: CL:1000399 def: "An epithelial cell found in the lining of the stomach." [GOC:tfm] xref: FMA:62948 is_a: CL:0002251 ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000945 ! stomach relationship: part_of UBERON:0000945 ! stomach created_by: tmeehan creation_date: 2010-08-25T03:22:08Z [Term] id: CL:0002179 name: foveolar cell of stomach namespace: cell def: "An epithelial cell within one of the pits in the embryonic gastric mucosa from which the gastric glands develop ." [GOC:tfm, http://www.merriam-webster.com/medical/foveolar] xref: FMA:86552 is_a: CL:0002178 ! epithelial cell of stomach created_by: tmeehan creation_date: 2010-08-25T03:23:22Z [Term] id: CL:0002180 name: mucous cell of stomach namespace: cell alt_id: CL:1000404 def: "A mucous cell in the epithelium of the stomach." [GOC:tfm] xref: FMA:63464 is_a: CL:0002659 ! glandular cell of stomach intersection_of: CL:0002178 ! epithelial cell of stomach intersection_of: part_of UBERON:0001199 ! mucosa of stomach relationship: part_of UBERON:0001199 ! mucosa of stomach created_by: tmeehan creation_date: 2010-08-25T03:38:51Z [Term] id: CL:0002181 name: mucus neck cell of gastric gland namespace: cell alt_id: CL:1000401 def: "A neck cell that secretes mucus within the stomach. Its products are distinct histochemically from those of the surface mucous cells of stomach." [GOC:tfm, ISBN:0517223651] xref: FMA:62954 is_a: CL:0000651 ! neck cell is_a: CL:0002180 ! mucous cell of stomach intersection_of: CL:0000651 ! neck cell intersection_of: part_of UBERON:0000325 ! gastric gland relationship: part_of UBERON:0000325 ! gastric gland created_by: tmeehan creation_date: 2010-08-25T03:41:30Z [Term] id: CL:0002182 name: surface mucosal cell of stomach namespace: cell def: "A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall." [GOC:tfm, ISBN:0517223651] xref: FMA:62949 is_a: CL:0000319 ! mucus secreting cell is_a: CL:0002180 ! mucous cell of stomach created_by: tmeehan creation_date: 2010-08-25T03:45:10Z [Term] id: CL:0002183 name: stem cell of gastric gland namespace: cell alt_id: CL:1000400 def: "A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit." [GOC:tfm, ISBN:0517223651] xref: FMA:62953 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002180 ! mucous cell of stomach intersection_of: CL:0000048 ! multi fate stem cell intersection_of: part_of UBERON:0000325 ! gastric gland relationship: part_of UBERON:0000325 ! gastric gland created_by: tmeehan creation_date: 2010-08-25T03:57:08Z [Term] id: CL:0002184 name: basal proper cell of olfactory epithelium namespace: cell def: "A flat or angular epithelial cell with condensed nuclei and darkly staining cytoplasm containing numerous intermediate filaments inserted into desmosomes contacting surrounding supporting cells; lie in contact with the basal lamina of olfactory epithelium." [GOC:tfm, PMID:0517223651, PMID:11891623] synonym: "horizontal basal cells" EXACT [] xref: FMA:62304 is_a: CL:0002169 ! basal cell of olfactory epithelium created_by: tmeehan creation_date: 2010-08-26T01:59:22Z [Term] id: CL:0002187 name: basal cell of epidermis namespace: cell alt_id: CL:1000439 def: "A basally situated, mitotically active, columnar-shaped keratinocyte attached to the basement membrane." [GOC:tfm, ISBN:0517223651] xref: FMA:70571 is_a: CL:0000312 ! keratinocyte is_a: CL:0000646 ! basal cell is_a: CL:1000428 ! stem cell of epidermis intersection_of: CL:0000646 ! basal cell intersection_of: part_of UBERON:0001003 ! epidermis relationship: part_of UBERON:0001003 ! epidermis created_by: tmeehan creation_date: 2010-08-26T03:12:49Z [Term] id: CL:0002188 name: glomerular endothelial cell namespace: cell def: "An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate." [GOC:tfm, PMID:15840009] xref: BTO:0004632 xref: FMA:70970 is_a: CL:0000115 ! endothelial cell is_a: CL:0000666 ! fenestrated cell is_a: CL:1000746 ! glomerular cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0000074 ! renal glomerulus created_by: tmeehan creation_date: 2010-08-26T10:59:44Z [Term] id: CL:0002189 name: granular cell of epidermis namespace: cell def: "A keratinocyte of the epidermis that is characterized by containing granules of keratohyalin and lamellar granules." [ISBN:1416031855] xref: FMA:70543 is_a: CL:0000312 ! keratinocyte created_by: tmeehan creation_date: 2010-08-26T03:19:00Z [Term] id: CL:0002190 name: squamous cell of epidermis namespace: cell def: "A flat keratinocyte immediately below the cornified layer." [GOC:tfm, ISBN:0517223651] xref: FMA:86925 is_a: CL:0000312 ! keratinocyte created_by: tmeehan creation_date: 2010-08-26T03:37:02Z [Term] id: CL:0002191 name: granulocytopoietic cell namespace: cell def: "A cell involved in the formation of a granulocyte." [GOC:tfm] xref: FMA:83519 is_a: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030851 ! granulocyte differentiation relationship: capable_of GO:0030851 ! granulocyte differentiation created_by: tmeehan creation_date: 2010-08-30T12:54:27Z [Term] id: CL:0002192 name: metamyelocyte namespace: cell def: "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare." [GOC:tfm, http://en.wikipedia.org/wiki/Metamyelocyte, ISBN:0721601464] xref: FMA:83541 is_a: CL:0002191 ! granulocytopoietic cell relationship: develops_from CL:0002193 ! myelocyte created_by: tmeehan creation_date: 2010-08-30T01:08:15Z [Term] id: CL:0002193 name: myelocyte namespace: cell def: "A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses." [GOC:tfm, http://en.wikipedia.org/wiki/Myelocyte, ISBN:0323052908] xref: BTO:0000734 xref: FMA:83525 is_a: CL:0002191 ! granulocytopoietic cell relationship: develops_from CL:0000836 ! promyelocyte created_by: tmeehan creation_date: 2010-08-30T01:08:19Z [Term] id: CL:0002194 name: monopoietic cell namespace: cell def: "A cell involved in the formation of a monocyte (monopoiesis)." [GOC:tfm] xref: FMA:83552 is_a: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0030224 ! monocyte differentiation created_by: tmeehan creation_date: 2010-08-30T01:27:48Z [Term] id: CL:0002195 name: hepatic stem cell namespace: cell def: "A stem cell that can give rise to the cells of the liver." [GOC:tfm] xref: FMA:86577 is_a: CL:0000048 ! multi fate stem cell intersection_of: CL:0000048 ! multi fate stem cell intersection_of: part_of UBERON:0002107 ! liver relationship: part_of UBERON:0002107 ! liver created_by: tmeehan creation_date: 2010-08-30T02:00:42Z [Term] id: CL:0002196 name: hepatic oval stem cell namespace: cell alt_id: CL:1000036 def: "A transient hepatic stem cell observed after liver injury with a high nuclear to cytoplasm ratio that can differentiate into mature hepatocytes and bile duct cells. Arises from more than one tissue." [PMID:17901986] synonym: "hepatic oval cell" EXACT [] xref: BTO:0004270 xref: FMA:86576 is_a: CL:0002195 ! hepatic stem cell created_by: tmeehan creation_date: 2010-08-30T02:01:49Z [Term] id: CL:0002197 name: inactive chief cell of parathyoid gland namespace: cell def: "A parathyroid chief cell that is not actively secreting hormone. Contains small Golgi complexes with only a few grouped vesicles and membrane-bound secretory granules; glycogen and many lipofuscin granules abound but sacs of granular endoplasmic reticulum are rare and dispersed. In normal humans, inactive chief cells out number active chief cells in a ratio of 3-5:1." [GOC:tfm, ISBN:0517223651] is_a: CL:0000446 ! chief cell of parathyroid gland created_by: tmeehan creation_date: 2010-09-02T11:14:01Z [Term] id: CL:0002198 name: oncocyte namespace: cell def: "A large epithelial cell with an extremely acidophilic and granular cytoplasm, containing vast numbers of mitochondria; such cells may undergo neoplastic transformation. From the Greek word onkos meaning swelling, this cell type is found in parathyroid, salivary and thyroid glands." [GOC:tfm, ISBN:0721662544, PMID:20013317] synonym: "oxyphil" EXACT [] xref: FMA:67606 is_a: CL:0002076 ! endo-epithelial cell created_by: tmeehan creation_date: 2010-09-02T11:26:49Z [Term] id: CL:0002199 name: oxyphil cell of parathyroid gland namespace: cell def: "An oncocyte located in the parathyroid gland." [PMID:20013317] xref: FMA:69084 is_a: CL:0002198 ! oncocyte is_a: CL:0002260 ! epithelial cell of parathyroid gland created_by: tmeehan creation_date: 2010-09-02T11:33:23Z [Term] id: CL:0002200 name: oxyphil cell of thyroid namespace: cell def: "An oncocyte located in the thyroid." [GOC:tfm, PMID:20013317] synonym: "Askanazy cells" EXACT [] synonym: "Hurthle cells" EXACT [] xref: FMA:87169 is_a: CL:0002198 ! oncocyte is_a: CL:0002257 ! epithelial cell of thyroid gland created_by: tmeehan creation_date: 2010-09-02T11:33:26Z [Term] id: CL:0002201 name: renal beta-intercalated cell namespace: cell def: "A renal intercalated cell that secretes base and reabsorbs acid in the coritcal collecting duct to mantain acid/base balance." [GOC:tfm, PMID:11781354] is_a: CL:0005010 ! renal intercalated cell created_by: tmeehan creation_date: 2010-09-02T01:43:55Z [Term] id: CL:0002202 name: epithelial cell of tracheobronchial tree namespace: cell alt_id: CL:1000407 def: "An epithelial cell of the tracheobronchial tree." [GOC:tfm] xref: FMA:66816 is_a: CL:0002632 ! epithelial cell of lower respiratory tract intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0007196 ! tracheobronchial tree relationship: part_of UBERON:0007196 ! tracheobronchial tree created_by: tmeehan creation_date: 2010-09-02T02:09:14Z [Term] id: CL:0002203 name: Brush cell of epithelium proper of large intestine namespace: cell alt_id: CL:1000387 def: "Brush cell found in the epithelial layer of the colon." [GOC:tfm] comment: Brush cells are a distinct cell type from brush border cell-types. xref: FMA:263222 is_a: CL:0002204 ! brush cell is_a: CL:0002253 ! epithelial cell of large intestine created_by: tmeehan creation_date: 2010-09-02T02:20:50Z [Term] id: CL:0002204 name: brush cell namespace: cell def: "A cell type found in the gastrointestinal and respiratory tracts that is characterized by the presence of a tuft of blunt, squat microvilli (120-140 per cell). Function of this cell type is not known." [GOC:tfm, ISBN:0517223651, PMID:15817800] synonym: "caveolated cell" EXACT [] synonym: "fibrillovesicular cell" EXACT [] synonym: "multivesicular cell" EXACT [] synonym: "tuft cell" EXACT [] xref: FMA:67978 is_a: CL:0002076 ! endo-epithelial cell created_by: tmeehan creation_date: 2010-09-02T02:28:53Z [Term] id: CL:0002205 name: brush cell of lobular bronchiole namespace: cell alt_id: CL:1000386 def: "A brush cell found in the epithelium of lobular bronchiole." [GOC:tfm] xref: FMA:263220 is_a: CL:0002208 ! brush cell of bronchus intersection_of: CL:0002075 ! brush cell of trachebronchial tree intersection_of: part_of UBERON:0002051 ! epithelium of bronchiole relationship: part_of UBERON:0002051 ! epithelium of bronchiole created_by: tmeehan creation_date: 2010-09-02T02:38:34Z [Term] id: CL:0002206 name: brush cell of terminal bronchiole namespace: cell alt_id: CL:1000390 def: "A brush cell of the epithelium in the terminal bronchiole." [GOC:tfm] xref: FMA:263228 is_a: CL:0002205 ! brush cell of lobular bronchiole intersection_of: CL:0002075 ! brush cell of trachebronchial tree intersection_of: part_of UBERON:0001958 ! epithelium of terminal bronchiole relationship: part_of UBERON:0001958 ! epithelium of terminal bronchiole created_by: tmeehan creation_date: 2010-09-02T02:38:36Z [Term] id: CL:0002207 name: brush cell of trachea namespace: cell alt_id: CL:1000388 def: "Brush cell of the epithelium in the trachea." [GOC:tfm] xref: FMA:263224 is_a: CL:0000307 ! tracheal epithelial cell is_a: CL:0002075 ! brush cell of trachebronchial tree intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0001901 ! epithelium of trachea relationship: part_of UBERON:0001901 ! epithelium of trachea created_by: tmeehan creation_date: 2010-09-02T02:38:37Z [Term] id: CL:0002208 name: brush cell of bronchus namespace: cell alt_id: CL:1000389 def: "A brush cell found in the epithelium of bronchus." [GOC:tfm] xref: FMA:263226 is_a: CL:0002075 ! brush cell of trachebronchial tree is_a: CL:0002328 ! bronchial epithelial cell intersection_of: CL:0002075 ! brush cell of trachebronchial tree intersection_of: part_of UBERON:0002031 ! epithelium of bronchus relationship: part_of UBERON:0002031 ! epithelium of bronchus created_by: tmeehan creation_date: 2010-09-02T02:38:42Z [Term] id: CL:0002209 name: intermediate epitheliocyte namespace: cell def: "An epithelial cell present in the trachea and bronchi; columnar in shape; generally lack cilia; immature forms of ciliated or secretory cells which have been formed from stem cells." [GOC:tfm, ISBN:0517223651] synonym: "undifferentiated columnar cell of tracheobronchial tree" EXACT [] xref: FMA:69060 is_a: CL:0002202 ! epithelial cell of tracheobronchial tree created_by: tmeehan creation_date: 2010-09-02T02:53:59Z [Term] id: CL:0002210 name: red muscle cell namespace: cell def: "A slow muscle cell that contains high levels of myoglobin and oxygen storing proteins giving the cell a red appearance." [GOC:tfm, ISBN:0517223651] synonym: "oxidative muscle fiber" EXACT [] synonym: "red muscle fiber" EXACT [] xref: FMA:84448 is_a: CL:0002372 ! myotube created_by: tmeehan creation_date: 2010-09-02T03:20:03Z [Term] id: CL:0002211 name: type I muscle cell namespace: cell def: "A slow muscle cell that has large amounts of myoglobin, stores energy as triglycerides, generates ATP by the oxidative method and is resistant to fatigue." [GOC:tfm, ISBN:0517223651] synonym: "intermediate muscle fiber" RELATED [MESH:A02.633.565.700] synonym: "slow twitch fiber" EXACT [] synonym: "slow twitch muscle cell" EXACT [] synonym: "slow twitch muscle fiber" RELATED [MESH:A02.633.565.700] synonym: "slow-twitch muscle fiber" RELATED [MESH:A02.633.565.700] synonym: "type 1 muscle cell" EXACT [] synonym: "type 1 muscle fiber" EXACT [] synonym: "type I muscle fiber" EXACT [] xref: BTO:0001812 xref: FMA:84413 xref: MESH:A02.633.565.700 is_a: CL:0000189 ! slow muscle cell is_a: CL:0002210 ! red muscle cell created_by: tmeehan creation_date: 2010-09-02T03:24:05Z [Term] id: CL:0002212 name: type II muscle cell namespace: cell def: "A fast muscle fiber cell that stores energy in the form of glycogen and creatine phosphate." [GOC:tfm] synonym: "type 2 muscle cell" EXACT [] synonym: "type 2 muscle fiber" EXACT [] synonym: "type II muscle fiber" EXACT [] xref: BTO:0001813 xref: FMA:84414 is_a: CL:0000190 ! fast muscle cell created_by: tmeehan creation_date: 2010-09-02T03:28:45Z [Term] id: CL:0002213 name: white muscle cell namespace: cell def: "A muscle cell with low content of myoglobin and other oxygen storing proteins. This muscle cell has a white appearance." [GOC:tfm, ISBN:0517223651] xref: FMA:84449 is_a: CL:0000190 ! fast muscle cell created_by: tmeehan creation_date: 2010-09-02T03:28:48Z [Term] id: CL:0002214 name: type IIa muscle cell namespace: cell def: "A type II muscle cell that contains large amounts of myoglobin, has many mitochondria and very many blood capillaries. Type II A cells are red, have a very high capacity for generating ATP by oxidative metabolic processes, split ATP at a very rapid rate, have a fast contraction velocity and are resistant to fatigue." [GOC:tfm] synonym: "fast twitch A" EXACT [] synonym: "fatigue resistant fast twitch muscle cell" EXACT [] synonym: "type 2a muscle cell" EXACT [] synonym: "type 2a muscle fiber" EXACT [] synonym: "type IIa muscle fiber" EXACT [] xref: BTO:0001813 xref: FMA:84415 is_a: CL:0002210 ! red muscle cell is_a: CL:0002212 ! type II muscle cell created_by: tmeehan creation_date: 2010-09-02T03:31:38Z [Term] id: CL:0002215 name: type IIb muscle cell namespace: cell def: "A type II muscle cell that contains a low content of myoglobin, relatively few mitochondria, relatively few blood capillaries and large amounts of glycogen. Type II B fibres are white, geared to generate ATP by anaerobic metabolic processes, not able to supply skeletal muscle fibres continuously with sufficient ATP, fatigue easily, split ATP at a fast rate and have a fast contraction velocity." [GOC:tfm, http://en.wikipedia.org/wiki/Skeletal_muscle, ISBN:0517223651] synonym: "type 2b muscle cell" EXACT [] synonym: "type 2b muscle fiber" EXACT [] synonym: "type IIb muscle fiber" EXACT [] xref: FMA:84416 is_a: CL:0002212 ! type II muscle cell is_a: CL:0002213 ! white muscle cell created_by: tmeehan creation_date: 2010-09-02T03:31:42Z [Term] id: CL:0002216 name: intermediate muscle cell namespace: cell def: "An intermediate muscle cell that has characteristics of both fast and slow muscle cells." [GOC:tfm] xref: FMA:84450 is_a: CL:0002372 ! myotube created_by: tmeehan creation_date: 2010-09-02T03:51:17Z [Term] id: CL:0002217 name: intermediate trophoblast namespace: cell def: "A trophoblast that leaves the placenta and invades the endometrium and myometrium. This cell type is crucial in increasing blood flow to the fetus." [GOC:tfm, http://www.med.yale.edu/obgyn/kliman/placenta/articles/EOR_Placenta/Trophtoplacenta.html] xref: BTO:0002366 xref: FMA:86564 is_a: CL:0000351 ! trophoblast cell created_by: tmeehan creation_date: 2010-09-02T04:04:36Z [Term] id: CL:0002218 name: immature dendritic epithelial T cell precursor namespace: cell def: "A double negative thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-positive. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18." [GOC:tfm, http://www.immgen.org] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "immature DEC precursor" EXACT [] synonym: "immature DETC precursor" EXACT [] is_a: CL:0002404 ! fetal thymocyte created_by: tmeehan creation_date: 2010-10-07T01:58:00Z [Term] id: CL:0002219 name: anchoring trophoblasts namespace: cell def: "A trophoblast found at the junction of the placenta. This cell type makes a unique fibronectin-trophouteronectin junction that helps mediate attachment of the placenta to the uterus. This cell type is also found junction of the chorion layer of the external membranes and the decidua." [GOC:tfm, http://www.med.yale.edu/obgyn/kliman/placenta/articles/EOR_Placenta/Trophtoplacenta.html] is_a: CL:0000351 ! trophoblast cell created_by: tmeehan creation_date: 2010-09-02T04:14:28Z [Term] id: CL:0002220 name: interstitial cell of pineal gland namespace: cell def: "A cell located between the pinealocytes." [GOC:tfm, ISBN:0517223651] xref: FMA:86575 is_a: CL:0000710 ! neurecto-epithelial cell created_by: tmeehan creation_date: 2010-09-02T04:28:41Z [Term] id: CL:0002221 name: keratinized squamous cell of esophagus namespace: cell def: "A squamous cell that has keratin in the esophagus." [GOC:tfm, PMID:11694559] xref: FMA:86549 is_a: CL:0000237 ! keratinizing barrier epithelial cell is_a: CL:0002252 ! epithelial cell of esophagus created_by: tmeehan creation_date: 2010-09-07T10:11:06Z [Term] id: CL:0002222 name: vertebrate lens cell namespace: cell def: "A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye." [GOC:tfm, ISBN:0721662544] xref: FMA:70950 is_a: CL:0000066 ! epithelial cell is_a: CL:0000306 ! crystallin accumulating cell is_a: CL:0002371 ! somatic cell relationship: part_of UBERON:0000965 ! lens of camera-type eye created_by: tmeehan creation_date: 2010-09-07T10:38:03Z [Term] id: CL:0002223 name: anterior lens cell namespace: cell def: "A cell of the transparent layer of simple cuboidal epithelium over the anterior surface of the lens; transform into lens fiber(s)." [GOC:tfm, ISBN:0517223651] xref: FMA:63181 is_a: CL:0002224 ! lens epithelial cell created_by: tmeehan creation_date: 2010-09-07T10:45:45Z [Term] id: CL:0002224 name: lens epithelial cell namespace: cell def: "A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth." [GOC:tfm, http://en.wikipedia.org/wiki/Lens_%28anatomy%29#Lens_epithelium, ISBN:0721662544] xref: FMA:67559 is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002222 ! vertebrate lens cell intersection_of: CL:0000075 ! columnar/cuboidal epithelial cell intersection_of: part_of UBERON:0001803 ! epithelium of lens relationship: part_of UBERON:0001803 ! epithelium of lens created_by: tmeehan creation_date: 2010-09-07T10:45:47Z [Term] id: CL:0002225 name: secondary lens fiber namespace: cell def: "A lens fiber cell that develops from primary lens fiber; located towards the center of lens; cell organelles are normally degraded or in the process of being degraded." [GOC:tfm, ISBN:0517223651] synonym: "secondary lens fibre" EXACT [] is_a: CL:0011004 ! lens fiber cell relationship: develops_from CL:0002228 ! primary lens fiber created_by: tmeehan creation_date: 2010-09-07T10:53:39Z [Term] id: CL:0002226 name: non-nucleated secondary lens fiber namespace: cell def: "A secondary lens fiber cell that lacks a nucleus." [GOC:tfm] synonym: "non-nucleated secondary lens fibre" EXACT [] xref: FMA:67561 is_a: CL:0002225 ! secondary lens fiber relationship: develops_from CL:0002227 ! nucleated secondary lens fiber created_by: tmeehan creation_date: 2010-09-07T11:15:23Z [Term] id: CL:0002227 name: nucleated secondary lens fiber namespace: cell def: "A secondary fiber cell that contains a nucleus." [GOC:tfm] synonym: "nucleated secondary lens fibre" EXACT [] xref: FMA:70949 is_a: CL:0002225 ! secondary lens fiber created_by: tmeehan creation_date: 2010-09-07T11:15:26Z [Term] id: CL:0002228 name: primary lens fiber namespace: cell def: "An elongating cell that rapidly obliterates the lumen of the lens vesicle. Subsequently, differentiation of this cell type at the lens equator leads to the formation of secondary fiber cells that come to overlie the primary fibers." [GOC:tfm, PMID:10711704] synonym: "primary lens fibre" EXACT [] xref: FMA:70613 is_a: CL:0011004 ! lens fiber cell relationship: develops_from CL:0002223 ! anterior lens cell created_by: tmeehan creation_date: 2010-09-07T11:19:01Z [Term] id: CL:0002229 name: light chief cell of parathyroid gland namespace: cell def: "A chief cell that is bigger than dark chief cells and has a larger and lighter nucleus and a cytoplasm with few granules." [GOC:tfm, ISBN:0721662544] xref: FMA:69079 is_a: CL:0000446 ! chief cell of parathyroid gland created_by: tmeehan creation_date: 2010-09-07T11:46:54Z [Term] id: CL:0002231 name: epithelial cell of prostate namespace: cell alt_id: CL:1000295 alt_id: CL:1000408 def: "An epithelial cell of the prostate." [GOC:tfm] synonym: "prostate epithelial cell" EXACT [] xref: FMA:256163 xref: FMA:66817 is_a: CL:0002076 ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0002367 ! prostate gland relationship: part_of UBERON:0002367 ! prostate gland created_by: tmeehan creation_date: 2010-09-07T01:49:29Z [Term] id: CL:0002232 name: epithelial cell of prostatic duct namespace: cell alt_id: CL:1000462 def: "An epithelial cell of prostatic duct." [GOC:tfm] synonym: "ductal epithelial cell of prostate" EXACT [FMA:74224] xref: FMA:74224 is_a: CL:0000072 ! non-branched duct epithelial cell is_a: CL:0002231 ! epithelial cell of prostate intersection_of: CL:0000072 ! non-branched duct epithelial cell intersection_of: part_of UBERON:0002485 ! prostate duct relationship: part_of UBERON:0002485 ! prostate duct created_by: tmeehan creation_date: 2010-09-07T01:55:51Z [Term] id: CL:0002233 name: epithelial cell of prostatic acinus namespace: cell alt_id: CL:1000461 def: "An epithelial cell of the prostatic acinus." [GOC:tfm, PMCID:PMC2673349] synonym: "acinar epithelial cell of prostate" EXACT [FMA:74223] xref: FMA:74223 is_a: CL:0002231 ! epithelial cell of prostate intersection_of: CL:0002231 ! epithelial cell of prostate intersection_of: part_of UBERON:0004179 ! prostate glandular acinus relationship: part_of UBERON:0004179 ! prostate glandular acinus created_by: tmeehan creation_date: 2010-09-07T01:55:53Z [Term] id: CL:0002234 name: basal cell of prostatic acinus namespace: cell alt_id: CL:1000464 def: "A cell of the basal layer of the epithelium in the prostatic acinus." [GOC:tfm] synonym: "basal epithelial cell of prostatic acinus" EXACT [FMA:74265] xref: FMA:74265 is_a: CL:0002233 ! epithelial cell of prostatic acinus is_a: CL:0002341 ! basal cell of prostate epithelium created_by: tmeehan creation_date: 2010-09-07T01:59:08Z [Term] id: CL:0002235 name: luminal cell of prostatic acinus namespace: cell def: "A cell of the luminal layer of the epithelium in the prostatic acinus." [GOC:tfm] xref: FMA:74266 is_a: CL:0002233 ! epithelial cell of prostatic acinus is_a: CL:0002340 ! luminal cell of prostate epithelium created_by: tmeehan creation_date: 2010-09-07T01:59:10Z [Term] id: CL:0002236 name: basal epithelial cell of prostatic duct namespace: cell alt_id: CL:1000463 def: "A cell that constitutes the basal layer of epithelium in the prostatic duct." [GOC:tfm, PMID:15226377] xref: FMA:74226 is_a: CL:0002232 ! epithelial cell of prostatic duct is_a: CL:0002341 ! basal cell of prostate epithelium intersection_of: CL:0002341 ! basal cell of prostate epithelium intersection_of: part_of UBERON:0002485 ! prostate duct relationship: part_of UBERON:0002485 ! prostate duct created_by: tmeehan creation_date: 2010-09-07T01:59:12Z [Term] id: CL:0002237 name: luminal epithelial cell of prostatic duct namespace: cell def: "A cell that constitutes the luminal layer of epithelium of prostatic duct." [GOC:tfm] xref: FMA:74225 is_a: CL:0002232 ! epithelial cell of prostatic duct is_a: CL:0002340 ! luminal cell of prostate epithelium created_by: tmeehan creation_date: 2010-09-07T01:59:16Z [Term] id: CL:0002238 name: male gonocyte namespace: cell def: "A primordial germ cell that is destined to become a male germ cell." [GOC:tfm] synonym: "male primordial germ cell" EXACT [] synonym: "testis primordial germ cell" EXACT [VHOG:0000662] xref: EHDAA2:0001053 xref: EMAPA:18686 xref: FMA:84771 xref: VHOG:0000662 is_a: CL:0000670 ! primordial germ cell relationship: part_of UBERON:0000473 ! testis created_by: tmeehan creation_date: 2010-09-07T02:11:13Z [Term] id: CL:0002239 name: ooblast namespace: cell def: "A primordial cell from which an oocyte (ovum) ultimately is developed." [GOC:tfm] synonym: "ovary primordial germ cell" EXACT [VHOG:0000661] synonym: "ovigerm" EXACT [FMA:84772] xref: EHDAA2:0000505 xref: EMAPA:17965 xref: FMA:84772 xref: ISBN:0721662544 xref: VHOG:0000661 is_a: CL:0000670 ! primordial germ cell relationship: part_of UBERON:0000992 ! female gonad created_by: tmeehan creation_date: 2010-09-07T02:11:16Z [Term] id: CL:0002240 name: marrow fibroblast namespace: cell def: "A fibroblast in the bone marrow." [GOC:tfm] xref: FMA:84377 is_a: CL:0000057 ! fibroblast created_by: tmeehan creation_date: 2010-09-07T02:25:18Z [Term] id: CL:0002241 name: pulmonary interstitial fibroblast namespace: cell def: "A fibroblasts found in interstitial spaces in the pulmonary tract. Greater numbers of these cells are found in idiopathic pulmonary fibrosis." [GOC:tfm] synonym: "pulmonary myofibroblast" EXACT [] synonym: "pulmonary septal cell" EXACT [] xref: FMA:84467 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0005169 ! interstitial tissue relationship: part_of UBERON:0005169 ! interstitial tissue created_by: tmeehan creation_date: 2010-09-07T02:29:38Z [Term] id: CL:0002242 name: nucleate cell namespace: cell def: "A cell containing at least one nucleus." [GOC:tfm] xref: FMA:67513 is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: has_part GO:0005634 ! nucleus relationship: has_part GO:0005634 ! nucleus created_by: tmeehan creation_date: 2010-09-07T03:32:33Z [Term] id: CL:0002243 name: smooth muscle cell of sphincter of pupil namespace: cell def: "A circular smooth muscle cell of the iris, innervated by the ciliary nerves (parasympathetic), and acting to contract the pupil. This muscle cell derives from neuroectoderm. This smooth muscle cell results from transformation of epithelial cells to smooth muscle cells." [GOC:tfm, ISBN:0721662544, ISBN:0721694128] synonym: "smooth muscle fiber of sphincter of pupil" EXACT [] synonym: "smooth muscle fibre of sphincter of pupil" RELATED [] xref: FMA:70611 is_a: CL:0000358 ! sphincter associated smooth muscle cell is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001607 ! sphincter pupillae relationship: develops_from CL:0000133 ! neurectodermal cell relationship: part_of UBERON:0001607 ! sphincter pupillae created_by: tmeehan creation_date: 2010-09-08T08:53:42Z [Term] id: CL:0002244 name: squamous cell of ectocervix namespace: cell def: "A nonstratified squamous cell located in the ectocervix." [GOC:tfm, http://www.bu.edu/histology/p/19404loa.htm] synonym: "ectocervical squamous cell" EXACT [] xref: FMA:86483 is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0002149 ! epithelial cell of uterus created_by: tmeehan creation_date: 2010-09-08T09:12:23Z [Term] id: CL:0002245 name: null lymphocyte namespace: cell def: "A lymphocyte that lacks T or B cell surface markers." [GOC:tfm, ISBN:068340007X] xref: FMA:83601 is_obsolete: true created_by: tmeehan creation_date: 2010-09-07T03:43:42Z [Term] id: CL:0002246 name: peripheral blood stem cell namespace: cell def: "A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells)." [GOC:tfm] synonym: "PBSC" EXACT [] xref: BTO:0002669 xref: FMA:86711 is_a: CL:0000037 ! hematopoietic stem cell is_a: CL:0000080 ! circulating cell intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: part_of UBERON:0000178 ! blood relationship: part_of UBERON:0000178 ! blood created_by: tmeehan creation_date: 2010-09-07T03:57:09Z [Term] id: CL:0002247 name: pleural macrophage namespace: cell def: "A tissue macrophage that is in the pleural space." [GOC:tfm] xref: FMA:83024 is_a: CL:0000864 ! tissue-resident macrophage created_by: tmeehan creation_date: 2010-09-07T04:16:43Z [Term] id: CL:0002248 name: pluripotent stem cell namespace: cell def: "A pluripotent stem cell has the ability to form cells from all three germ layers (ectoderm, mesoderm, and endoderm). However, unlike totipotent stem cells, they cell can not generate all the cells of the whole organism such as placenta." [GOC:tfm, PMID:19343304] xref: FMA:70570 is_a: CL:0000723 ! somatic stem cell created_by: tmeehan creation_date: 2010-09-07T04:26:06Z [Term] id: CL:0002249 name: primitive cardiac myocyte namespace: cell def: "A stem cell that can differentiate into a cardiac myocyte." [GOC:tfm, PMID:16938308] xref: FMA:75620 is_a: CL:0000035 ! single fate stem cell is_a: CL:0002078 ! meso-epithelial cell created_by: tmeehan creation_date: 2010-09-07T04:40:32Z [Term] id: CL:0002250 name: intestinal crypt stem cell namespace: cell def: "A cell that is found in a zone occupying the bottom region of the crypt; provide the source of most of the cell types of the intestinal epithelium; proliferate by mitotic division; differentiates into columnar or goblet cells." [GOC:tfm, ISBN:0517223651] synonym: "stem cell of intestinal crypt of lieberkuhn" EXACT [] xref: FMA:63379 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002563 ! intestinal epithelial cell created_by: tmeehan creation_date: 2010-09-08T09:21:22Z [Term] id: CL:0002251 name: epithelial cell of alimentary canal namespace: cell def: "An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus." [GOC:tfm, ISBN:0721662544] is_a: CL:0002076 ! endo-epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract created_by: tmeehan creation_date: 2010-09-08T09:26:53Z [Term] id: CL:0002252 name: epithelial cell of esophagus namespace: cell alt_id: CL:1000402 def: "An epithelial cell of the esophagus." [GOC:tfm] xref: FMA:63071 is_a: CL:0002251 ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001043 ! esophagus created_by: tmeehan creation_date: 2010-09-08T09:28:20Z [Term] id: CL:0002253 name: epithelial cell of large intestine namespace: cell alt_id: CL:1000292 def: "An epithelial cell of the large intestine." [GOC:tfm] synonym: "epithelial cell of colon" RELATED [] xref: BTO:0004297 xref: FMA:256157 is_a: CL:0002563 ! intestinal epithelial cell intersection_of: CL:0002563 ! intestinal epithelial cell intersection_of: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0000059 ! large intestine created_by: tmeehan creation_date: 2010-09-08T09:28:22Z [Term] id: CL:0002254 name: epithelial cell of small intestine namespace: cell alt_id: CL:1000293 def: "An epithelial cell of the small intestine." [GOC:tfm] xref: FMA:256159 is_a: CL:0002563 ! intestinal epithelial cell intersection_of: CL:0002563 ! intestinal epithelial cell intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0002108 ! small intestine created_by: tmeehan creation_date: 2010-09-08T09:41:46Z [Term] id: CL:0002255 name: stromal cell of endometrium namespace: cell def: "An epithelial cell that regulates growth and differentiation of the overlying epithelium." [GOC:tfm, PMID:11331626] xref: FMA:86490 is_a: CL:0000499 ! stromal cell is_a: CL:0002149 ! epithelial cell of uterus created_by: tmeehan creation_date: 2010-09-08T09:50:04Z [Term] id: CL:0002256 name: supporting cell of carotid body namespace: cell def: "A supportive cell that has characteristics of glial cell. Processes of this cell envelope the junctions between glomus cells and nerve endings." [GOC:tfm, http://www.copewithcytokines.de/cope.cgi?key=glomus%20cells, PMID:8985136] synonym: "carotid body sustentacular cell" EXACT [] xref: FMA:84188 is_a: CL:0000630 ! supportive cell is_a: CL:0000710 ! neurecto-epithelial cell created_by: tmeehan creation_date: 2010-09-08T10:34:45Z [Term] id: CL:0002257 name: epithelial cell of thyroid gland namespace: cell alt_id: CL:1000297 def: "An epithelial cell of thyroid gland." [GOC:tfm] xref: FMA:256167 is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0002076 ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0002046 ! thyroid gland relationship: part_of UBERON:0002046 ! thyroid gland created_by: tmeehan creation_date: 2010-09-08T01:46:51Z [Term] id: CL:0002258 name: thyroid follicular cell namespace: cell def: "A cell type that varies from squamous to columnar, depending on their activity with microvillus directed luminally. This cell produces and secretes thyroid hormones." [GOC:tfm, ISBN:0517223651] synonym: "follicular cell of thyroid gland" EXACT [] synonym: "principal cell of thyroid gland" EXACT [] synonym: "thyroid gland follicular cell" EXACT [] xref: BTO:0003736 xref: FMA:68782 is_a: CL:0002257 ! epithelial cell of thyroid gland created_by: tmeehan creation_date: 2010-09-08T01:50:08Z [Term] id: CL:0002259 name: neuroepithelial stem cell namespace: cell def: "The stem cell from which glial precursor cell arises from." [GOC:tfm, PMID:11687496] synonym: "totipotent neuroepithelial stem cell" NARROW [] xref: FMA:87171 is_a: CL:0000723 ! somatic stem cell created_by: tmeehan creation_date: 2010-09-08T02:14:14Z [Term] id: CL:0002260 name: epithelial cell of parathyroid gland namespace: cell alt_id: CL:1000429 def: "An epithelial cell of the parathyroid gland." [GOC:tfm] xref: FMA:70547 is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0002076 ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0001132 ! parathyroid gland relationship: part_of UBERON:0001132 ! parathyroid gland created_by: tmeehan creation_date: 2010-09-08T02:29:38Z [Term] id: CL:0002261 name: endothelial cell of viscerocranial mucosa namespace: cell alt_id: CL:1000446 def: "An endothelial cell found in the mucosa associated with the facial skeleton." [GOC:tfm, ISBN:0618947256] xref: FMA:70627 is_a: CL:0002076 ! endo-epithelial cell created_by: tmeehan creation_date: 2010-09-14T10:40:12Z [Term] id: CL:0002262 name: endothelial cell of sinusoid namespace: cell alt_id: CL:1000403 def: "An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver." [GOC:tfm, ISBN:0618947256] xref: FMA:63134 is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0003909 ! sinusoid relationship: part_of UBERON:0003909 ! sinusoid created_by: tmeehan creation_date: 2010-09-14T10:57:26Z [Term] id: CL:0002263 name: transitional cell of parathyroid gland namespace: cell def: "One of three types of epithelial cells that populate the parathyroid gland; cytological characteristics intermediate between those of the chief cell and of the oxyphil cell. Because only one hormone is produced, the three cell forms are widely believed to be different phases in the life cycle of a single cell type, with the chief cell being its physiologically active stage." [GOC:tfm, ISBN:0412046911] xref: FMA:69324 is_a: CL:0002260 ! epithelial cell of parathyroid gland created_by: tmeehan creation_date: 2010-09-08T02:33:50Z [Term] id: CL:0002264 name: type A cell of stomach namespace: cell def: "A type of enteroendocrine cell found in the stomach that secretes glucagon." [GOC:tfm] xref: FMA:83411 is_a: CL:0002067 ! type A enterocrine cell is_a: CL:0002659 ! glandular cell of stomach created_by: tmeehan creation_date: 2010-09-10T10:54:42Z [Term] id: CL:0002265 name: type D cell of colon namespace: cell def: "A D cell located in the colon." [GOC:tfm] xref: FMA:268744 is_a: CL:0000502 ! type D enteroendocrine cell is_a: CL:0002658 ! glandular cell of the large intestine created_by: tmeehan creation_date: 2010-09-10T11:37:35Z [Term] id: CL:0002266 name: type D cell of small intestine namespace: cell def: "A type D cell of the small intestine." [GOC:tfm] xref: FMA:268736 is_a: CL:0000502 ! type D enteroendocrine cell is_a: CL:0002254 ! epithelial cell of small intestine is_a: CL:1001516 ! intestinal enteroendocrine cell created_by: tmeehan creation_date: 2010-09-10T01:34:22Z [Term] id: CL:0002267 name: type D cell of stomach namespace: cell def: "A type D cell found in the stomach." [GOC:tfm] xref: FMA:83410 is_a: CL:0000502 ! type D enteroendocrine cell is_a: CL:0002659 ! glandular cell of stomach created_by: tmeehan creation_date: 2010-09-10T01:36:03Z [Term] id: CL:0002268 name: P/D1 enteroendocrine cell namespace: cell def: "An enteroendocrine cell that stores and secretes Ghrelin." [GOC:tfm, ISBN:0517223651, PMID:15153415] xref: FMA:63207 xref: FMA:63418 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0002269 ! vasoactive intestinal peptide secreting cell created_by: tmeehan creation_date: 2010-09-10T01:47:45Z [Term] id: CL:0002269 name: vasoactive intestinal peptide secreting cell namespace: cell def: "An endocrine cell that secretes vasoactive intestinal peptide." [GOC:tfm] is_a: CL:0000167 ! peptide hormone secreting cell created_by: tmeehan creation_date: 2010-09-10T01:52:20Z [Term] id: CL:0002270 name: type EC2 enteroendocrine cell namespace: cell def: "A type EC enteroendocrine cell in the duodenum and jejunum that stores and secretes motilin and 5-hydroxytryptamine." [GOC:tfm, ISBN:0517223651, PMID:15153415] synonym: "Mo enteroendocrine cell" BROAD [] xref: FMA:62941 is_a: CL:0000577 ! type EC enteroendocrine cell is_a: CL:0002272 ! motilin secreting cell created_by: tmeehan creation_date: 2010-09-10T02:13:47Z [Term] id: CL:0002271 name: type EC1 enteroendocrine cell namespace: cell def: "A type EC enteredocrine cell in the intestines that stores and secretes substance P and 5-hydroxytryptamine." [GOC:tfm, ISBN:0517223651] xref: FMA:62940 is_a: CL:0000505 ! substance P secreting cell is_a: CL:0000577 ! type EC enteroendocrine cell created_by: tmeehan creation_date: 2010-09-10T02:13:49Z [Term] id: CL:0002272 name: motilin secreting cell namespace: cell def: "A cell that secretes motilin, a gastric hormone that at low pH inhibits gastric motor activity, whereas at high pH has a stimulating effect." [GOC:tfm, MESH:D06.472.317.525] is_a: CL:0000167 ! peptide hormone secreting cell created_by: tmeehan creation_date: 2010-09-10T02:31:13Z [Term] id: CL:0002273 name: type ECL enteroendocrine cell namespace: cell def: "A type EC enteroendocrine cell type that is numerous in the fundus of the stomach; stores 5-hydroxytryptamine and histamine." [GOC:tfm, ISBN:0517223651, PMID:15153415] xref: FMA:63208 is_a: CL:0000577 ! type EC enteroendocrine cell is_a: CL:0002274 ! histamine secreting cell created_by: tmeehan creation_date: 2010-09-10T02:35:17Z [Term] id: CL:0002274 name: histamine secreting cell namespace: cell def: "A cell type that secretes histamine." [GOC:tfm] is_a: CL:0000457 ! biogenic amine secreting cell created_by: tmeehan creation_date: 2010-09-10T03:04:42Z [Term] id: CL:0002275 name: pancreatic PP cell namespace: cell def: "A PP cell located in the islets of the pancreas." [GOC:tfm] comment: The term PP cell of pancreatic acinus was obsoleted due to a lack of evidence, making PP cell of pancreatic islets synonymous with pancreatic PP cell. synonym: "pancreatic polypeptide-secreting cell" EXACT [] synonym: "PP cell of pancreatic islet" EXACT [] synonym: "PP-cell of pancreatic islet" EXACT [] xref: BTO:0000805 xref: FMA:70588 is_a: CL:0000083 ! epithelial cell of pancreas is_a: CL:0000696 ! PP cell intersection_of: CL:0000696 ! PP cell intersection_of: part_of UBERON:0000006 ! islet of Langerhans intersection_of: part_of UBERON:0001264 ! pancreas relationship: part_of UBERON:0000006 ! islet of Langerhans relationship: part_of UBERON:0001264 ! pancreas created_by: tmeehan creation_date: 2010-09-10T03:30:31Z [Term] id: CL:0002276 name: PP cell of pancreatic acinus namespace: cell def: "A PP cell located in the pancreatic acinus. Obsoleted due to a lack of published evidence that this cell type is actually found in the pancreatic acinus." [GOC:tfm] synonym: "type F cell of pancreatic acinus" EXACT [] xref: FMA:85400 is_obsolete: true created_by: tmeehan creation_date: 2010-09-10T03:30:33Z [Term] id: CL:0002277 name: type I enteroendocrine cell namespace: cell def: "An enteroendocrine cell commonest in the duodenum and jejunum, rare in ileum, that secretes cholecystokinin. This cell type is involved in the regulation of digestive enzymes and bile." [GOC:tfm] synonym: "CCK cell" EXACT [] xref: FMA:62937 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell created_by: tmeehan creation_date: 2010-09-10T03:44:36Z [Term] id: CL:0002278 name: GIP cell namespace: cell def: "An enteroendocrine cell of duodenum and jejunum that produces gastric inhibitory peptide." [GOC:tfm] synonym: "type K enteroendocrine cell" EXACT [] xref: FMA:62942 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell created_by: tmeehan creation_date: 2010-09-10T03:51:47Z [Term] id: CL:0002279 name: type L enteroendocrine cell namespace: cell def: "A enteroendocrine cell type that is numerous in ileum, present in jejunum and large intestine, few in duodenum. This cell type produces glucagon-like immunoreactants (glicentin, glucagon-37, glucagon-29, GLP-1 and -2) and PYY." [ISBN:0517223651, PMID:15153415] xref: FMA:62944 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell created_by: tmeehan creation_date: 2010-09-10T03:59:09Z [Term] id: CL:0002280 name: type N enteroendocrine cell namespace: cell def: "An enteroendorcine cell found in the ileum and jejunum that produces neurotensin." [GOC:tfm] synonym: "N cell" EXACT [] xref: FMA:62943 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell created_by: tmeehan creation_date: 2010-09-10T04:08:29Z [Term] id: CL:0002281 name: type S enteroendocrine cell namespace: cell def: "Scattered in duodenojejunal mucosa, this enteroendocrine cell secretes secretin and serotonin." [GOC:tfm, PMID:15153415] xref: FMA:62936 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell is_a: CL:0000458 ! serotonin secreting cell created_by: tmeehan creation_date: 2010-09-10T04:44:46Z [Term] id: CL:0002282 name: type TG enteroendocrine cell namespace: cell def: "An enteroendocrine cell which produces a gastrin- and cholecystokinin-like peptide. The apical microvilli-rich plasma membrane is in open contact with the small intestine mucosa. This cell type is devoid of gastrin-17 but contains other fragments of the gastrin polypeptide." [DOI:10.1007/978-3-211-99390-3, GOC:tfm, PMID:7013499] xref: FMA:63421 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000509 ! gastrin secreting cell created_by: tmeehan creation_date: 2010-09-13T09:48:34Z [Term] id: CL:0002283 name: ecto-epithelial cell of viscerocranial mucosa namespace: cell alt_id: CL:1000440 def: "An epithelial cell of the mucosa associated with facial skeleton." [GOC:tfm, ISBN:0323052908] xref: FMA:70581 is_a: CL:0002159 ! general ecto-epithelial cell created_by: tmeehan creation_date: 2010-09-14T11:04:02Z [Term] id: CL:0002284 name: type X enteroendocrine cell namespace: cell def: "An enteroendorcine cell found in the fundus and pylorus, this cell type has dense round secretory granules that contain ghrelin." [GOC:tfm, PMID:20616512] synonym: "A-like" EXACT [] synonym: "X/A-like" EXACT [] xref: FMA:63209 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0005018 ! ghrelin secreting cell created_by: tmeehan creation_date: 2010-09-13T10:12:12Z [Term] id: CL:0002285 name: type III taste bud cell namespace: cell def: "A taste receptor cell that is characterized by morphologically identifiable synaptic contacts with the gustatory nerve fibers and expression of the synaptic membrane protein-25 (SNAP-25) and NCAM." [GOC:tfm, ISBN:0517223651, PMID:15738192] synonym: "taste bud basal cell" BROAD [] synonym: "type 3 taste cell" EXACT [] xref: FMA:67940 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0000209 ! taste receptor cell created_by: tmeehan creation_date: 2010-09-13T10:57:21Z [Term] id: CL:0002286 name: type II taste cell namespace: cell def: "A taste receptor cell that has a short microvilli, a projecting apical region, a large rounded nucleus, and expresses taste chemoreceptors thus making them the transducing cell for taste qualities." [GOC:tfm, PMID:15738192] synonym: "type 2 taste cell" EXACT [] xref: FMA:62381 is_a: CL:0000209 ! taste receptor cell created_by: tmeehan creation_date: 2010-09-13T10:57:26Z [Term] id: CL:0002287 name: type IV taste receptor cell namespace: cell def: "A rounded, mitotically active stem cell which is the source of new cells of the taste bud; located basally." [GOC:tfm, ISBN:0517223651, PMID:15738192] comment: There is debate about the exact lineage of these cell types from this progenitor. See PMID:15738192. synonym: "taste bud basal cell" BROAD [] synonym: "type 4 taste cell" EXACT [] xref: FMA:62380 is_a: CL:0000209 ! taste receptor cell created_by: tmeehan creation_date: 2010-09-13T10:57:29Z [Term] id: CL:0002288 name: type V taste receptor cell namespace: cell def: "A cell type that forms the boundary with the surrounding epithelium." [GOC:tfm, ISBN:0517223651] xref: FMA:67941 is_a: CL:0000209 ! taste receptor cell created_by: tmeehan creation_date: 2010-09-13T10:57:31Z [Term] id: CL:0002289 name: type I taste bud cell namespace: cell def: "A densely staining taste receptor cell that contains many dense vacuoles in their apical regions which project into the apical space and bear microvilli. This cell type serves as a supporting cell by surrounding and isolating the other cell types from each other; secrete a dense amorphous material that surrounds the microvilli in the taste pore. This cell type expresses a glial glutumate transporter, GLAST." [GOC:tfm, ISBN:0412046911, ISBN:0517223651, PMID:15738192] synonym: "dark tongue cell" EXACT [] synonym: "type I taste cell" EXACT [] synonym: "type taste 1 cell" EXACT [] xref: FMA:62356 is_a: CL:0000209 ! taste receptor cell is_a: CL:0000703 ! sustentacular cell created_by: tmeehan creation_date: 2010-09-13T10:57:35Z [Term] id: CL:0002290 name: Y chromosome-bearing sperm cell namespace: cell def: "A sperm bearing a Y chromosome. Chromosomal and genetic sex is established at fertilization in mammals and depends upon whether an X-bearing sperm or a Y-bearing sperm fertilizes the X-bearing ovum." [GOC:tfm, ISBN:0721669743] synonym: "Y bearing sperm" EXACT [] synonym: "Y-bearing sperm" EXACT [] xref: FMA:84058 is_a: CL:0000019 ! sperm created_by: tmeehan creation_date: 2010-09-13T11:35:24Z [Term] id: CL:0002291 name: X chromosome-bearing sperm cell namespace: cell def: "A sperm bearing an X chromosome. Chromosomal and genetic sex is established at fertilization in mammals and depends upon whether an X-bearing sperm or a Y-bearing sperm fertilizes the X-bearing ovum." [GOC:tfm, ISBN:0721669743] synonym: "X bearing sperm" EXACT [] synonym: "X-bearing sperm" EXACT [] xref: FMA:84057 is_a: CL:0000019 ! sperm created_by: tmeehan creation_date: 2010-09-13T11:35:26Z [Term] id: CL:0002292 name: type I cell of carotid body namespace: cell def: "A round or oval neuroepithelial cell that contacts other type I cells or capillaries. They occur in clusters that are surrounded by sheath cells (type-II cells) in the carotid body. This cell type is capable of secreting a number of neurotransmitters." [GOC:tfm, ISBN:0517223651] synonym: "glomus cell" EXACT [] xref: FMA:84186 is_a: CL:0000710 ! neurecto-epithelial cell created_by: tmeehan creation_date: 2010-09-13T01:40:21Z [Term] id: CL:0002293 name: epithelial cell of thymus namespace: cell alt_id: CL:1000459 def: "An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies." [FMA:72208, GOC:tfm] synonym: "epithelial cell of thymus gland" EXACT [] synonym: "epithelial reticular cell" EXACT [] synonym: "epithelial reticular cell of thymus" EXACT [] synonym: "thymic epithelial cell" EXACT [] xref: FMA:72208 is_a: CL:0002076 ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0002370 ! thymus relationship: part_of UBERON:0002370 ! thymus created_by: tmeehan creation_date: 2010-09-13T02:34:22Z [Term] id: CL:0002294 name: type-1 epithelial cell of thymus namespace: cell def: "An epithelial cell with a well defined Golgi apparatus that makes up the continuous layer of cells bordering the thymic tissue beneath the capsule." [GOC:tfm, PMID:9264335] synonym: "subcapsular thymic epithelial cell" EXACT [] xref: FMA:72209 is_a: CL:0002364 ! cortical thymic epithelial cell created_by: tmeehan creation_date: 2010-09-13T02:37:23Z [Term] id: CL:0002295 name: type-6 epithelial cell of thymus namespace: cell def: "A thymic epithelial cell that has an eccentric, round, or irregularly shaped hetero or euchromatic nucleus. The hallmark of this cell type is the presence of vacuoles, which are clustered in one area of the cytoplasm in the vicinity of the nucleus. The vacuoles are small and acquire a grape-like form, occasionally showing delicate internal microvillous projections." [GOC:tfm, PMID:19721455, PMID:9264335] synonym: "cystic thymic epithelial cells" EXACT [] synonym: "large medullary thymic epithelial cells" EXACT [] synonym: "large mTEC" EXACT [] xref: FMA:72214 is_a: CL:0002365 ! medullary thymic epithelial cell created_by: tmeehan creation_date: 2010-09-13T02:37:26Z [Term] id: CL:0002296 name: type-4 epithelial cell of thymus namespace: cell def: "An epithelial cell with high nuclear and cytoplasmic electron-density. This cell type is found in the deeper portions of the cortex but is more abundant in the medulla of the thymus." [FMA:0412046911, GOC:tfm, PMID:9264335] synonym: "dark thymic epithelial cell" EXACT [] xref: FMA:72212 is_a: CL:0002364 ! cortical thymic epithelial cell is_a: CL:0002365 ! medullary thymic epithelial cell created_by: tmeehan creation_date: 2010-09-13T02:37:45Z [Term] id: CL:0002297 name: type-3 epithelial cell of thymus namespace: cell def: "A thymic epithelial cell with moderate nuclear and cytoplasmic electron-density. Scattered in the cortex, this cell type is predominant in the mid and deep cortex." [PMID:9264335] synonym: "intermediate thymic epithelial cell" EXACT [] xref: FMA:72211 is_a: CL:0002364 ! cortical thymic epithelial cell created_by: tmeehan creation_date: 2010-09-13T02:37:51Z [Term] id: CL:0002298 name: type-5 epithelial cell of thymus namespace: cell def: "A thymic epithelial cell type with low nuclear and cytoplasmic electrondensity; has a round, euchromatic nucleus and occurs in small groups at the corticomedullary junction or scattered singly in the medulla." [GOC:tfm, ISBN:0412046911, PMID:19721455, PMID:9264335] synonym: "undifferentiated medullary thymic epithelial cell" EXACT [] synonym: "undifferentiated mTEC" EXACT [] synonym: "undifferentiated thymic epithelial cell" EXACT [] xref: FMA:72213 is_a: CL:0002365 ! medullary thymic epithelial cell created_by: tmeehan creation_date: 2010-09-13T02:37:54Z [Term] id: CL:0002299 name: type-2 epithelial cell of thymus namespace: cell def: "An epithelial cell scattered in the cortex, predominant in the outer cortex with a large pale nucleus and a prominent nucleolus." [GOC:tfm, ISBN:0412046911, PMID:9264335] synonym: "pale thymic epithelial cell" EXACT [] xref: FMA:72210 is_a: CL:0002364 ! cortical thymic epithelial cell created_by: tmeehan creation_date: 2010-09-13T02:37:58Z [Term] id: CL:0002300 name: type-7 epithelial cell of thymus namespace: cell def: "A small medullary thymic epithelial cell with a spindle shape, often arranged in groups and connected to each other by large desmosomes and interdigitations. The cytoplasm is sparse, with scanty organelles and thick bundles of cytokeratin." [GOC:tfm, PMID:19721455] synonym: "spindle shaped medullary thymic epithelial cell" EXACT [] synonym: "spindle shaped mTEC" EXACT [] is_a: CL:0002365 ! medullary thymic epithelial cell created_by: tmeehan creation_date: 2010-09-13T03:23:25Z [Term] id: CL:0002301 name: type B synovial cell namespace: cell def: "A synovial cell type that resembles fibroblasts, has abundant granular endoplasmic reticulum but contains fewer vacuoles and vesicles. This cell type secretes glycoproteins and hyaluronic acid." [GOC:tfm, ISBN:0517223651] xref: FMA:66788 is_a: CL:0000214 ! synovial cell created_by: tmeehan creation_date: 2010-09-13T03:39:14Z [Term] id: CL:0002302 name: type A synovial cell namespace: cell def: "A synovial cell that is macrophage-like, characterized by surface ruffles or lamellipodia, plasma membrane invaginations and associated micropinocytotic vesicles, Golgi apparatus and little granular endoplasmic reticulum." [GOC:tfm, ISBN:0517223651] synonym: "type A synoviocyte" EXACT [] xref: FMA:66787 is_a: CL:0000214 ! synovial cell created_by: tmeehan creation_date: 2010-09-13T03:39:17Z [Term] id: CL:0002303 name: pigmented ciliary epithelial cell namespace: cell def: "A ciliated epithelial cell of the retina, this cell type uptakes sodium chloride and passes it to non-pigmented ciliary epithelial cells." [PMID:15106942] synonym: "PE" EXACT [] xref: FMA:70606 is_a: CL:0000067 ! ciliated epithelial cell is_a: CL:0000710 ! neurecto-epithelial cell is_a: CL:0005012 ! multi-ciliated epithelial cell created_by: tmeehan creation_date: 2010-09-13T04:09:27Z [Term] id: CL:0002304 name: non-pigmented ciliary epithelial cell namespace: cell def: "A multi-ciliated cell of the retina that lacks visual pigment and contributes to aqueous humor by secreting chloride ions. This cell type maintains gap junctions with pigmented epithelial cells." [GOC:tfm, PMID:15106942] synonym: "NPE" EXACT [] xref: FMA:70607 is_a: CL:0000067 ! ciliated epithelial cell is_a: CL:0000710 ! neurecto-epithelial cell is_a: CL:0005012 ! multi-ciliated epithelial cell intersection_of: CL:0000710 ! neurecto-epithelial cell intersection_of: part_of UBERON:0001778 ! ciliary epithelium relationship: part_of UBERON:0001778 ! ciliary epithelium created_by: tmeehan creation_date: 2010-09-13T04:09:31Z [Term] id: CL:0002305 name: epithelial cell of distal tubule namespace: cell def: "An epithelial cell of the distal convoluted tubule of the kidney that helps regulate systemic levels of potassium, sodium, calcium, and pH." [GOC:tfm, ISBN:0517223651] synonym: "kidney distal tubule epithelial cell" EXACT [] xref: FMA:62125 xref: FMA:70981 xref: KUPO:0001055 is_a: CL:0002078 ! meso-epithelial cell is_a: CL:1000615 ! kidney cortex tubule cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0004135 ! distal tubule relationship: part_of UBERON:0004135 ! distal tubule [Term] id: CL:0002306 name: epithelial cell of proximal tubule namespace: cell def: "An epithelial cell of the proximal tubule of the kidney." [GOC:tfm, ISBN:1-4160-2328-3] synonym: "kidney proximal tubule epithelial cell" EXACT [] xref: FMA:62125 xref: FMA:70973 xref: KUPO:0001044 is_a: CL:0000239 ! brush border epithelial cell is_a: CL:0002078 ! meso-epithelial cell is_a: CL:1000615 ! kidney cortex tubule cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0004134 ! proximal tubule relationship: part_of UBERON:0004134 ! proximal tubule [Term] id: CL:0002307 name: brush border cell of the proximal tubule namespace: cell def: "A brush border epithelial cell located in the proximal tubule of the kidney that detects fluid flow." [GOC:tfm, ISBN:1-4160-2328-3] is_a: CL:0002306 ! epithelial cell of proximal tubule created_by: tmeehan creation_date: 2010-09-14T11:29:20Z [Term] id: CL:0002308 name: epithelial cell of skin gland namespace: cell def: "An epithelial cell of a skin gland." [GOC:tfm] synonym: "epithelial cell of gland of skin" EXACT [] xref: FMA:70657 is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002419 ! skin gland relationship: part_of UBERON:0002419 ! skin gland created_by: tmeehan creation_date: 2010-09-14T12:00:07Z [Term] id: CL:0002309 name: corticotroph namespace: cell def: "A basophil chromphil cell of the anterior pitiutary gland that produce adrenocorticotropic hormone, melanocyte-stimulating hormone and lipotropin. This cell type is irregular in shape and has short dendritic processes which are inserted among other neighboring cells;" [GOC:tfm, ISBN:0517223651] xref: BTO:0002509 xref: FMA:83098 is_a: CL:0000467 ! adrenocorticotropic hormone secreting cell is_a: CL:0000639 ! basophil cell of pars distalis of adenohypophysis created_by: tmeehan creation_date: 2010-09-14T02:08:23Z [Term] id: CL:0002310 name: mammosomatotroph namespace: cell def: "An acidophil cell of the anterior pitiuatry gland that produces both prolactin and growth hormone." [GOC:tfm] xref: FMA:83097 is_a: CL:0000295 ! somatotropin secreting cell is_a: CL:0000439 ! prolactin secreting cell is_a: CL:0000638 ! acidophil cell of pars distalis of adenohypophysis created_by: tmeehan creation_date: 2010-09-14T02:25:34Z [Term] id: CL:0002311 name: mammotroph namespace: cell def: "An acidophilic cell of the anterior pituitary that produces prolactin." [SANBI:mhl] synonym: "epsilon-acidophil" EXACT [] synonym: "lactotrope" EXACT [] synonym: "lactotroph" EXACT [] synonym: "lactotropic cell" EXACT [] synonym: "mammotrope" EXACT [] synonym: "mammotrophic cell" EXACT [] synonym: "mammotropic cell" EXACT [] xref: FMA:83096 is_a: CL:0000439 ! prolactin secreting cell is_a: CL:0000638 ! acidophil cell of pars distalis of adenohypophysis created_by: tmeehan creation_date: 2010-09-14T02:30:57Z [Term] id: CL:0002312 name: somatotroph namespace: cell def: "An acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin." [SANBI:mhl] synonym: "somatotrope" EXACT [] synonym: "somatotropic cell" EXACT [] synonym: "somatrophic cell" EXACT [] xref: FMA:83095 is_a: CL:0000295 ! somatotropin secreting cell is_a: CL:0000638 ! acidophil cell of pars distalis of adenohypophysis created_by: tmeehan creation_date: 2010-09-14T02:33:09Z [Term] id: CL:0002313 name: endocrine-paracrine cell of prostate gland namespace: cell def: "An ecto-epithelial cell of the prostate gland that secretes hormones." [GOC:tfm] synonym: "glandular cell of prostate" EXACT [] synonym: "neuro-epithelial cell of prostate gland" EXACT [] xref: FMA:74390 xref: FMA:86774 is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0002159 ! general ecto-epithelial cell created_by: tmeehan creation_date: 2010-09-14T03:01:58Z [Term] id: CL:0002314 name: external supporting cell of vestibular epithelium namespace: cell def: "An auditory epithelial support cell located in the vestibular epithelium that has many hallmarks of glial cells. This cell type express glial markers such as vimentin, S100, glutamate-aspartate transporter, low affinity neurotrophin receptor p75, glial fibrillary acidic protein, and proteolipid protein." [GOC:tfm, PMID:20837532] xref: FMA:75809 is_a: CL:0002316 ! supporting cell of vestibular epithelium created_by: tmeehan creation_date: 2010-09-14T03:20:01Z [Term] id: CL:0002315 name: supporting cell of cochlea namespace: cell def: "An epithelial supporting cell located in the cochlea." [GOC:tfm] xref: FMA:79796 is_a: CL:0005014 ! auditory epithelial support cell created_by: tmeehan creation_date: 2010-09-14T03:31:38Z [Term] id: CL:0002316 name: supporting cell of vestibular epithelium namespace: cell def: "A supporting cell of the vestibular epithelium." [GOC:tfm, PMID:20837532] xref: FMA:75607 is_a: CL:0005014 ! auditory epithelial support cell created_by: tmeehan creation_date: 2010-09-14T03:31:44Z [Term] id: CL:0002317 name: external limiting cell of vestibular epithelium namespace: cell def: "An external limiting cell found in the vestibular epithelium." [GOC:tfm] xref: FMA:75808 is_a: CL:0002316 ! supporting cell of vestibular epithelium created_by: tmeehan creation_date: 2010-09-14T03:33:50Z [Term] id: CL:0002318 name: periperhal blood mesothelial cell namespace: cell def: "A mesothelial cell capable of circulating in the blood by first losing its squamous character. This cell can incorporate into the regenerating mesothelium." [GOC:tfm, PMID:14592528] xref: FMA:86712 is_a: CL:0000081 ! blood cell relationship: develops_from CL:0000077 ! mesothelial cell created_by: tmeehan creation_date: 2010-09-15T10:47:11Z [Term] id: CL:0002319 name: neural cell namespace: cell def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] xref: FMA:70333 is_a: CL:0000548 ! animal cell is_a: CL:0002371 ! somatic cell created_by: tmeehan creation_date: 2010-09-15T01:34:57Z [Term] id: CL:0002320 name: connective tissue cell namespace: cell alt_id: CL:1000406 def: "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." [GOC:tfm, ISBN:0618947256] xref: FMA:63875 is_a: CL:0000548 ! animal cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0002371 ! somatic cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue created_by: tmeehan creation_date: 2010-09-15T03:01:54Z [Term] id: CL:0002321 name: embryonic cell namespace: cell def: "A cell of the embryo." [FMA:0618947256] xref: FMA:82840 xref: FMA:82841 xref: WBbt:0007028 is_a: CL:0000548 ! animal cell created_by: tmeehan creation_date: 2010-09-15T03:39:21Z [Term] id: CL:0002322 name: embryonic stem cell namespace: cell def: "A stem cell of embryonic origin." [GOC:dsd, GOC:tfm, ISBN:068340007X, PMID:18179856] comment: This is an in vitro cell type and may be removed in future releases. These cells are reportedly SSEA-4-positive, CD73-negative, and CD324-positive. synonym: "ESC" EXACT [] xref: BTO:0001086 xref: FMA:82841 is_a: CL:0000034 ! stem cell is_a: CL:0002321 ! embryonic cell created_by: tmeehan creation_date: 2010-09-15T03:44:35Z [Term] id: CL:0002323 name: amniocyte namespace: cell def: "A cell of a fetus which is suspended in the amniotic fluid. Amniocytes are considered to arise from several tissues including fetal skin, the fetal urinary tract, umbilical cord, and the inner amniotic surface." [BFO:0000066, GOC:tfm, PMID:3211847] xref: BTO:0000066 is_a: CL:0000349 ! extraembryonic cell intersection_of: CL:0000349 ! extraembryonic cell intersection_of: located_in UBERON:0000173 ! amniotic fluid relationship: located_in UBERON:0000173 ! amniotic fluid created_by: tmeehan creation_date: 2010-09-20T10:13:37Z [Term] id: CL:0002324 name: myoepithelial cell of mammary gland namespace: cell def: "A myoepithelial cell that surrounds milk-secreting luminal epithelial cells. This cell type contracts under the stimulation of oxytocin and is attached to the basement membrane by hemidesmosomes and to the adjacent luminal cells by desmosomes. This cell type expresses high level of keratin-14 and is estrogen receptor alpha negative." [GOC:tfm, PMID:11250738, PMID:19022771] is_a: CL:1000416 ! myoepithelial cell of lactiferous gland created_by: tmeehan creation_date: 2010-09-20T11:42:14Z [Term] id: CL:0002325 name: mammary alveolar cell namespace: cell alt_id: CL:0002230 alt_id: CL:1000476 def: "The milk-producing cell of the alveolar unit that emerges during pregnancy." [GOC:tfm, PMID:19022771] synonym: "epithelial cell of lactiferous gland" EXACT [] synonym: "luminal cell of alveolus of lactiferous gland" EXACT [] xref: FMA:74506 xref: FMA:79866 is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000314 ! milk secreting cell is_a: CL:0002159 ! general ecto-epithelial cell is_a: CL:0002327 ! mammary epithelial cell intersection_of: CL:0002159 ! general ecto-epithelial cell intersection_of: part_of UBERON:0001911 ! mammary gland relationship: part_of UBERON:0001911 ! mammary gland created_by: tmeehan creation_date: 2010-09-20T01:30:57Z [Term] id: CL:0002326 name: luminal epithelial cell of mammary gland namespace: cell def: "A mammary epithelial cell that occurs in the lumen of the ductal and alveoli structure in the breast." [GOC:tfm, PMID:19022771] xref: FMA:73280 is_a: CL:0000069 ! branched duct epithelial cell is_a: CL:0002327 ! mammary epithelial cell created_by: tmeehan creation_date: 2010-09-20T01:37:53Z [Term] id: CL:0002327 name: mammary epithelial cell namespace: cell def: "An epithelial cell of the mammary gland." [GOC:tfm, PMID:19022771] synonym: "breast epithelial cell" EXACT [] xref: BTO:0004300 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001911 ! mammary gland relationship: part_of UBERON:0001911 ! mammary gland created_by: tmeehan creation_date: 2010-09-20T01:49:37Z [Term] id: CL:0002328 name: bronchial epithelial cell namespace: cell def: "An epithelial cell of the bronchus." [GOC:tfm] xref: BTO:0002922 is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0002202 ! epithelial cell of tracheobronchial tree intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002185 ! bronchus relationship: part_of UBERON:0002031 ! epithelium of bronchus relationship: part_of UBERON:0002185 ! bronchus created_by: tmeehan creation_date: 2010-09-20T02:00:00Z [Term] id: CL:0002329 name: basal epithelial cell of tracheobronchial tree namespace: cell def: "An epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury." [GOC:tfm] is_a: CL:0002202 ! epithelial cell of tracheobronchial tree created_by: tmeehan creation_date: 2010-09-20T02:10:36Z [Term] id: CL:0002330 name: undifferentiated cell of bronchus epithelium namespace: cell def: "An undifferentiated columnar cell of the bronchus epithelium" [GOC:tfm, PMID:18757316] is_a: CL:0002328 ! bronchial epithelial cell created_by: tmeehan creation_date: 2010-09-20T02:17:58Z [Term] id: CL:0002332 name: ciliated cell of the bronchus namespace: cell def: "A ciliated cell of the bronchus." [GOC:tfm, PMID:18757316] is_a: CL:0002145 ! ciliated columnar cell of tracheobronchial tree is_a: CL:0002328 ! bronchial epithelial cell created_by: tmeehan creation_date: 2010-09-20T02:21:12Z [Term] id: CL:0002333 name: neural crest derived fat cell namespace: cell def: "A fat cell derived from a neural crest cell." [GOC:tfm, PMID:17507398] is_a: CL:0000136 ! fat cell relationship: develops_from CL:0000005 ! fibroblast neural crest derived created_by: tmeehan creation_date: 2010-09-20T02:25:25Z [Term] id: CL:0002334 name: preadipocyte namespace: cell def: "An undifferentiated fibroblast that can be stimulated to form a fat cell." [GOC:tfm, PMID:18793119] xref: BTO:0001107 is_a: CL:0000057 ! fibroblast created_by: tmeehan creation_date: 2010-09-20T02:31:53Z [Term] id: CL:0002335 name: brown preadipocyte namespace: cell def: "A preadipocyte that is capable of differentiating into a brown adipocyte. This cell type expresses uncoupling protein-1, PPAR-gamma, PR-domain-containing 16; and PGC-1alpha (peroxisome proliferator-activated receptor-gamma (PPARgamma) coactivator-1alpha)." [GOC:tfm, PMID:18719589] is_a: CL:0002334 ! preadipocyte created_by: tmeehan creation_date: 2010-09-20T02:38:38Z [Term] id: CL:0002336 name: buccal mucosa cell namespace: cell def: "An endothelial cell that lines the oral cavitiy including the mucosa of the gums, the palate, the lip, and the cheek." [GOC:tfm, MESH:A10.615.550.599] is_a: CL:0002261 ! endothelial cell of viscerocranial mucosa created_by: tmeehan creation_date: 2010-09-20T02:52:54Z [Term] id: CL:0002337 name: keratinocyte stem cell namespace: cell def: "A stem cell located in the bulge of the hair follicle that can give rise to regenerate the new follicle with each hair cycle and to reepithelialize the epidermis during wound repair." [PMID:15339667] synonym: "bulge keratinocyte" EXACT [] is_a: CL:0000048 ! multi fate stem cell is_a: CL:0000312 ! keratinocyte is_a: CL:1000428 ! stem cell of epidermis created_by: tmeehan creation_date: 2010-09-20T03:07:03Z [Term] id: CL:0002338 name: CD56-positive, CD161-positive immature natural killer cell namespace: cell def: "A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-negative, CD117-positive, CD122-positive,and CD161-positive." [GO_REF:0000031, GOC:add, ISBN:0781735149, PMID:12457618] comment: Human markers; killer cell immunoglobulin-like receptor 2DL1 is used as a representative example (PRO at this time lacks a KIR superfamily). synonym: "p-NK" RELATED [PMID:12457618] is_a: CL:0000823 ! immature natural killer cell intersection_of: CL:0000823 ! immature natural killer cell intersection_of: has_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 intersection_of: has_plasma_membrane_part PR:000001381 ! interleukin-2 receptor subunit beta intersection_of: has_plasma_membrane_part PR:000001874 ! KLRB1-like protein intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: develops_from CL:0002344 ! CD56-negative, CD161-positive immature natural killer cell relationship: has_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: has_plasma_membrane_part PR:000001381 ! interleukin-2 receptor subunit beta relationship: has_plasma_membrane_part PR:000001874 ! KLRB1-like protein relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule created_by: tmeehan creation_date: 2010-09-21T10:06:53Z [Term] id: CL:0002339 name: prostate stem cell namespace: cell def: "A prostate epithelial cell that is CD133-positive, CD44-positive, integrin A2beta3-high. This cell is a stem cell for the prostate epithelium." [GOC:tfm, PMID:15226377] synonym: "CD133-positive prostate epithelial cell" EXACT [] is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002341 ! basal cell of prostate epithelium created_by: tmeehan creation_date: 2010-09-20T03:21:06Z [Term] id: CL:0002340 name: luminal cell of prostate epithelium namespace: cell def: "The exocrine cell of the prostate, this epithelial cell secretes prostatic acid phosphotase and PSA, and is dependent on androgen hormones for survival." [GOC:tfm] is_a: CL:0002231 ! epithelial cell of prostate created_by: tmeehan creation_date: 2010-09-20T03:34:05Z [Term] id: CL:0002341 name: basal cell of prostate epithelium namespace: cell def: "An undifferentiated cell of the prostate epithelium that lacks secretory activity." [GOC:tfm, PMCID:PMC2673349] is_a: CL:0002231 ! epithelial cell of prostate created_by: tmeehan creation_date: 2010-09-20T03:34:10Z [Term] id: CL:0002342 name: circulating endothelial cell namespace: cell def: "A circulating endothelial cell of the phenotype CD146-positive, CD105-positive, CD45-negative. This cell type is indicative of recent vascular damage." [GOC:tfm, PMID:19652886] is_a: CL:0000115 ! endothelial cell created_by: tmeehan creation_date: 2010-09-20T03:49:58Z [Term] id: CL:0002343 name: decidual natural killer cell namespace: cell def: "A natural killer cell subset that is found in the decidual of the uterus and is CD56-high, Galectin-1-positive and CD16-negative. This cell type represents the most abundant immune cell type in the decidual during the first trimester of pregnancy." [PMID:14568979, PMID:19800965] synonym: "decidual NK cell" EXACT [] synonym: "dNK cell" EXACT [] is_a: CL:0000824 ! mature natural killer cell intersection_of: CL:0000824 ! mature natural killer cell intersection_of: has_high_plasma_membrane_amount PR:000001024 ! neural cell adhesion molecule 1 intersection_of: has_plasma_membrane_part PR:000009766 ! galectin-1 intersection_of: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: has_high_plasma_membrane_amount PR:000001024 ! neural cell adhesion molecule 1 relationship: has_plasma_membrane_part PR:000009766 ! galectin-1 relationship: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III created_by: tmeehan creation_date: 2010-09-20T04:00:02Z [Term] id: CL:0002344 name: CD56-negative, CD161-positive immature natural killer cell namespace: cell def: "A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-negative, CD117-positive, CD122-positive,and CD161-positive." [GO_REF:0000031, GOC:add, ISBN:0781735149, PMID:12457618] comment: Human markers; killer cell immunoglobulin-like receptor 2DL1 is used as a representative example (PRO at this time lacks a KIR superfamily). synonym: "p-NK" RELATED [PMID:12457618] is_a: CL:0000823 ! immature natural killer cell intersection_of: CL:0000823 ! immature natural killer cell intersection_of: has_plasma_membrane_part PR:000001381 ! interleukin-2 receptor subunit beta intersection_of: has_plasma_membrane_part PR:000001874 ! KLRB1-like protein intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule intersection_of: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 relationship: has_plasma_membrane_part PR:000001381 ! interleukin-2 receptor subunit beta relationship: has_plasma_membrane_part PR:000001874 ! KLRB1-like protein relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part PR:000001003 ! CD34 molecule relationship: lacks_plasma_membrane_part PR:000001024 ! neural cell adhesion molecule 1 created_by: tmeehan creation_date: 2010-09-20T04:33:11Z [Term] id: CL:0002345 name: CD27-low, CD11b-low immature natural killer cell namespace: cell def: "An immature natural killer cell that is NK1.1-positive, DX5-positive, Ly49-positive, CD27-low and CD11b-low. This cell type is found in high numbers in the liver." [GOC:tfm, http:www.immgen.org/index_content.html, PMID:19949422] comment: Markers are associated with mouse cells. synonym: "preNK.BM" BROAD [] is_a: CL:0000823 ! immature natural killer cell intersection_of: CL:0000823 ! immature natural killer cell intersection_of: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M intersection_of: has_low_plasma_membrane_amount PR:000001963 ! CD27 molecule intersection_of: has_plasma_membrane_part PR:000001008 ! integrin alpha-2 intersection_of: has_plasma_membrane_part PR:000002977 ! killer cell lectin-like receptor subfamily B member 1C intersection_of: has_plasma_membrane_part PR:000009616 ! T-cell surface glycoprotein YE1/48 relationship: develops_from CL:0002346 ! Dx5-negative, NK1.1-positive immature natural killer cell relationship: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: has_low_plasma_membrane_amount PR:000001963 ! CD27 molecule relationship: has_plasma_membrane_part PR:000001008 ! integrin alpha-2 relationship: has_plasma_membrane_part PR:000002977 ! killer cell lectin-like receptor subfamily B member 1C relationship: has_plasma_membrane_part PR:000009616 ! T-cell surface glycoprotein YE1/48 created_by: tmeehan creation_date: 2010-09-20T04:41:01Z [Term] id: CL:0002346 name: Dx5-negative, NK1.1-positive immature natural killer cell namespace: cell def: "An immature natural killer cell that is NK1.1-positive and DX-5 negative." [GOC:tfm, PMID:12766763] is_a: CL:0000823 ! immature natural killer cell intersection_of: CL:0000823 ! immature natural killer cell intersection_of: has_plasma_membrane_part PR:000002977 ! killer cell lectin-like receptor subfamily B member 1C intersection_of: lacks_plasma_membrane_part PR:000001008 ! integrin alpha-2 relationship: has_plasma_membrane_part PR:000002977 ! killer cell lectin-like receptor subfamily B member 1C relationship: lacks_plasma_membrane_part PR:000001008 ! integrin alpha-2 created_by: tmeehan creation_date: 2010-09-21T10:11:44Z [Term] id: CL:0002347 name: CD27-high, CD11b-high natural killer cell namespace: cell def: "A mature natural killer cell that is CD27-high and CD11b-high. This cell type is capable of interferon-gamma secretion." [GOC:tfm, PMID:19949422] is_a: CL:0002426 ! CD11b-positive, CD27-positive natural killer cell intersection_of: CL:0000824 ! mature natural killer cell intersection_of: capable_of GO:0032609 ! interferon-gamma production intersection_of: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M intersection_of: has_high_plasma_membrane_amount PR:000001963 ! CD27 molecule relationship: capable_of GO:0032609 ! interferon-gamma production relationship: develops_from CL:0002349 ! CD27-high, CD11b-low natural killer cell relationship: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: has_high_plasma_membrane_amount PR:000001963 ! CD27 molecule created_by: tmeehan creation_date: 2010-09-21T10:19:49Z [Term] id: CL:0002348 name: CD27-low, CD11b-high natural killer cell namespace: cell def: "A CD27-low, CD11b-high natural killer cell that has a higher threshold of activation due to higher expression of inhibitory receptors." [GOC:tfm, PMID:1994922] is_a: CL:0002426 ! CD11b-positive, CD27-positive natural killer cell intersection_of: CL:0000824 ! mature natural killer cell intersection_of: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M intersection_of: has_low_plasma_membrane_amount PR:000001963 ! CD27 molecule relationship: develops_from CL:0002347 ! CD27-high, CD11b-high natural killer cell relationship: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: has_low_plasma_membrane_amount PR:000001963 ! CD27 molecule created_by: tmeehan creation_date: 2010-09-21T10:19:54Z [Term] id: CL:0002349 name: CD27-high, CD11b-low natural killer cell namespace: cell def: "A natural killer cell that is CD27-high and CD11b-low." [GOC:tfm, PMID:1994922] is_a: CL:0002426 ! CD11b-positive, CD27-positive natural killer cell intersection_of: CL:0000824 ! mature natural killer cell intersection_of: has_high_plasma_membrane_amount PR:000001963 ! CD27 molecule intersection_of: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: develops_from CL:0002345 ! CD27-low, CD11b-low immature natural killer cell relationship: has_high_plasma_membrane_amount PR:000001963 ! CD27 molecule relationship: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M created_by: tmeehan creation_date: 2010-09-21T10:20:00Z [Term] id: CL:0002350 name: endocardial cell namespace: cell alt_id: CL:1000475 def: "An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin." [GOC:tfm, ISSN:0452-3458] synonym: "endocardial endothelial cell" EXACT [] synonym: "endothelial cell of endocardium" EXACT [FMA:75621] xref: FMA:75621 is_a: CL:0000115 ! endothelial cell is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0002165 ! endocardium relationship: part_of UBERON:0002165 ! endocardium created_by: tmeehan creation_date: 2010-09-21T04:33:05Z [Term] id: CL:0002351 name: progenitor cell of endocrine pancreas namespace: cell def: "A multi-fate stem cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1." [GOC:tfm, PMID:20025937, PMID:20217494] synonym: "pancreatic endocrine progenitor" EXACT [] synonym: "pancreatic islet progenitor cell" EXACT [] is_a: CL:0000048 ! multi fate stem cell created_by: tmeehan creation_date: 2010-09-21T04:41:06Z [Term] id: CL:0002352 name: gestational hematopoietic stem cell namespace: cell def: "A hematopoietic stem cell that exists during embryogenesis." [GOC:tfm, ISBN:978-60327-246-6] is_a: CL:0000037 ! hematopoietic stem cell created_by: tmeehan creation_date: 2010-09-22T09:05:13Z [Term] id: CL:0002353 name: fetal liver hematopoietic progenitor cell namespace: cell def: "A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative." [GOC:tfm, ISBN:978-1-60327-346-6, PMID:16569764] is_a: CL:0002352 ! gestational hematopoietic stem cell intersection_of: CL:0002352 ! gestational hematopoietic stem cell intersection_of: has_plasma_membrane_part GO:0042611 ! MHC protein complex intersection_of: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C intersection_of: has_plasma_membrane_part PR:000001833 ! SLAM family member 1 intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor intersection_of: has_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 intersection_of: lacks_plasma_membrane_part PR:000001308 ! CD48 molecule intersection_of: lacks_plasma_membrane_part PR:000001896 ! natural killer cell receptor 2B4 relationship: has_plasma_membrane_part GO:0042611 ! MHC protein complex relationship: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C relationship: has_plasma_membrane_part PR:000001833 ! SLAM family member 1 relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor relationship: has_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: lacks_plasma_membrane_part PR:000001308 ! CD48 molecule relationship: lacks_plasma_membrane_part PR:000001896 ! natural killer cell receptor 2B4 created_by: tmeehan creation_date: 2010-09-22T09:08:32Z [Term] id: CL:0002354 name: yolk sac hematopoietic stem cell namespace: cell def: "A hematopoietic stem found in the yolk sac. In mice, this cell type is Sca-1-negative, CD45-negative, MHC-negative, HSA-positive, AA4.1-positive, CD44-positive." [doi:10.1097/MOH.0b013e3282f97ae1, GOC:tfm] synonym: "hemangioblast precursor" EXACT [] is_a: CL:0002352 ! gestational hematopoietic stem cell intersection_of: CL:0002352 ! gestational hematopoietic stem cell intersection_of: has_plasma_membrane_part PR:000001307 ! CD44 molecule intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor intersection_of: lacks_plasma_membrane_part GO:0042611 ! MHC protein complex intersection_of: lacks_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C intersection_of: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: has_plasma_membrane_part PR:000001307 ! CD44 molecule relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor relationship: lacks_plasma_membrane_part GO:0042611 ! MHC protein complex relationship: lacks_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C relationship: lacks_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 created_by: tmeehan creation_date: 2010-09-22T09:08:34Z [Term] id: CL:0002355 name: primitive red blood cell namespace: cell def: "A large nucleated basophilic erythrocyte found in mammalian embryos. This cell type arises from the blood islands of yolk sacs and expresses different types of hemoglobins (beta-H1, gamma-1 and zeta) than adult erythrocytes. Considered a type of erythroblast as this cell type can enucleate in circulation." [DOI:10.1097/MOH.0b013e3282f97ae1, GOC:tfm, PMID:11495698] synonym: "primitive erythroblast" EXACT [] synonym: "primitive erythrocyte" EXACT [] synonym: "primitive erythroid cell" EXACT [] is_a: CL:0002417 ! primitive erythroid lineage cell intersection_of: CL:0002417 ! primitive erythroid lineage cell intersection_of: has_part PR:000008467 ! hemoglobin subunit zeta intersection_of: has_part PR:000008857 ! hemoglobin subunit beta-1 intersection_of: has_quality PATO:0000586 ! increased size intersection_of: part_of UBERON:0000922 ! embryo relationship: develops_from CL:0002361 ! primitive erythroid progenitor relationship: has_part PR:000008467 ! hemoglobin subunit zeta relationship: has_part PR:000008857 ! hemoglobin subunit beta-1 relationship: has_quality PATO:0000586 ! increased size relationship: part_of UBERON:0000922 ! embryo created_by: tmeehan creation_date: 2010-09-22T09:27:05Z [Term] id: CL:0002356 name: primitive reticulocyte namespace: cell def: "A primitive erythrocyte that has undergone enucleation. This cell type is 3-6 fold bigger than the fetal derived erythrocytes that they co-circulate with during fetal development. Expresses epsilon-gamma hemoglobin chains." [doi:10.1097/MOH.0b013e3282f97ae1, GOC:tfm, PMID:11495698] synonym: "megalocyte" EXACT [] is_a: CL:0002417 ! primitive erythroid lineage cell intersection_of: CL:0002417 ! primitive erythroid lineage cell intersection_of: develops_from CL:0002355 ! primitive red blood cell intersection_of: has_quality PATO:0000586 ! increased size relationship: develops_from CL:0002355 ! primitive red blood cell relationship: has_quality PATO:0000586 ! increased size created_by: tmeehan creation_date: 2010-09-22T09:35:16Z [Term] id: CL:0002357 name: fetal derived definitive erythrocyte namespace: cell def: "A fetal liver derived enucleated erythrocyte. This erythrocyte resembles adult erythrocytes in that they are small (3- to 6- times smaller than primitive erythrocytes) and produce adult hemaglobins." [GOC:tfm, PMID:11495698] synonym: "macrocyte" EXACT [] is_a: CL:0000595 ! enucleate erythrocyte intersection_of: CL:0000595 ! enucleate erythrocyte intersection_of: has_part PR:000008857 ! hemoglobin subunit beta-1 intersection_of: part_of UBERON:0000922 ! embryo relationship: develops_from CL:0002353 ! fetal liver hematopoietic progenitor cell relationship: has_part PR:000008857 ! hemoglobin subunit beta-1 relationship: part_of UBERON:0000922 ! embryo created_by: tmeehan creation_date: 2010-09-22T09:38:32Z [Term] id: CL:0002358 name: pyrenocyte namespace: cell def: "Derived from the Greek word pyren (the pit of a stone fruit), this is a transient nucleated cell type that results from exclusion of the nucleus from the primitive erythrocyte." [GOC:tfm] is_a: CL:0002417 ! primitive erythroid lineage cell intersection_of: CL:0002417 ! primitive erythroid lineage cell intersection_of: develops_from CL:0002355 ! primitive red blood cell intersection_of: has_quality PATO:0000587 ! decreased size relationship: develops_from CL:0002355 ! primitive red blood cell relationship: has_quality PATO:0000587 ! decreased size created_by: tmeehan creation_date: 2010-09-22T10:02:37Z [Term] id: CL:0002359 name: placental hematopoietic stem cell namespace: cell def: "A hematopoietic stem cell of the placenta. This cell type is first observed E10.5 This cell type may give rise to fetal liver hematopoietic stem cells." [GOC:tfm, ISBN:978-1-60327-346-6] is_a: CL:0002352 ! gestational hematopoietic stem cell created_by: tmeehan creation_date: 2010-09-22T10:30:02Z [Term] id: CL:0002360 name: AGM hematopoietic stem cell namespace: cell def: "A hematopoietic stem cell from the aorta-gonad-mesonephros region of the developing embryo. First seen at E10.5 in mouse embryos. May give rise to fetal liver HSC." [GOC:tfm, ISBN:978-1-60327-346-6] is_a: CL:0002352 ! gestational hematopoietic stem cell created_by: tmeehan creation_date: 2010-09-22T10:31:49Z [Term] id: CL:0002361 name: primitive erythroid progenitor namespace: cell def: "A progenitor cell that is capable of forming colonies of primitive erythrocytes in the blood island of the yolk sac. First arrive at E7.5 in mouse and expresses CD41." [GOC:tfm, ISBN:0813817986, PMID:20711979] synonym: "EryP-CFC" EXACT [] synonym: "inner blood island hemangioblast" EXACT [] is_a: CL:0002417 ! primitive erythroid lineage cell intersection_of: CL:0002417 ! primitive erythroid lineage cell intersection_of: has_plasma_membrane_part PR:000009127 ! integrin alpha-IIb relationship: develops_from CL:0002418 ! hemangioblast relationship: has_plasma_membrane_part PR:000009127 ! integrin alpha-IIb created_by: tmeehan creation_date: 2010-09-22T10:47:28Z [Term] id: CL:0002362 name: granule cell precursor namespace: cell def: "A cell located in the outermost proliferative zone of the external germinal layer that can differentiate into astroglial cells and granule cells. This cell type is glial fibrillary acidic protein-positive and NK1-positive." [GOC:tfm, PMID:14745007] is_a: CL:0000337 ! neuroblast (sensu Vertebrata) created_by: tmeehan creation_date: 2010-09-22T01:40:44Z [Term] id: CL:0002363 name: keratocyte namespace: cell def: "A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic cell located between the lamellae with a large flattened nucleus and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratin sulfate." [GOC:tfm, ISBN:978-0-7020-2958-5] synonym: "corneal fibroblast" EXACT [] synonym: "corneal keratocyte" EXACT [] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001777 ! substantia propria of cornea relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001777 ! substantia propria of cornea created_by: tmeehan creation_date: 2010-09-22T01:57:40Z [Term] id: CL:0002364 name: cortical thymic epithelial cell namespace: cell def: "An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells." [GOC:tfm, PMID:18403190] synonym: "cTEC" EXACT [] xref: BTO:0004562 is_a: CL:0002293 ! epithelial cell of thymus created_by: tmeehan creation_date: 2010-09-23T03:17:12Z [Term] id: CL:0002365 name: medullary thymic epithelial cell namespace: cell def: "An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output." [GOC:tfm, PMID:18180458] synonym: "mTEC" EXACT [] xref: BTO:0004563 is_a: CL:0002293 ! epithelial cell of thymus created_by: tmeehan creation_date: 2010-09-23T03:17:14Z [Term] id: CL:0002366 name: myometrial cell namespace: cell def: "A smooth muscle cell of the myometrium that enlarges and stretches during pregnancy, and contracts in response to oxytocin." [GOC:tfm, PMID:11429640] synonym: "myometrium smooth muscle cell" EXACT [] xref: BTO:0004519 is_a: CL:0002601 ! uterine smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001296 ! myometrium relationship: part_of UBERON:0001296 ! myometrium created_by: tmeehan creation_date: 2010-09-23T03:46:34Z [Term] id: CL:0002367 name: trabecular meshwork cell namespace: cell def: "A cell that lines the trabecular meshwork, which is an area of tissue in the eye located around the base of the cornea, near the ciliary body, and is responsible for draining the aqueous humor from the eye via the anterior chamber (the chamber on the front of the eye covered by the cornea). This cell may play a role in regulating intraocular pressure." [GOC:tfm, PMID:14500801] synonym: "trabeculocyte" EXACT [] is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0005969 ! reticulum trabeculare relationship: part_of UBERON:0005969 ! reticulum trabeculare created_by: tmeehan creation_date: 2010-09-23T04:18:50Z [Term] id: CL:0002368 name: respiratory epithelial cell namespace: cell def: "An endo-epithelial cell of the respiratory tract." [GOC:tfm] synonym: "airway epithelial cell" EXACT [] xref: BTO:0004533 is_a: CL:0002076 ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0000065 ! respiratory tract relationship: part_of UBERON:0000065 ! respiratory tract created_by: tmeehan creation_date: 2010-09-23T04:38:49Z [Term] id: CL:0002369 name: fungal spore namespace: cell def: "A differentiated form of a fungus produced during or as a result of an asexual or sexual reproductive process; usually a cell with a thick cell wall that stores and protects one or more nuclei. Spores may be produced in response to, and are characteristically resistant to, adverse environmental conditions." [FAO:0000019, GOC:tfm] is_a: CL:0000521 ! fungal cell created_by: tmeehan creation_date: 2010-10-01T09:02:42Z [Term] id: CL:0002370 name: respiratory goblet cell namespace: cell def: "A simple columnar epithelial cell that secretes mucin. Rough endoplasmic reticulum, mitochondria, the nucleus, and other organelles are concentrated in the basal portion. The apical plasma membrane projects microvilli to increase surface area for secretion." [GOC:tfm, ISBN:0721662544] synonym: "respiratory mucosa goblet cells" EXACT [MP:0010863] is_a: CL:0000160 ! goblet cell is_a: CL:0002202 ! epithelial cell of tracheobronchial tree created_by: tmeehan creation_date: 2010-09-23T04:42:27Z [Term] id: CL:0002371 name: somatic cell namespace: cell def: "A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell)." [GOC:tfm, ISBN:0721662544] subset: ubprop:upper_level xref: BTO:0001268 xref: FMA:72300 xref: WBbt:0008378 is_a: CL:0000003 ! native cell created_by: tmeehan creation_date: 2010-09-24T09:44:42Z [Term] id: CL:0002372 name: myotube namespace: cell alt_id: CL:0000369 def: "A myotube is a multinucleated cells that is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." [GOC:tfm, ISBN:0323052908] synonym: "myotubule" EXACT [] synonym: "single cell sarcomere" EXACT [] synonym: "skeletal muscle fiber" EXACT [] is_a: CL:0000188 ! skeletal muscle cell is_a: CL:0000228 ! multinucleate cell is_a: CL:0000737 ! striated muscle cell relationship: develops_from CL:0000515 ! skeletal muscle myoblast created_by: tmeehan creation_date: 2010-09-24T01:13:01Z [Term] id: CL:0002373 name: growth hormone releasing hormone secreting cell namespace: cell def: "A peptide hormone secreting cell that secretes growth hormone releasing hormone." [GOC:dph, GOC:tfm] synonym: "GHRH secreting cell" EXACT [] synonym: "somatocrinin secreting cell" EXACT [] is_a: CL:0000167 ! peptide hormone secreting cell created_by: tmeehan creation_date: 2010-09-24T01:36:44Z [Term] id: CL:0002374 name: ear hair cell namespace: cell def: "A hair cell of the ear that contains the organs of balance and hearing." [GOC:dph, GOC:tfm, ISBN:0192801023] synonym: "ear receptor cell" EXACT [] is_a: CL:0000855 ! sensory hair cell created_by: tmeehan creation_date: 2010-09-24T01:49:31Z [Term] id: CL:0002375 name: Schwann cell precursor namespace: cell def: "A giioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19." [GOC:tfm] synonym: "Schwann cell precursor cell" EXACT [] is_a: CL:0000030 ! glioblast relationship: develops_from CL:0000333 ! migratory neural crest cell created_by: tmeehan creation_date: 2010-09-24T02:06:10Z [Term] id: CL:0002376 name: non-myelinating Schwann cell namespace: cell def: "A glial cell that ensheaths multiple small diameter axons in the peripheral nervous system. The non-myelinating Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. These cells can de-differentiate into immature Schwann cells." [GOC:cvs, GOC:tfm, ISBN:0721662544] synonym: "Schwann cell" BROAD [] is_a: CL:0002573 ! Schwann cell relationship: develops_from CL:0002377 ! immature Schwann cell created_by: tmeehan creation_date: 2010-09-24T02:10:26Z [Term] id: CL:0002377 name: immature Schwann cell namespace: cell def: "A glial cell that develops from a Schwann cell precursor. The immature Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. Immature Schwann cell can be found communally ensheathing large groups of axons." [GOC:cvs, GOC:tfm, ISBN:0721662544] synonym: "Schwann cell" BROAD [] xref: ZFA:0001725 is_a: CL:0002573 ! Schwann cell relationship: develops_from CL:0002375 ! Schwann cell precursor created_by: tmeehan creation_date: 2010-09-24T02:10:31Z [Term] id: CL:0002378 name: immature Vgamma2-positive fetal thymocyte namespace: cell def: "A double negative thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-positive and is found in the fetal thymus." [GOC:tfm, http://www.immgen.org] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "fetal Vgamma2+ thymocyte" BROAD [] is_a: CL:0002404 ! fetal thymocyte created_by: tmeehan creation_date: 2010-10-07T02:21:07Z [Term] id: CL:0002379 name: meningothelial cell namespace: cell def: "A neurecto-epithelial cell found in the arachnoid villi of dura mater. This cell type facilitates flow of cerebrospinal fluid into the blood." [GOC:tfm, http://www.aippg.net/forum/viewtopic.php?t=62590] synonym: "arachnoid cap cell" EXACT [] xref: FMA:86588 is_a: CL:0000710 ! neurecto-epithelial cell created_by: tmeehan creation_date: 2010-09-28T02:23:46Z [Term] id: CL:0002380 name: oospore namespace: cell def: "An asexual spore formed by Oomycetes; formed upon fertilization of an oosphere." [GOC:tfm, ISBN:0851988857, SGD:clt] xref: FAO:0000039 is_a: CL:0000605 ! fungal asexual spore created_by: tmeehan creation_date: 2010-10-01T09:22:45Z [Term] id: CL:0002381 name: uninucleate conidium namespace: cell def: "A conidium that has only one nucleus." [GOC:tfm, SGD:clt] xref: FAO:0000025 is_a: CL:0000599 ! conidium created_by: tmeehan creation_date: 2010-10-01T09:26:39Z [Term] id: CL:0002382 name: multinucleate conidium namespace: cell def: "A conidium that has more than one nucleus." [GOC:tfm, SGD:clt] xref: FAO:0000033 is_a: CL:0000599 ! conidium created_by: tmeehan creation_date: 2010-10-01T09:31:28Z [Term] id: CL:0002383 name: conidium of conidiophore head namespace: cell def: "A uninucleate spore formed on specialized cells or projections, sterigma, of a conidiophore head." [GOC:tfm, PMID:9529886, SGD:clt] xref: FAO:0000033 is_a: CL:0002381 ! uninucleate conidium [Term] id: CL:0002384 name: uninucleate macroconidium namespace: cell def: "A macroconidium that has only one nucleus." [GOC:tfm, SGD:clt] xref: FAO:0000029 is_a: CL:0000606 ! macroconidium is_a: CL:0002381 ! uninucleate conidium [Term] id: CL:0002385 name: blastoconidium namespace: cell def: "An oblong or round asexual spore formed from conidial chains." [GOC:tfm, PMID:2524423, SGD:clt] synonym: "blastospore" RELATED [] xref: BTO:0000127 xref: FAO:0000042 is_a: CL:0000606 ! macroconidium [Term] id: CL:0002386 name: multinucleate macroconidium namespace: cell def: "A macroconidium that has more than one nucleus." [GOC:tfm, SGD:clt] xref: FAO:0000035 is_a: CL:0000606 ! macroconidium is_a: CL:0002382 ! multinucleate conidium [Term] id: CL:0002387 name: arthroconidium namespace: cell def: "Cylindrical spore formed by development and compartmentation of hyphae; the hyphae are often supporting blastoconidiophores." [GOC:tfm, PMID:2524423, SGD:clt] synonym: "arthrospore" RELATED [] xref: FAO:0000041 is_a: CL:0000606 ! macroconidium [Term] id: CL:0002388 name: multinucleate arthroconidium namespace: cell def: "An arthroconidium that has more than one nucleus." [GOC:tfm, SGD:clt] xref: FAO:0000037 is_a: CL:0002386 ! multinucleate macroconidium is_a: CL:0002387 ! arthroconidium [Term] id: CL:0002389 name: uninucleate arthroconidium namespace: cell def: "An arthroconidium that has only one nucleus." [GOC:tfm, SGD:clt] xref: FAO:0000031 is_a: CL:0002384 ! uninucleate macroconidium is_a: CL:0002387 ! arthroconidium [Term] id: CL:0002390 name: uninucleate blastconidium namespace: cell def: "A blastoconidium that has only one nucleus." [GOC:tfm, SGD:clt] xref: FAO:0000030 is_a: CL:0002384 ! uninucleate macroconidium is_a: CL:0002385 ! blastoconidium [Term] id: CL:0002391 name: multinucleate blastoconidium namespace: cell def: "A blastoconidium that has more than one nucleus." [GOC:tfm, SGD:clt] xref: FAO:0000036 is_a: CL:0002385 ! blastoconidium is_a: CL:0002386 ! multinucleate macroconidium [Term] id: CL:0002392 name: plant spore namespace: cell def: "Obsolete. Use PO:0025017 from Plant Ontology instead. A plant cell that arises through meiosis and develops into a gametophyte." [GOC:tfm, PO:0025017] comment: replaced_by: PO:0025017 is_obsolete: true [Term] id: CL:0002393 name: intermediate monocyte namespace: cell def: "A monocyte that has characteristics of both patrolling and inflammatory monocytes." [GOC:tfm, PMID:20628149, PMID:20870168] is_a: CL:0000576 ! monocyte created_by: tmeehan creation_date: 2010-10-04T10:52:03Z [Term] id: CL:0002394 name: CD141-positive myeloid dendritic cell namespace: cell def: "A myeloid dendritic cell found in the blood, lymph nodes, tonsil, bone marrow, and spleen that is CD141-positive (BDCA-3), XCR1-positive, and Clec9A-positive. This cell-type can cross-present antigen to CD8-positive T cells and can produce inteferon-beta." [GOC:dsd, GOC:tfm, PMCID:PMC2882828, PMCID:PMC2882837, PMID:17332250, PMID:20628149] comment: Markers are found in human cells. Normally they represent 3-5% of peripheral blood mDCs (human). These cells express high levels of CD283 (TLR3), are capable of producing IL-12p70 and IFN-beta upon stimulation, and inducing a TH1 response [PMCID:PMC2882828]. They are also Necl2-positive. May be human equivalent of murine CD8alpha-positive DCs. is_a: CL:0000782 ! myeloid dendritic cell is_a: CL:0000784 ! plasmacytoid dendritic cell intersection_of: CL:0000782 ! myeloid dendritic cell intersection_of: capable_of GO:0002827 ! positive regulation of T-helper 1 type immune response intersection_of: capable_of GO:0032606 ! type I interferon production intersection_of: capable_of GO:0042590 ! antigen processing and presentation of exogenous peptide antigen via MHC class I intersection_of: has_plasma_membrane_part PR:000002105 ! thrombomodulin relationship: capable_of GO:0002827 ! positive regulation of T-helper 1 type immune response relationship: capable_of GO:0032606 ! type I interferon production relationship: capable_of GO:0042590 ! antigen processing and presentation of exogenous peptide antigen via MHC class I relationship: has_plasma_membrane_part PR:000002105 ! thrombomodulin created_by: tmeehan creation_date: 2010-10-04T02:38:58Z [Term] id: CL:0002395 name: Gr1-high classical monocyte namespace: cell def: "A resident monocyte that is Gr-1 high, CD43-negative, CX3CR1-negative, CD115-positive, and B220-negative." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:20628149, PMID:8890901] comment: Markers are associated with mice. The Gr epitope is used to describe this cell type is found on both Ly6c and Ly6g. However, its the Ly6c that is considered the specific marker, and thus used in the cross-product. is_a: CL:0000860 ! classical monocyte is_a: CL:0001022 ! CD115-positive monocyte intersection_of: CL:0000860 ! classical monocyte intersection_of: has_high_plasma_membrane_amount PR:000002980 ! lymphocyte antigen 6C intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor intersection_of: lacks_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R intersection_of: lacks_plasma_membrane_part PR:000001206 ! CX3C chemokine receptor 1 intersection_of: lacks_plasma_membrane_part PR:000001879 ! leukosialin relationship: has_high_plasma_membrane_amount PR:000002980 ! lymphocyte antigen 6C relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor relationship: lacks_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: lacks_plasma_membrane_part PR:000001206 ! CX3C chemokine receptor 1 relationship: lacks_plasma_membrane_part PR:000001879 ! leukosialin created_by: tmeehan creation_date: 2010-10-04T11:26:18Z [Term] id: CL:0002396 name: CD14-low, CD16-positive monocyte namespace: cell def: "A patrolling monocyte that is CD14-low and CD16-positive." [GOC:tfm, PMID:20870168] comment: Markers are associated with human monocytes. is_a: CL:0000875 ! non-classical monocyte intersection_of: CL:0000875 ! non-classical monocyte intersection_of: has_low_plasma_membrane_amount PR:000001889 ! CD14 molecule intersection_of: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: develops_from CL:0002397 ! CD14-positive, CD16-positive monocyte relationship: has_low_plasma_membrane_amount PR:000001889 ! CD14 molecule relationship: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III created_by: tmeehan creation_date: 2010-10-04T12:25:42Z [Term] id: CL:0002397 name: CD14-positive, CD16-positive monocyte namespace: cell def: "An intermediate monocyte that is CD14-positive, CD16-positive." [GOC:tfm, PMID:20628149] comment: Markers are associated with human cells. is_a: CL:0002393 ! intermediate monocyte intersection_of: CL:0002393 ! intermediate monocyte intersection_of: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III intersection_of: has_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: develops_from CL:0002057 ! CD14-positive, CD16-negative classical monocyte relationship: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: has_plasma_membrane_part PR:000001889 ! CD14 molecule created_by: tmeehan creation_date: 2010-10-04T12:49:47Z [Term] id: CL:0002398 name: Gr1-positive, CD43-positive monocyte namespace: cell def: "An intermediate monocyte that is Gr1-positive, CD43-positive." [GOC:tfm, PMID:20628149] is_a: CL:0001022 ! CD115-positive monocyte is_a: CL:0002393 ! intermediate monocyte intersection_of: CL:0000576 ! monocyte intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001879 ! leukosialin intersection_of: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor intersection_of: has_plasma_membrane_part PR:000002980 ! lymphocyte antigen 6C relationship: develops_from CL:0002395 ! Gr1-high classical monocyte relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001879 ! leukosialin relationship: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor relationship: has_plasma_membrane_part PR:000002980 ! lymphocyte antigen 6C created_by: tmeehan creation_date: 2010-10-04T12:49:49Z [Term] id: CL:0002399 name: CD1c-positive myeloid dendritic cell namespace: cell def: "A myeloid dendritic cell found in the blood that is CD1c-positive." [GOC:dsd, GOC:tfm, PMID:20204387, PMID:20628149] comment: Normally represent 10-20% of peripheral blood mDCs (human). They are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD285-positive (TLR5), CD286-positive (TLR6), CD288-positive (TLR8), and CD290-positive (TLR10) [PMID:20204387]. Upon TLR stimulation, these cells were potent producers of CXCL8 (IL-8), while producing little TNF-alpha. is_a: CL:0000782 ! myeloid dendritic cell intersection_of: CL:0000782 ! myeloid dendritic cell intersection_of: capable_of GO:0032637 ! interleukin-8 production intersection_of: has_plasma_membrane_part PR:000002027 ! T-cell surface glycoprotein CD1c relationship: capable_of GO:0032637 ! interleukin-8 production relationship: has_plasma_membrane_part PR:000002027 ! T-cell surface glycoprotein CD1c created_by: tmeehan creation_date: 2010-10-04T02:39:01Z [Term] id: CL:0002400 name: Fraction B/C precursor B cell namespace: cell def: "A precursor B cell that is AA4-positive, IgM-negative, CD19-positive, CD43-positive and HSA-positive." [GOC:tfm, http://www.immgen.org/index_content.html] is_a: CL:0000817 ! precursor B cell intersection_of: CL:0000817 ! precursor B cell intersection_of: has_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: has_plasma_membrane_part PR:000001879 ! leukosialin intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 intersection_of: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor intersection_of: lacks_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex relationship: has_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: has_plasma_membrane_part PR:000001879 ! leukosialin relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: has_plasma_membrane_part PR:000002037 ! complement component C1q receptor relationship: lacks_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex created_by: tmeehan creation_date: 2010-10-05T10:11:38Z [Term] id: CL:0002401 name: mature dendritic epithelial T cell precursor namespace: cell def: "A thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18." [GOC:tfm, http://www.immgen.org/index_content.html] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "mature DEC precursor" EXACT [] synonym: "mature DETC precursor" EXACT [] is_a: CL:0002404 ! fetal thymocyte relationship: develops_from CL:0002218 ! immature dendritic epithelial T cell precursor created_by: tmeehan creation_date: 2010-10-07T02:05:46Z [Term] id: CL:0002402 name: Peyer's patch B cell namespace: cell def: "A resting mature B cell within the Peyer's patch that is CD19-positive, B220-positive, IgM-positive, AA4-negative, CD23-positive, CD43-negative, and CD5-negative." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "Peyers patch B cell" EXACT [] is_a: CL:0000822 ! B-2 B cell intersection_of: CL:0000785 ! mature B cell intersection_of: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex intersection_of: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R intersection_of: has_plasma_membrane_part PR:000001338 ! complement receptor type 2 intersection_of: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 intersection_of: lacks_plasma_membrane_part PR:000001879 ! leukosialin intersection_of: lacks_plasma_membrane_part PR:000002037 ! complement component C1q receptor intersection_of: part_of UBERON:0001211 ! Peyer's patch relationship: has_plasma_membrane_part GO:0071753 ! IgM immunoglobulin complex relationship: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: has_plasma_membrane_part PR:000001338 ! complement receptor type 2 relationship: lacks_plasma_membrane_part PR:000001839 ! T-cell surface glycoprotein CD5 relationship: lacks_plasma_membrane_part PR:000001879 ! leukosialin relationship: lacks_plasma_membrane_part PR:000002037 ! complement component C1q receptor relationship: part_of UBERON:0001211 ! Peyer's patch created_by: tmeehan creation_date: 2010-10-05T11:18:03Z [Term] id: CL:0002403 name: mature Vgamma2-positive fetal thymocyte namespace: cell def: "A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus." [GOC:tfm, http://www.immgen.org/index_content.html] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "fetal Vgamma2-positive" EXACT [] is_a: CL:0002404 ! fetal thymocyte relationship: develops_from CL:0002378 ! immature Vgamma2-positive fetal thymocyte created_by: tmeehan creation_date: 2010-10-07T02:24:36Z [Term] id: CL:0002404 name: fetal thymocyte namespace: cell def: "A thymocyte found in the fetal thymus." [GOC:tfm] is_a: CL:0000893 ! thymocyte created_by: tmeehan creation_date: 2010-10-07T02:28:25Z [Term] id: CL:0002405 name: gamma-delta thymocyte namespace: cell def: "A post-natal thymocyte expressing components of the gamma-delta T cell receptor. This cell type is always double-negative (i.e. CD4-negative, CD8-negative)." [GOC:tfm, PMID:20725107] synonym: "gammadelta thymocyte" EXACT [] synonym: "gd thymocyte" EXACT [] is_a: CL:0000798 ! gamma-delta T cell is_a: CL:0002489 ! double negative thymocyte intersection_of: CL:0000893 ! thymocyte intersection_of: has_plasma_membrane_part GO:0042106 ! gamma-delta T cell receptor complex intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 relationship: has_plasma_membrane_part GO:0042106 ! gamma-delta T cell receptor complex relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 created_by: tmeehan creation_date: 2010-10-07T02:33:39Z [Term] id: CL:0002406 name: immature Vgamma2-positive thymocyte namespace: cell def: "A double negative post-natal thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-positive." [GOC:tfm, http://www.immgen.org] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "Vgamma2-positive thymocyte" BROAD [] is_a: CL:0002405 ! gamma-delta thymocyte created_by: tmeehan creation_date: 2010-10-07T02:53:44Z [Term] id: CL:0002407 name: mature Vgamma2-positive thymocyte namespace: cell def: "A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus." [GOC:tfm, http://www.immgen.org/index_content.html] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "Vgamma2-positive" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte relationship: develops_from CL:0002406 ! immature Vgamma2-positive thymocyte created_by: tmeehan creation_date: 2010-10-07T02:53:48Z [Term] id: CL:0002408 name: immature Vgamma2-negative thymocyte namespace: cell def: "A double negative post-natal thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-positive." [GOC:tfm, http://www.immgen.org] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "Vgamma2-negative thymocyte" BROAD [] is_a: CL:0002405 ! gamma-delta thymocyte created_by: tmeehan creation_date: 2010-10-07T02:59:05Z [Term] id: CL:0002409 name: mature Vgamma2-negative thymocyte namespace: cell def: "A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus." [GOC:tfm, http://www.immgen.org/index_content.html] comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "Vgamma2-negative" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte relationship: develops_from CL:0002408 ! immature Vgamma2-negative thymocyte created_by: tmeehan creation_date: 2010-10-07T02:59:08Z [Term] id: CL:0002410 name: pancreatic stellate cell namespace: cell def: "A cell that is found in the periacinar space of the exocrine pancreas and in perivascular and periductal regions of the pancreas, and has long cytoplasmic processes that encircle the base of the acinus. Expresses several intermediate filament proteins including vimentin and nestin. Shares many of the characteristics of hepatatic stellate cells, but not stellate cells of the central nervous system. Upon activation, this cell type undergoes morphological and gene expression changes that make the cell suggestive of being a type of myofibroblast." [GOC:mah, GOC:tfm, PMID:17200706] synonym: "PaSC" EXACT [] is_a: CL:0000057 ! fibroblast created_by: tmeehan creation_date: 2010-11-10T09:40:33Z [Term] id: CL:0002411 name: Vgamma1.1-positive, Vdelta6.3-negative thymocyte namespace: cell def: "A gamma-delta receptor that expresses Vgamma1.1 but does not express Vdelta6.3 chains in the T-cell receptor." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "Vg1.1-positive, Vd6.3-negative T cell" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte created_by: tmeehan creation_date: 2010-10-07T03:07:44Z [Term] id: CL:0002412 name: Vgamma1.1-positive, Vdelta6.3-positive thymocyte namespace: cell def: "A gamma-delta receptor that expresses Vgamma1.1-Vdelta6.3 chains in the T-cell receptor." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "Vg1.1+Vd6.3+ T cell" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte created_by: tmeehan creation_date: 2010-10-07T03:03:00Z [Term] id: CL:0002413 name: mature Vgamma1.1-positive, Vdelta6.3-negative thymocyte namespace: cell def: "A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-negative." [GOC:tfm, http://www.immgen.org] synonym: "mature Vg1.1-positive, Vd6.3-negative T cell" RELATED [] is_a: CL:0002411 ! Vgamma1.1-positive, Vdelta6.3-negative thymocyte created_by: tmeehan creation_date: 2010-10-07T03:10:32Z [Term] id: CL:0002414 name: immature Vgamma1.1-positive, Vdelta6.3-negative thymocyte namespace: cell def: "A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "immature Vg1.1-positive, Vd6.3-negative T cell" RELATED [] is_a: CL:0002411 ! Vgamma1.1-positive, Vdelta6.3-negative thymocyte created_by: tmeehan creation_date: 2010-10-07T03:10:35Z [Term] id: CL:0002415 name: immature Vgamma1.1-positive, Vdelta6.3-positive thymocyte namespace: cell def: "A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "immature Vg1.1+Vd6.3+ T cell" EXACT [] is_a: CL:0002412 ! Vgamma1.1-positive, Vdelta6.3-positive thymocyte created_by: tmeehan creation_date: 2010-10-07T03:10:39Z [Term] id: CL:0002416 name: mature Vgamma1.1-positive, Vdelta6.3-positive thymocyte namespace: cell def: "A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-negative." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "mature Vg1.1+Vd6.3+ T cell" EXACT [] is_a: CL:0002412 ! Vgamma1.1-positive, Vdelta6.3-positive thymocyte created_by: tmeehan creation_date: 2010-10-07T03:10:41Z [Term] id: CL:0002417 name: primitive erythroid lineage cell namespace: cell def: "An immature or mature cell of the first erythroid lineage to arise during embryonic development." [GOC:tfm] is_a: CL:0000764 ! erythroid lineage cell created_by: tmeehan creation_date: 2010-10-12T11:22:41Z [Term] id: CL:0002418 name: hemangioblast namespace: cell def: "A pluripotent cell in the yolk sac that can give rise to mesenchymal cells including erythrocytes and endothelial cells." [GOC:tfm, ISBN:0813817986, PMID:11495698] is_a: CL:0000222 ! mesodermal cell relationship: develops_from CL:0002354 ! yolk sac hematopoietic stem cell created_by: tmeehan creation_date: 2010-10-12T12:21:16Z [Term] id: CL:0002419 name: mature T cell namespace: cell def: "A T cell that expresses a T cell receptor complex and has completed T cell selection." [GOC:tfm] synonym: "CD3e-positive T cell" EXACT [] synonym: "CD3epsilon T cell" RELATED [] synonym: "mature T-cell" EXACT [] is_a: CL:0000084 ! T cell intersection_of: CL:0000084 ! T cell intersection_of: has_completed GO:0045058 ! T cell selection intersection_of: has_plasma_membrane_part GO:0042101 ! T cell receptor complex relationship: has_completed GO:0045058 ! T cell selection relationship: has_plasma_membrane_part GO:0042101 ! T cell receptor complex created_by: tmeehan creation_date: 2010-10-12T01:56:15Z [Term] id: CL:0002420 name: immature T cell namespace: cell def: "A T cell that has not completed T cell selection." [GOC:tfm] synonym: "immature T-cell" EXACT [] xref: BTO:0001372 is_a: CL:0000084 ! T cell intersection_of: CL:0000084 ! T cell intersection_of: has_not_completed GO:0045058 ! T cell selection relationship: has_not_completed GO:0045058 ! T cell selection created_by: tmeehan creation_date: 2010-10-12T01:56:17Z [Term] id: CL:0002421 name: nucleated reticulocyte namespace: cell def: "A reticulocyte that retains the nucleus and other organelles. Found in birds, fish, amphibians and reptiles." [GOC:tfm, PMID:18182572, PMID:9011180, PMID:9046052] is_a: CL:0000558 ! reticulocyte is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000558 ! reticulocyte intersection_of: has_part GO:0005634 ! nucleus relationship: has_part GO:0005634 ! nucleus created_by: tmeehan creation_date: 2010-10-15T09:24:05Z [Term] id: CL:0002422 name: enucleated reticulocyte namespace: cell def: "A reticulocyte lacking a nucleus and showing a basophilic reticulum under vital staining due to the presence of ribosomes." [GOC:tfm, ISBN:0-12203-052-4, ISBN:0721601464] xref: FMA:66785 is_a: CL:0000558 ! reticulocyte intersection_of: CL:0000558 ! reticulocyte intersection_of: has_part GO:0005840 ! ribosome intersection_of: lacks_part GO:0005634 ! nucleus relationship: has_part GO:0005840 ! ribosome relationship: lacks_part GO:0005634 ! nucleus created_by: tmeehan creation_date: 2010-10-15T09:24:08Z [Term] id: CL:0002423 name: DN2a thymocyte namespace: cell def: "A DN2 thymocyte that is Kit-hi." [GOC:tfm, PMID:20595614] comment: Observed in mice. is_a: CL:0000806 ! DN2 thymocyte intersection_of: CL:0000806 ! DN2 thymocyte intersection_of: has_high_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor relationship: has_high_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor created_by: tmeehan creation_date: 2010-10-21T10:12:05Z [Term] id: CL:0002424 name: DN2b thymocyte namespace: cell def: "A DN2 thymocyte that is Kit-low." [GOC:tfm, PMID:20595614] comment: Observed in mice. is_a: CL:0000806 ! DN2 thymocyte intersection_of: CL:0000806 ! DN2 thymocyte intersection_of: has_low_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor relationship: develops_from CL:0002423 ! DN2a thymocyte relationship: has_low_plasma_membrane_amount PR:000002065 ! mast/stem cell growth factor receptor created_by: tmeehan creation_date: 2010-10-21T10:12:08Z [Term] id: CL:0002425 name: early T lineage precursor namespace: cell def: "A pro-T cell that is lin-negative, CD25-negative, CD127-negative, CD44-positive and kit-positive." [GOC:dsd, GOC:tfm, http://www.immgen.org/index_content.html, PMID:16551251] comment: ETPs are reportedly CD1a-negative, CD4-negative, CD7-positive, CD8a-negative, CD8b-negative, CD33-low, CD34-high, CD38-low, CD45RA-positive, and CD45RO-negative. synonym: "ETP" EXACT [] synonym: "preT.ETP.Th" EXACT [] is_a: CL:0000827 ! pro-T cell intersection_of: CL:0000827 ! pro-T cell intersection_of: has_plasma_membrane_part PR:000001307 ! CD44 molecule intersection_of: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha relationship: has_plasma_membrane_part PR:000001307 ! CD44 molecule relationship: has_plasma_membrane_part PR:000001869 ! interleukin-7 receptor subunit alpha relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: lacks_plasma_membrane_part PR:000001380 ! interleukin-2 receptor subunit alpha created_by: tmeehan creation_date: 2010-10-21T01:16:24Z [Term] id: CL:0002426 name: CD11b-positive, CD27-positive natural killer cell namespace: cell def: "A mature natural killer cell that is CD11b-positive and CD27-positive." [GOC:tfm, http://www.immgen.org/index_content.html] comment: A natural killer cell that is NK1.1-positive, CD11b-positive, and CD27-positive. is_a: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001963 ! CD27 molecule relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001963 ! CD27 molecule created_by: tmeehan creation_date: 2010-10-25T03:07:59Z [Term] id: CL:0002427 name: resting double-positive thymocyte namespace: cell def: "A double-positive, alpha-beta thymocyte that is small and not proliferating." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "T.DP.sm.Th" EXACT [] is_a: CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: has_quality PATO:0000587 ! decreased size relationship: has_quality PATO:0000587 ! decreased size created_by: tmeehan creation_date: 2010-10-21T01:59:06Z [Term] id: CL:0002428 name: double-positive blast namespace: cell def: "A double-positive thymocyte that is large (i.e. has a high forward scatter signal in flow cytometry) and is actively proliferating." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "activated double-positive thymocyte" EXACT [] synonym: "T.DPb.Th" EXACT [] is_a: CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: has_quality PATO:0000586 ! increased size intersection_of: participates_in GO:0008283 ! cell proliferation relationship: develops_from CL:0002427 ! resting double-positive thymocyte relationship: has_quality PATO:0000586 ! increased size relationship: participates_in GO:0008283 ! cell proliferation created_by: tmeehan creation_date: 2010-10-21T01:59:11Z [Term] id: CL:0002429 name: CD69-positive double-positive thymocyte namespace: cell def: "A double-positive thymocyte that is CD69-positive and has begun positive selection." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "T.DP69+.Th" EXACT [] is_a: CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: has_low_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex intersection_of: has_plasma_membrane_part PR:000001343 ! CD69 molecule intersection_of: participates_in GO:0043368 ! positive T cell selection relationship: develops_from CL:0002428 ! double-positive blast relationship: has_low_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex relationship: has_plasma_membrane_part PR:000001343 ! CD69 molecule relationship: participates_in GO:0043368 ! positive T cell selection created_by: tmeehan creation_date: 2010-10-21T02:11:52Z [Term] id: CL:0002430 name: CD4-intermediate, CD8-positive double-positive thymocyte namespace: cell def: "A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD4 co-receptor." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "T.4int8+.Th" EXACT [] is_a: CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex intersection_of: has_low_plasma_membrane_amount PR:000001004 ! CD4 molecule intersection_of: has_plasma_membrane_part PR:000001343 ! CD69 molecule intersection_of: participates_in GO:0043368 ! positive T cell selection relationship: develops_from CL:0002429 ! CD69-positive double-positive thymocyte relationship: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex relationship: has_low_plasma_membrane_amount PR:000001004 ! CD4 molecule relationship: has_plasma_membrane_part PR:000001343 ! CD69 molecule relationship: participates_in GO:0043368 ! positive T cell selection created_by: tmeehan creation_date: 2010-10-21T02:29:19Z [Term] id: CL:0002431 name: CD4-positive, CD8-intermediate double-positive thymocyte namespace: cell def: "A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD4 co-receptor." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "T.4int8+.th" EXACT [] is_a: CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex intersection_of: has_low_plasma_membrane_amount PR:000025402 ! T cell receptor co-receptor CD8 intersection_of: has_plasma_membrane_part PR:000001343 ! CD69 molecule intersection_of: participates_in GO:0043368 ! positive T cell selection relationship: develops_from CL:0002429 ! CD69-positive double-positive thymocyte relationship: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex relationship: has_low_plasma_membrane_amount PR:000025402 ! T cell receptor co-receptor CD8 relationship: has_plasma_membrane_part PR:000001343 ! CD69 molecule relationship: participates_in GO:0043368 ! positive T cell selection created_by: tmeehan creation_date: 2010-10-21T02:29:23Z [Term] id: CL:0002432 name: CD24-positive, CD4 single-positive thymocyte namespace: cell def: "A CD4-positive, CD8-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor." [GOC:tfm, http://www.immgen.org/index_content.html] comment: Described in the immgene database as being CD24-intermediate. synonym: "CD24-positive, CD4 single-positive semimature thymocyte" EXACT [] synonym: "T.4SP24int.Th" EXACT [] is_a: CL:0000810 ! CD4-positive, alpha-beta thymocyte intersection_of: CL:0000810 ! CD4-positive, alpha-beta thymocyte intersection_of: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: develops_from CL:0002433 ! CD69-positive, CD4-positive single-positive thymocyte relationship: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 created_by: tmeehan creation_date: 2010-10-21T02:43:52Z [Term] id: CL:0002433 name: CD69-positive, CD4-positive single-positive thymocyte namespace: cell def: "A CD4-positive, CD8-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "intermediate CD4-single-positive" EXACT [] synonym: "T.4SP69+.Th" EXACT [] is_a: CL:0000810 ! CD4-positive, alpha-beta thymocyte intersection_of: CL:0000810 ! CD4-positive, alpha-beta thymocyte intersection_of: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex intersection_of: has_plasma_membrane_part PR:000001343 ! CD69 molecule relationship: develops_from CL:0002431 ! CD4-positive, CD8-intermediate double-positive thymocyte relationship: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex relationship: has_plasma_membrane_part PR:000001343 ! CD69 molecule created_by: tmeehan creation_date: 2010-10-21T02:46:02Z [Term] id: CL:0002434 name: CD24-positive, CD8 single-positive thymocyte namespace: cell def: "A CD8-positive, CD4-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor." [GOC:tfm, http://www.immgen.org/index_content.html] comment: Described in the immgene database as being CD24-intermediate. synonym: "CD24-positive, CD8 single-positive semimature thymocyte" EXACT [] synonym: "T.8SP24int.Th" EXACT [] is_a: CL:0000811 ! CD8-positive, alpha-beta thymocyte intersection_of: CL:0000811 ! CD8-positive, alpha-beta thymocyte intersection_of: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex intersection_of: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 relationship: develops_from CL:0002435 ! CD69-positive, CD8-positive single-positive thymocyte relationship: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex relationship: has_plasma_membrane_part PR:000001932 ! signal transducer CD24 created_by: tmeehan creation_date: 2010-10-21T02:59:10Z [Term] id: CL:0002435 name: CD69-positive, CD8-positive single-positive thymocyte namespace: cell def: "A CD4-positive, CD8-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "intermediate CD8-single-positive" EXACT [] synonym: "T.8SP69+.Th" EXACT [] is_a: CL:0000811 ! CD8-positive, alpha-beta thymocyte intersection_of: CL:0000811 ! CD8-positive, alpha-beta thymocyte intersection_of: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex intersection_of: has_plasma_membrane_part PR:000001343 ! CD69 molecule relationship: develops_from CL:0002430 ! CD4-intermediate, CD8-positive double-positive thymocyte relationship: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex relationship: has_plasma_membrane_part PR:000001343 ! CD69 molecule created_by: tmeehan creation_date: 2010-10-21T02:59:14Z [Term] id: CL:0002436 name: mature CD4 single-positive thymocyte namespace: cell def: "A mature CD4-positive, CD8-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "T.4SP24-.Th" RELATED [] is_a: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex intersection_of: has_low_plasma_membrane_amount PR:000001932 ! signal transducer CD24 relationship: develops_from CL:0002432 ! CD24-positive, CD4 single-positive thymocyte relationship: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex relationship: has_low_plasma_membrane_amount PR:000001932 ! signal transducer CD24 created_by: tmeehan creation_date: 2010-10-21T03:31:19Z [Term] id: CL:0002437 name: mature CD8 single-positive thymocyte namespace: cell def: "A mature CD8-positive, CD4-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor." [GOC:tfm, http:www.immgen.org/index_content.html] synonym: "T.8SP24-.Th" EXACT [] is_a: CL:0000625 ! CD8-positive, alpha-beta T cell intersection_of: CL:0000625 ! CD8-positive, alpha-beta T cell intersection_of: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex intersection_of: has_low_plasma_membrane_amount PR:000001932 ! signal transducer CD24 relationship: develops_from CL:0002434 ! CD24-positive, CD8 single-positive thymocyte relationship: has_high_plasma_membrane_amount GO:0042105 ! alpha-beta T cell receptor complex relationship: has_low_plasma_membrane_amount PR:000001932 ! signal transducer CD24 created_by: tmeehan creation_date: 2010-10-21T03:51:50Z [Term] id: CL:0002438 name: NK1.1-positive natural killer cell namespace: cell def: "A mature NK cell that is NK1.1-positive." [GOC:tfm] comment: Note: Nk1.1 expression is restricted to C57BL strains of laboratory mice. synonym: "NK.sp" EXACT [] synonym: "NK1.1-positive NK cell" EXACT [] is_a: CL:0000824 ! mature natural killer cell intersection_of: CL:0000824 ! mature natural killer cell intersection_of: has_plasma_membrane_part PR:000002977 ! killer cell lectin-like receptor subfamily B member 1C relationship: has_plasma_membrane_part PR:000002977 ! killer cell lectin-like receptor subfamily B member 1C created_by: tmeehan creation_date: 2010-10-25T03:18:04Z [Term] id: CL:0002439 name: NKGA2-positive natural killer cell namespace: cell def: "A NK1.1-positive T cell that is NKGA2-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "NK.G2A+.SP" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: has_plasma_membrane_part PR:000002023 ! NKG2-A/NKG2-B type II integral membrane protein relationship: has_plasma_membrane_part PR:000002023 ! NKG2-A/NKG2-B type II integral membrane protein created_by: tmeehan creation_date: 2010-10-25T03:31:09Z [Term] id: CL:0002440 name: Ly49D-positive natural killer cell namespace: cell def: "A NK1.1-positive T cell that is Ly49D-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "NK.49D+.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: has_plasma_membrane_part PR:000009619 ! killer cell lectin-like receptor 4 relationship: has_plasma_membrane_part PR:000009619 ! killer cell lectin-like receptor 4 created_by: tmeehan creation_date: 2010-10-25T03:36:19Z [Term] id: CL:0002441 name: CD94-positive natural killer cell namespace: cell def: "A NK1.1-positive T cell that is CD94-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "NK.94+.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: has_plasma_membrane_part PR:000001402 ! killer cell lectin-like receptor subfamily D member 1 relationship: has_plasma_membrane_part PR:000001402 ! killer cell lectin-like receptor subfamily D member 1 created_by: tmeehan creation_date: 2010-10-25T03:36:28Z [Term] id: CL:0002442 name: CD94-negative, Ly49CI-negative natural killer cell namespace: cell def: "A NK1.1-positive T cell that is CD94-negative and Ly49Cl-negative." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "CD94- Ly49I-negative NK cell" EXACT [] synonym: "NK.49Cl-94-.Sp" EXACT [] is_a: CL:0002446 ! Ly49CI-negative natural killer cell is_a: CL:0002447 ! CD94-negative natural killer cell intersection_of: CL:0000623 ! natural killer cell intersection_of: lacks_plasma_membrane_part PR:000001402 ! killer cell lectin-like receptor subfamily D member 1 intersection_of: lacks_plasma_membrane_part PR:000009618 ! killer cell lectin-like receptor 3 relationship: lacks_plasma_membrane_part PR:000001402 ! killer cell lectin-like receptor subfamily D member 1 relationship: lacks_plasma_membrane_part PR:000009618 ! killer cell lectin-like receptor 3 created_by: tmeehan creation_date: 2010-10-25T03:56:21Z [Term] id: CL:0002443 name: Ly49CI-positive natural killer cell namespace: cell def: "A NK1.1-positive T cell that is Ly49Cl-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "Ly49I-positive NK cell" EXACT [] synonym: "NK.49Cl+.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: has_plasma_membrane_part PR:000009618 ! killer cell lectin-like receptor 3 relationship: has_plasma_membrane_part PR:000009618 ! killer cell lectin-like receptor 3 created_by: tmeehan creation_date: 2010-10-25T03:36:38Z [Term] id: CL:0002444 name: Ly49H-positive natural killer cell namespace: cell def: "A NK1.1-positive T cell that is Ly49H-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "LyH49H-positive" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: has_plasma_membrane_part PR:000009623 ! killer cell lectin-like receptor 8 relationship: has_plasma_membrane_part PR:000009623 ! killer cell lectin-like receptor 8 created_by: tmeehan creation_date: 2010-10-25T03:36:43Z [Term] id: CL:0002445 name: Ly49D-negative natural killer cell namespace: cell def: "A NK1.1-positive T cell that is Ly49D-negative." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "NK.49D-.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: lacks_plasma_membrane_part PR:000009619 ! killer cell lectin-like receptor 4 relationship: lacks_plasma_membrane_part PR:000009619 ! killer cell lectin-like receptor 4 created_by: tmeehan creation_date: 2010-10-25T03:39:02Z [Term] id: CL:0002446 name: Ly49CI-negative natural killer cell namespace: cell def: "A NK1.1-positive T cell that is Ly49Cl-negative." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "Ly49I-negative NK cell" EXACT [] synonym: "NK.49Cl-.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: lacks_plasma_membrane_part PR:000009618 ! killer cell lectin-like receptor 3 relationship: lacks_plasma_membrane_part PR:000009618 ! killer cell lectin-like receptor 3 created_by: tmeehan creation_date: 2010-10-25T03:52:04Z [Term] id: CL:0002447 name: CD94-negative natural killer cell namespace: cell def: "A NK1.1-positive T cell that is CD94-negative." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "NK.94-.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: lacks_plasma_membrane_part PR:000001402 ! killer cell lectin-like receptor subfamily D member 1 relationship: lacks_plasma_membrane_part PR:000001402 ! killer cell lectin-like receptor subfamily D member 1 created_by: tmeehan creation_date: 2010-10-25T03:54:18Z [Term] id: CL:0002448 name: Ly49H-negative natural killer cell namespace: cell def: "A NK1.1-positive T cell that is Ly49H-negative." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "LyH49H-negative" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: lacks_plasma_membrane_part PR:000009623 ! killer cell lectin-like receptor 8 relationship: lacks_plasma_membrane_part PR:000009623 ! killer cell lectin-like receptor 8 created_by: tmeehan creation_date: 2010-10-25T03:42:42Z [Term] id: CL:0002449 name: CD94-positive Ly49CI-positive natural killer cell namespace: cell def: "A NK1.1-positive T cell that is CD94-positive and Ly49Cl-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "NK.49Cl+94+.Sp" EXACT [] is_a: CL:0002441 ! CD94-positive natural killer cell is_a: CL:0002443 ! Ly49CI-positive natural killer cell intersection_of: CL:0002438 ! NK1.1-positive natural killer cell intersection_of: has_plasma_membrane_part PR:000001402 ! killer cell lectin-like receptor subfamily D member 1 intersection_of: has_plasma_membrane_part PR:000009618 ! killer cell lectin-like receptor 3 relationship: has_plasma_membrane_part PR:000001402 ! killer cell lectin-like receptor subfamily D member 1 relationship: has_plasma_membrane_part PR:000009618 ! killer cell lectin-like receptor 3 created_by: tmeehan creation_date: 2010-10-25T03:56:27Z [Term] id: CL:0002450 name: tether cell namespace: cell def: "A specialized hair cell that has an elongated kinocilium upon which an otolith accretes. The tether cell then anchors the otolith in place." [GOC:cvs, GOC:tfm, PMID:9398434] is_a: CL:0002374 ! ear hair cell created_by: tmeehan creation_date: 2010-11-10T01:41:00Z [Term] id: CL:0002451 name: mammary stem cell namespace: cell def: "A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi." [GOC:hjd, GOC:tfm, PMID:15987436, PMID:16397499, PMID:17851544] is_a: CL:0000048 ! multi fate stem cell created_by: tmeehan creation_date: 2010-11-10T01:46:51Z [Term] id: CL:0002453 name: oligodendrocyte precursor cell namespace: cell def: "The cell type from which oligodendrocytes develop. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons." [GOC:tfm, PMID:20142420] is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) intersection_of: CL:0000123 ! neuron associated cell (sensu Vertebrata) intersection_of: part_of UBERON:0001017 ! central nervous system relationship: develops_from CL:0000339 ! glioblast (sensu Vertebrata) relationship: part_of UBERON:0001017 ! central nervous system created_by: tmeehan creation_date: 2010-11-10T02:51:34Z [Term] id: CL:0002454 name: Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell namespace: cell def: "Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8_alpha-negative and is CD205-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "DC.8-4-11b+" EXACT [] synonym: "spleen double-negative dendritic cell" EXACT [] is_a: CL:0002465 ! CD11b-positive dendritic cell intersection_of: CL:0002465 ! CD11b-positive dendritic cell intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain created_by: tmeehan creation_date: 2010-11-22T01:10:28Z [Term] id: CL:0002455 name: CD8_alpha-negative plasmactyoid dendritic cell namespace: cell def: "A CD11c-low plasmacytoid dendritic cell that is CD8alpha-negative and CD4-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "DC.pDC.8-" EXACT [] is_a: CL:0000989 ! CD11c-low plasmacytoid dendritic cell intersection_of: CL:0000989 ! CD11c-low plasmacytoid dendritic cell intersection_of: has_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: has_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain created_by: tmeehan creation_date: 2010-11-22T01:27:37Z [Term] id: CL:0002456 name: CD8_alpha-positive plasmactyoid dendritic cell namespace: cell def: "A CD11c-low plasmacytoid dendritic cell that is CD8alpha-positive and CD4-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "DC.pDC.8+" EXACT [] is_a: CL:0000989 ! CD11c-low plasmacytoid dendritic cell intersection_of: CL:0000989 ! CD11c-low plasmacytoid dendritic cell intersection_of: has_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: has_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: has_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: has_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain created_by: tmeehan creation_date: 2010-11-22T01:23:07Z [Term] id: CL:0002457 name: epidermal Langerhans cell namespace: cell def: "A Langerhans cell that is in the epidermis and is CD45-positive, MHCII-positive, and CD11b-positive." [GOC:tfm, http://www.immgen.org/index_content.html] is_a: CL:0000453 ! Langerhans cell is_a: CL:0002465 ! CD11b-positive dendritic cell intersection_of: CL:0000453 ! Langerhans cell intersection_of: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R intersection_of: part_of UBERON:0001003 ! epidermis relationship: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: part_of UBERON:0001003 ! epidermis created_by: tmeehan creation_date: 2010-11-22T03:57:57Z [Term] id: CL:0002458 name: langerin-positive dermal dendritic cell namespace: cell def: "A dermal dendritic cell that is langerin-positive, CD103-positive, and CD11b-negative." [GOC:tfm, http://www.immgen.org/index_content.html] is_a: CL:0001006 ! dermal dendritic cell is_a: CL:0002461 ! CD103-positive dendritic cell intersection_of: CL:0001006 ! dermal dendritic cell intersection_of: has_plasma_membrane_part PR:000001010 ! integrin alpha-E intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001010 ! integrin alpha-E relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M created_by: tmeehan creation_date: 2010-11-22T04:06:22Z [Term] id: CL:0002459 name: langerin-negative dermal dendritic cell namespace: cell def: "A dermal dendritic cell that is langerin-negative, CD103-negative, and CD11b-positive." [GOC:tfm, http://www.immgen.org/index_content.html] is_a: CL:0001006 ! dermal dendritic cell intersection_of: CL:0001006 ! dermal dendritic cell intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part CL:0002458 ! langerin-positive dermal dendritic cell intersection_of: lacks_plasma_membrane_part PR:000001010 ! integrin alpha-E relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part CL:0002458 ! langerin-positive dermal dendritic cell relationship: lacks_plasma_membrane_part CL:0002507 ! langerin-positive lymph node dendritic cell relationship: lacks_plasma_membrane_part CL:0002508 ! langerin-negative, CD103-negative lymph node dendritic cell relationship: lacks_plasma_membrane_part PR:000001010 ! integrin alpha-E created_by: tmeehan creation_date: 2010-11-22T04:09:44Z [Term] id: CL:0002460 name: CD8alpha-negative thymic conventional dendritic cell namespace: cell def: "A conventional thymic dendritic cell that is CD8alpha-negative." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:19273629] synonym: "DC.8-.Th" EXACT [] is_a: CL:0000941 ! thymic conventional dendritic cell intersection_of: CL:0000941 ! thymic conventional dendritic cell intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain created_by: tmeehan creation_date: 2010-11-23T10:58:53Z [Term] id: CL:0002461 name: CD103-positive dendritic cell namespace: cell def: "A conventional dendritic cell that is CD103-positive. This cell type is usually found in non-lymphoid tissue." [GOC:tfm, http://www.immgen.org/index_content.html] is_a: CL:0000990 ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: has_plasma_membrane_part PR:000001010 ! integrin alpha-E relationship: develops_from CL:0002010 ! pre-conventional dendritic cell relationship: has_plasma_membrane_part PR:000001010 ! integrin alpha-E created_by: tmeehan creation_date: 2010-11-23T01:32:43Z [Term] id: CL:0002462 name: adipose dendritic cell namespace: cell def: "A F4/80-negative dendritic cell located in adipose tissue." [GOC:tfm, http://www.immgen.org/index_content.html] is_a: CL:0000990 ! conventional dendritic cell is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: lacks_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 intersection_of: part_of UBERON:0001013 ! adipose tissue relationship: develops_from CL:0002010 ! pre-conventional dendritic cell relationship: lacks_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 relationship: part_of UBERON:0001013 ! adipose tissue created_by: tmeehan creation_date: 2010-11-23T01:38:21Z [Term] id: CL:0002463 name: SIRPa-positive adipose dendritic cell namespace: cell def: "An adipose dendritic cell that is SIRPa-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "DC.SIRPa+.Ad" EXACT [] is_a: CL:0002462 ! adipose dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: has_plasma_membrane_part PR:000001968 ! tyrosine-protein phosphatase non-receptor type substrate 1 relationship: has_plasma_membrane_part PR:000001968 ! tyrosine-protein phosphatase non-receptor type substrate 1 created_by: tmeehan creation_date: 2010-11-23T01:40:44Z [Term] id: CL:0002464 name: SIRPa-negative adipose dendritic cell namespace: cell def: "An adipose dendritic cell that is SIRPa-negative." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "DC.SIRPa-.Ad" EXACT [] is_a: CL:0002462 ! adipose dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: lacks_plasma_membrane_part PR:000001968 ! tyrosine-protein phosphatase non-receptor type substrate 1 relationship: lacks_plasma_membrane_part PR:000001968 ! tyrosine-protein phosphatase non-receptor type substrate 1 created_by: tmeehan creation_date: 2010-11-23T01:40:46Z [Term] id: CL:0002465 name: CD11b-positive dendritic cell namespace: cell def: "A conventional dendritic cell that expresses CD11b (ITGAM)." [GOC:tfm, http://www.immgen.org/index_content.html] is_a: CL:0000990 ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: has_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001012 ! integrin alpha-M created_by: tmeehan creation_date: 2010-11-23T01:50:05Z [Term] id: CL:0002466 name: small intestine serosal dendritic cell namespace: cell def: "A CD11b-positive dendritic cell located in the serosal portion of the small intestine epithelium. This cell type is CD45-positive, MHC-II-positive, CD11c-low, CD103-negative." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "DC.11cloSer.SI" EXACT [] is_a: CL:0002465 ! CD11b-positive dendritic cell intersection_of: CL:0002465 ! CD11b-positive dendritic cell intersection_of: has_low_plasma_membrane_amount PR:000001013 ! integrin alpha-X intersection_of: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex intersection_of: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C intersection_of: lacks_plasma_membrane_part PR:000001010 ! integrin alpha-E relationship: has_low_plasma_membrane_amount PR:000001013 ! integrin alpha-X relationship: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C relationship: lacks_plasma_membrane_part PR:000001010 ! integrin alpha-E created_by: tmeehan creation_date: 2010-11-23T02:00:21Z [Term] id: CL:0002467 name: Gr1-high myeloid suppressor cell namespace: cell def: "A myeloid suppressor cell that is Gr1-high and CD11c-negative." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "MDS.Gr1hi" EXACT [] is_a: CL:0000889 ! myeloid suppressor cell intersection_of: CL:0000889 ! myeloid suppressor cell intersection_of: has_high_plasma_membrane_amount PR:000002980 ! lymphocyte antigen 6C intersection_of: lacks_plasma_membrane_part PR:000001013 ! integrin alpha-X relationship: has_high_plasma_membrane_amount PR:000002980 ! lymphocyte antigen 6C relationship: lacks_plasma_membrane_part PR:000001013 ! integrin alpha-X created_by: tmeehan creation_date: 2010-11-23T02:15:12Z [Term] id: CL:0002468 name: Gr1-low myeloid suppressor cell namespace: cell def: "A myeloid suppressor cell that is Gr1-low and CD11c-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "MDS.Gr1lo" EXACT [] is_a: CL:0000889 ! myeloid suppressor cell intersection_of: CL:0000889 ! myeloid suppressor cell intersection_of: has_low_plasma_membrane_amount PR:000002980 ! lymphocyte antigen 6C intersection_of: has_plasma_membrane_part PR:000001013 ! integrin alpha-X relationship: has_low_plasma_membrane_amount PR:000002980 ! lymphocyte antigen 6C relationship: has_plasma_membrane_part PR:000001013 ! integrin alpha-X created_by: tmeehan creation_date: 2010-11-23T02:19:43Z [Term] id: CL:0002469 name: MHC-II-negative classical monocyte namespace: cell def: "Gr1-high monocyte that lacks MHC-II receptor complex." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "Mo.6C+II-" EXACT [] is_a: CL:0002395 ! Gr1-high classical monocyte intersection_of: CL:0002395 ! Gr1-high classical monocyte intersection_of: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex created_by: tmeehan creation_date: 2010-11-23T03:27:12Z [Term] id: CL:0002470 name: MHC-II-positive classical monocyte namespace: cell def: "Gr1-high monocyte that has a MHC-II receptor complex." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "Mo.6c+II" EXACT [] is_a: CL:0002395 ! Gr1-high classical monocyte intersection_of: CL:0002395 ! Gr1-high classical monocyte intersection_of: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex created_by: tmeehan creation_date: 2010-11-23T03:30:21Z [Term] id: CL:0002471 name: MHC-II-negative non-classical monocyte namespace: cell def: "Gr1-low non-classical monocyte that lacks expression of a MHC-II complex." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "Mo.6C-II-" EXACT [] is_a: CL:0002058 ! Gr1-low non-classical monocyte intersection_of: CL:0002058 ! Gr1-low non-classical monocyte intersection_of: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex created_by: tmeehan creation_date: 2010-11-23T03:38:15Z [Term] id: CL:0002472 name: MHC-II-low non-classical monocyte namespace: cell def: "Gr1-low non-classical monocyte that has low to intermediate expression of the MHC-II complex." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "Mo.6C-IIint" EXACT [] is_a: CL:0002058 ! Gr1-low non-classical monocyte intersection_of: CL:0002058 ! Gr1-low non-classical monocyte intersection_of: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex created_by: tmeehan creation_date: 2010-11-23T03:47:53Z [Term] id: CL:0002473 name: MHC-II-high non-classical monocyte namespace: cell def: "Gr1-low non-classical monocyte that has high surface expression of a MHC-II complex." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "Mo.6C-II+" EXACT [] is_a: CL:0002058 ! Gr1-low non-classical monocyte intersection_of: CL:0002058 ! Gr1-low non-classical monocyte intersection_of: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex created_by: tmeehan creation_date: 2010-11-23T03:47:55Z [Term] id: CL:0002474 name: lymphoid MHC-II-negative classical monocyte namespace: cell def: "A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-negative, and CD11b-high." [GOC:tfm, http://www.immgen.org/index_content.html] is_a: CL:0002469 ! MHC-II-negative classical monocyte intersection_of: CL:0002469 ! MHC-II-negative classical monocyte intersection_of: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 intersection_of: lacks_plasma_membrane_part PR:000001013 ! integrin alpha-X relationship: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 relationship: lacks_plasma_membrane_part PR:000001013 ! integrin alpha-X created_by: tmeehan creation_date: 2010-11-23T04:00:52Z [Term] id: CL:0002475 name: lymphoid MHC-II-negative non-classical monocyte namespace: cell def: "A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-intermediate, and CD11b-high." [GOC:tfm, http://www.immgen.org/index_content.html] is_a: CL:0002469 ! MHC-II-negative classical monocyte is_a: CL:0002471 ! MHC-II-negative non-classical monocyte intersection_of: CL:0002469 ! MHC-II-negative classical monocyte intersection_of: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001013 ! integrin alpha-X intersection_of: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 relationship: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001013 ! integrin alpha-X relationship: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 created_by: tmeehan creation_date: 2010-11-23T04:09:09Z [Term] id: CL:0002476 name: bone marrow macrophage namespace: cell def: "A tissue-resident macrophage located in the bone marrow. This cell type is B220-negative, CD3e-negative, Ly-6C-negative, CD115-positive, F4/80-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "MF.BM" RELATED [] xref: BTO:0004732 is_a: CL:0000864 ! tissue-resident macrophage is_a: CL:0002092 ! bone marrow cell intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 intersection_of: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor intersection_of: lacks_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000002980 ! lymphocyte antigen 6C relationship: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 relationship: has_plasma_membrane_part PR:000002062 ! macrophage colony-stimulating factor 1 receptor relationship: lacks_plasma_membrane_part PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45R relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000002980 ! lymphocyte antigen 6C relationship: part_of UBERON:0002371 ! bone marrow created_by: tmeehan creation_date: 2010-11-23T04:19:25Z [Term] id: CL:0002477 name: adipose macrophage namespace: cell def: "A macrophage located in adipose tissue that is CD45-positive, CD11c-positive, and SIRPa-positive." [GOC:tfm] is_a: CL:0000864 ! tissue-resident macrophage intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C intersection_of: has_plasma_membrane_part PR:000001013 ! integrin alpha-X intersection_of: has_plasma_membrane_part PR:000001968 ! tyrosine-protein phosphatase non-receptor type substrate 1 relationship: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C relationship: has_plasma_membrane_part PR:000001013 ! integrin alpha-X relationship: has_plasma_membrane_part PR:000001968 ! tyrosine-protein phosphatase non-receptor type substrate 1 created_by: tmeehan creation_date: 2010-11-23T04:31:28Z [Term] id: CL:0002478 name: F4/80-negative adipose macrophage namespace: cell def: "An adipose macrophage that does not express F4/80but is MHC-II-positive. This cell type exhibits autofluorescence under typical flow cyometry conditions." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "MF.Autofl.Ad" EXACT [] is_a: CL:0002477 ! adipose macrophage intersection_of: CL:0002477 ! adipose macrophage intersection_of: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex intersection_of: lacks_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 relationship: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: lacks_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 created_by: tmeehan creation_date: 2010-11-23T04:40:50Z [Term] id: CL:0002479 name: F4/80-positive adipose macrophage namespace: cell def: "An adipose macrophage that does not express MHC-II but is F4/80-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "MF.F480+.Ad" EXACT [] is_a: CL:0002477 ! adipose macrophage intersection_of: CL:0002477 ! adipose macrophage intersection_of: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 intersection_of: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: has_plasma_membrane_part PR:000001813 ! EGF-like module-containing mucin-like hormone receptor-like 1 relationship: lacks_plasma_membrane_part GO:0042613 ! MHC class II protein complex created_by: tmeehan creation_date: 2010-11-23T04:35:53Z [Term] id: CL:0002480 name: nasal mucosa goblet cell namespace: cell def: "A goblet cell located in the nasal epithelium." [GOC:cjm, GOC:tfm] xref: MP:0002262 is_a: CL:0000160 ! goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0005384 ! nasal cavity epithelium relationship: part_of UBERON:0005384 ! nasal cavity epithelium created_by: tmeehan creation_date: 2010-12-03T03:03:02Z [Term] id: CL:0002481 name: peritubular myoid cell namespace: cell def: "The flattened smooth myoepithelial cells of mesodermal origin that lie just outside the basal lamina of the seminiferous tubule." [GOC:cjm, GOC:tfm, MP:0006420] is_a: CL:0000185 ! myoepithelial cell intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:0001343 ! seminiferous tubule of testis relationship: part_of UBERON:0001343 ! seminiferous tubule of testis created_by: tmeehan creation_date: 2010-12-03T03:11:48Z [Term] id: CL:0002482 name: dermal melanocyte namespace: cell def: "A melanocyte that produces pigment in the dermis." [GOC:cjm, GOC:tfm, MP:0009386] is_a: CL:1000458 ! melanocyte of skin intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0002067 ! dermis relationship: part_of UBERON:0002067 ! dermis created_by: tmeehan creation_date: 2010-12-03T03:17:05Z [Term] id: CL:0002483 name: hair follicle melanocyte namespace: cell def: "A melanocyte that produces pigment within the hair follicle." [GOC:tfm, MP:0004381] is_a: CL:0000362 ! epidermal cell is_a: CL:0002484 ! epithelial melanocyte is_a: CL:0002559 ! hair follicle cell is_a: CL:1000458 ! melanocyte of skin intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0002073 ! hair follicle relationship: part_of UBERON:0002073 ! hair follicle created_by: tmeehan creation_date: 2010-12-03T03:17:09Z [Term] id: CL:0002484 name: epithelial melanocyte namespace: cell def: "A melanocyte that produces pigment in the epithelium." [GOC:tfm, MP:0009388] is_a: CL:0000148 ! melanocyte intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0000483 ! epithelium relationship: part_of UBERON:0000483 ! epithelium created_by: tmeehan creation_date: 2010-12-03T03:17:14Z [Term] id: CL:0002485 name: retinal melanocyte namespace: cell def: "A melanocyte of the retina. This cell type is distinct from pigmented retinal epithelium." [GOC:tfm, MP:0010190] is_a: CL:0000148 ! melanocyte intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina created_by: tmeehan creation_date: 2010-12-03T03:25:32Z [Term] id: CL:0002486 name: strial intermediate cell namespace: cell def: "A melanocyte located between the epithelial marginal cell layer and the mesodermal basal cell layer within the intrastrial space; the predominant cellular component of the electrogenic machinery that generates an endocochlear potential (80-100 mV) ." [GOC:tfm, MP:0000048] is_a: CL:0000148 ! melanocyte is_a: CL:0001035 ! bone cell is_a: CL:0002491 ! auditory epithelial cell intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0002282 ! stria vascularis of cochlear duct relationship: part_of UBERON:0002282 ! stria vascularis of cochlear duct created_by: tmeehan creation_date: 2010-12-03T03:29:15Z [Term] id: CL:0002487 name: cutaneous/subcutaneous mechanoreceptor cell namespace: cell def: "A neuronal receptor that respond to mechanical pressure or distortion in the skin." [GOC:tfm, MP:0000973] is_a: CL:0000199 ! mechanoreceptor cell created_by: tmeehan creation_date: 2010-12-06T02:53:30Z [Term] id: CL:0002488 name: trophoblast giant cell namespace: cell def: "A trophoblast cell that has a large volume of cytoplasm, is polyploidy and is usually mononuclear but is also occasionally multi-nucleate. This cell type is important in establishing maternal physiology and remodeling of the vasculature of the placenta." [GOC:tfm, MP:0001714, MP:19876834] synonym: "giant trophoblast cell" EXACT [] is_a: CL:0000351 ! trophoblast cell intersection_of: CL:0000351 ! trophoblast cell intersection_of: capable_of GO:0001974 ! blood vessel remodeling intersection_of: has_quality PATO:0000586 ! increased size relationship: capable_of GO:0001974 ! blood vessel remodeling relationship: has_quality PATO:0000586 ! increased size created_by: tmeehan creation_date: 2010-12-06T02:55:24Z [Term] id: CL:0002489 name: double negative thymocyte namespace: cell def: "A thymocyte that lacks expression of CD4 and CD8." [GOC:tfm, MP:0002407] synonym: "double negative T cell" BROAD [] is_a: CL:0000893 ! thymocyte intersection_of: CL:0000893 ! thymocyte intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000025402 ! T cell receptor co-receptor CD8 created_by: tmeehan creation_date: 2010-12-06T03:03:38Z [Term] id: CL:0002490 name: organ of Corti supporting cell namespace: cell def: "A supporting cell of the organ of Corti." [GOC:tfm, MP:0004300] is_a: CL:0001035 ! bone cell is_a: CL:0002315 ! supporting cell of cochlea intersection_of: CL:0005014 ! auditory epithelial support cell intersection_of: part_of UBERON:0002227 ! spiral organ of cochlea relationship: part_of UBERON:0002227 ! spiral organ of cochlea created_by: tmeehan creation_date: 2010-12-06T03:09:01Z [Term] id: CL:0002491 name: auditory epithelial cell namespace: cell def: "A specialized cell involved in auditory sensory perception." [GOC:tfm] is_a: CL:0000098 ! sensory epithelial cell created_by: tmeehan creation_date: 2010-12-06T03:18:43Z [Term] id: CL:0002492 name: strial marginal cell namespace: cell def: "A polarized columnar cell that covesr the lateral surface of the cochlear duct, secretes potassium ions and forms a continuous sheet in contact with the endolymph; marginal cells form extensive interdigitations with the basal and intermediate cells in the normal adult stria." [GOC:tfm, MP:0004366] is_a: CL:0002491 ! auditory epithelial cell created_by: tmeehan creation_date: 2010-12-06T03:20:41Z [Term] id: CL:0002493 name: strial basal cell namespace: cell def: "A polarized cell that is juxtaposed to fibrocytes in the underlying spiral ligament. This cell type secretes potassium ions derived from fibrocytes through gap junctions." [GOC:tfm, MP:0004365] comment: Basal cells form a multi-layered epithelial barrier that separates the extracellular spaces of the stria vascularis and the spiral ligament[PMID:18353863] is_a: CL:0001035 ! bone cell is_a: CL:0002491 ! auditory epithelial cell relationship: part_of UBERON:0002282 ! stria vascularis of cochlear duct created_by: tmeehan creation_date: 2010-12-06T03:26:53Z [Term] id: CL:0002494 name: cardiocyte namespace: cell def: "A cell located in the heart, including both muscle and non muscle cells." [GOC:tfm] comment: From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. synonym: "heart cell" EXACT [] xref: BTO:0001539 xref: FMA:83808 xref: FMA:84791 is_a: CL:0000548 ! animal cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0002371 ! somatic cell intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart created_by: tmeehan creation_date: 2010-12-07T09:37:22Z [Term] id: CL:0002495 name: fetal cardiomyocyte namespace: cell def: "A fetal and neonatal heart cell that undergoes proliferation and is not yet terminally differentiated into a binucleate or a multinucleate cardiac myocyte." [GOC:tfm, MP:0008788] synonym: "embryonic cardiomyocyte" EXACT [] synonym: "neonatal cardiomyocyte" EXACT [] is_a: CL:0000746 ! cardiac muscle cell created_by: tmeehan creation_date: 2010-12-07T09:50:41Z [Term] id: CL:0002496 name: intraepithelial lymphocyte namespace: cell def: "A T cell that is located in the intestinal epithelium and is capable of a mucosal immune response." [GOC:tfm, MP:0008894] synonym: "IEL" EXACT [] synonym: "intraepithelial T cell" EXACT [] synonym: "intraepithelial T-cell" EXACT [] is_a: CL:0002419 ! mature T cell intersection_of: CL:0002419 ! mature T cell intersection_of: capable_of GO:0002385 ! mucosal immune response intersection_of: part_of UBERON:0001277 ! intestinal epithelium relationship: capable_of GO:0002385 ! mucosal immune response relationship: part_of UBERON:0001277 ! intestinal epithelium created_by: tmeehan creation_date: 2010-12-07T09:54:50Z [Term] id: CL:0002497 name: primary trophoblast giant cell namespace: cell def: "A trophoblast giant cell derived from the mural trophectoderm." [GOC:tfm, PMCID:PMC85124] xref: EMAPA:16066 is_a: CL:0002488 ! trophoblast giant cell created_by: tmeehan creation_date: 2010-12-07T10:07:47Z [Term] id: CL:0002498 name: secondary trophoblast giant cell namespace: cell def: "A trophoblast giant cell that is derived from ectoplacental cone and, later in gestation, the spongiotrophoblast." [GOC:tfm, PMCID:PMC85124] is_a: CL:0002488 ! trophoblast giant cell created_by: tmeehan creation_date: 2010-12-07T10:07:52Z [Term] id: CL:0002499 name: spongiotrophoblast cell namespace: cell def: "A trophoblast cell that arises in the junctional zone (basal plate) of the placenta." [GOC:tfm, MP:0008959] is_a: CL:0000351 ! trophoblast cell created_by: tmeehan creation_date: 2010-12-07T12:56:56Z [Term] id: CL:0002500 name: P enteroendocrine cell namespace: cell def: "A P/D1 enteroendocrine cell that is Grimelius positive and stores bombesin-like polypeptide." [FMA:63418, GOC:tfm] is_a: CL:0002268 ! P/D1 enteroendocrine cell created_by: tmeehan creation_date: 2010-12-07T03:42:06Z [Term] id: CL:0002501 name: type D1 enteroendocrine cell namespace: cell def: "A P/D1 enteroendocrine cell that is argyrophilic and stores vasoactive intestinal polypeptide." [FMA:63207, GOC:tfm] xref: FMA:63207 is_a: CL:0002268 ! P/D1 enteroendocrine cell created_by: tmeehan creation_date: 2010-12-07T03:42:09Z [Term] id: CL:0002502 name: type M enteroendocrine cell namespace: cell def: "An enteroendocrine cell of the small intestine that secretes motilin." [GOC:tfm, PMID:15153415] synonym: "Mo enteroendocrine cell" BROAD [] xref: FMA:63420 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0002272 ! motilin secreting cell created_by: tmeehan creation_date: 2010-12-07T03:55:49Z [Term] id: CL:0002503 name: adventitial cell namespace: cell def: "A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc" [GOC:tfm] xref: BTO:0002441 xref: FMA:84639 is_a: CL:0000630 ! supportive cell is_a: CL:0002320 ! connective tissue cell created_by: tmeehan creation_date: 2010-12-07T04:03:56Z [Term] id: CL:0002504 name: enteric smooth muscle cell namespace: cell def: "A smooth muscle cell of the intestine." [GOC:tfm] synonym: "intestinal smooth muscle cell" EXACT [] is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0000160 ! intestine created_by: tmeehan creation_date: 2011-01-17T03:39:38Z [Term] id: CL:0002505 name: liver CD103-negative dendritic cell namespace: cell def: "A CD11b-positive dendritic cell that is CD11b-high, CD45-positive, MHC-II-positive and CD103-negative." [GOC:tfm, http:http\://www.immgen.org/index_content.html] synonym: "DC.103-11b+.Lv" EXACT [] is_a: CL:0002454 ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell intersection_of: CL:0002454 ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell intersection_of: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex intersection_of: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C intersection_of: lacks_plasma_membrane_part PR:000001010 ! integrin alpha-E intersection_of: part_of UBERON:0001281 ! hepatic sinusoid relationship: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C relationship: lacks_plasma_membrane_part PR:000001010 ! integrin alpha-E relationship: part_of UBERON:0001281 ! hepatic sinusoid created_by: tmeehan creation_date: 2011-01-21T01:27:41Z [Term] id: CL:0002506 name: liver CD103-positive dendritic cell namespace: cell def: "A CD11b-positive dendritic cell that is CD11b-low, CD45-positive, MHC-II-high and CD103-positive that is located in the liver." [GOC:tfm, http:http\://www.immgen.org/index_content.html] synonym: "DC.103+11b-.Lv" EXACT [] is_a: CL:0002454 ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell is_a: CL:0002461 ! CD103-positive dendritic cell intersection_of: CL:0002454 ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell intersection_of: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex intersection_of: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C intersection_of: has_plasma_membrane_part PR:000001010 ! integrin alpha-E intersection_of: part_of UBERON:0001281 ! hepatic sinusoid relationship: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein phosphatase C relationship: has_plasma_membrane_part PR:000001010 ! integrin alpha-E relationship: part_of UBERON:0001281 ! hepatic sinusoid created_by: tmeehan creation_date: 2011-01-21T01:27:45Z [Term] id: CL:0002507 name: langerin-positive lymph node dendritic cell namespace: cell def: "A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-positive, MHC-II-positive, and CD4-negative and CD8a-negative." [GOC:tfm, http://www.immgen.org/index_content.html] is_a: CL:0000990 ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex intersection_of: has_plasma_membrane_part PR:000001293 ! C-type lectin domain family 4 member K intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: has_plasma_membrane_part PR:000001293 ! C-type lectin domain family 4 member K relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain created_by: tmeehan creation_date: 2011-01-21T01:57:00Z [Term] id: CL:0002508 name: langerin-negative, CD103-negative lymph node dendritic cell namespace: cell def: "A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-negative, MHC-II-positive, and CD4-negative and CD8a-negative." [GOC:tfm, http://www.immgen.org/index_content.html] is_a: CL:0000990 ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex intersection_of: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule intersection_of: lacks_plasma_membrane_part PR:000001010 ! integrin alpha-E intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001293 ! C-type lectin domain family 4 member K relationship: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex relationship: lacks_plasma_membrane_part PR:000001004 ! CD4 molecule relationship: lacks_plasma_membrane_part PR:000001010 ! integrin alpha-E relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001293 ! C-type lectin domain family 4 member K created_by: tmeehan creation_date: 2011-01-21T02:13:58Z [Term] id: CL:0002509 name: CD103-positive, langerin-positive lymph node dendritic cell namespace: cell def: "A langerin-positive lymph node dendritic cell that is CD103-positive and CD11b-low." [GOC:tfm, http://www.immgen.org/index_content.html] is_a: CL:0002461 ! CD103-positive dendritic cell is_a: CL:0002507 ! langerin-positive lymph node dendritic cell intersection_of: CL:0002507 ! langerin-positive lymph node dendritic cell intersection_of: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M intersection_of: has_plasma_membrane_part PR:000001010 ! integrin alpha-E relationship: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: has_plasma_membrane_part PR:000001010 ! integrin alpha-E created_by: tmeehan creation_date: 2011-01-21T02:07:54Z [Term] id: CL:0002510 name: CD103-negative, langerin-positive lymph node dendritic cell namespace: cell def: "A langerin-positive lymph node dendritic cell that is CD103-negative and CD11b-high." [GOC:tfm, http://www.immgen.org/index_content.html] is_a: CL:0002507 ! langerin-positive lymph node dendritic cell intersection_of: CL:0002507 ! langerin-positive lymph node dendritic cell intersection_of: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001010 ! integrin alpha-E relationship: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001010 ! integrin alpha-E created_by: tmeehan creation_date: 2011-01-21T02:11:14Z [Term] id: CL:0002511 name: CD11b-low, CD103-negative, langerin-negative lymph node dendritic cell namespace: cell def: "A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-low." [GOC:tfm, http://www.immgen.org/index_content.html] is_a: CL:0002508 ! langerin-negative, CD103-negative lymph node dendritic cell intersection_of: CL:0002508 ! langerin-negative, CD103-negative lymph node dendritic cell intersection_of: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: has_low_plasma_membrane_amount PR:000001012 ! integrin alpha-M created_by: tmeehan creation_date: 2011-01-21T02:22:15Z [Term] id: CL:0002512 name: CD11b-high, CD103-negative, langerin-negative lymph node dendritic cell namespace: cell def: "A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-high." [GOC:tfm, http://www.immgen.org/index_content.html] is_a: CL:0002508 ! langerin-negative, CD103-negative lymph node dendritic cell intersection_of: CL:0002508 ! langerin-negative, CD103-negative lymph node dendritic cell intersection_of: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M relationship: has_high_plasma_membrane_amount PR:000001012 ! integrin alpha-M created_by: tmeehan creation_date: 2011-01-21T02:16:21Z [Term] id: CL:0002513 name: Vgamma5-positive CD8alpha alpha positive gamma-delta intraepithelial T cell namespace: cell def: "A CD8alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "tgd.vg5+.IEL" EXACT [] is_a: CL:0000802 ! CD8-alpha alpha positive, gamma-delta intraepithelial T cell created_by: tmeehan creation_date: 2011-01-24T10:22:18Z [Term] id: CL:0002514 name: Vgamma5-negative CD8alpha alpha positive gamma-delta intraepithelial T cell namespace: cell def: "A CD8alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "tgd.vg5-.IEL" EXACT [] is_a: CL:0000802 ! CD8-alpha alpha positive, gamma-delta intraepithelial T cell created_by: tmeehan creation_date: 2011-01-24T10:25:44Z [Term] id: CL:0002515 name: interrenal norepinephrine type cell namespace: cell def: "An interrenal chromaffin cell found in teleosts that contain heterogeneous vesicles with electron-dense granules located asymmetrically within the vesicular membrane." [GOC:MH, GOC:tfm, PMID:12668625] synonym: "interrenal noradrenaline type cell" EXACT [] synonym: "type n interrenal cell" EXACT [] is_a: CL:0000459 ! norepinephrin secreting cell is_a: CL:0002516 ! interrenal chromaffin cell created_by: tmeehan creation_date: 2011-02-08T10:11:55Z [Term] id: CL:0002516 name: interrenal chromaffin cell namespace: cell def: "A chromaffin cell interspersed among the interrenal epithelial layer of the anterior kidney of teloest fish." [GOC:MH, GOC:tfm, PMID:12668625] is_a: CL:0000166 ! chromaffin cell created_by: tmeehan creation_date: 2011-02-08T10:21:35Z [Term] id: CL:0002517 name: interrenal epinephrin secreting cell namespace: cell def: "An interrenal chromaffin cell found in teleosts that contain small, homogeneous electron-lucent granules that are separated from the vesicular membrane by a visible halo." [GOC:MH, GOC:tfm, PMID:12668625] synonym: "interrenal adrenaline secreting cell" RELATED [] synonym: "type a interrenal cell" EXACT [] is_a: CL:0000454 ! epinephrine secreting cell is_a: CL:0002516 ! interrenal chromaffin cell created_by: tmeehan creation_date: 2011-02-08T10:27:05Z [Term] id: CL:0002518 name: kidney epithelial cell namespace: cell def: "An epithelial cell of the kidney." [GOC:tfm, KUPO:SJ] xref: KUPO:0001019 is_a: CL:0000066 ! epithelial cell is_a: CL:1000497 ! kidney cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney created_by: tmeehan creation_date: 2011-02-08T10:46:34Z [Term] id: CL:0002519 name: interrenal epithelial cell namespace: cell def: "The interrenal epithelial kidney cell is an epithelial cell found in the anterior kidney of teleosts fish. This cell type is arranged in layers around the posterior cardinal vein and contains many mitochondria with tubulovesicular cristae. Interrenal chromaffin cells are interspersed among the tissue layer created by this cell type." [GOC:mh, GOC:tfm, PMID:12668625] is_a: CL:0002518 ! kidney epithelial cell created_by: tmeehan creation_date: 2011-02-08T11:03:32Z [Term] id: CL:0002520 name: nephrocyte namespace: cell def: "An insect excretory cell that regulates haemolymph composition by filtration and filtrate endocytosis." [GOC:tfm, PMID:19783135] xref: BTO:0004597 xref: FMA:83807 is_a: CL:0002522 ! renal filtration cell created_by: tmeehan creation_date: 2011-02-08T01:34:56Z [Term] id: CL:0002521 name: subcutaneous fat cell namespace: cell def: "A fat cell that is part of subcutaneous adipose tissue." [GOC:tfm] synonym: "subcutaneous adipocyte" EXACT [] is_a: CL:0000136 ! fat cell intersection_of: CL:0000136 ! fat cell intersection_of: part_of UBERON:0002190 ! subcutaneous adipose tissue relationship: part_of UBERON:0002190 ! subcutaneous adipose tissue created_by: tmeehan creation_date: 2011-02-21T02:51:22Z [Term] id: CL:0002522 name: renal filtration cell namespace: cell def: "A renal filtration cell is a specialized cell of the renal system that filter fluids by charge, size or both." [GOC:tfm] is_a: CL:0000424 ! excretory cell created_by: tmeehan creation_date: 2011-02-08T01:37:59Z [Term] id: CL:0002523 name: mesonephric glomerular visceral epithelial cell namespace: cell def: "A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the mesonephros" [GOC:tfm] is_a: CL:0000653 ! glomerular visceral epithelial cell created_by: tmeehan creation_date: 2011-02-08T01:58:30Z [Term] id: CL:0002524 name: disseminated nephrocyte namespace: cell def: "A disseminated nephrocyte is a nephrocyte that filters hemolymph and is found at scattered locations in the fat body or other tissues." [GOC:tfm, PMID:19783135] is_a: CL:0002520 ! nephrocyte created_by: tmeehan creation_date: 2011-02-08T02:07:33Z [Term] id: CL:0002525 name: metanephric glomerular visceral epithelial cell namespace: cell def: "A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the metanephros." [GOC:tfm] is_a: CL:0000653 ! glomerular visceral epithelial cell created_by: tmeehan creation_date: 2011-02-08T02:02:13Z [Term] id: CL:0002526 name: CD14-positive dermal dendritic cell namespace: cell def: "A dermal dendritic cell that is CD1a-negative and CD14-positive." [GOC:dsd, PMID:19236899, PMID:20309010] comment: They are also CD11c-positive, CD40-positive, CD85j-positive (ILT-2), CD163-positive, CD205-positive (DEC205), CD207-negative (langerin), CD209-positive (DC-SIGN), CD274-positive (PD-L1), CD324-negative (E-cadherin), Factor XIIIa-positive, LOX-I-positive, CLEC6-positive, Dectin-1-positive, and DCIR-positive. Upon stimulation, these cells are capable of producing IL1-beta, IL6, IL8, IL10, IL12p40, IL19, IL20, IL24, TGF-beta, TNF-alpha, GM-CSF, and MCP1. They reside in the dermis. synonym: "CD14+ dermal DC" EXACT [] is_a: CL:0001006 ! dermal dendritic cell intersection_of: CL:0001006 ! dermal dendritic cell intersection_of: capable_of GO:0045191 ! regulation of isotype switching intersection_of: has_plasma_membrane_part PR:000001889 ! CD14 molecule intersection_of: lacks_plasma_membrane_part PR:000002025 ! T-cell surface glycoprotein CD1a relationship: capable_of GO:0045191 ! regulation of isotype switching relationship: has_plasma_membrane_part PR:000001889 ! CD14 molecule relationship: lacks_plasma_membrane_part PR:000002025 ! T-cell surface glycoprotein CD1a [Term] id: CL:0002527 name: immature CD14-positive dermal dendritic cell namespace: cell def: "An immature CD14-positive dermal dendritic cell is CD80-low, CD86-low, and MHCII-low." [GOC:dsd] is_a: CL:0001009 ! immature dermal dendritic cell is_a: CL:0002526 ! CD14-positive dermal dendritic cell intersection_of: CL:0002526 ! CD14-positive dermal dendritic cell intersection_of: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule [Term] id: CL:0002528 name: mature CD14-positive dermal dendritic cell namespace: cell def: "A mature CD14-positive dermal dendritic cell is CD80-high, CD86-high, MHCII-high and is CD83-positive." [GOC:dsd] is_a: CL:0001010 ! mature dermal dendritic cell is_a: CL:0002526 ! CD14-positive dermal dendritic cell intersection_of: CL:0002526 ! CD14-positive dermal dendritic cell intersection_of: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule intersection_of: has_plasma_membrane_part PR:000001310 ! CD83 molecule relationship: develops_from CL:0002527 ! immature CD14-positive dermal dendritic cell relationship: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_plasma_membrane_part PR:000001310 ! CD83 molecule [Term] id: CL:0002529 name: CD1a-positive dermal dendritic cell namespace: cell def: "A dermal dendritic cell that is CD1a-positive and CD14-negative." [GOC:dsd, PMID:20309010] comment: Reside in the dermis. They are also CD11c-positive, CD40-positive, CD207-negative (langerin), CD209-negative (DC-SIGN), and CD324-negative (E-cadherin). When activated, they are capable of producing CXCL8 (IL-8) and IL-15. Possibly a precursor of Langerhans cells or equivalent of langerin-positive dermal DCs in the mouse. synonym: "CD1a+ dermal DC" EXACT [] is_a: CL:0001006 ! dermal dendritic cell intersection_of: CL:0001006 ! dermal dendritic cell intersection_of: has_plasma_membrane_part PR:000002025 ! T-cell surface glycoprotein CD1a relationship: has_plasma_membrane_part PR:000002025 ! T-cell surface glycoprotein CD1a [Term] id: CL:0002530 name: immature CD1a-positive dermal dendritic cell namespace: cell def: "An immature CD1a-positive dermal dendritic cell is CD80-low, CD86-low, and MHCII-low." [GOC:dsd] is_a: CL:0001009 ! immature dermal dendritic cell is_a: CL:0002529 ! CD1a-positive dermal dendritic cell intersection_of: CL:0002529 ! CD1a-positive dermal dendritic cell intersection_of: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule [Term] id: CL:0002531 name: mature CD1a-positive dermal dendritic cell namespace: cell def: "A mature CD1a-positive dermal dendritic cell is CD80-high, CD83-positive, CD86-high, and MHCII-high." [GOC:dsd] is_a: CL:0001010 ! mature dermal dendritic cell is_a: CL:0002529 ! CD1a-positive dermal dendritic cell intersection_of: CL:0002529 ! CD1a-positive dermal dendritic cell intersection_of: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule intersection_of: has_plasma_membrane_part PR:000001310 ! CD83 molecule relationship: develops_from CL:0002530 ! immature CD1a-positive dermal dendritic cell relationship: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_plasma_membrane_part PR:000001310 ! CD83 molecule [Term] id: CL:0002532 name: CD16-positive myeloid dendritic cell namespace: cell def: "A myeloid dendritic cell found in the blood that is CD16-positive." [GOC:dsd, PMID:17332250] comment: Normally represent 65-75% of peripheral blood mDCs (human). They are also CD281-positive (TLR1), CD282-positive (TLR2), CD284-positive (TLR4), CD285-positive (TLR5), CD286-positive (TLR6), CD288-positive (TLR8), CD289-positive (TLR9), and CD290-positive (TLR10) by RT-PCR [PMID:17332250]. Upon TLR stimulation, these cells are potent producers of TNF-alpha, while producing little CXCL8 (IL8). synonym: "CD16+ mDC" EXACT [] synonym: "CD16-mDC" EXACT [] is_a: CL:0000782 ! myeloid dendritic cell intersection_of: CL:0000782 ! myeloid dendritic cell intersection_of: capable_of GO:0032640 ! tumor necrosis factor production intersection_of: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III relationship: capable_of GO:0032640 ! tumor necrosis factor production relationship: has_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III [Term] id: CL:0002533 name: immature CD16-positive myeloid dendritic cell namespace: cell def: "An immature CD16-positive myeloid dendritic cell is CD80-low, CD86-low, and MHCII-low." [GOC:dsd] is_a: CL:0000840 ! immature conventional dendritic cell is_a: CL:0002532 ! CD16-positive myeloid dendritic cell intersection_of: CL:0002532 ! CD16-positive myeloid dendritic cell intersection_of: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_low_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_low_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_low_plasma_membrane_amount PR:000001438 ! CD80 molecule [Term] id: CL:0002534 name: mature CD16-positive myeloid dendritic cell namespace: cell def: "A mature CD16-positive myeloid dendritic cell is CD80-high, CD83-positive, CD86-high, and MHCII-high." [GOC:dsd] is_a: CL:0000841 ! mature conventional dendritic cell is_a: CL:0002532 ! CD16-positive myeloid dendritic cell intersection_of: CL:0002532 ! CD16-positive myeloid dendritic cell intersection_of: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex intersection_of: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule intersection_of: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule intersection_of: has_plasma_membrane_part PR:000001310 ! CD83 molecule relationship: develops_from CL:0002533 ! immature CD16-positive myeloid dendritic cell relationship: has_high_plasma_membrane_amount GO:0042613 ! MHC class II protein complex relationship: has_high_plasma_membrane_amount PR:000001412 ! CD86 molecule relationship: has_high_plasma_membrane_amount PR:000001438 ! CD80 molecule relationship: has_plasma_membrane_part PR:000001310 ! CD83 molecule [Term] id: CL:0002535 name: epithelial cell of cervix namespace: cell def: "An epithelial cell of the cervix." [GOC:tfm] synonym: "cervical canal epithelial cell" EXACT [GOC:tfm] synonym: "cervical canal of uterus epithelial cell" EXACT [GOC:tfm] synonym: "cervix epithelial cell" EXACT [GOC:tfm] synonym: "cervix of uterus epithelial cell" EXACT [GOC:tfm] synonym: "epithelial cell of cervical canal" EXACT [GOC:tfm] synonym: "epithelial cell of cervical canal of uterus" EXACT [GOC:tfm] synonym: "epithelial cell of cervix of uterus" EXACT [GOC:tfm] synonym: "epithelial cell of neck of uterus" EXACT [GOC:tfm] synonym: "epithelial cell of uterine cervix" EXACT [GOC:tfm] synonym: "neck of uterus epithelial cell" EXACT [GOC:tfm] synonym: "uterine cervix epithelial cell" EXACT [GOC:tfm] is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000002 ! uterine cervix relationship: part_of UBERON:0000002 ! uterine cervix relationship: part_of UBERON:0004801 ! cervix epithelium created_by: tmeehan creation_date: 2011-02-24T08:20:08Z [Term] id: CL:0002536 name: amniotic epithelial cell namespace: cell def: "An epithelial cell that is part of the amnion." [GOC:tfm] is_a: CL:0000066 ! epithelial cell is_a: CL:0000349 ! extraembryonic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000305 ! amnion relationship: part_of UBERON:0000305 ! amnion created_by: tmeehan creation_date: 2011-02-28T12:38:01Z [Term] id: CL:0002537 name: amnion mesenchymal stem cell namespace: cell def: "A mesenchymal stem cell of the amnion membrane." [GOC:tfm, PMID:20446274, PMID:21339039] synonym: "amniotic membrane stem cell" EXACT [] is_a: CL:0000134 ! mesenchymal cell is_a: CL:0000349 ! extraembryonic cell intersection_of: CL:0000134 ! mesenchymal cell intersection_of: part_of UBERON:0000305 ! amnion relationship: part_of UBERON:0000305 ! amnion created_by: tmeehan creation_date: 2011-02-28T12:44:24Z [Term] id: CL:0002538 name: intrahepatic bile duct epithelial cell namespace: cell def: "An epithelial cell of the intrahepatic portion of the bile duct." [GOC:tfm] is_a: CL:0000069 ! branched duct epithelial cell is_a: CL:0000182 ! hepatocyte intersection_of: CL:0000069 ! branched duct epithelial cell intersection_of: part_of UBERON:0004823 ! intrahepatic bile duct epithelium relationship: part_of UBERON:0004823 ! intrahepatic bile duct epithelium created_by: tmeehan creation_date: 2011-02-28T01:20:20Z [Term] id: CL:0002539 name: aortic smooth muscle cell namespace: cell def: "A smooth muscle cell of the aorta." [GOC:tfm] xref: BTO:0004577 is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0004178 ! aorta smooth muscle tissue relationship: part_of UBERON:0004178 ! aorta smooth muscle tissue created_by: tmeehan creation_date: 2011-02-28T01:42:12Z [Term] id: CL:0002540 name: mesenchymal stem cell of the bone marrow namespace: cell def: "A mesenchymal stem cell that is part of the bone marrow." [GOC:tfm] is_a: CL:0000134 ! mesenchymal cell is_a: CL:0002092 ! bone marrow cell intersection_of: CL:0000134 ! mesenchymal cell intersection_of: part_of UBERON:0002371 ! bone marrow relationship: part_of UBERON:0002371 ! bone marrow created_by: tmeehan creation_date: 2011-02-28T01:47:47Z [Term] id: CL:0002541 name: chorionic membrane mesenchymal stem cell namespace: cell def: "A mesenchymal stem cell of the chorionic membrane." [GOC:tfm] is_a: CL:0000134 ! mesenchymal cell is_a: CL:0000349 ! extraembryonic cell intersection_of: CL:0000134 ! mesenchymal cell intersection_of: part_of UBERON:0003124 ! chorion relationship: part_of UBERON:0003124 ! chorion created_by: tmeehan creation_date: 2011-02-28T03:04:35Z [Term] id: CL:0002543 name: vein endothelial cell namespace: cell alt_id: CL:1000393 def: "An endothelial cell that is part of the vein." [GOC:tfm] synonym: "endothelial cell of vein" EXACT [] xref: FMA:62104 xref: KUPO:0001099 is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0001638 ! vein relationship: part_of UBERON:0001638 ! vein created_by: tmeehan creation_date: 2011-02-28T03:48:11Z [Term] id: CL:0002544 name: aortic endothelial cell namespace: cell def: "An arterial endothelial cell that is part of the aorta endothelium." [GOC:tfm] xref: BTO:0003245 is_a: CL:1000413 ! endothelial cell of artery created_by: tmeehan creation_date: 2011-02-28T03:54:42Z [Term] id: CL:0002545 name: thoracic aorta endothelial cell namespace: cell def: "An endothelial cell that is part of the thoracic endothelium." [GOC:tfm] is_a: CL:0002544 ! aortic endothelial cell intersection_of: CL:0002544 ! aortic endothelial cell intersection_of: part_of UBERON:0001515 ! thoracic aorta relationship: part_of UBERON:0001515 ! thoracic aorta created_by: tmeehan creation_date: 2011-02-28T03:59:09Z [Term] id: CL:0002546 name: embryonic blood vessel endothelial progenitor cell namespace: cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. is_a: CL:0000222 ! mesodermal cell is_a: CL:0002371 ! somatic cell created_by: tmeehan creation_date: 2011-02-28T04:20:39Z [Term] id: CL:0002547 name: fibroblast of the aortic adventitia namespace: cell def: "A fibroblast of the aortic adventitia." [GOC:tfm] is_a: CL:1000306 ! fibroblast of tunica adventitia of artery intersection_of: CL:1000306 ! fibroblast of tunica adventitia of artery intersection_of: part_of UBERON:0004664 ! aorta tunica adventitia relationship: part_of UBERON:0004664 ! aorta tunica adventitia created_by: tmeehan creation_date: 2011-02-28T04:43:41Z [Term] id: CL:0002548 name: cardiac fibroblast namespace: cell def: "A fibroblast that is part of the heart." [GOC:tfm] is_a: CL:0000057 ! fibroblast is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart created_by: tmeehan creation_date: 2011-02-28T04:57:44Z [Term] id: CL:0002549 name: fibroblast of choroid plexus namespace: cell def: "A fibroblast that is part of the choroid plexus." [GOC:tfm] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001886 ! choroid plexus relationship: part_of UBERON:0001886 ! choroid plexus created_by: tmeehan creation_date: 2011-02-28T05:01:39Z [Term] id: CL:0002550 name: fibroblast of the conjuctiva namespace: cell def: "A fibroblast that is part of the conjuctiva of the eye." [GOC:tfm] is_a: CL:0000057 ! fibroblast created_by: tmeehan creation_date: 2011-02-28T05:03:44Z [Term] id: CL:0002551 name: fibroblast of dermis namespace: cell is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0002067 ! dermis relationship: part_of UBERON:0002067 ! dermis created_by: tmeehan creation_date: 2011-02-28T05:05:33Z [Term] id: CL:0002552 name: fibroblast of gingiva namespace: cell is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001828 ! gingiva relationship: part_of UBERON:0001828 ! gingiva created_by: tmeehan creation_date: 2011-02-28T05:09:12Z [Term] id: CL:0002553 name: fibroblast of lung namespace: cell def: "A fibroblast that is part of lung." [GOC:tfm] xref: BTO:0000764 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung created_by: tmeehan creation_date: 2011-02-28T05:11:03Z [Term] id: CL:0002554 name: fibroblast of lymphatic vessel namespace: cell def: "A fibroblast of the lymphatic system." [GOC:tfm] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001473 ! lymphatic vessel relationship: part_of UBERON:0001473 ! lymphatic vessel created_by: tmeehan creation_date: 2011-02-28T05:16:18Z [Term] id: CL:0002555 name: fibroblast of mammary gland namespace: cell def: "A fibroblast that is part of the mammary gland." [GOC:tfm] is_a: CL:0000057 ! fibroblast created_by: tmeehan creation_date: 2011-02-28T05:18:38Z [Term] id: CL:0002556 name: fibroblast of periodontium namespace: cell def: "A fibroblast of the periodontium." [GOC:tfm] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001758 ! periodontium relationship: part_of UBERON:0001758 ! periodontium created_by: tmeehan creation_date: 2011-02-28T05:19:48Z [Term] id: CL:0002557 name: fibroblast of pulmonary artery namespace: cell def: "A fibroblast of pulmonary artery." [GOC:tfm] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002012 ! pulmonary artery relationship: part_of UBERON:0002012 ! pulmonary artery created_by: tmeehan creation_date: 2011-02-28T05:22:27Z [Term] id: CL:0002558 name: fibroblast of villous mesenchymal namespace: cell def: "A fibroblast that is part of villous mesenchymal." [GOC:tfm] is_a: CL:0000057 ! fibroblast created_by: tmeehan creation_date: 2011-02-28T05:24:28Z [Term] id: CL:0002559 name: hair follicle cell namespace: cell def: "An animal cell that is part of a hair follicle." [GOC:tfm] is_a: CL:0002371 ! somatic cell intersection_of: CL:0002371 ! somatic cell intersection_of: part_of UBERON:0002073 ! hair follicle relationship: part_of UBERON:0002073 ! hair follicle created_by: tmeehan creation_date: 2011-03-01T04:11:01Z [Term] id: CL:0002560 name: inner root sheath cell namespace: cell def: "An epithelial cell that resides in the inner root sheath of the hair follicle." [GOC:tfm] is_a: CL:0000362 ! epidermal cell is_a: CL:0002559 ! hair follicle cell intersection_of: CL:0002559 ! hair follicle cell intersection_of: part_of UBERON:0005941 ! hair inner root sheath relationship: part_of UBERON:0005941 ! hair inner root sheath created_by: tmeehan creation_date: 2011-03-01T04:27:51Z [Term] id: CL:0002561 name: outer root sheath cell namespace: cell def: "An epithelial cell that is part of the outer root sheath." [GOC:tfm] is_a: CL:0000362 ! epidermal cell is_a: CL:0002559 ! hair follicle cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0005942 ! hair outer root sheath relationship: part_of UBERON:0005942 ! hair outer root sheath created_by: tmeehan creation_date: 2011-03-01T04:29:47Z [Term] id: CL:0002562 name: hair germinal matrix cell namespace: cell def: "An epidermal cell that is part of the germinal matrix." [GOC:tfm] synonym: "trichocyte" EXACT [] is_a: CL:0000362 ! epidermal cell is_a: CL:0002559 ! hair follicle cell intersection_of: CL:0000362 ! epidermal cell intersection_of: part_of UBERON:0006004 ! hair follicle matrix region relationship: part_of UBERON:0006004 ! hair follicle matrix region created_by: tmeehan creation_date: 2011-03-01T04:31:06Z [Term] id: CL:0002563 name: intestinal epithelial cell namespace: cell def: "An epithelial cell of the intestine." [GOC:tfm] is_a: CL:0002251 ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0001277 ! intestinal epithelium created_by: tmeehan creation_date: 2011-03-01T05:18:31Z [Term] id: CL:0002564 name: nucleus pulposus cell of intervertebral disc namespace: cell def: "A connective tissue cell of the nucleus pulposus cell of intervertebral disc." [GOC:tfm] is_a: CL:0002320 ! connective tissue cell is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002242 ! nucleus pulposus relationship: part_of UBERON:0002242 ! nucleus pulposus created_by: tmeehan creation_date: 2011-03-02T02:12:23Z [Term] id: CL:0002565 name: iris pigment epithelial cell namespace: cell def: "A pigment cell located in the epithelium of the iris." [GOC:tfm] is_a: CL:0000066 ! epithelial cell is_a: CL:0000342 ! pigment cell (sensu Vertebrata) intersection_of: CL:0000342 ! pigment cell (sensu Vertebrata) intersection_of: part_of UBERON:0002506 ! iris epithelium relationship: part_of UBERON:0002506 ! iris epithelium created_by: tmeehan creation_date: 2011-03-01T05:28:52Z [Term] id: CL:0002566 name: dark melanocyte namespace: cell def: "A melanocyte that appears darker due to content or amount of melanin granules." [GOC:tfm] is_a: CL:0000148 ! melanocyte created_by: tmeehan creation_date: 2011-03-01T05:57:11Z [Term] id: CL:0002567 name: light melanocyte namespace: cell def: "A melanocyte that appears lighter in color." [GOC:tfm] is_a: CL:0000148 ! melanocyte created_by: tmeehan creation_date: 2011-03-01T05:58:23Z [Term] id: CL:0002568 name: mesenchymal stem cell of Wharton's jelly namespace: cell def: "A mesenchymal stem cell that is part of Wharton's jelly." [GOC:tfm] is_a: CL:0002569 ! mesenchymal stem cell of umbilical cord created_by: tmeehan creation_date: 2011-03-01T09:51:18Z [Term] id: CL:0002569 name: mesenchymal stem cell of umbilical cord namespace: cell def: "A mesenchymal stem cell of the umbilical cord." [GOC:tfm] is_a: CL:0000134 ! mesenchymal cell is_a: CL:0000349 ! extraembryonic cell intersection_of: CL:0000134 ! mesenchymal cell intersection_of: part_of UBERON:0003422 ! mesenchyme of umbilical cord relationship: part_of UBERON:0003422 ! mesenchyme of umbilical cord created_by: tmeehan creation_date: 2011-03-01T09:55:12Z [Term] id: CL:0002570 name: mesenchymal stem cell of adipose namespace: cell def: "A mesenchymal stem cell of adipose tissue." [GOC:tfm] is_a: CL:0000134 ! mesenchymal cell intersection_of: CL:0000134 ! mesenchymal cell intersection_of: part_of UBERON:0001013 ! adipose tissue relationship: part_of UBERON:0001013 ! adipose tissue created_by: tmeehan creation_date: 2011-03-01T09:57:17Z [Term] id: CL:0002571 name: hepatic mesenchymal stem cell namespace: cell def: "A mesenchymal stem cell of liver." [GOC:tfm] is_a: CL:0000134 ! mesenchymal cell is_a: CL:0002195 ! hepatic stem cell intersection_of: CL:0000134 ! mesenchymal cell intersection_of: part_of UBERON:0002107 ! liver relationship: part_of UBERON:0002107 ! liver created_by: tmeehan creation_date: 2011-03-01T09:58:51Z [Term] id: CL:0002572 name: vertebral mesenchymal stem cell namespace: cell def: "A mesenchymal stem cell of the vertebrae." [GOC:tfm] is_a: CL:0000134 ! mesenchymal cell is_a: CL:0001035 ! bone cell intersection_of: CL:0000134 ! mesenchymal cell intersection_of: part_of UBERON:0002412 ! vertebra relationship: part_of UBERON:0002412 ! vertebra created_by: tmeehan creation_date: 2011-03-01T10:40:27Z [Term] id: CL:0002573 name: Schwann cell namespace: cell def: "A glial cell that ensheathes axons of neuron in the peripheral nervous system and are necessary for their maintainance and function." [GOC:tfm] xref: BTO:0001220 is_a: CL:0000243 ! glial cell (sensu Vertebrata) intersection_of: CL:0000243 ! glial cell (sensu Vertebrata) intersection_of: part_of UBERON:0000010 ! peripheral nervous system relationship: part_of UBERON:0000010 ! peripheral nervous system created_by: tmeehan creation_date: 2011-03-02T01:19:27Z [Term] id: CL:0002574 name: stromal cell of pancreas namespace: cell def: "A stromal cell of the pancreas." [GOC:tfm] is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0001264 ! pancreas relationship: part_of UBERON:0001264 ! pancreas created_by: tmeehan creation_date: 2011-03-02T02:40:41Z [Term] id: CL:0002575 name: central nervous system pericyte namespace: cell def: "A pericyte of the central nervous system." [GOC:tfm] is_a: CL:0000669 ! pericyte cell created_by: tmeehan creation_date: 2011-03-02T02:54:18Z [Term] id: CL:0002576 name: perineural cell namespace: cell def: "A myofibroblast that lies in the connective tissue of the spinal cord that has a distinctly lamellar arrangement." [GO:tfm, http://en.wikipedia.org/wiki/Perineurium] is_a: CL:0000186 ! myofibroblast cell is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0000186 ! myofibroblast cell intersection_of: part_of UBERON:0000121 ! perineurium relationship: part_of UBERON:0000121 ! perineurium created_by: tmeehan creation_date: 2011-03-02T03:03:58Z [Term] id: CL:0002577 name: placental epithelial cell namespace: cell def: "An epithelial cell of the placenta." [GOC:tfm] is_a: CL:0000066 ! epithelial cell is_a: CL:0000349 ! extraembryonic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001987 ! placenta relationship: part_of UBERON:0001987 ! placenta created_by: tmeehan creation_date: 2011-03-02T03:21:30Z [Term] id: CL:0002578 name: mesenteric preadipocyte namespace: cell def: "A preadipocyte found in mesenteric tissue." [GOC:tfm] is_a: CL:0002334 ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0002095 ! mesentery relationship: part_of UBERON:0002095 ! mesentery created_by: tmeehan creation_date: 2011-03-03T04:19:40Z [Term] id: CL:0002579 name: omentum preadipocyte namespace: cell is_a: CL:0002334 ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0003688 ! omentum relationship: part_of UBERON:0003688 ! omentum created_by: tmeehan creation_date: 2011-03-03T04:19:42Z [Term] id: CL:0002580 name: preadipocyte of the breast namespace: cell def: "A preadipocyte that is part of the breast." [GOC:tfm] is_a: CL:0002334 ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0000310 ! breast relationship: part_of UBERON:0000310 ! breast created_by: tmeehan creation_date: 2011-03-03T04:19:46Z [Term] id: CL:0002581 name: perirenal preadipocyte namespace: cell is_a: CL:0002334 ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0005406 ! perirenal fat relationship: part_of UBERON:0005406 ! perirenal fat created_by: tmeehan creation_date: 2011-03-03T04:20:04Z [Term] id: CL:0002582 name: visceral preadipocyte namespace: cell def: "A preadipocyte that is part of visceral tissue." [GOC:tfm] is_a: CL:0002334 ! preadipocyte created_by: tmeehan creation_date: 2011-03-03T04:32:56Z [Term] id: CL:0002583 name: subcutaneous preadipocyte namespace: cell def: "A preadipocyte that is part of subcutaneous tissue." [GOC:tfm] is_a: CL:0002334 ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0002072 ! hypodermis relationship: part_of UBERON:0002072 ! hypodermis created_by: tmeehan creation_date: 2011-03-03T04:33:01Z [Term] id: CL:0002584 name: renal cortical epithelial cell namespace: cell def: "An epithelial cell of the kidney cortex." [GOC:tfm] xref: KUPO:0001016 is_a: CL:0002518 ! kidney epithelial cell is_a: CL:0002681 ! kidney cortical cell intersection_of: CL:0002518 ! kidney epithelial cell intersection_of: part_of UBERON:0001225 ! cortex of kidney relationship: part_of UBERON:0001225 ! cortex of kidney [Term] id: CL:0002585 name: retinal blood vessel endothelial cell namespace: cell def: "A blood vessel endothelial cell that is part of the retina." [GOC:tfm] is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina created_by: tmeehan creation_date: 2011-03-06T03:28:27Z [Term] id: CL:0002586 name: retinal pigment epithelial cell namespace: cell def: "An epithelial cell of the retinal pigmented epithelium." [GOC:tfm] xref: BTO:0004910 xref: FMA:75802 is_a: CL:0000066 ! epithelial cell is_a: CL:0000149 ! visual pigment cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001782 ! pigmented layer of retina relationship: part_of UBERON:0001782 ! pigmented layer of retina created_by: tmeehan creation_date: 2011-03-06T03:37:09Z [Term] id: CL:0002588 name: smooth muscle cell of the umbilical vein namespace: cell def: "A smooth muscle cell of the umbilical vein." [GOC:tfm] is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0002066 ! umbilical vein relationship: part_of UBERON:0002066 ! umbilical vein created_by: tmeehan creation_date: 2011-03-06T05:00:51Z [Term] id: CL:0002589 name: smooth muscle cell of the brachiocephalic vasculature namespace: cell def: "A smooth muscle cell of the bachiocephalic vasculature." [GOC:tfm] is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0001529 ! brachiocephalic artery relationship: part_of UBERON:0001529 ! brachiocephalic artery created_by: tmeehan creation_date: 2011-03-06T05:00:58Z [Term] id: CL:0002590 name: smooth muscle cell of the brain vasculature namespace: cell def: "A vascular associated smooth muscle cell of the brain vasculature." [GOC:tfm] is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0005284 ! brain vasculature relationship: part_of UBERON:0005284 ! brain vasculature created_by: tmeehan creation_date: 2011-03-06T05:01:20Z [Term] id: CL:0002591 name: smooth muscle cell of the pulmonary artery namespace: cell def: "A smooth muscle of the pulmonary artery." [GOC:tfm] xref: BTO:0003336 is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0002012 ! pulmonary artery relationship: part_of UBERON:0002012 ! pulmonary artery created_by: tmeehan creation_date: 2011-03-06T05:01:28Z [Term] id: CL:0002592 name: smooth muscle cell of the coronary artery namespace: cell def: "A smooth muscle cell of the coronary artery." [GOC:tfm] is_a: CL:0000359 ! vascular associated smooth muscle cell is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0001621 ! coronary artery relationship: part_of UBERON:0001621 ! coronary artery created_by: tmeehan creation_date: 2011-03-06T05:01:34Z [Term] id: CL:0002593 name: smooth muscle cell of the internal thoracic artery namespace: cell def: "A smooth muscle of the internal thoracic artery." [GOC:tfm] is_a: CL:0002595 ! smooth muscle cell of the subclavian artery intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0002456 ! internal thoracic artery relationship: part_of UBERON:0002456 ! internal thoracic artery created_by: tmeehan creation_date: 2011-03-06T05:01:41Z [Term] id: CL:0002594 name: smooth muscle cell of the umbilical artery namespace: cell def: "A smooth muscle cell of the umbilical artery." [GOC:tfm] is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0001310 ! umbilical artery relationship: part_of UBERON:0001310 ! umbilical artery created_by: tmeehan creation_date: 2011-03-06T05:01:48Z [Term] id: CL:0002595 name: smooth muscle cell of the subclavian artery namespace: cell def: "A smooth muscle cell of the subclavian artery." [GOC:tfm] is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0001533 ! subclavian artery relationship: part_of UBERON:0001533 ! subclavian artery created_by: tmeehan creation_date: 2011-03-06T05:01:52Z [Term] id: CL:0002596 name: smooth muscle cell of the carotid artery namespace: cell def: "Smooth muscle cell of the carotid artery." [GOC:tfm] is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0005396 ! carotid artery segment relationship: part_of UBERON:0005396 ! carotid artery segment created_by: tmeehan creation_date: 2011-03-06T05:01:56Z [Term] id: CL:0002597 name: smooth muscle cell of bladder namespace: cell def: "A smooth muscle cell of the bladder." [GC:tfm] xref: KUPO:0001122 is_a: CL:0000192 ! smooth muscle cell is_a: CL:1001319 ! bladder cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001255 ! urinary bladder created_by: tmeehan creation_date: 2011-03-06T05:43:24Z [Term] id: CL:0002598 name: bronchial smooth muscle cell namespace: cell xref: BTO:0004402 is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0002185 ! bronchus relationship: part_of UBERON:0002185 ! bronchus created_by: tmeehan creation_date: 2011-03-06T05:46:39Z [Term] id: CL:0002599 name: smooth muscle cell of the esophagus namespace: cell def: "A smooth muscle cell of the esophagus." [GOC:tfm] is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001043 ! esophagus created_by: tmeehan creation_date: 2011-03-06T05:48:17Z [Term] id: CL:0002600 name: smooth muscle cell of trachea namespace: cell def: "A smooth muscle cell of the trachea." [GOC:tfm] is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0003126 ! trachea relationship: part_of UBERON:0003126 ! trachea created_by: tmeehan creation_date: 2011-03-06T05:50:28Z [Term] id: CL:0002601 name: uterine smooth muscle cell namespace: cell def: "A smooth muscle cell of the uterus." [GOC:tfm] is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0000995 ! uterus relationship: part_of UBERON:0000995 ! uterus created_by: tmeehan creation_date: 2011-03-06T05:53:28Z [Term] id: CL:0002602 name: annulus pulposus cell namespace: cell synonym: "anulus pulposus cell" EXACT [] is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0004715 ! annulus fibrosus disci intervertebralis relationship: part_of UBERON:0004715 ! annulus fibrosus disci intervertebralis created_by: tmeehan creation_date: 2011-03-06T06:50:53Z [Term] id: CL:0002603 name: astrocyte of the cerebellum namespace: cell def: "An astrocyte of the cerebellum." [GOC:tfm] is_a: CL:0000127 ! astrocyte intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0002037 ! cerebellum relationship: part_of UBERON:0002037 ! cerebellum created_by: tmeehan creation_date: 2011-03-06T06:57:27Z [Term] id: CL:0002604 name: astrocyte of the hippocampus namespace: cell is_a: CL:0002605 ! astrocyte of the cerebral cortex intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0001954 ! Ammon's horn relationship: part_of UBERON:0001954 ! Ammon's horn created_by: tmeehan creation_date: 2011-03-06T06:57:33Z [Term] id: CL:0002605 name: astrocyte of the cerebral cortex namespace: cell def: "An astrocyte of the cerebral cortex." [GOC:tfm] is_a: CL:0000127 ! astrocyte intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0000956 ! cerebral cortex relationship: part_of UBERON:0000956 ! cerebral cortex created_by: tmeehan creation_date: 2011-03-06T06:57:36Z [Term] id: CL:0002606 name: astrocyte of the spinal cord namespace: cell def: "An astrocyte of the spinal cord." [GOC:tfm] is_a: CL:0000127 ! astrocyte intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0002240 ! spinal cord relationship: part_of UBERON:0002240 ! spinal cord created_by: tmeehan creation_date: 2011-03-06T07:11:26Z [Term] id: CL:0002607 name: migratory enteric neural crest cell namespace: cell def: "A neural crest cell that gives rise to cells of the enteric nervous system." [GOC:tfm] is_a: CL:0000333 ! migratory neural crest cell created_by: tmeehan creation_date: 2011-03-06T07:24:35Z [Term] id: CL:0002608 name: hippocampal neuron namespace: cell def: "A neuron of the hippocampus." [GOC:tfm] is_a: CL:0002609 ! neuron of cerebral cortex intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: part_of UBERON:0001954 ! Ammon's horn relationship: part_of UBERON:0001954 ! Ammon's horn created_by: tmeehan creation_date: 2011-03-06T07:31:49Z [Term] id: CL:0002609 name: neuron of cerebral cortex namespace: cell def: "A CNS neuron of the cerebral cortex." [GOC:tfm] synonym: "cortical neuron" EXACT [] xref: BTO:0004102 xref: FMA:84104 is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: part_of UBERON:0000956 ! cerebral cortex relationship: part_of UBERON:0000956 ! cerebral cortex created_by: tmeehan creation_date: 2011-03-06T07:37:08Z [Term] id: CL:0002610 name: raphe nuclei neuron namespace: cell def: "A neuron of the raphe nuclei." [GOC:tfm] is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: part_of UBERON:0004684 ! raphe nuclei relationship: part_of UBERON:0004684 ! raphe nuclei created_by: tmeehan creation_date: 2011-03-06T07:42:06Z [Term] id: CL:0002611 name: neuron of the dorsal spinal cord namespace: cell def: "A CNS neuron of the dorsal spinal cord." [GOC:tfm] is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: part_of UBERON:0002256 ! dorsal horn of spinal cord relationship: part_of UBERON:0002256 ! dorsal horn of spinal cord created_by: tmeehan creation_date: 2011-03-06T07:43:34Z [Term] id: CL:0002612 name: neuron of the ventral spinal cord namespace: cell def: "A neuron of the ventral spinal cord." [GOC:tfm] is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: part_of UBERON:0002257 ! ventral horn of spinal cord relationship: part_of UBERON:0002257 ! ventral horn of spinal cord created_by: tmeehan creation_date: 2011-03-06T07:46:03Z [Term] id: CL:0002613 name: striatum neuron namespace: cell def: "A neuron of the striatum." [GOC:tfm] is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: part_of UBERON:0002435 ! striatum relationship: part_of UBERON:0002435 ! striatum created_by: tmeehan creation_date: 2011-03-06T07:47:12Z [Term] id: CL:0002614 name: neuron of the substantia nigra namespace: cell def: "A neuron of the substantia nigra." [GOC:tfm] is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: part_of UBERON:0002038 ! substantia nigra relationship: part_of UBERON:0002038 ! substantia nigra created_by: tmeehan creation_date: 2011-03-06T07:48:42Z [Term] id: CL:0002615 name: adipocyte of omentum tissue namespace: cell def: "A fat cell that is part of omentum tissue." [GOC:tfm] synonym: "omental adipocyte" EXACT [] synonym: "omental fat cell" EXACT [] is_a: CL:0000136 ! fat cell intersection_of: CL:0000136 ! fat cell intersection_of: part_of UBERON:0003688 ! omentum relationship: part_of UBERON:0003688 ! omentum created_by: tmeehan creation_date: 2011-03-14T10:17:00Z [Term] id: CL:0002616 name: perirenal adipocyte cell namespace: cell def: "A fat cell of perirenal fat tissue." [GOC:tfm] synonym: "perirenal fat cell" EXACT [] is_a: CL:0000136 ! fat cell intersection_of: CL:0000136 ! fat cell intersection_of: part_of UBERON:0005406 ! perirenal fat relationship: part_of UBERON:0005406 ! perirenal fat created_by: tmeehan creation_date: 2011-03-14T10:17:05Z [Term] id: CL:0002617 name: adipocyte of breast namespace: cell def: "A fat cell that is part of the breast." [GOC:tfm] synonym: "fat cell of breast" EXACT [] is_a: CL:0000136 ! fat cell intersection_of: CL:0000136 ! fat cell intersection_of: part_of UBERON:0000310 ! breast relationship: part_of UBERON:0000310 ! breast created_by: tmeehan creation_date: 2011-03-14T10:17:07Z [Term] id: CL:0002618 name: endothelial cell of umbilical vein namespace: cell def: "An endothelial cell of the umbilical vein." [GOC:tfm] xref: BTO:0004296 is_a: CL:0002543 ! vein endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0002066 ! umbilical vein relationship: part_of UBERON:0002066 ! umbilical vein created_by: tmeehan creation_date: 2011-03-14T11:36:51Z [Term] id: CL:0002619 name: adult endothelial progenitor cell namespace: cell def: "An adult angioblastic cell released from the bone marrow, capable of blood circulation and participation in angiogenesis by differentiating into blood vessel endothelial cells. Their existence is controversial." [GOC:tfm, PMID:20807818, PMID:9020076] synonym: "EPC" EXACT [] is_a: CL:0000566 ! angioblastic mesenchymal cell created_by: tmeehan creation_date: 2011-03-14T12:11:18Z [Term] id: CL:0002620 name: skin fibroblast namespace: cell def: "A fibroblast of skin." [GOC:tfm] xref: BTO:0001255 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002097 ! skin of body relationship: part_of UBERON:0002097 ! skin of body created_by: tmeehan creation_date: 2011-03-14T12:31:49Z [Term] id: CL:0002621 name: gingival epithelial cell namespace: cell is_a: CL:0002251 ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001949 ! gingival epithelium relationship: part_of UBERON:0001949 ! gingival epithelium created_by: tmeehan creation_date: 2011-03-14T12:46:28Z [Term] id: CL:0002622 name: prostate stromal cell namespace: cell def: "A stromal cell of the prostate." [GOC:tfm] xref: BTO:0003972 is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0002367 ! prostate gland relationship: part_of UBERON:0002367 ! prostate gland created_by: tmeehan creation_date: 2011-03-14T02:11:10Z [Term] id: CL:0002623 name: acinar cell of salivary gland namespace: cell def: "An acinar cell of salivary gland." [GOC:tfm] is_a: CL:0000622 ! acinar cell is_a: CL:0002251 ! epithelial cell of alimentary canal intersection_of: CL:0000622 ! acinar cell intersection_of: part_of UBERON:0001044 ! salivary gland relationship: part_of UBERON:0001044 ! salivary gland created_by: tmeehan creation_date: 2011-03-14T02:22:22Z [Term] id: CL:0002624 name: paneth cell of the appendix namespace: cell def: "A paneth cell of the appendix." [GOC:tfm] is_a: CL:0000510 ! paneth cell is_a: CL:1000405 ! epithelial cell of appendix intersection_of: CL:0000510 ! paneth cell intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix created_by: tmeehan creation_date: 2011-03-15T09:38:18Z [Term] id: CL:0002625 name: seminiferous tubule epithelial cell namespace: cell def: "A cell of the seminiferous tubule epithelium." [GOC:tfm] is_a: CL:0000077 ! mesothelial cell intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0004813 ! seminiferous tubule epithelium relationship: part_of UBERON:0004813 ! seminiferous tubule epithelium created_by: tmeehan creation_date: 2011-03-15T11:59:23Z [Term] id: CL:0002626 name: immature astrocyte namespace: cell def: "An immature astrocyte." [GOC:dsd] synonym: "immature astrocytic glia" EXACT [] is_a: CL:0000127 ! astrocyte [Term] id: CL:0002627 name: mature astrocyte namespace: cell def: "A mature astrocyte that is capable of producing cytokines." [GOC:dsd, PMID:12898703, PMID:8734446] comment: Mature astrocytes are reportedly able to produce aspartate, ATP, BDNF, BMP-2a, BMP-3, CCL2, CCL3, CCL4, CCL5, CCL19, CCL20,CD40L, CNTF, CTGF, CXCL1, CXCL2, CXCL8, edn-1, aFGF, bFGF, G-CSF, glutamate, GM-CSF, IFN-alpha, IFN-beta, IFN-gamma, IGF-1, IL-1alpha, IL-1beta, IL-2, Il-4, IL-6, IL-10, IL-12, LIF, MIP-2, NGF, nitric oxide, NT3, taurine, TGF-beta, TNF-alpha, TNF-beta. synonym: "activated astrocyte" EXACT [] synonym: "mature astrocytic glia" EXACT [] is_a: CL:0000127 ! astrocyte [Term] id: CL:0002628 name: immature microglial cell namespace: cell def: "An immature microglial cell with a ramified morphology." [GOC:dsd, PMID:18396103, PMID:19461673] comment: Immature microglia are reportedly CD34-positive, CD163-negative, MHCI-negative, MHCII-negative. synonym: "immature microglia" EXACT [] synonym: "quiescent microglia" EXACT [PMID:18396103] synonym: "resting microglia" EXACT [PMID:18396103] is_a: CL:0000129 ! microglial cell [Term] id: CL:0002629 name: mature microglial cell namespace: cell def: "A mature microglial cell that has changed shape to an amoeboid morphology and is capable of cytokine production and antigen presentation." [GOC:dsd, PMID:11517395, PMID:14612429, PMID:15246020, PMID:16177057, PMID:18396103, PMID:20021364] comment: Mature microglia are reportedly CCR2-positive, CD4-positive, CD9-positive, CD11a-positive, CD11b-positive, CD11c-positive, CD13-positive, CD16-positive, CDw17-positive, CD18-positive, CD21-positive, CD26-negative, CD32-positive, CD35-positive, CD36-positive, CD40-positive, CD44-positive, CD45-positive, CD53-positive, CD54-positive, CD56-negative, CD58-positive, CD63-positive, CD64-positive, CD66-positive, CD80-positive, CD86-positive, CD87-positive, CD92-positive, CD106-positive, CD107a-positive, CD147-positive, CD155-positive, CD162-positive, CD163-positive, CD171-negative, CD200R-positive, CXCR3-positive, CX3CR1-positive, fibronectin-positive, GD3-positive, GLUT1-positive, GLUT3-negative, GLUT5-positive, MHCI-positive, MHCII-positive, P2X4-positive, RFD7-negative, RGS5-negative, alpha-SMA-negative, vimentin-positive, and vwf-negative. Mature microglia are capable of producing BDNF, CCL3, CCL5, CCL7, CCL8, CCL9, CCL19, CCL20,CD40L, CSF, CXCL1, CXCL2, CXCL4, CXCL5, CXCL8, CXCL9, CXCL10, glutamate, IL-1beta, IL-1ra, IL-3, IL-6, IL-10, IL-12, LT, MMP-2, MMP-9, NGF, nitric oxide, ROS, TGF-beta, TNF-alpha. synonym: "activated microglia" EXACT [PMID:18396103] synonym: "mature microglia" EXACT [] synonym: "reactive microglia" EXACT [PMID:18396103] is_a: CL:0000129 ! microglial cell intersection_of: CL:0000129 ! microglial cell intersection_of: capable_of GO:0001816 ! cytokine production intersection_of: capable_of GO:0002536 ! respiratory burst involved in inflammatory response intersection_of: capable_of GO:0002537 ! nitric oxide production involved in inflammatory response intersection_of: capable_of GO:0006909 ! phagocytosis intersection_of: capable_of GO:0019882 ! antigen processing and presentation relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0002536 ! respiratory burst involved in inflammatory response relationship: capable_of GO:0002537 ! nitric oxide production involved in inflammatory response relationship: capable_of GO:0006909 ! phagocytosis relationship: capable_of GO:0019882 ! antigen processing and presentation [Term] id: CL:0002630 name: actinomycete-type spore namespace: cell def: "A spore formed from bacteria in the order Actinomycetales." [GO:0034304, GOC:tfm] is_a: CL:0000520 ! prokaryotic cell created_by: tmeehan creation_date: 2011-06-16T01:01:41Z [Term] id: CL:0002631 name: epithelial cell of upper respiratory tract namespace: cell is_a: CL:0002368 ! respiratory epithelial cell intersection_of: CL:0002368 ! respiratory epithelial cell intersection_of: part_of UBERON:0001557 ! upper respiratory tract relationship: part_of UBERON:0001557 ! upper respiratory tract created_by: tmeehan creation_date: 2011-06-21T12:28:55Z [Term] id: CL:0002632 name: epithelial cell of lower respiratory tract namespace: cell is_a: CL:0002368 ! respiratory epithelial cell intersection_of: CL:0002368 ! respiratory epithelial cell intersection_of: part_of UBERON:0001558 ! lower respiratory tract relationship: part_of UBERON:0001558 ! lower respiratory tract created_by: tmeehan creation_date: 2011-06-21T12:29:31Z [Term] id: CL:0002633 name: respiratory basal cell namespace: cell def: "A basal cell in the respiratory tract." [GOC:tfm, PMID:20699479] synonym: "airway basal cell" EXACT [] synonym: "airway basal stem cell" EXACT [] is_a: CL:0000646 ! basal cell is_a: CL:0002368 ! respiratory epithelial cell created_by: tmeehan creation_date: 2011-06-21T03:11:10Z [Term] id: CL:0002634 name: epithelial cell of anal column namespace: cell def: "An epithelial cell of the anal column." [GOC:tfm] is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell created_by: tmeehan creation_date: 2011-07-08T12:11:38Z [Term] id: CL:0002635 name: nonkeratinized epithelial cell of anal column namespace: cell def: "A nonkeratinized epithelial cell of the anal canal." [GOC:tfm] xref: FMA:263146 is_a: CL:0002634 ! epithelial cell of anal column created_by: tmeehan creation_date: 2011-07-08T02:05:33Z [Term] id: CL:0002636 name: nonkeratinized epithelial cell of inferior part of anal canal namespace: cell def: "A nonkeratinized cell epithleial cell of the inferior part of the anal canal." [GOC:tfm] xref: FMA:263144 is_a: CL:0002635 ! nonkeratinized epithelial cell of anal column is_a: CL:1000438 ! epithelial cell of wall of inferior part of anal canal created_by: tmeehan creation_date: 2011-07-08T02:06:53Z [Term] id: CL:0002637 name: keratinized epithelial cell of the anal canal namespace: cell def: "An epithelial cell of the anal canal that is keratinized. This cell type is found towards the lower, rectal end of the anal canal." [GOC:tfm] is_a: CL:0000237 ! keratinizing barrier epithelial cell is_a: CL:0002634 ! epithelial cell of anal column created_by: tmeehan creation_date: 2011-07-08T02:08:40Z [Term] id: CL:0002638 name: bronchioalveolar stem cell namespace: cell def: "A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole. This cell types gives rise to alveolar cell types and Clara cells in response to lung injury. This cell type expresses markers Scgb1a1 and Sftpc." [GOC:tfm, PMID:15960971] synonym: "basal epithelial cell of bronchioalveolar duct junction" EXACT [] synonym: "BASC" EXACT [] is_a: CL:1000350 ! basal cell of epithelium of terminal bronchiole is_a: CL:1000351 ! basal cell of epithelium of respiratory bronchiole intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0001955 ! epithelium of respiratory bronchiole intersection_of: part_of UBERON:0001958 ! epithelium of terminal bronchiole relationship: part_of UBERON:0001955 ! epithelium of respiratory bronchiole relationship: part_of UBERON:0001958 ! epithelium of terminal bronchiole created_by: tmeehan creation_date: 2011-06-21T03:26:08Z [Term] id: CL:0002639 name: amniotic stem cell namespace: cell def: "An amniotic stem cell is a mesenchymalstem cell extracted from amniotic fluid. Amniotic stem cells are able to differentiate into various tissue type such as skin, cartilage, cardiac tissue, nerves, muscle, and bone" [GOC:tfm, PMID:20942606] comment: Not clear to me if amniotic stem cell is a different cell type from amnion mesenchymal stem cells. They are treated as distinct in the literature as isolations methods are different, so I will keep them as separate terms for now. is_a: CL:0000134 ! mesenchymal cell is_a: CL:0002323 ! amniocyte created_by: tmeehan creation_date: 2011-06-21T03:55:39Z [Term] id: CL:0002640 name: amniotic epithelial stem cell namespace: cell def: "An epithelial fate stem cell derived form the amnion membrane." [GOC:tfm, PMID:20446274] is_a: CL:0000036 ! epithelial fate stem cell created_by: tmeehan creation_date: 2011-06-21T04:06:17Z [Term] id: CL:0002641 name: epithelial cell of esophageal gland proper namespace: cell def: "An epithelial cell of the esophageal gland proper." [GOC:tfm] xref: FMA:256141 is_a: CL:0002657 ! glandular cell of esophagus created_by: tmeehan creation_date: 2011-07-08T02:16:51Z [Term] id: CL:0002642 name: epithelial cell of esophageal cardiac gland namespace: cell def: "An epithelial cell of the esophageal cardiac gland that occurs both in the proximal and distal esophagusm, within the lamina propia." [GOC:tfm, http://web.mac.com/wjkrause/iWeb/Histology/Blog/E3FA5916-1AA9-4885-B579-5051838D98CB.html] xref: FMA:256143 is_a: CL:0002657 ! glandular cell of esophagus created_by: tmeehan creation_date: 2011-07-08T02:16:54Z [Term] id: CL:0002643 name: nonkeratinized cell of stratum corneum of esophageal epithelium namespace: cell def: "An epithelial cell of stratum corneum of esophageal epithelium that lacks keratin." [GOC:tfm] xref: FMA:263148 is_a: CL:0002654 ! epithelial cell of stratum corneum of esophageal epithelium created_by: tmeehan creation_date: 2011-07-08T02:22:09Z [Term] id: CL:0002644 name: endo-epithelial cell of tympanic part of viscerocranial mucosa namespace: cell def: "An endothelial cell of viscerocranial mucosa that is part of the tympanic region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70628 is_a: CL:0002261 ! endothelial cell of viscerocranial mucosa created_by: tmeehan creation_date: 2011-07-08T02:25:44Z [Term] id: CL:0002645 name: endo-epithelial cell of pharyngotympanic part of viscerocranial mucosa namespace: cell def: "An endocranial viscerocranial mucosa cell that is part of viscerocranial mucosa." [GOC:tfm] xref: FMA:70629 is_a: CL:0002261 ! endothelial cell of viscerocranial mucosa created_by: tmeehan creation_date: 2011-07-08T02:25:46Z [Term] id: CL:0002646 name: epithelial cell of buccal part of viscerocranial mucosa namespace: cell def: "An ecto-epithelial cell of the buccal region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70577 is_a: CL:0002283 ! ecto-epithelial cell of viscerocranial mucosa created_by: tmeehan creation_date: 2011-07-08T02:34:12Z [Term] id: CL:0002647 name: epithelial cell of anterior palatal part of viscerocranial mucosa namespace: cell def: "An ecto-epithelial cell of the palatal region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70580 is_a: CL:0002283 ! ecto-epithelial cell of viscerocranial mucosa created_by: tmeehan creation_date: 2011-07-08T02:34:14Z [Term] id: CL:0002648 name: epithelial cell of nasal part of viscerocranial mucosa namespace: cell def: "An ecto-epithelial cell of the nasal region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70554 is_a: CL:0002283 ! ecto-epithelial cell of viscerocranial mucosa created_by: tmeehan creation_date: 2011-07-08T02:36:06Z [Term] id: CL:0002649 name: epithelial cell of gingival part of viscerocranial mucosa namespace: cell def: "An ecto-epithelial cell of the gingival region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70579 is_a: CL:0002283 ! ecto-epithelial cell of viscerocranial mucosa created_by: tmeehan creation_date: 2011-07-08T02:36:11Z [Term] id: CL:0002650 name: epithelial cell of paranasal sinus part of viscerocranial mucosa namespace: cell def: "An ecto-epithelial cell of the paranasal region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70578 is_a: CL:0002283 ! ecto-epithelial cell of viscerocranial mucosa created_by: tmeehan creation_date: 2011-07-08T02:38:18Z [Term] id: CL:0002651 name: endothelial cell of venous sinus of spleen namespace: cell def: "An endothelial cell that is part of the venous sinus of spleen. This endothelial cell has an elongated, spindle-shaped, flattened morphology that is parallel to long axis of sinus. This cell type rests on a basement membrane interrupted by numerous narrow slits." [GOC:tfm] synonym: "stave cell" EXACT [FMA:62817] xref: FMA:72140 is_a: CL:0002262 ! endothelial cell of sinusoid created_by: tmeehan creation_date: 2011-07-08T03:06:49Z [Term] id: CL:0002652 name: endothelial cell of high endothelial venule namespace: cell def: "A venule endothelial cell that is cubodial, expresses leukocyte-specific receptors, and allows for passage of lymphocytes into bloodstream." [GOC:tfm, PMID:20726857] comment: Markers expressed on HEV include: MAdCAM-1,PNAd (sulfated and glycosylated molecules, i.e. GlyCAM-1, CD34, endomucin, nepmucin), ICAM-1, ICAM-2,Fuc-TVII, beta 3GlcNAcT-3, GlcNAc6ST2,CCL21, CCL19, CXCL13, CXCL12, Autotaxin, DARC, angiomodulin, LRHG. synonym: "endothelial cell of postcapillary venule of lymph node" EXACT [] synonym: "HEV cell" EXACT [] xref: FMA:67759 is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:1000414 ! endothelial cell of venule created_by: tmeehan creation_date: 2011-07-08T03:14:10Z [Term] id: CL:0002653 name: squamous endothelial cell namespace: cell def: "A endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells." [GOC:tfm] is_a: CL:0000076 ! squamous epithelial cell is_a: CL:1000414 ! endothelial cell of venule created_by: tmeehan creation_date: 2011-07-08T03:31:25Z [Term] id: CL:0002654 name: epithelial cell of stratum corneum of esophageal epithelium namespace: cell def: "An epithelial cell of stratum corneum of esophageal epithelium." [GOC:tfm] xref: FMA:70733 is_a: CL:0002252 ! epithelial cell of esophagus created_by: tmeehan creation_date: 2011-07-08T03:46:35Z [Term] id: CL:0002655 name: epithelial cell of stratum spinosum of esophageal epithelium namespace: cell def: "An epithelial cell of stratum spinosum of esophageal epithelium." [GOC:tfm] xref: FMA:70732 is_a: CL:0002252 ! epithelial cell of esophagus created_by: tmeehan creation_date: 2011-07-08T03:48:26Z [Term] id: CL:0002656 name: glandular cell of endometrium namespace: cell def: "A glandular epithelial cell of the endometrium." [GOC:tfm] xref: FMA:86489 is_a: CL:0000150 ! glandular epithelial cell created_by: tmeehan creation_date: 2011-07-08T03:54:08Z [Term] id: CL:0002657 name: glandular cell of esophagus namespace: cell def: "A glandular epithelial cell of the endometrium." [GOC:tfm] xref: FMA:86489 xref: FMA:86548 is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0002252 ! epithelial cell of esophagus created_by: tmeehan creation_date: 2011-07-08T03:55:57Z [Term] id: CL:0002658 name: glandular cell of the large intestine namespace: cell def: "A glandular epithelial cell of the large intestine." [GOC:tfm] xref: FMA:87194 is_a: CL:0000150 ! glandular epithelial cell created_by: tmeehan creation_date: 2011-07-08T04:03:01Z [Term] id: CL:0002659 name: glandular cell of stomach namespace: cell def: "A glandular epithelial cell that is part of the stomach." [GOC:tfm] xref: FMA:86554 is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0002178 ! epithelial cell of stomach intersection_of: CL:0000150 ! glandular epithelial cell intersection_of: part_of UBERON:0000945 ! stomach relationship: part_of UBERON:0000945 ! stomach created_by: tmeehan creation_date: 2011-07-11T01:20:35Z [Term] id: CL:0002660 name: luminal cell of acinus of lactiferous gland namespace: cell def: "A luminal epithelial cell of mammary gland located in acinus of structure." [GOC:tfm] comment: Consider if synonymous with mammary alveolar cell CL:0002325. Some use this term to refer to the non-lactating cell type that gives rise to the lactating cell type. xref: FMA:74505 is_a: CL:0002326 ! luminal epithelial cell of mammary gland created_by: tmeehan creation_date: 2011-07-11T01:44:31Z [Term] id: CL:0002661 name: luminal cell of lactiferous terminal ductal lobular unit namespace: cell def: "A luminal cell of terminal ducts, i.e.e the terminal branch of a lactiferous duct which alveolar cells drain into." [GOC:tfm] xref: FMA:87168 is_a: CL:0002662 ! luminal cell of lactiferous duct created_by: tmeehan creation_date: 2011-07-11T01:44:33Z [Term] id: CL:0002662 name: luminal cell of lactiferous duct namespace: cell def: "A luminal epithelial cell of the lactiferous duct. This cuboidal epithelial cell expresses keratin-18 and is estrogen-receptor alpha positive." [GOC:tfm, PMID:19022771] xref: FMA:74504 xref: FMA:74505 is_a: CL:0002326 ! luminal epithelial cell of mammary gland created_by: tmeehan creation_date: 2011-07-11T01:44:48Z [Term] id: CL:0002663 name: myocardial endocrine cell of atrium namespace: cell def: "A myocardial endocrine cell that is part of the atrium." [GOC:tfm] xref: FMA:83389 is_a: CL:0002074 ! myocardial endocrine cell created_by: tmeehan creation_date: 2011-07-11T02:45:39Z [Term] id: CL:0002664 name: cardioblast namespace: cell def: "A stem cell that can give rise to multiple cell types (i.e. smooth muscle, endothelial) in the developing heart." [GOC:tfm, PMID:19745164] comment: Discrepancy in develops from origins prevents me from making the assertion that cardioblasts give rise to all instances of cardiocytes as we state cardiac muscle cells develop from cardiac myoblast, which in turn develop from muscle stem cell. is_a: CL:0000048 ! multi fate stem cell created_by: tmeehan creation_date: 2011-07-11T03:15:38Z [Term] id: CL:0002665 name: otic fibrocyte namespace: cell def: "A fibrocyte of the cochlea that has specialized structural and molecular adaptions." [GOC:tfm, PMID:18353863] is_a: CL:0000135 ! fibrocyte is_a: CL:0001035 ! bone cell relationship: part_of UBERON:0006725 ! spiral ligament created_by: tmeehan creation_date: 2011-07-11T03:35:01Z [Term] id: CL:0002666 name: type 2 otic fibrocyte namespace: cell def: "An otic fibrocyte that underlies the spiral prominence and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph." [GOC:tfm, PMID:18353863] synonym: "type II otic fibrocyte" EXACT [] synonym: "type II spiral ligament fibrocyte" EXACT [MP:0004488] is_a: CL:0002665 ! otic fibrocyte created_by: tmeehan creation_date: 2011-07-11T03:40:40Z [Term] id: CL:0002667 name: type 5 otic fibrocyte namespace: cell def: "An otic fibrocyte that resides above the stria vasularis and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph." [GOC:tfm, PMID:18353863] synonym: "type V otic fibrocyte" EXACT [] synonym: "type V spiral ligament fibrocyte" EXACT [] is_a: CL:0002665 ! otic fibrocyte created_by: tmeehan creation_date: 2011-07-11T03:40:42Z [Term] id: CL:0002668 name: type 4 otic fibrocyte namespace: cell def: "An otic fibrocyte that is lateral to the basilar membrane and anchoris it to the lateral wall." [GOC:tfm, PMID:18353863] synonym: "type IV otic fibrocyte" EXACT [] synonym: "type IV spiral ligament fibrocyte" EXACT [MP:0004490] is_a: CL:0002665 ! otic fibrocyte created_by: tmeehan creation_date: 2011-07-11T03:40:46Z [Term] id: CL:0002669 name: type 3 otic fibrocyte namespace: cell def: "An otic fibrocyte that lines the otic capsule." [GOC:tfm, PMID:18353863] synonym: "type III otic fibrocyte" EXACT [] synonym: "type III spiral ligament fibrocyte" EXACT [MP:0004489] is_a: CL:0002665 ! otic fibrocyte created_by: tmeehan creation_date: 2011-07-11T03:40:50Z [Term] id: CL:0002670 name: type 1 otic fibrocyte namespace: cell def: "An otic fibrocyte that underlies the stria vascularis and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph." [GOC:tfm, PMID:18353863] synonym: "type I otic fibrocyte" EXACT [] synonym: "type I spiral ligament fibrocyte" EXACT [MP:0004487] is_a: CL:0002665 ! otic fibrocyte created_by: tmeehan creation_date: 2011-07-11T03:39:27Z [Term] id: CL:0002671 name: endothelial stalk cell namespace: cell def: "An endothelial stalk cell is a specialized endothelial cell that follows behind the tip cell of an angiogenic sprout." [GOC:tfm, PMID:21521739] is_a: CL:0000071 ! blood vessel endothelial cell created_by: tmeehan creation_date: 2011-08-16T01:49:32Z [Term] id: CL:0002672 name: retinal progenitor cell namespace: cell def: "A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells." [GOC:tfm, PMID:20959166, PMID:21148186] is_a: CL:0000048 ! multi fate stem cell relationship: develops_from CL:0000133 ! neurectodermal cell created_by: tmeehan creation_date: 2011-08-16T02:38:01Z [Term] id: CL:0002673 name: tongue muscle cell namespace: cell def: "A skeletal muscle cell that is part of the tongue." [GOC:tfm, PMID:18816858] is_a: CL:0000188 ! skeletal muscle cell created_by: tmeehan creation_date: 2011-08-16T03:10:02Z [Term] id: CL:0002674 name: H minus namespace: cell def: "A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus." [GOC:tfm] synonym: "H- cell" EXACT [] is_a: CL:0000521 ! fungal cell created_by: tmeehan creation_date: 2011-08-16T03:20:53Z [Term] id: CL:0002675 name: H plus namespace: cell def: "A S. pombe cell type determined by mat1-Pc and mat1-Pi on the mat1 locus." [GOC:tfm] is_a: CL:0000521 ! fungal cell created_by: tmeehan creation_date: 2011-08-16T03:20:58Z [Term] id: CL:0002676 name: neural crest derived neuroblast namespace: cell def: "A neuroblast derived from a neural crest cell." [GOC:tfm, PMID:17407019] is_a: CL:0000337 ! neuroblast (sensu Vertebrata) relationship: develops_from CL:0000333 ! migratory neural crest cell created_by: tmeehan creation_date: 2011-08-22T09:24:15Z [Term] id: CL:0002677 name: naive regulatory T cell namespace: cell def: "A regulatory T cell that has not encountered antigen." [GOC:tfm] comment: This cell type has been described as CD45RA-negative, but this doesn't fit with our current definition of naive T cell. is_a: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell is_a: CL:0000898 ! naive T cell created_by: tmeehan creation_date: 2011-08-25T03:17:21Z [Term] id: CL:0002678 name: memory regulatory T cell namespace: cell def: "A CD4-positive, CD25-positive alpha-beta regulatory T cell that has encountered antigen." [GOC:tfm, PMID:21739668] comment: Cell has been described as being CD45RA-positive in human, but this doesn't fit with our current definition memory T cell. is_a: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell is_a: CL:0000813 ! memory T cell created_by: tmeehan creation_date: 2011-08-25T03:17:34Z [Term] id: CL:0002679 name: natural helper lymphocyte namespace: cell def: "A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13" [GOC:tfm, PMID:20023630] is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor intersection_of: has_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 intersection_of: lacks_plasma_membrane_part GO:0042105 ! alpha-beta T cell receptor complex intersection_of: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule intersection_of: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M intersection_of: lacks_plasma_membrane_part PR:000001013 ! integrin alpha-X intersection_of: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon intersection_of: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain intersection_of: lacks_plasma_membrane_part PR:000001874 ! KLRB1-like protein intersection_of: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 relationship: has_plasma_membrane_part PR:000002065 ! mast/stem cell growth factor receptor relationship: has_plasma_membrane_part PR:000002979 ! lymphocyte antigen 6A-2/6E-1 relationship: lacks_plasma_membrane_part GO:0042105 ! alpha-beta T cell receptor complex relationship: lacks_plasma_membrane_part PR:000001002 ! CD19 molecule relationship: lacks_plasma_membrane_part PR:000001012 ! integrin alpha-M relationship: lacks_plasma_membrane_part PR:000001013 ! integrin alpha-X relationship: lacks_plasma_membrane_part PR:000001020 ! CD3 epsilon relationship: lacks_plasma_membrane_part PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain relationship: lacks_plasma_membrane_part PR:000001874 ! KLRB1-like protein relationship: lacks_plasma_membrane_part PR:000002981 ! lymphocyte antigen 76 created_by: tmeehan creation_date: 2011-08-29T10:08:02Z [Term] id: CL:0002680 name: PP cell of intestine namespace: cell def: "A PP cell found in intestine." [GOC:tfm, PMID:2420136, PMID:728970] is_a: CL:0000696 ! PP cell is_a: CL:1001516 ! intestinal enteroendocrine cell intersection_of: CL:0000696 ! PP cell intersection_of: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0000160 ! intestine created_by: tmeehan creation_date: 2011-09-27T11:59:01Z [Term] id: CL:0002681 name: kidney cortical cell namespace: cell is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0001225 ! cortex of kidney relationship: part_of UBERON:0001225 ! cortex of kidney created_by: terryh creation_date: 2011-10-25T03:49:41Z [Term] id: CL:0005000 name: spinal cord interneuron namespace: cell def: "A CNS interneuron located in the spinal cord." [CL:CVS] comment: Is_a interneuron, part_of UBERON:0002240. is_a: CL:0000402 ! CNS interneuron [Term] id: CL:0005001 name: iridoblast namespace: cell def: "A non-terminally differentiated cell that originates from the neural crest and differentiates into an iridophore." [CL:CVS] comment: Derived from UBERON:0002342 neural crest. is_a: CL:0000055 ! non-terminally differentiated cell relationship: develops_from CL:0000333 ! migratory neural crest cell [Term] id: CL:0005002 name: xanthoblast namespace: cell def: "A non-terminally differentiated cell that differentiates into a xanthophore." [CL:CVS] is_a: CL:0000055 ! non-terminally differentiated cell relationship: develops_from CL:0000333 ! migratory neural crest cell [Term] id: CL:0005003 name: leucoblast namespace: cell def: "A non-terminally differentiated cell that originates from the neural crest and differentiates into a leucophore." [CL:CVS] is_a: CL:0000055 ! non-terminally differentiated cell relationship: develops_from CL:0000333 ! migratory neural crest cell [Term] id: CL:0005004 name: pigment erythroblast namespace: cell def: "A non-terminally differentiated cell that originates from the neural crest and differentiates into an erythrophore." [CL:CVS] is_a: CL:0000055 ! non-terminally differentiated cell relationship: develops_from CL:0000333 ! migratory neural crest cell [Term] id: CL:0005005 name: cyanoblast namespace: cell def: "A non-terminally differentiated cell that originates from the neural crest and differentiates into a cyanophore." [CL:CVS] is_a: CL:0000055 ! non-terminally differentiated cell relationship: develops_from CL:0000333 ! migratory neural crest cell [Term] id: CL:0005006 name: ionocyte namespace: cell def: "Specialized epithelial cells involved in the maintenance of osmotic homeostasis. They are characterized by abundant mitochondria and ion transporters. In amniotes, they are present in the renal system. In freshwater fish, ionocytes in the skin and gills help maintain osmotic homeostasis by absorbing salt from the external environment." [PMID:17555741, PMID:19268451] is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell [Term] id: CL:0005007 name: Kolmer-Agduhr neuron namespace: cell def: "Kolmer-Agduhr neurons are ciliated GABAergic neurons that contact the central canal of the spinal cord and have ipsilateral ascending axons." [PMID:18680739] synonym: "KA cell" EXACT [] synonym: "KA interneuron" EXACT [PMID:15539490] synonym: "KA neuron" EXACT [PMID:9634146] synonym: "Kolmer-Agduhr cell" EXACT [] is_a: CL:0000617 ! GABAergic neuron is_a: CL:0005000 ! spinal cord interneuron [Term] id: CL:0005008 name: macular hair cell namespace: cell def: "An auditory hair cell located in the macula that is sensitive to auditory stimuli." [GO:cvs] is_a: CL:0000202 ! auditory hair cell [Term] id: CL:0005009 name: renal principal cell namespace: cell def: "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the cells apical membrane is regulated by aldosterone and vasopressin. In mammals these cells are located in the renal collecting ducts." [CL:CVS] is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002518 ! kidney epithelial cell [Term] id: CL:0005010 name: renal intercalated cell namespace: cell def: "A cuboidal epithelial cell of the kidney that regulates acid/base balance." [CL:CVS] synonym: "intercalated cell" EXACT [] xref: FMA:86560 is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002078 ! meso-epithelial cell is_a: CL:0002518 ! kidney epithelial cell [Term] id: CL:0005011 name: renal alpha-intercalated cell namespace: cell def: "A cuboidal epithelial cell of the kidney which secretes acid and reabsorbs base to regulate acid/base balance." [CL:CVS] is_a: CL:0005010 ! renal intercalated cell [Term] id: CL:0005012 name: multi-ciliated epithelial cell namespace: cell def: "A ciliated epithelial cell with many cilium." [CL:CVS] is_a: CL:0000064 ! ciliated cell is_a: CL:0000066 ! epithelial cell relationship: has_plasma_membrane_part GO:0005929 ! cilium [Term] id: CL:0005013 name: single ciliated epithelial cell namespace: cell def: "A ciliated epithelial cell with a single cilium." [CL:CVS] is_a: CL:0000064 ! ciliated cell is_a: CL:0000066 ! epithelial cell relationship: has_plasma_membrane_part GO:0005929 ! cilium [Term] id: CL:0005014 name: auditory epithelial support cell namespace: cell def: "A non-sensory cell that extends from the basement membrane to the apical surface of the auditory epithelium and provides support for auditory hair cells." [CL:CVS, GOC:tfm] is_a: CL:0000630 ! supportive cell is_a: CL:0000710 ! neurecto-epithelial cell is_a: CL:0002491 ! auditory epithelial cell [Term] id: CL:0005015 name: inner phalangeal cell namespace: cell def: "An auditory epithelial support cell that surrounds the nerve fibers and synapses of the auditory inner hair cells." [CL:CVS] xref: FMA:79801 is_a: CL:0002165 ! phalangeal cell [Term] id: CL:0005016 name: apical cell namespace: cell def: "Obsolete. Use PO:0030007 from Plant Ontology instead. The apical cell is the upper cell formed after the first division of a plant zygote." [TAIR:TB] comment: replaced_by: PO:0030007 is_obsolete: true [Term] id: CL:0005017 name: plant basal cell namespace: cell def: "Obsolete. Use PO:0002002 from Plant Ontology instead. The lower cell formed after the first division of a plant zygote." [TAIR:TB] comment: replaced_by: PO:0002002 is_obsolete: true [Term] id: CL:0005018 name: ghrelin secreting cell namespace: cell def: "A cell that secretes ghrelin, the peptide hormone that stimulates hunger." [CL:curator] is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0005019 name: pancreatic epsilon cell namespace: cell def: "Ghrelin secreting cells found in the found in the exocrine pancreas." [PMID:14970313] comment: In mammals the endocrine pancreas is called the Islets of Langerhans. synonym: "pancreatic e cell" EXACT [] is_a: CL:0005018 ! ghrelin secreting cell [Term] id: CL:0005020 name: lymphangioblast namespace: cell def: "Lymphatic progenitor cells. Usually express Prox1, or prox1b." [CL:CVS] is_a: CL:0000048 ! multi fate stem cell intersection_of: CL:0000048 ! multi fate stem cell intersection_of: derives_from UBERON:0004536 ! lymph vasculature relationship: derives_from UBERON:0004536 ! lymph vasculature created_by: Ceri creation_date: 2012-01-12T04:44:34Z [Term] id: CL:0005021 name: mesenchymal lymphangioblast namespace: cell def: "Mesenchymal derived lymphatic progenitor cells that give rise to the superficial lymphatics." [PMID:15624319, PMID:18430230] is_a: CL:0000134 ! mesenchymal cell is_a: CL:0005020 ! lymphangioblast created_by: Ceri creation_date: 2012-01-12T05:01:22Z [Term] id: CL:0005022 name: vascular lymphangioblast namespace: cell def: "Lymphatic progenitor cells, derived from the veins, that give rise to lymphatic endothelial cells." [CL:CVS] is_a: CL:0005020 ! lymphangioblast intersection_of: CL:0005020 ! lymphangioblast intersection_of: derives_from UBERON:0001638 ! vein relationship: derives_from UBERON:0001638 ! vein created_by: Ceri creation_date: 2012-01-12T05:21:09Z [Term] id: CL:0007000 name: preameloblast namespace: cell def: "Skeletogenic cell that has the potential to develop into an ameloblast. Located in the inner enamel epithelium, these cells elongate, their nuclei shift distally (away from the dental papilla), and their cytoplasm becomes filled with organelles needed for synthesis and secretion of enamel proteins." [GO_REF:0000034, PMCID:PMC2737325] comment: unsure of neural crest contribution. In VSAO we have develops_from CL:0000008 is_a: CL:0000055 ! non-terminally differentiated cell relationship: adjacent_to UBERON:0001763 ! odontogenic papilla relationship: develops_from CL:0002077 ! ecto-epithelial cell relationship: part_of UBERON:0005176 ! tooth enamel organ created_by: haendel creation_date: 2012-06-15T01:27:01Z [Term] id: CL:0007001 name: skeletogenic cell namespace: cell def: "Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized)." [GO_REF:0000034] comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000003 ! native cell created_by: haendel creation_date: 2012-06-15T02:51:27Z [Term] id: CL:0007002 name: precementoblast namespace: cell def: "Skeletogenic cell that has the potential to develop into a cementoblast." [GO_REF:0000034] is_a: CL:0000055 ! non-terminally differentiated cell relationship: part_of UBERON:0005176 ! tooth enamel organ created_by: haendel creation_date: 2012-06-15T04:37:13Z [Term] id: CL:0007003 name: preodontoblast namespace: cell def: "Skeletogenic cell that has the potential to form an odontoblast, deposits predentine, and arises from a cranial neural crest cell." [GO_REF:0000034] is_a: CL:0000055 ! non-terminally differentiated cell relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0005176 ! tooth enamel organ created_by: haendel creation_date: 2012-06-15T05:15:11Z [Term] id: CL:0007004 name: premigratory neural crest cell namespace: cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] is_a: CL:0000003 ! native cell relationship: part_of UBERON:0002342 ! neural crest created_by: haendel creation_date: 2012-06-27T08:27:35Z [Term] id: CL:0007005 name: notochordal cell namespace: cell def: "Cell that is part of the notochord." [GO_REF:0000034] comment: NOTE: TO DO, notochord development still needs work. is_a: CL:0000003 ! native cell relationship: develops_from CL:0007006 ! chordamesodermal cell relationship: part_of UBERON:0002328 ! notochord created_by: haendel creation_date: 2012-06-27T08:47:31Z [Term] id: CL:0007006 name: chordamesodermal cell namespace: cell def: "Mesodermal cell that is axially located and gives rise to the cells of the notochord." [GO_REF:0000034] is_a: CL:0000222 ! mesodermal cell relationship: part_of UBERON:0004880 ! chordamesoderm created_by: haendel creation_date: 2012-06-27T08:52:41Z [Term] id: CL:0007007 name: notochordal sheath cell namespace: cell def: "Notochordal cell that is part of the outer epithelium of the notochord and surrounds the vacuolated notochord cells." [CL:MAH] is_a: CL:0007005 ! notochordal cell created_by: haendel creation_date: 2012-06-27T09:26:37Z [Term] id: CL:0007008 name: notochordal vacuole cell namespace: cell def: "Notochordal cell that is inner portion of the notochord and becomes vacuolated as development proceeds." [CL:MAH] synonym: "chordablast" EXACT [GO_REF:0000034] synonym: "chordoblast" EXACT [PMID:14574572] is_a: CL:0007005 ! notochordal cell created_by: haendel creation_date: 2012-06-27T09:29:30Z [Term] id: CL:0007009 name: prechondroblast namespace: cell def: "Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells." [GO_REF:0000034] is_a: CL:0000055 ! non-terminally differentiated cell created_by: haendel creation_date: 2012-06-27T10:44:01Z [Term] id: CL:0007010 name: preosteoblast namespace: cell def: "Skeletogenic cell that has the potential to transform into an osteoblast, and develops from neural crest or mesodermal cells." [GO_REF:0000034] synonym: "osteoprogenitor cell" EXACT [] is_a: CL:0000055 ! non-terminally differentiated cell relationship: develops_from CL:0000222 ! mesodermal cell relationship: develops_from CL:0000333 ! migratory neural crest cell relationship: part_of UBERON:0008883 ! osteoid created_by: haendel creation_date: 2012-06-27T10:57:21Z [Term] id: CL:0007011 name: enteric neuron namespace: cell def: "Neuron that is part of the enteric nervous system." [CL:MAH] is_a: CL:0000029 ! neuron neural crest derived relationship: develops_from CL:0002607 ! migratory enteric neural crest cell relationship: part_of UBERON:0002005 ! enteric nervous system created_by: haendel creation_date: 2012-06-28T08:20:31Z [Term] id: CL:0007012 name: non-terminally differentiated odontoblast def: "Odontoblast that non-terminally differentiated, located in the odontogenic papilla and dentine tissue, and transforms from a odontoblast cell." [GO_REF:0000034, PSPUB:0000170] is_a: CL:0000060 ! odontoblast [Term] id: CL:0007013 name: terminally differentiated odontoblast def: "Odontoblast that is terminally differentiated and derived from an odontogenic papilla and associated with dentine." [GO_REF:0000034] is_a: CL:0000060 ! odontoblast [Term] id: CL:0007014 name: cell line cell namespace: cell def: "A cultured cell that has been passaged at least one time in culture." [ReO:mhb] comment: Covers cells actively being cultured or stored in a quiescent state for future use. synonym: "passaged cultured cell" EXACT [] is_a: CL:0000010 ! cultured cell created_by: haendel creation_date: 2012-11-28T11:54:59Z [Term] id: CL:0007015 name: mortal cell line cell namespace: cell def: "A cell line cell that is expected to be capable of replicating a limited number of times in culture before undergoing senescence. Mortal cell line cells cannot be propagated indefinitely (as immortal cell line cells can)." [ReO:mhb] comment: Covers cells actively being cultured or stored in a quiescent state for future use. synonym: "finite cell line cell" EXACT [] synonym: "primary cell line cell" RELATED [] is_a: CL:0007014 ! cell line cell created_by: haendel creation_date: 2012-11-28T11:56:20Z [Term] id: CL:0007016 name: adaxial cell namespace: cell def: "Muscle precursor cell that is adjacent to the notochord and part of the presomitic mesoderm." [PMID:8951054] comment: In teleosts, adaxial cells give rise to slow muscle myoblasts. is_a: CL:0000680 ! muscle precursor cell relationship: part_of UBERON:0003059 ! presomitic mesoderm created_by: haendel creation_date: 2012-12-30T12:43:15Z [Term] id: CL:0009000 name: sensory neuron of spinal nerve def: "A sensory neuron of the spinal nerve that senses body position and sends information about how much the muscle is stretched to the spinal cord." [GOC:nv, GOC:pr] synonym: "spinal sensory neuron" EXACT [] is_a: CL:0000101 ! sensory neuron intersection_of: CL:0000101 ! sensory neuron intersection_of: part_of UBERON:0001780 ! spinal nerve relationship: part_of UBERON:0001780 ! spinal nerve [Term] id: CL:0011000 name: dorsal horn interneuron def: "A CNS interneuron located in the dorsal horn of the spinal cord." [GOC:nv] synonym: "dorsal spinal cord interneuron" RELATED [] is_a: CL:0002611 ! neuron of the dorsal spinal cord is_a: CL:0005000 ! spinal cord interneuron intersection_of: CL:0000099 ! interneuron intersection_of: part_of UBERON:0002256 ! dorsal horn of spinal cord relationship: part_of UBERON:0002256 ! dorsal horn of spinal cord [Term] id: CL:0011001 name: spinal cord motor neuron def: "A motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement." [GOC:nv] is_a: CL:0000100 ! motor neuron intersection_of: CL:0000100 ! motor neuron intersection_of: part_of UBERON:0002240 ! spinal cord relationship: part_of UBERON:0002240 ! spinal cord [Term] id: CL:0011002 name: lateral motor column neuron def: "A motor neuron that is generated only on limb levels and send axons into the limb mesenchyme." [GOC:nv] comment: Need to MIREOT in 'spinal cord lateral column' from Uberon is_a: CL:0011001 ! spinal cord motor neuron [Term] id: CL:0011003 name: magnocellular neurosecretory cell def: "A neurosecretory neuron residing mainly in the hypothalamic supraoptic and paraventricular nuclei and in a number of smaller accessory cell groups between these two nuclei, that secretes the hormones oxytocin and vasopressin." [GOC:nv, MP:0009467] synonym: "magnocellular neuron" EXACT [] is_a: CL:0000381 ! neurosecretory neuron relationship: part_of UBERON:0001930 ! paraventricular nucleus of hypothalamus relationship: part_of UBERON:0006568 ! hypothalamic nucleus [Term] id: CL:0011004 name: lens fiber cell def: "A vetebrate lens cell that is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye." [GO:0070307, GOC:nv] synonym: "lens fibre cell" EXACT [] is_a: CL:0002222 ! vertebrate lens cell [Term] id: CL:0011005 name: GABAergic interneuron def: "An interneuron that uses GABA as a vesicular neurotransmitter." [GOC:nv] is_a: CL:0000617 ! GABAergic neuron [Term] id: CL:0011006 name: lugaro cell def: "An inhibitory GABAergic interneuron found in the cerebellar cortex." [GOC:nv] is_a: CL:0011005 ! GABAergic interneuron relationship: has_part UBERON:0002037 ! cerebellum [Term] id: CL:1000082 name: stretch receptor cell namespace: cell is_a: CL:0000006 ! neuronal receptor cell [Term] id: CL:1000083 name: stratified keratinized epithelial stem cell namespace: cell is_a: CL:0000357 ! stratified epithelial stem cell [Term] id: CL:1000085 name: stratified non keratinized epithelial stem cell namespace: cell is_a: CL:0000357 ! stratified epithelial stem cell [Term] id: CL:1000191 name: pillar cell namespace: cell def: "A rod-like cell in the inner ear, having their heads joined and their bases on the basilar membrane widely separated so as to form a spiral tunnel known as the tunnel of Corti." [GOC:tfm, PMID:12417662] synonym: "cochlear pillar cell" RELATED [] synonym: "pillar cell of cochlea" EXACT [] synonym: "pillar cell of corti" EXACT [] synonym: "rod cell of Corti" EXACT [] xref: FMA:75722 is_a: CL:0002490 ! organ of Corti supporting cell [Term] id: CL:1000274 name: trophectodermal cell namespace: cell synonym: "trophectoderm cell" EXACT [] is_a: CL:0000349 ! extraembryonic cell [Term] id: CL:1000275 name: smooth muscle cell of small intestine namespace: cell def: "A smooth muscle cell that is part of the small intestine." [GOC:tfm] synonym: "non-striated muscle fiber of small intestine" EXACT [FMA:15050] xref: FMA:15050 is_a: CL:0002504 ! enteric smooth muscle cell intersection_of: CL:0002504 ! enteric smooth muscle cell intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0002108 ! small intestine [Term] id: CL:1000276 name: smooth muscle fiber of duodenum namespace: cell def: "A smooth muscle cell that is part of the duodenum." [GOC:tfm] synonym: "non-striated muscle fiber of duodenum" EXACT [FMA:15058] xref: FMA:15058 is_a: CL:1000275 ! smooth muscle cell of small intestine intersection_of: CL:1000275 ! smooth muscle cell of small intestine intersection_of: part_of UBERON:0002114 ! duodenum relationship: part_of UBERON:0002114 ! duodenum [Term] id: CL:1000277 name: smooth muscle fiber of jejunum namespace: cell def: "A smooth muscle cell that is part of the jejunum." [GOC:tfm] synonym: "non-striated muscle fiber of jejunum" EXACT [FMA:15062] xref: FMA:15062 is_a: CL:1000275 ! smooth muscle cell of small intestine intersection_of: CL:1000275 ! smooth muscle cell of small intestine intersection_of: part_of UBERON:0002115 ! jejunum relationship: part_of UBERON:0002115 ! jejunum [Term] id: CL:1000278 name: smooth muscle fiber of ileum namespace: cell def: "A smooth muscle cell that is part of the ileum." [GOC:tfm] synonym: "non-striated muscle fiber of ileum" EXACT [FMA:15066] xref: FMA:15066 is_a: CL:1000275 ! smooth muscle cell of small intestine intersection_of: CL:1000275 ! smooth muscle cell of small intestine intersection_of: part_of UBERON:0002116 ! ileum relationship: part_of UBERON:0002116 ! ileum [Term] id: CL:1000279 name: smooth muscle cell of large intestine namespace: cell def: "A smooth muscle cell that is part of the large intestine." [GOC:tfm] synonym: "non-striated muscle fiber of large intestine" EXACT [FMA:15653] xref: FMA:15653 is_a: CL:0002504 ! enteric smooth muscle cell intersection_of: CL:0002504 ! enteric smooth muscle cell intersection_of: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0000059 ! large intestine [Term] id: CL:1000280 name: smooth muscle cell of colon namespace: cell def: "A smooth muscle cell that is part of the colon." [GOC:tfm] synonym: "non-striated muscle fiber of colon" EXACT [FMA:15663] xref: FMA:15663 is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0002504 ! enteric smooth muscle cell intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon [Term] id: CL:1000281 name: smooth muscle cell of cecum namespace: cell def: "A smooth muscle cell that is part of the cecum." [GOC:tfm] synonym: "non-striated muscle fiber of cecum" EXACT [FMA:15681] synonym: "smooth muscle fiber of cecum" EXACT [] xref: FMA:15681 is_a: CL:1000280 ! smooth muscle cell of colon intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001153 ! caecum relationship: part_of UBERON:0001153 ! caecum [Term] id: CL:1000282 name: smooth muscle fiber of ascending colon namespace: cell def: "A smooth muscle cell that is part of the ascending colon." [GOC:tfm] synonym: "non-striated muscle fiber of ascending colon" EXACT [FMA:17518] xref: FMA:17518 is_a: CL:1000280 ! smooth muscle cell of colon intersection_of: CL:1000280 ! smooth muscle cell of colon intersection_of: part_of UBERON:0001156 ! ascending colon relationship: part_of UBERON:0001156 ! ascending colon [Term] id: CL:1000283 name: smooth muscle fiber of transverse colon namespace: cell def: "A smooth muscle cell that is part of the transverse colon." [GOC:tfm] synonym: "non-striated muscle fiber of transverse colon" EXACT [FMA:17519] xref: FMA:17519 is_a: CL:1000280 ! smooth muscle cell of colon intersection_of: CL:1000280 ! smooth muscle cell of colon intersection_of: part_of UBERON:0001157 ! transverse colon relationship: part_of UBERON:0001157 ! transverse colon [Term] id: CL:1000284 name: smooth muscle fiber of descending colon namespace: cell def: "A smooth muscle cell that is part of the descending colon." [GOC:tfm] synonym: "non-striated muscle fiber of descending colon" EXACT [FMA:17520] xref: FMA:17520 is_a: CL:1000280 ! smooth muscle cell of colon intersection_of: CL:1000280 ! smooth muscle cell of colon intersection_of: part_of UBERON:0001158 ! descending colon relationship: part_of UBERON:0001158 ! descending colon [Term] id: CL:1000285 name: smooth muscle cell of sigmoid colon namespace: cell def: "A smooth muscle cell that is part of the sigmoid colon." [GOC:tfm] synonym: "non-striated muscle fiber of sigmoid colon" EXACT [FMA:17521] xref: FMA:17521 is_a: CL:1000280 ! smooth muscle cell of colon intersection_of: CL:1000280 ! smooth muscle cell of colon intersection_of: part_of UBERON:0001159 ! sigmoid colon relationship: part_of UBERON:0001159 ! sigmoid colon [Term] id: CL:1000286 name: smooth muscle cell of rectum namespace: cell def: "A smooth muscle cell that is part of the rectum." [GOC:tfm] synonym: "non-striated muscle fiber of rectum" EXACT [FMA:17522] synonym: "smooth muscle fiber of rectum" EXACT [] xref: FMA:17522 is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001052 ! rectum relationship: part_of UBERON:0001052 ! rectum [Term] id: CL:1000287 name: myocyte of anterior internodal tract namespace: cell def: "A muscle cell that is part of the anterior internodal tract." [GOC:tfm] xref: FMA:223276 is_a: CL:0002096 ! internodal tract myocyte [Term] id: CL:1000288 name: myocyte of atrial branch of anterior internodal tract namespace: cell def: "A muscle cell that is part of the atrial branch of anterior internodal tract." [GOC:tfm] xref: FMA:223277 is_a: CL:0002096 ! internodal tract myocyte [Term] id: CL:1000289 name: myocyte of atrial septal branch of anterior internodal tract namespace: cell def: "A muscle cell that is part of the atrial septal branch of anterior internodal tract." [GOC:tfm] xref: FMA:223278 is_a: CL:0002096 ! internodal tract myocyte [Term] id: CL:1000290 name: myocyte of middle internodal tract namespace: cell def: "A muscle cell that is part of the middle internodal tract." [GOC:tfm] xref: FMA:223279 is_a: CL:0002096 ! internodal tract myocyte [Term] id: CL:1000291 name: myocyte of posterior internodal tract namespace: cell def: "A muscle cell that is part of the posterior internodal tract." [GOC:tfm] xref: FMA:223280 is_a: CL:0002096 ! internodal tract myocyte [Term] id: CL:1000296 name: epithelial cell of urethra namespace: cell def: "An epithelial cell that is part of the urethra." [GOC:tfm] xref: FMA:256165 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell is_a: CL:1001320 ! urethra cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000057 ! urethra relationship: part_of UBERON:0000057 ! urethra [Term] id: CL:1000298 name: mesothelial cell of dura mater namespace: cell def: "A mesothelial cell that is part of the dura mater." [GOC:tfm] synonym: "squamous mesothelial cell of dura mater" EXACT [FMA:256516] xref: FMA:256516 is_a: CL:0000077 ! mesothelial cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0002363 ! dura mater relationship: part_of UBERON:0002363 ! dura mater [Term] id: CL:1000299 name: fibroblast of connective tissue of prostate namespace: cell def: "A fibroblast that is part of the connective tissue of prostate." [GOC:tfm] xref: FMA:261271 is_a: CL:0000057 ! fibroblast relationship: part_of UBERON:0002367 ! prostate gland [Term] id: CL:1000300 name: fibroblast of outer membrane of prostatic capsule namespace: cell def: "A fibroblast that is part of the outer membrane of prostatic capsule." [GOC:tfm] xref: FMA:261273 is_a: CL:0000057 ! fibroblast relationship: part_of UBERON:0002367 ! prostate gland [Term] id: CL:1000301 name: fibroblast of subepithelial connective tissue of prostatic gland namespace: cell def: "A fibroblast that is part of the subepithelial connective tissue of prostatic gland." [GOC:tfm] xref: FMA:261275 is_a: CL:0000057 ! fibroblast relationship: part_of UBERON:0002367 ! prostate gland [Term] id: CL:1000302 name: fibroblast of papillary layer of dermis namespace: cell def: "A fibroblast that is part of the papillary layer of dermis." [GOC:tfm] xref: FMA:261277 is_a: CL:0002551 ! fibroblast of dermis intersection_of: CL:0002551 ! fibroblast of dermis intersection_of: part_of UBERON:0001992 ! papillary layer of dermis relationship: part_of UBERON:0001992 ! papillary layer of dermis [Term] id: CL:1000303 name: fibroblast of areolar connective tissue namespace: cell def: "A fibroblast that is part of the areolar connective tissue." [GOC:tfm] xref: FMA:261279 is_a: CL:0000057 ! fibroblast relationship: part_of UBERON:0006815 ! areolar connective tissue [Term] id: CL:1000304 name: fibroblast of connective tissue of nonglandular part of prostate namespace: cell def: "A fibroblast that is part of the connective tissue of nonglandular part of prostate." [GOC:tfm] xref: FMA:261281 is_a: CL:0000057 ! fibroblast relationship: part_of UBERON:0002367 ! prostate gland [Term] id: CL:1000305 name: fibroblast of connective tissue of glandular part of prostate namespace: cell def: "A fibroblast that is part of the connective tissue of glandular part of prostate." [GOC:tfm] xref: FMA:261283 is_a: CL:0000057 ! fibroblast relationship: part_of UBERON:0002367 ! prostate gland [Term] id: CL:1000306 name: fibroblast of tunica adventitia of artery namespace: cell def: "A fibroblast that is part of the tunica adventitia of artery." [GOC:tfm] xref: FMA:261285 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0005734 ! tunica adventitia of blood vessel relationship: part_of UBERON:0005734 ! tunica adventitia of blood vessel [Term] id: CL:1000307 name: fibroblast of dense regular elastic tissue namespace: cell def: "A fibroblast that is part of the dense regular elastic tissue." [GOC:tfm] xref: FMA:261287 is_a: CL:0000057 ! fibroblast relationship: part_of UBERON:0002521 ! elastic tissue [Term] id: CL:1000308 name: fibrocyte of adventitia of ureter namespace: cell def: "A fibrocyte that is part of the adventitia of ureter." [GOC:tfm] xref: FMA:261289 is_a: CL:0000135 ! fibrocyte is_a: CL:1000708 ! ureter adventitial cell intersection_of: CL:0000135 ! fibrocyte intersection_of: part_of UBERON:0001252 ! adventitia of ureter relationship: part_of UBERON:0001252 ! adventitia of ureter [Term] id: CL:1000309 name: epicardial adipocyte namespace: cell def: "A fat cell that is part of the epicardial fat." [GOC:tfm] synonym: "adipocyte of epicardial fat" EXACT [FMA:261293] synonym: "epicardial fat cell" EXACT [FMA:261293] xref: FMA:261293 is_a: CL:0000136 ! fat cell is_a: CL:0002494 ! cardiocyte relationship: part_of UBERON:0002348 ! epicardium [Term] id: CL:1000310 name: adipocyte of epicardial fat of right ventricle namespace: cell def: "A fat cell that is part of the epicardial fat of right ventricle." [GOC:tfm] synonym: "epicardial adipocyte of right ventricle" EXACT [FMA:261297] synonym: "epicardial fat cell of right ventricle" EXACT [FMA:261297] xref: FMA:261297 is_a: CL:0000136 ! fat cell is_a: CL:0002494 ! cardiocyte relationship: part_of UBERON:0002080 ! heart right ventricle [Term] id: CL:1000311 name: adipocyte of epicardial fat of left ventricle namespace: cell def: "A fat cell that is part of the epicardial fat of left ventricle." [GOC:tfm] synonym: "epicardial adipocyte of left ventricle" EXACT [FMA:261300] synonym: "epicardial fat cell of left ventricle" EXACT [FMA:261300] xref: FMA:261300 is_a: CL:0000136 ! fat cell is_a: CL:0002494 ! cardiocyte relationship: part_of UBERON:0002084 ! heart left ventricle [Term] id: CL:1000312 name: bronchial goblet cell namespace: cell def: "A goblet cell that is part of the epithelium of bronchus." [GOC:tfm] synonym: "goblet cell of epithelium of bronchus" EXACT [FMA:263032] xref: FMA:263032 is_a: CL:0000160 ! goblet cell is_a: CL:0002328 ! bronchial epithelial cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0002031 ! epithelium of bronchus relationship: part_of UBERON:0002031 ! epithelium of bronchus [Term] id: CL:1000313 name: gastric goblet cell namespace: cell def: "A goblet cell that is part of the epithelium of stomach." [GOC:tfm] synonym: "goblet cell of epithelium of stomach" EXACT [FMA:263035] xref: FMA:263035 is_a: CL:0000160 ! goblet cell is_a: CL:0002180 ! mucous cell of stomach intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001276 ! epithelium of stomach relationship: part_of UBERON:0001276 ! epithelium of stomach [Term] id: CL:1000314 name: goblet cell of epithelium of gastric cardiac gland namespace: cell def: "A goblet cell that is part of the epithelium of gastric cardiac gland." [GOC:tfm] xref: FMA:263038 is_a: CL:1000313 ! gastric goblet cell relationship: part_of UBERON:0008859 ! cardiac gastric gland [Term] id: CL:1000315 name: goblet cell of epithelium of principal gastric gland namespace: cell def: "A goblet cell that is part of the epithelium of principal gastric gland." [GOC:tfm] xref: FMA:263040 is_a: CL:1000313 ! gastric goblet cell [Term] id: CL:1000316 name: goblet cell of epithelium of small intestine namespace: cell def: "A goblet cell that is part of the epithelium of small intestine." [GOC:tfm] xref: FMA:263042 is_a: CL:1000343 ! paneth cell of epithelium of small intestine is_a: CL:1000495 ! goblet cell of small intestine intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001902 ! epithelium of small intestine relationship: part_of UBERON:0001902 ! epithelium of small intestine [Term] id: CL:1000317 name: goblet cell of epithelium of intestinal villus namespace: cell def: "A goblet cell that is part of the epithelium of intestinal villus." [GOC:tfm] xref: FMA:263046 is_a: CL:0000160 ! goblet cell is_a: CL:0000510 ! paneth cell relationship: part_of UBERON:0001213 ! intestinal villus [Term] id: CL:1000318 name: goblet cell of epithelium of crypt of lieberkuhn of small intestine namespace: cell def: "A goblet cell that is part of the epithelium of crypt of lieberkuhn of small intestine." [GOC:tfm] xref: FMA:263050 is_a: CL:1000316 ! goblet cell of epithelium of small intestine relationship: part_of UBERON:0001983 ! crypt of Lieberkuhn [Term] id: CL:1000319 name: goblet cell of epithelium proper of small intestine namespace: cell def: "A goblet cell that is part of the epithelium proper of small intestine." [GOC:tfm] xref: FMA:263052 is_a: CL:1000316 ! goblet cell of epithelium of small intestine [Term] id: CL:1000320 name: goblet cell of epithelium of large intestine namespace: cell def: "A goblet cell that is part of the epithelium of large intestine." [GOC:tfm] xref: FMA:263054 is_a: CL:0000160 ! goblet cell is_a: CL:0000510 ! paneth cell is_a: CL:0002253 ! epithelial cell of large intestine is_a: CL:0002658 ! glandular cell of the large intestine intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001278 ! epithelium of large intestine relationship: part_of UBERON:0001278 ! epithelium of large intestine [Term] id: CL:1000321 name: goblet cell of epithelium of crypt of lieberkuhn of large intestine namespace: cell def: "A goblet cell that is part of the epithelium of crypt of lieberkuhn of large intestine." [GOC:tfm] xref: FMA:263056 is_a: CL:1000320 ! goblet cell of epithelium of large intestine relationship: part_of UBERON:0001983 ! crypt of Lieberkuhn [Term] id: CL:1000322 name: pancreatic goblet cell namespace: cell def: "A goblet cell that is part of the epithelium of pancreatic duct." [GOC:tfm] synonym: "goblet cell of epithelium of pancreatic duct" EXACT [FMA:263058] xref: FMA:263058 is_a: CL:0000069 ! branched duct epithelial cell is_a: CL:0000160 ! goblet cell [Term] id: CL:1000323 name: goblet cell of epithelium of pyloric gland namespace: cell def: "A goblet cell that is part of the epithelium of pyloric gland." [GOC:tfm] xref: FMA:263061 is_a: CL:1000313 ! gastric goblet cell relationship: part_of UBERON:0008861 ! pyloric gastric gland [Term] id: CL:1000324 name: goblet cell of epithelium proper of duodenum namespace: cell def: "A goblet cell that is part of the epithelium proper of duodenum." [GOC:tfm] xref: FMA:263063 is_a: CL:1000495 ! goblet cell of small intestine relationship: part_of UBERON:0002114 ! duodenum [Term] id: CL:1000325 name: goblet cell of epithelium proper of jejunum namespace: cell def: "A goblet cell that is part of the epithelium proper of jejunum." [GOC:tfm] xref: FMA:263065 is_a: CL:1000495 ! goblet cell of small intestine relationship: part_of UBERON:0002115 ! jejunum [Term] id: CL:1000326 name: goblet cell of epithelium proper of ileum namespace: cell def: "A goblet cell that is part of the epithelium proper of ileum." [GOC:tfm] xref: FMA:263067 is_a: CL:1000495 ! goblet cell of small intestine relationship: part_of UBERON:0002116 ! ileum [Term] id: CL:1000327 name: goblet cell of epithelium proper of appendix namespace: cell def: "A goblet cell that is part of the epithelium proper of appendix." [GOC:tfm] xref: FMA:263069 is_a: CL:0000160 ! goblet cell is_a: CL:0002624 ! paneth cell of the appendix relationship: part_of UBERON:0001154 ! vermiform appendix [Term] id: CL:1000328 name: goblet cell of epithelium proper of large intestine namespace: cell def: "A goblet cell that is part of the epithelium proper of large intestine." [GOC:tfm] xref: FMA:263071 is_a: CL:1000320 ! goblet cell of epithelium of large intestine [Term] id: CL:1000329 name: tracheal goblet cell namespace: cell def: "A goblet cell that is part of the epithelium of trachea." [GOC:tfm] synonym: "goblet cell of epithelium of trachea" EXACT [FMA:263075] xref: FMA:263075 is_a: CL:0000160 ! goblet cell is_a: CL:0000307 ! tracheal epithelial cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001901 ! epithelium of trachea relationship: part_of UBERON:0001901 ! epithelium of trachea [Term] id: CL:1000330 name: serous cell of epithelium of trachea namespace: cell def: "A serous secreting cell that is part of the epithelium of trachea." [GOC:tfm] xref: FMA:263078 is_a: CL:0000313 ! serous secreting cell intersection_of: CL:0000313 ! serous secreting cell intersection_of: part_of UBERON:0001901 ! epithelium of trachea relationship: part_of UBERON:0001901 ! epithelium of trachea [Term] id: CL:1000331 name: serous cell of epithelium of bronchus namespace: cell def: "A serous secreting cell that is part of the epithelium of bronchus." [GOC:tfm] xref: FMA:263080 is_a: CL:0000313 ! serous secreting cell intersection_of: CL:0000313 ! serous secreting cell intersection_of: part_of UBERON:0002031 ! epithelium of bronchus relationship: part_of UBERON:0002031 ! epithelium of bronchus [Term] id: CL:1000332 name: serous cell of epithelium of terminal bronchiole namespace: cell def: "A serous secreting cell that is part of the epithelium of terminal bronchiole." [GOC:tfm] xref: FMA:263082 is_a: CL:1000333 ! serous cell of epithelium of lobular bronchiole intersection_of: CL:0000313 ! serous secreting cell intersection_of: part_of UBERON:0001958 ! epithelium of terminal bronchiole relationship: part_of UBERON:0001958 ! epithelium of terminal bronchiole [Term] id: CL:1000333 name: serous cell of epithelium of lobular bronchiole namespace: cell def: "A serous secreting cell that is part of the epithelium of bronchiole." [GOC:tfm] xref: FMA:263084 is_a: CL:1000331 ! serous cell of epithelium of bronchus intersection_of: CL:0000313 ! serous secreting cell intersection_of: part_of UBERON:0002051 ! epithelium of bronchiole relationship: part_of UBERON:0002051 ! epithelium of bronchiole [Term] id: CL:1000334 name: enterocyte of epithelium of small intestine namespace: cell def: "An enterocyte that is part of the epithelium of small intestine." [GOC:tfm] xref: FMA:263086 is_a: CL:0000584 ! enterocyte is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:0001902 ! epithelium of small intestine relationship: part_of UBERON:0001902 ! epithelium of small intestine [Term] id: CL:1000335 name: enterocyte of epithelium of intestinal villus namespace: cell def: "An enterocyte that is part of the epithelium of intestinal villus." [GOC:tfm] xref: FMA:263088 is_a: CL:0000584 ! enterocyte relationship: part_of UBERON:0001213 ! intestinal villus [Term] id: CL:1000337 name: enterocyte of epithelium of duodenal gland namespace: cell def: "An enterocyte that is part of the epithelium of duodenal gland." [GOC:tfm] xref: FMA:263092 is_a: CL:1000334 ! enterocyte of epithelium of small intestine relationship: part_of UBERON:0001212 ! duodenal gland [Term] id: CL:1000338 name: enterocyte of epithelium of crypt of lieberkuhn of small intestine namespace: cell def: "An enterocyte that is part of the epithelium of crypt of lieberkuhn of small intestine." [GOC:tfm] xref: FMA:263094 is_a: CL:1000334 ! enterocyte of epithelium of small intestine relationship: part_of UBERON:0001983 ! crypt of Lieberkuhn [Term] id: CL:1000339 name: enterocyte of epithelium proper of small intestine namespace: cell def: "An enterocyte that is part of the epithelium proper of small intestine." [GOC:tfm] xref: FMA:263096 is_a: CL:1000334 ! enterocyte of epithelium of small intestine [Term] id: CL:1000340 name: enterocyte of epithelium proper of duodenum namespace: cell def: "An enterocyte that is part of the epithelium proper of duodenum." [GOC:tfm] xref: FMA:263098 is_a: CL:1000337 ! enterocyte of epithelium of duodenal gland is_a: CL:1000339 ! enterocyte of epithelium proper of small intestine [Term] id: CL:1000341 name: enterocyte of epithelium proper of jejunum namespace: cell def: "An enterocyte that is part of the epithelium proper of jejunum." [GOC:tfm] xref: FMA:263100 is_a: CL:1000339 ! enterocyte of epithelium proper of small intestine [Term] id: CL:1000342 name: enterocyte of epithelium proper of ileum namespace: cell def: "An enterocyte that is part of the epithelium proper of ileum." [GOC:tfm] xref: FMA:263102 is_a: CL:1000339 ! enterocyte of epithelium proper of small intestine [Term] id: CL:1000343 name: paneth cell of epithelium of small intestine namespace: cell def: "A paneth cell that is part of the epithelium of small intestine." [GOC:tfm] xref: FMA:263104 is_a: CL:0000510 ! paneth cell is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0000510 ! paneth cell intersection_of: part_of UBERON:0001902 ! epithelium of small intestine relationship: part_of UBERON:0001902 ! epithelium of small intestine [Term] id: CL:1000344 name: paneth cell of epithelium proper of small intestine namespace: cell def: "A Paneth cell that is part of the epithelium proper of small intestine." [GOC:tfm] xref: FMA:263106 is_a: CL:1000343 ! paneth cell of epithelium of small intestine [Term] id: CL:1000345 name: paneth cell of epithelium of crypt of lieberkuhn of small intestine namespace: cell def: "A Paneth cell that is part of the epithelium of crypt of lieberkuhn of small intestine." [GOC:tfm] xref: FMA:263108 is_a: CL:1000343 ! paneth cell of epithelium of small intestine relationship: part_of UBERON:0001983 ! crypt of Lieberkuhn [Term] id: CL:1000346 name: vacuolar absorptive cell of epithelium proper of large intestine namespace: cell alt_id: CL:1000336 def: "MERGED DEFINITION: TARGET DEFINITION: A columnar cell of the colon that is part of the epithelium proper of large intestine. SOURCE DEFINITION: An enterocyte that is part of the epithelium proper of large intestine." [GOC:tfm] synonym: "enterocyte of epithelium proper of large intestine" EXACT [] xref: FMA:263090 xref: FMA:263112 is_a: CL:0002071 ! enterocyte of epithelium of large intestine [Term] id: CL:1000347 name: vacuolar absorptive cell of epithelium of colon namespace: cell def: "A columnar cell of the colon that is part of the colonic epithelium." [GOC:tfm] xref: FMA:263114 is_a: CL:0002071 ! enterocyte of epithelium of large intestine intersection_of: CL:0002071 ! enterocyte of epithelium of large intestine intersection_of: part_of UBERON:0000397 ! colonic epithelium relationship: part_of UBERON:0000397 ! colonic epithelium [Term] id: CL:1000348 name: basal cell of epithelium of trachea namespace: cell def: "A basal cell that is part of the epithelium of trachea." [GOC:tfm] xref: FMA:263118 is_a: CL:0000307 ! tracheal epithelial cell is_a: CL:0002633 ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0001901 ! epithelium of trachea relationship: part_of UBERON:0001901 ! epithelium of trachea [Term] id: CL:1000349 name: basal cell of epithelium of bronchus namespace: cell alt_id: CL:0002331 def: "A basal cell found in the bronchus epithelium." [GOC:tfm] synonym: "basal cell of bronchus" EXACT [] xref: FMA:263120 is_a: CL:0002328 ! bronchial epithelial cell is_a: CL:0002329 ! basal epithelial cell of tracheobronchial tree is_a: CL:0002633 ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0002031 ! epithelium of bronchus relationship: part_of UBERON:0002031 ! epithelium of bronchus [Term] id: CL:1000350 name: basal cell of epithelium of terminal bronchiole namespace: cell def: "A basal cell that is part of the epithelium of terminal bronchiole." [GOC:tfm] xref: FMA:263122 is_a: CL:1000352 ! basal cell of epithelium of lobular bronchiole intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0001958 ! epithelium of terminal bronchiole relationship: part_of UBERON:0001958 ! epithelium of terminal bronchiole [Term] id: CL:1000351 name: basal cell of epithelium of respiratory bronchiole namespace: cell def: "A basal cell that is part of the epithelium of respiratory bronchiole." [GOC:tfm] xref: FMA:263124 is_a: CL:1000352 ! basal cell of epithelium of lobular bronchiole intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0001955 ! epithelium of respiratory bronchiole relationship: part_of UBERON:0001955 ! epithelium of respiratory bronchiole [Term] id: CL:1000352 name: basal cell of epithelium of lobular bronchiole namespace: cell def: "A basal cell that is part of the epithelium of bronchiole." [GOC:tfm] xref: FMA:263126 is_a: CL:1000349 ! basal cell of epithelium of bronchus intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0002051 ! epithelium of bronchiole relationship: part_of UBERON:0002051 ! epithelium of bronchiole [Term] id: CL:1000353 name: microfold cell of epithelium of small intestine namespace: cell def: "A M cell that is part of the epithelium of small intestine." [GOC:tfm] xref: FMA:263128 is_a: CL:0000682 ! M cell is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0000682 ! M cell intersection_of: part_of UBERON:0001902 ! epithelium of small intestine relationship: part_of UBERON:0001902 ! epithelium of small intestine [Term] id: CL:1000354 name: microfold cell of epithelium of intestinal villus namespace: cell def: "A M cell that is part of the epithelium of intestinal villus." [GOC:tfm] xref: FMA:263130 is_a: CL:0000682 ! M cell is_a: CL:0002563 ! intestinal epithelial cell relationship: part_of UBERON:0001213 ! intestinal villus [Term] id: CL:1000355 name: microfold cell of epithelium proper of small intestine namespace: cell def: "A M cell that is part of the epithelium proper of small intestine." [GOC:tfm] xref: FMA:263132 is_a: CL:1000353 ! microfold cell of epithelium of small intestine [Term] id: CL:1000356 name: microfold cell of epithelium proper of duodenum namespace: cell def: "A M cell that is part of the epithelium proper of duodenum." [GOC:tfm] xref: FMA:263134 is_a: CL:0000682 ! M cell [Term] id: CL:1000357 name: microfold cell of epithelium proper of jejunum namespace: cell def: "A M cell that is part of the epithelium proper of jejunum." [GOC:tfm] xref: FMA:263136 is_a: CL:0000682 ! M cell [Term] id: CL:1000358 name: microfold cell of epithelium proper of ileum namespace: cell def: "A M cell that is part of the epithelium proper of ileum." [GOC:tfm] xref: FMA:263138 is_a: CL:0000682 ! M cell [Term] id: CL:1000359 name: microfold cell of epithelium proper of appendix namespace: cell def: "A M cell that is part of the epithelium proper of appendix." [GOC:tfm] xref: FMA:263140 is_a: CL:0000682 ! M cell [Term] id: CL:1000360 name: microfold cell of epithelium proper of large intestine namespace: cell def: "A M cell that is part of the epithelium proper of large intestine." [GOC:tfm] xref: FMA:263142 is_a: CL:0000682 ! M cell is_a: CL:0002253 ! epithelial cell of large intestine [Term] id: CL:1000361 name: transitional myocyte of interatrial septum namespace: cell def: "A transitional myocyte that is part of the interatrial septum." [GOC:tfm] xref: FMA:263152 is_a: CL:0002073 ! transitional myocyte intersection_of: CL:0002073 ! transitional myocyte intersection_of: part_of UBERON:0002085 ! interatrial septum relationship: part_of UBERON:0002085 ! interatrial septum [Term] id: CL:1000362 name: transitional myocyte of interventricular septum namespace: cell def: "A transitional myocyte that is part of the interventricular septum." [GOC:tfm] xref: FMA:263154 is_a: CL:0002073 ! transitional myocyte intersection_of: CL:0002073 ! transitional myocyte intersection_of: part_of UBERON:0002094 ! interventricular septum relationship: part_of UBERON:0002094 ! interventricular septum [Term] id: CL:1000363 name: transitional myocyte of atrial branch of anterior internodal tract namespace: cell def: "A transitional myocyte that is part of the atrial branch of anterior internodal tract." [GOC:tfm] xref: FMA:263156 is_a: CL:1000480 ! transitional myocyte of internodal tract [Term] id: CL:1000364 name: transitional myocyte of anterior internodal tract namespace: cell def: "A transitional myocyte that is part of the anterior internodal tract." [GOC:tfm] xref: FMA:263158 is_a: CL:1000480 ! transitional myocyte of internodal tract [Term] id: CL:1000365 name: transitional myocyte of atrial septal branch of anterior internodal tract namespace: cell def: "A transitional myocyte that is part of the atrial septal branch of anterior internodal tract." [GOC:tfm] xref: FMA:263160 is_a: CL:1000480 ! transitional myocyte of internodal tract [Term] id: CL:1000366 name: transitional myocyte of middle internodal tract namespace: cell def: "A transitional myocyte that is part of the middle internodal tract." [GOC:tfm] xref: FMA:263162 is_a: CL:1000480 ! transitional myocyte of internodal tract [Term] id: CL:1000367 name: transitional myocyte of posterior internodal tract namespace: cell def: "A transitional myocyte that is part of the posterior internodal tract." [GOC:tfm] xref: FMA:263164 is_a: CL:1000480 ! transitional myocyte of internodal tract [Term] id: CL:1000368 name: transitional myocyte of anterior division of left branch of atrioventricular bundle namespace: cell def: "A transitional myocyte that is part of the anterior division of left branch of atrioventricular bundle." [GOC:tfm] xref: FMA:263166 is_a: CL:1000481 ! transitional myocyte of atrioventricular bundle relationship: part_of UBERON:0005986 ! left branch of atrioventricular bundle [Term] id: CL:1000369 name: transitional myocyte of septal division of left branch of atrioventricular bundle namespace: cell def: "A transitional myocyte that is part of the septal division of left branch of atrioventricular bundle." [GOC:tfm] xref: FMA:263168 is_a: CL:1000481 ! transitional myocyte of atrioventricular bundle relationship: part_of UBERON:0005986 ! left branch of atrioventricular bundle [Term] id: CL:1000370 name: transitional myocyte of left branch of atrioventricular bundle namespace: cell def: "A transitional myocyte that is part of the left branch of atrioventricular bundle." [GOC:tfm] xref: FMA:263170 is_a: CL:1000481 ! transitional myocyte of atrioventricular bundle relationship: part_of UBERON:0005986 ! left branch of atrioventricular bundle [Term] id: CL:1000371 name: transitional myocyte of right branch of atrioventricular bundle namespace: cell def: "A transitional myocyte that is part of the right branch of atrioventricular bundle." [GOC:tfm] xref: FMA:263172 is_a: CL:1000481 ! transitional myocyte of atrioventricular bundle relationship: part_of UBERON:0005987 ! right branch of atrioventricular bundle [Term] id: CL:1000372 name: transitional myocyte of atrial part of atrioventricular bundle namespace: cell def: "A transitional myocyte that is part of the atrial part of atrioventricular bundle." [GOC:tfm] xref: FMA:263174 is_a: CL:1000481 ! transitional myocyte of atrioventricular bundle [Term] id: CL:1000373 name: transitional myocyte of ventricular part of atrioventricular bundle namespace: cell def: "A transitional myocyte that is part of the ventricular part of atrioventricular bundle." [GOC:tfm] xref: FMA:263176 is_a: CL:1000481 ! transitional myocyte of atrioventricular bundle [Term] id: CL:1000374 name: transitional myocyte of posterior division of left branch of atrioventricular bundle namespace: cell def: "A transitional myocyte that is part of the posterior division of left branch of atrioventricular bundle." [GOC:tfm] xref: FMA:263178 is_a: CL:1000481 ! transitional myocyte of atrioventricular bundle relationship: part_of UBERON:0005986 ! left branch of atrioventricular bundle [Term] id: CL:1000375 name: myocardial endocrine cell of septal division of left branch of atrioventricular bundle namespace: cell def: "A myocardial endocrine cell that is part of the septal division of left branch of atrioventricular bundle." [GOC:tfm] xref: FMA:263180 is_a: CL:0002074 ! myocardial endocrine cell relationship: part_of UBERON:0005986 ! left branch of atrioventricular bundle [Term] id: CL:1000376 name: purkinje myocyte of interventricular septum namespace: cell def: "A Purkinje myocyte that is part of the interventricular septum." [GOC:tfm] xref: FMA:263182 is_a: CL:0002068 ! Purkinje myocyte intersection_of: CL:0002068 ! Purkinje myocyte intersection_of: part_of UBERON:0002094 ! interventricular septum relationship: part_of UBERON:0002094 ! interventricular septum [Term] id: CL:1000377 name: dense-core granulated cell of epithelium of trachea namespace: cell def: "A Feyrter cell that is part of the epithelium of trachea." [GOC:tfm] xref: FMA:263184 is_a: CL:0000307 ! tracheal epithelial cell is_a: CL:0002066 ! Feyrter cell intersection_of: CL:0002066 ! Feyrter cell intersection_of: part_of UBERON:0001901 ! epithelium of trachea relationship: part_of UBERON:0001901 ! epithelium of trachea [Term] id: CL:1000378 name: type 1 vestibular sensory cell of stato-acoustic epithelium namespace: cell def: "A type I vestibular sensory cell that is part of the stato-acoustic epithelium." [GOC:tfm] xref: FMA:263186 is_a: CL:0002070 ! type I vestibular sensory cell [Term] id: CL:1000379 name: type 1 vestibular sensory cell of epithelium of macula of utricle of membranous labyrinth namespace: cell def: "A type I vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth." [GOC:tfm] xref: FMA:263188 is_a: CL:0002070 ! type I vestibular sensory cell relationship: part_of UBERON:0003241 ! epithelium of utricle [Term] id: CL:1000380 name: type 1 vestibular sensory cell of epithelium of macula of saccule of membranous labyrinth namespace: cell def: "A type I vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth." [GOC:tfm] xref: FMA:263190 is_a: CL:0002070 ! type I vestibular sensory cell relationship: part_of UBERON:0003242 ! epithelium of saccule [Term] id: CL:1000381 name: type 1 vestibular sensory cell of epithelium of crista of ampulla of semicircular duct of membranous labyrinth namespace: cell def: "A type I vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth." [GOC:tfm] xref: FMA:263192 is_a: CL:0002070 ! type I vestibular sensory cell relationship: part_of UBERON:0006935 ! crista ampullaris neuroepithelium [Term] id: CL:1000382 name: type 2 vestibular sensory cell of stato-acoustic epithelium namespace: cell def: "A type II vestibular sensory cell that is part of the stato-acoustic epithelium." [GOC:tfm] xref: FMA:263194 is_a: CL:0002069 ! type II vestibular sensory cell [Term] id: CL:1000383 name: type 2 vestibular sensory cell of epithelium of macula of utricle of membranous labyrinth namespace: cell def: "A type II vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth." [GOC:tfm] xref: FMA:263196 is_a: CL:0002069 ! type II vestibular sensory cell relationship: part_of UBERON:0003241 ! epithelium of utricle [Term] id: CL:1000384 name: type 2 vestibular sensory cell of epithelium of macula of saccule of membranous labyrinth namespace: cell def: "A type II vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth." [GOC:tfm] xref: FMA:263198 is_a: CL:0002069 ! type II vestibular sensory cell relationship: part_of UBERON:0003242 ! epithelium of saccule [Term] id: CL:1000385 name: type 2 vestibular sensory cell of epithelium of crista of ampulla of semicircular duct of membranous labyrinth namespace: cell def: "A type II vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth." [GOC:tfm] xref: FMA:263200 is_a: CL:0002069 ! type II vestibular sensory cell [Term] id: CL:1000391 name: melanocyte of eyelid namespace: cell def: "A melanocyte that is part of the eyelid." [GOC:tfm] synonym: "eyelid melanocyte" EXACT [FMA:59175] synonym: "sebaceous gland of wolff" EXACT [FMA:59175] xref: FMA:59175 is_a: CL:0000148 ! melanocyte intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0001711 ! eyelid relationship: part_of UBERON:0001711 ! eyelid [Term] id: CL:1000394 name: myoepithelial cell of intralobular lactiferous duct namespace: cell def: "A myoepithelial cell that is part of the intralobular part of terminal lactiferous duct." [GOC:tfm] xref: FMA:62158 is_a: CL:0000185 ! myoepithelial cell [Term] id: CL:1000397 name: endothelial cell of venous sinus of red pulp of spleen namespace: cell def: "An endothelial cell that is part of the venous sinus of red pulp of spleen." [GOC:tfm] comment: todo - add logical definition to UBERON:0009967 xref: FMA:62817 is_a: CL:0002651 ! endothelial cell of venous sinus of spleen [Term] id: CL:1000398 name: endothelial cell of hepatic sinusoid namespace: cell def: "An endothelial cell that is part of the hepatic sinusoid." [GOC:tfm] synonym: "endotheliocyte of hepatic sinusoid" EXACT [FMA:62911] xref: FMA:62911 is_a: CL:0000182 ! hepatocyte is_a: CL:0002262 ! endothelial cell of sinusoid intersection_of: CL:0002262 ! endothelial cell of sinusoid intersection_of: part_of UBERON:0001281 ! hepatic sinusoid relationship: part_of UBERON:0001281 ! hepatic sinusoid [Term] id: CL:1000405 name: epithelial cell of appendix namespace: cell def: "An epithelial cell that is part of the appendix." [GOC:tfm] synonym: "columnar epitheliocyte of appendix" EXACT [FMA:63602] synonym: "epithelial cell of vermiform appendix" EXACT [FMA:63602] xref: FMA:63602 is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix [Term] id: CL:1000409 name: myocyte of sinoatrial node namespace: cell def: "A muscle cell that is part of the sinoatrial node." [FMA:67102, GOC:tfm] synonym: "myocyte of sinoatrial node" EXACT [FMA:67102] synonym: "SA nodal myocyte" EXACT [FMA:67102] synonym: "SA node cardiac muscle cell" EXACT [GOC:pr] synonym: "sinoatrial node cell" EXACT [GOC:pr] synonym: "sinoatrial node myocyte" EXACT [] synonym: "sinuatrial node myocyte" EXACT [FMA:67102] xref: FMA:67102 is_a: CL:0002072 ! nodal myocyte intersection_of: CL:0000187 ! muscle cell intersection_of: part_of UBERON:0002351 ! sinoatrial node relationship: part_of UBERON:0002351 ! sinoatrial node [Term] id: CL:1000410 name: myocyte of atrioventricular node namespace: cell def: "A muscle cell that is part of the atrioventricular node." [FMA:67106, GOC:tfm] synonym: "atrioventricular node cell" EXACT [GOC:pr] synonym: "atrioventricular node myocyte" EXACT [FMA:67106] synonym: "AV nodal myocyte" EXACT [FMA:67106] synonym: "AV node cardiac muscle cell" EXACT [GOC:pr] synonym: "AV node cell" EXACT [GOC:pr] xref: FMA:67106 is_a: CL:0002072 ! nodal myocyte intersection_of: CL:0000187 ! muscle cell intersection_of: part_of UBERON:0002352 ! atrioventricular node relationship: part_of UBERON:0002352 ! atrioventricular node [Term] id: CL:1000411 name: endothelial cell of peyer's patch namespace: cell def: "An endothelial cell that is part of the small intestine Peyer's patch." [GOC:tfm] xref: FMA:67757 is_a: CL:0000115 ! endothelial cell is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0003454 ! small intestine Peyer's patch relationship: part_of UBERON:0003454 ! small intestine Peyer's patch [Term] id: CL:1000412 name: endothelial cell of arteriole namespace: cell def: "An endothelial cell that is part of the arteriole." [GOC:tfm] xref: FMA:67760 xref: KUPO:0001097 is_a: CL:1000413 ! endothelial cell of artery intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001980 ! arteriole relationship: part_of UBERON:0001980 ! arteriole [Term] id: CL:1000413 name: endothelial cell of artery namespace: cell alt_id: CL:0002542 def: "A blood vessel endothelial cell that is part of an arterial endothelium." [GOC:tfm] synonym: "arterial endothelial cell" EXACT [] xref: BTO:0004758 xref: FMA:67761 xref: KUPO:0001095 is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001637 ! artery relationship: part_of UBERON:0001637 ! artery relationship: part_of UBERON:0001917 ! endothelium of artery [Term] id: CL:1000414 name: endothelial cell of venule namespace: cell def: "An endothelial cell that is part of the venule." [GOC:tfm] xref: FMA:67762 is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0002139 ! endothelial cell of vascular tree intersection_of: part_of UBERON:0001979 ! venule relationship: part_of UBERON:0001979 ! venule [Term] id: CL:1000415 name: epithelial cell of gall bladder namespace: cell def: "An epithelial cell that is part of the gallbladder." [GOC:tfm] xref: FMA:67780 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002110 ! gallbladder relationship: part_of UBERON:0002110 ! gallbladder [Term] id: CL:1000416 name: myoepithelial cell of lactiferous gland namespace: cell def: "A myoepithelial cell that is part of the mammary gland." [GOC:tfm] synonym: "basal cell of lactiferous duct" EXACT [FMA:67800] xref: FMA:67800 is_a: CL:0000185 ! myoepithelial cell is_a: CL:0002327 ! mammary epithelial cell intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:0001911 ! mammary gland relationship: part_of UBERON:0001911 ! mammary gland [Term] id: CL:1000417 name: myoepithelial cell of sweat gland namespace: cell def: "A myoepithelial cell that is part of the sweat gland." [GOC:tfm] xref: FMA:67801 is_a: CL:0000185 ! myoepithelial cell is_a: CL:1000448 ! epithelial cell of sweat gland intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:0001820 ! sweat gland relationship: part_of UBERON:0001820 ! sweat gland [Term] id: CL:1000418 name: myoepithelial cell of lactiferous alveolus namespace: cell def: "A myoepithelial cell that is part of the mammary gland alveolus." [GOC:tfm] synonym: "basal cell of alveolus of lactiferous gland" EXACT [FMA:67802] synonym: "myoepithelial cell of mammary alveolus" EXACT [FMA:67802] xref: FMA:67802 is_a: CL:1000416 ! myoepithelial cell of lactiferous gland intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:0003214 ! mammary gland alveolus relationship: part_of UBERON:0003214 ! mammary gland alveolus [Term] id: CL:1000419 name: myoepithelial cell of lactiferous duct namespace: cell def: "A myoepithelial cell that is part of the lactiferous duct." [GOC:tfm] xref: FMA:67803 is_a: CL:1000416 ! myoepithelial cell of lactiferous gland intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:0001765 ! mammary duct relationship: part_of UBERON:0001765 ! mammary duct [Term] id: CL:1000420 name: myoepithelial cell of terminal lactiferous duct namespace: cell def: "A myoepithelial cell that is part of the terminal lactiferous duct." [GOC:tfm] xref: FMA:67804 is_a: CL:0000185 ! myoepithelial cell [Term] id: CL:1000424 name: chromaffin cell of paraaortic body namespace: cell def: "A chromaffin cell that is part of the paraaortic body." [GOC:tfm] synonym: "chromaffin cell of para-aortic body" EXACT [FMA:69328] xref: FMA:69328 is_a: CL:0000166 ! chromaffin cell intersection_of: CL:0000166 ! chromaffin cell intersection_of: part_of UBERON:0001237 ! paraaortic body relationship: part_of UBERON:0001237 ! paraaortic body [Term] id: CL:1000425 name: chromaffin cell of paraganglion namespace: cell def: "A chromaffin cell that is part of the paraganglion." [GOC:tfm] xref: FMA:69335 is_a: CL:0000166 ! chromaffin cell [Term] id: CL:1000426 name: chromaffin cell of adrenal gland namespace: cell def: "A chromaffin cell that is part of the adrenal gland." [GOC:tfm] xref: FMA:69794 is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000166 ! chromaffin cell intersection_of: CL:0000166 ! chromaffin cell intersection_of: part_of UBERON:0002369 ! adrenal gland relationship: part_of UBERON:0002369 ! adrenal gland [Term] id: CL:1000427 name: adrenal cortex chromaffin cell namespace: cell def: "A chromaffin cell that is part of the adrenal cortex." [GOC:tfm] comment: Not clear this cell type exists. Can't call it a cortical adrenal cell because of different germ layer origin. synonym: "chromaffin cell of adrenal cortex" EXACT [] xref: FMA:69795 is_a: CL:1000426 ! chromaffin cell of adrenal gland intersection_of: CL:0000166 ! chromaffin cell intersection_of: part_of UBERON:0001235 ! adrenal cortex relationship: part_of UBERON:0001235 ! adrenal cortex [Term] id: CL:1000428 name: stem cell of epidermis namespace: cell def: "A somatic stem cell that is part of the epidermis." [GOC:tfm] synonym: "epidermal stem cell" EXACT [FMA:70541] xref: FMA:70541 is_a: CL:0000723 ! somatic stem cell intersection_of: CL:0000723 ! somatic stem cell intersection_of: part_of UBERON:0001003 ! epidermis relationship: part_of UBERON:0001003 ! epidermis [Term] id: CL:1000432 name: conjunctival epithelial cell namespace: cell def: "An epithelial cell that is part of the conjunctiva." [GOC:tfm] synonym: "epithelial cell of conjunctiva" EXACT [FMA:70552] xref: FMA:70552 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001811 ! conjunctiva relationship: part_of UBERON:0001811 ! conjunctiva [Term] id: CL:1000433 name: epithelial cell of lacrimal canaliculus namespace: cell def: "An epithelial cell that is part of the lacrimal canaliculus." [GOC:tfm] xref: FMA:70553 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001770 ! lacrimal canaliculus relationship: part_of UBERON:0001770 ! lacrimal canaliculus [Term] id: CL:1000434 name: epithelial cell of external acoustic meatus namespace: cell def: "An epithelial cell that is part of the external acoustic meatus." [GOC:tfm] xref: FMA:70555 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001352 ! external acoustic meatus relationship: part_of UBERON:0001352 ! external acoustic meatus [Term] id: CL:1000435 name: epithelial cell of lacrimal duct namespace: cell def: "An epithelial cell that is part of the lacrimal duct." [GOC:tfm] xref: FMA:70559 is_a: CL:0000072 ! non-branched duct epithelial cell intersection_of: CL:0000072 ! non-branched duct epithelial cell intersection_of: part_of UBERON:0001850 ! lacrimal duct relationship: part_of UBERON:0001850 ! lacrimal duct [Term] id: CL:1000436 name: epithelial cell of lacrimal sac namespace: cell def: "An epithelial cell that is part of the lacrimal sac." [GOC:tfm] xref: FMA:70560 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001351 ! lacrimal sac relationship: part_of UBERON:0001351 ! lacrimal sac [Term] id: CL:1000437 name: epithelial cell of nasolacrimal duct namespace: cell def: "An epithelial cell that is part of the nasolacrimal duct." [GOC:tfm] xref: FMA:70561 is_a: CL:1000435 ! epithelial cell of lacrimal duct intersection_of: CL:0000072 ! non-branched duct epithelial cell intersection_of: part_of UBERON:0002392 ! nasolacrimal duct relationship: part_of UBERON:0002392 ! nasolacrimal duct [Term] id: CL:1000438 name: epithelial cell of wall of inferior part of anal canal namespace: cell def: "An epithelial cell that is part of the wall of inferior part of anal canal." [GOC:tfm] xref: FMA:70562 is_a: CL:0002634 ! epithelial cell of anal column [Term] id: CL:1000441 name: epithelial cell of viscerocranial mucosa namespace: cell def: "An epithelial cell that is part of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70583 is_a: CL:0000066 ! epithelial cell is_a: CL:0002371 ! somatic cell [Term] id: CL:1000442 name: urothelial cell of trigone of urinary bladder namespace: cell def: "An urothelial cell that is part of the trigone of urinary bladder." [GOC:tfm] synonym: "epithelial cell of vesical trigone" EXACT [FMA:70598] xref: FMA:70598 is_a: CL:0000731 ! urothelial cell is_a: CL:1001319 ! bladder cell intersection_of: CL:0000731 ! urothelial cell intersection_of: part_of UBERON:0001257 ! trigone of urinary bladder relationship: part_of UBERON:0001257 ! trigone of urinary bladder [Term] id: CL:1000443 name: ciliary muscle cell namespace: cell def: "A smooth muscle cell that is part of the ciliary body." [GOC:tfm] synonym: "smooth muscle cell of ciliary body" EXACT [FMA:70610] xref: FMA:70610 is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001775 ! ciliary body relationship: part_of UBERON:0001775 ! ciliary body [Term] id: CL:1000444 name: mesothelial cell of anterior chamber of eye namespace: cell def: "A mesothelial cell that is part of the anterior chamber of eyeball." [GOC:tfm] xref: FMA:70615 is_a: CL:0000077 ! mesothelial cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0001766 ! anterior chamber of eyeball relationship: part_of UBERON:0001766 ! anterior chamber of eyeball [Term] id: CL:1000445 name: myoepithelial cell of dilator pupillae namespace: cell def: "A myoepithelial cell that is part of the dilatator pupillae." [GOC:tfm] xref: FMA:70619 is_a: CL:0000185 ! myoepithelial cell intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:0001608 ! dilatator pupillae relationship: part_of UBERON:0001608 ! dilatator pupillae [Term] id: CL:1000447 name: epithelial cell of stratum germinativum of esophagus namespace: cell def: "A basal cell that is part of the epithelium of esophagus." [GOC:tfm] synonym: "basal cell of esophageal epithelium" EXACT [FMA:70731] xref: FMA:70731 is_a: CL:0000646 ! basal cell intersection_of: CL:0000646 ! basal cell intersection_of: part_of UBERON:0001976 ! epithelium of esophagus relationship: part_of UBERON:0001976 ! epithelium of esophagus [Term] id: CL:1000448 name: epithelial cell of sweat gland namespace: cell def: "An epithelial cell that is part of the sweat gland." [GOC:tfm] xref: FMA:70952 is_a: CL:0000362 ! epidermal cell is_a: CL:0002308 ! epithelial cell of skin gland intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001820 ! sweat gland relationship: part_of UBERON:0001820 ! sweat gland [Term] id: CL:1000449 name: epithelial cell of nephron namespace: cell def: "An epithelial cell that is part of the nephron." [GOC:tfm] xref: FMA:70965 is_a: CL:0002518 ! kidney epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001285 ! nephron relationship: part_of UBERON:0001285 ! nephron [Term] id: CL:1000450 name: epithelial cell of glomerular capsule namespace: cell def: "An epithelial cell that is part of the glomerular capsule." [GOC:tfm] synonym: "Bowmans capsule epithelial cell" EXACT [] synonym: "epithelial cell of Bowman's capsule" EXACT [FMA:70966] xref: FMA:70966 xref: KUPO:0001034 is_a: CL:1000510 ! kidney glomerular epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001230 ! glomerular capsule relationship: part_of UBERON:0001230 ! glomerular capsule [Term] id: CL:1000451 name: epithelial cell of visceral layer of glomerular capsule namespace: cell def: "An epithelial cell that is part of the visceral layer of glomerular capsule." [GOC:tfm] comment: consider merging into CL:0000653 synonym: "glomerular podocyte" NARROW [FMA:70967] xref: FMA:70967 is_a: CL:1000450 ! epithelial cell of glomerular capsule intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0005751 ! visceral layer of glomerular capsule relationship: part_of UBERON:0005751 ! visceral layer of glomerular capsule [Term] id: CL:1000452 name: parietal epithelial cell namespace: cell alt_id: CL:1000897 def: "An epithelial cell that is part of the glomerular parietal epithelium." [GOC:tfm] synonym: "epithelial cell of parietal layer of glomerular capsule" EXACT [FMA:70968] xref: FMA:70968 xref: KUPO:0001035 is_a: CL:1000450 ! epithelial cell of glomerular capsule intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0005750 ! glomerular parietal epithelium relationship: part_of UBERON:0005750 ! glomerular parietal epithelium [Term] id: CL:1000453 name: epithelial cell of intermediate tubule namespace: cell def: "An epithelial cell that is part of the intermediate tubule." [GOC:tfm] xref: FMA:70980 is_a: CL:1000909 ! kidney loop of henle epithelial cell intersection_of: CL:1000494 ! epithelial cell of renal tubule intersection_of: part_of UBERON:0004136 ! intermediate tubule relationship: part_of UBERON:0004136 ! intermediate tubule [Term] id: CL:1000454 name: kidney collecting duct epithelial cell namespace: cell def: "An epithelial cell that is part of the collecting duct of renal tubule." [GOC:tfm] synonym: "epithelial cell of renal collecting tubule" EXACT [FMA:70982] xref: FMA:70982 xref: KUPO:0001059 is_a: CL:0000072 ! non-branched duct epithelial cell is_a: CL:1000449 ! epithelial cell of nephron is_a: CL:1001225 ! kidney collecting duct cell intersection_of: CL:0000072 ! non-branched duct epithelial cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule relationship: part_of UBERON:0001232 ! collecting duct of renal tubule [Term] id: CL:1000456 name: mesothelial cell of parietal peritoneum namespace: cell def: "A mesothelial cell that is part of the parietal peritoneum." [GOC:tfm] xref: FMA:72142 is_a: CL:1000490 ! mesothelial cell of peritoneum intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0001366 ! parietal peritoneum relationship: part_of UBERON:0001366 ! parietal peritoneum [Term] id: CL:1000457 name: mesothelial cell of visceral peritoneum namespace: cell def: "A mesothelial cell that is part of the visceral peritoneum." [GOC:tfm] xref: FMA:72143 is_a: CL:1000490 ! mesothelial cell of peritoneum intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0001178 ! visceral peritoneum relationship: part_of UBERON:0001178 ! visceral peritoneum [Term] id: CL:1000458 name: melanocyte of skin namespace: cell def: "A melanocyte that is part of the skin of body." [GOC:tfm] synonym: "skin melanocyte" EXACT [FMA:72144] xref: FMA:72144 is_a: CL:0000148 ! melanocyte intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0002097 ! skin of body relationship: part_of UBERON:0002097 ! skin of body [Term] id: CL:1000465 name: chromaffin cell of ovary namespace: cell def: "A chromaffin cell that is part of the ovary." [GOC:tfm] xref: FMA:74319 is_a: CL:0000166 ! chromaffin cell intersection_of: CL:0000166 ! chromaffin cell intersection_of: part_of UBERON:0000992 ! female gonad relationship: part_of UBERON:0000992 ! female gonad [Term] id: CL:1000466 name: chromaffin cell of right ovary namespace: cell def: "A chromaffin cell that is part of the right ovary." [GOC:tfm] xref: FMA:74320 is_a: CL:1000465 ! chromaffin cell of ovary intersection_of: CL:0000166 ! chromaffin cell intersection_of: part_of UBERON:0002118 ! right ovary relationship: part_of UBERON:0002118 ! right ovary [Term] id: CL:1000467 name: chromaffin cell of left ovary namespace: cell def: "A chromaffin cell that is part of the left ovary." [GOC:tfm] xref: FMA:74321 is_a: CL:1000465 ! chromaffin cell of ovary intersection_of: CL:0000166 ! chromaffin cell intersection_of: part_of UBERON:0002119 ! left ovary relationship: part_of UBERON:0002119 ! left ovary [Term] id: CL:1000468 name: myoepithelial cell of acinus of lactiferous gland namespace: cell def: "A myoepithelial cell that is part of the acinus of lactiferous gland." [GOC:tfm] synonym: "basal cell of acinus of lactiferous gland" EXACT [FMA:74469] xref: FMA:74469 is_a: CL:1000416 ! myoepithelial cell of lactiferous gland relationship: part_of UBERON:0001912 ! lobule of lactiferous gland [Term] id: CL:1000469 name: myoepithelial cell of main lactiferous duct namespace: cell def: "A myoepithelial cell that is part of the main lactiferous duct." [GOC:tfm] xref: FMA:74499 is_a: CL:0000185 ! myoepithelial cell [Term] id: CL:1000470 name: myoepithelial cell of primary lactiferous duct namespace: cell def: "A myoepithelial cell that is part of the primary lactiferous duct." [GOC:tfm] xref: FMA:74500 is_a: CL:0000185 ! myoepithelial cell [Term] id: CL:1000471 name: myoepithelial cell of secondary lactiferous duct namespace: cell def: "A myoepithelial cell that is part of the secondary lactiferous duct." [GOC:tfm] xref: FMA:74501 is_a: CL:0000185 ! myoepithelial cell [Term] id: CL:1000472 name: myoepithelial cell of tertiary lactiferous duct namespace: cell def: "A myoepithelial cell that is part of the tertiary lactiferous duct." [GOC:tfm] xref: FMA:74502 is_a: CL:0000185 ! myoepithelial cell [Term] id: CL:1000473 name: myoepithelial cell of quarternary lactiferous duct namespace: cell def: "A myoepithelial cell that is part of the quarternary lactiferous duct." [GOC:tfm] xref: FMA:74503 is_a: CL:0000185 ! myoepithelial cell [Term] id: CL:1000477 name: cardiac pacemaker cell of sinoatrial node namespace: cell def: "A nodal myocyte that is part of the sinoatrial node." [GOC:tfm] synonym: "cardiac pacemaker cell of sinuatrial node" EXACT [] synonym: "pacemaker cell of sinoatrial node" EXACT [] synonym: "pacemaker cell of sinuatrial node" EXACT [] xref: FMA:83383 is_a: CL:1000409 ! myocyte of sinoatrial node relationship: part_of UBERON:0002351 ! sinoatrial node [Term] id: CL:1000478 name: transitional myocyte of sinoatrial node namespace: cell def: "A transitional myocyte that is part of the sinoatrial node." [GOC:tfm] synonym: "transitinal myocyte of sinuatrial node" EXACT [] xref: FMA:83384 is_a: CL:0002073 ! transitional myocyte is_a: CL:1000409 ! myocyte of sinoatrial node intersection_of: CL:0002073 ! transitional myocyte intersection_of: part_of UBERON:0002351 ! sinoatrial node relationship: part_of UBERON:0002351 ! sinoatrial node [Term] id: CL:1000479 name: purkinje myocyte of atrioventricular node namespace: cell def: "A Purkinje myocyte that is part of the atrioventricular node." [GOC:tfm] xref: FMA:83386 is_a: CL:0002068 ! Purkinje myocyte is_a: CL:1000410 ! myocyte of atrioventricular node intersection_of: CL:0002068 ! Purkinje myocyte intersection_of: part_of UBERON:0002352 ! atrioventricular node relationship: part_of UBERON:0002352 ! atrioventricular node [Term] id: CL:1000480 name: transitional myocyte of internodal tract namespace: cell def: "A transitional myocyte that is part of the internodal tract." [GOC:tfm] xref: FMA:83387 is_a: CL:0002073 ! transitional myocyte [Term] id: CL:1000481 name: transitional myocyte of atrioventricular bundle namespace: cell def: "A transitional myocyte that is part of the atrioventricular bundle." [GOC:tfm] xref: FMA:83388 xref: FMA:83885 is_a: CL:0002073 ! transitional myocyte intersection_of: CL:0002073 ! transitional myocyte intersection_of: part_of UBERON:0002353 ! atrioventricular bundle relationship: part_of UBERON:0002353 ! atrioventricular bundle [Term] id: CL:1000482 name: myocardial endocrine cell of interventricular septum namespace: cell def: "A myocardial endocrine cell that is part of the interventricular septum." [GOC:tfm] xref: FMA:83390 is_a: CL:0002074 ! myocardial endocrine cell intersection_of: CL:0002074 ! myocardial endocrine cell intersection_of: part_of UBERON:0002094 ! interventricular septum relationship: part_of UBERON:0002094 ! interventricular septum [Term] id: CL:1000483 name: purkinje myocyte of internodal tract namespace: cell def: "A Purkinje myocyte that is part of the internodal tract." [GOC:tfm] xref: FMA:83392 is_a: CL:0002068 ! Purkinje myocyte [Term] id: CL:1000484 name: purkinje myocyte of atrioventricular bundle namespace: cell def: "A Purkinje myocyte that is part of the atrioventricular bundle." [GOC:tfm] xref: FMA:83393 is_a: CL:0002068 ! Purkinje myocyte intersection_of: CL:0002068 ! Purkinje myocyte intersection_of: part_of UBERON:0002353 ! atrioventricular bundle relationship: part_of UBERON:0002353 ! atrioventricular bundle [Term] id: CL:1000486 name: basal cell of urothelium namespace: cell def: "A basal cell that is part of the urothelium." [GOC:tfm] xref: FMA:84150 is_a: CL:0000646 ! basal cell intersection_of: CL:0000646 ! basal cell intersection_of: part_of UBERON:0000365 ! urothelium relationship: part_of UBERON:0000365 ! urothelium [Term] id: CL:1000487 name: smooth muscle cell of prostate namespace: cell def: "A smooth muscle cell that is part of the prostate gland." [GOC:tfm] synonym: "smooth muscle fiber of prostate" EXACT [FMA:84583] xref: FMA:84583 is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0002367 ! prostate gland relationship: part_of UBERON:0002367 ! prostate gland [Term] id: CL:1000488 name: cholangiocyte namespace: cell def: "An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts." [GOC:tfm, PMID:16550043, PMID:18356246] synonym: "epithelial cell of bile duct" EXACT [] synonym: "hepatoblast" EXACT [] xref: FMA:86481 is_a: CL:0000069 ! branched duct epithelial cell intersection_of: CL:0000069 ! branched duct epithelial cell intersection_of: capable_of GO:0015106 ! bicarbonate transmembrane transporter activity intersection_of: part_of UBERON:0002394 ! bile duct relationship: capable_of GO:0015106 ! bicarbonate transmembrane transporter activity relationship: part_of UBERON:0002394 ! bile duct [Term] id: CL:1000489 name: reticular cell of splenic cord namespace: cell def: "A reticular cell that is part of the splenic cord." [GOC:tfm] xref: FMA:86497 is_a: CL:0000432 ! reticular cell intersection_of: CL:0000432 ! reticular cell intersection_of: part_of UBERON:0001266 ! splenic cord relationship: part_of UBERON:0001266 ! splenic cord [Term] id: CL:1000490 name: mesothelial cell of peritoneum namespace: cell def: "A mesothelial cell that is part of the peritoneum." [GOC:tfm] synonym: "peritoneal mesothelial cell" EXACT [FMA:86736] xref: FMA:86736 is_a: CL:0000077 ! mesothelial cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0002358 ! peritoneum relationship: part_of UBERON:0002358 ! peritoneum [Term] id: CL:1000491 name: mesothelial cell of pleura namespace: cell def: "A mesothelial cell that is part of the pleura." [GOC:tfm] synonym: "pleural mesothelial cell" EXACT [FMA:86737] xref: FMA:86737 is_a: CL:0000077 ! mesothelial cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0000977 ! pleura relationship: part_of UBERON:0000977 ! pleura [Term] id: CL:1000492 name: mesothelial cell of parietal pleura namespace: cell def: "A mesothelial cell that is part of the parietal pleura." [GOC:tfm] xref: FMA:86738 is_a: CL:1000491 ! mesothelial cell of pleura intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0002400 ! parietal pleura relationship: part_of UBERON:0002400 ! parietal pleura [Term] id: CL:1000493 name: mesothelial cell of visceral pleura namespace: cell def: "A mesothelial cell that is part of the visceral pleura." [GOC:tfm] xref: FMA:86739 is_a: CL:0000082 ! epithelial cell of lung is_a: CL:1000491 ! mesothelial cell of pleura intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0002401 ! visceral pleura relationship: part_of UBERON:0002401 ! visceral pleura [Term] id: CL:1000494 name: epithelial cell of renal tubule namespace: cell def: "An epithelial cell that is part of the renal tubule." [GOC:tfm] synonym: "kidney tubule epithelial cell" EXACT [] xref: FMA:86785 xref: KUPO:0001022 is_a: CL:1000449 ! epithelial cell of nephron is_a: CL:1000507 ! kidney tubule cell intersection_of: CL:0002518 ! kidney epithelial cell intersection_of: part_of UBERON:0001231 ! nephron tubule relationship: part_of UBERON:0001231 ! nephron tubule relationship: part_of UBERON:0004810 ! nephron tubule epithelium [Term] id: CL:1000495 name: goblet cell of small intestine namespace: cell def: "A goblet cell that is part of the small intestine." [GOC:tfm] synonym: "small intestinal goblet cell" EXACT [FMA:86929] xref: FMA:86929 is_a: CL:0000160 ! goblet cell is_a: CL:0000510 ! paneth cell is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0002108 ! small intestine [Term] id: CL:1000497 name: kidney cell namespace: cell xref: KUPO:0001010 is_a: CL:0000548 ! animal cell is_a: CL:0002371 ! somatic cell intersection_of: CL:0000548 ! animal cell intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney [Term] id: CL:1000500 name: kidney interstitial cell namespace: cell xref: KUPO:0001013 is_a: CL:0002320 ! connective tissue cell is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0005215 ! kidney interstitium relationship: part_of UBERON:0005215 ! kidney interstitium [Term] id: CL:1000504 name: kidney medulla cell namespace: cell xref: KUPO:0001017 is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0000362 ! renal medulla relationship: part_of UBERON:0000362 ! renal medulla [Term] id: CL:1000505 name: kidney pelvis cell namespace: cell xref: KUPO:0001018 is_a: CL:1000497 ! kidney cell is_a: CL:1000601 ! ureteral cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0001224 ! renal pelvis relationship: part_of UBERON:0001224 ! renal pelvis [Term] id: CL:1000507 name: kidney tubule cell namespace: cell xref: KUPO:0001020 is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0001231 ! nephron tubule relationship: part_of UBERON:0001231 ! nephron tubule [Term] id: CL:1000510 name: kidney glomerular epithelial cell namespace: cell xref: KUPO:0001023 is_a: CL:1000746 ! glomerular cell intersection_of: CL:0002518 ! kidney epithelial cell intersection_of: part_of UBERON:0004188 ! glomerular epithelium relationship: part_of UBERON:0004188 ! glomerular epithelium [Term] id: CL:1000546 name: kidney medulla collecting duct epithelial cell namespace: cell xref: KUPO:0001060 is_a: CL:1000504 ! kidney medulla cell is_a: CL:1001225 ! kidney collecting duct cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0005185 ! renal medulla collecting duct relationship: part_of UBERON:0005185 ! renal medulla collecting duct [Term] id: CL:1000547 name: kidney inner medulla collecting duct epithelial cell namespace: cell xref: KUPO:0001061 is_a: CL:1000546 ! kidney medulla collecting duct epithelial cell is_a: CL:1000617 ! kidney inner medulla cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0005187 ! inner renal medulla collecting duct relationship: part_of UBERON:0005187 ! inner renal medulla collecting duct [Term] id: CL:1000548 name: kidney outer medulla collecting duct epithelial cell namespace: cell xref: KUPO:0001062 is_a: CL:1000546 ! kidney medulla collecting duct epithelial cell is_a: CL:1000616 ! kidney outer medulla cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0005186 ! outer renal medulla collecting duct relationship: part_of UBERON:0005186 ! outer renal medulla collecting duct [Term] id: CL:1000549 name: kidney cortex collecting duct epithelial cell namespace: cell xref: KUPO:0001063 is_a: CL:0002681 ! kidney cortical cell is_a: CL:1001225 ! kidney collecting duct cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0005267 ! renal cortex collecting duct relationship: part_of UBERON:0005267 ! renal cortex collecting duct [Term] id: CL:1000550 name: kidney papillary duct principal epithelial cell namespace: cell xref: KUPO:0001064 is_a: CL:1001225 ! kidney collecting duct cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0005167 ! papillary duct relationship: part_of UBERON:0005167 ! papillary duct [Term] id: CL:1000596 name: inner renal cortex cell namespace: cell xref: KUPO:0001111 is_a: CL:0002681 ! kidney cortical cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0005271 ! juxtamedullary cortex relationship: part_of UBERON:0005271 ! juxtamedullary cortex [Term] id: CL:1000597 name: papillary tips cell namespace: cell xref: KUPO:0001112 is_a: CL:1000505 ! kidney pelvis cell is_a: CL:1000617 ! kidney inner medulla cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0009095 ! tip of renal papilla relationship: part_of UBERON:0009095 ! tip of renal papilla [Term] id: CL:1000600 name: lower urinary tract cell namespace: cell xref: KUPO:0001115 is_a: CL:0000548 ! animal cell intersection_of: CL:0000548 ! animal cell intersection_of: part_of UBERON:0001556 ! lower urinary tract relationship: part_of UBERON:0001556 ! lower urinary tract [Term] id: CL:1000601 name: ureteral cell namespace: cell xref: KUPO:0001116 is_a: CL:0000548 ! animal cell intersection_of: CL:0000548 ! animal cell intersection_of: part_of UBERON:0000056 ! ureter relationship: part_of UBERON:0000056 ! ureter [Term] id: CL:1000606 name: kidney nerve cell namespace: cell xref: KUPO:0001015 is_a: CL:0000540 ! neuron is_a: CL:1000500 ! kidney interstitial cell intersection_of: CL:0000540 ! neuron intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney [Term] id: CL:1000612 name: kidney corpuscule cell namespace: cell xref: KUPO:0001021 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000449 ! epithelial cell of nephron intersection_of: CL:0002584 ! renal cortical epithelial cell intersection_of: part_of UBERON:0001229 ! renal corpuscle relationship: part_of UBERON:0001229 ! renal corpuscle [Term] id: CL:1000615 name: kidney cortex tubule cell namespace: cell xref: KUPO:0001024 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000494 ! epithelial cell of renal tubule intersection_of: CL:1000507 ! kidney tubule cell intersection_of: part_of UBERON:0006853 ! renal cortex tubule relationship: part_of UBERON:0006853 ! renal cortex tubule [Term] id: CL:1000616 name: kidney outer medulla cell namespace: cell xref: KUPO:0001025 is_a: CL:1000504 ! kidney medulla cell intersection_of: CL:1000504 ! kidney medulla cell intersection_of: part_of UBERON:0001293 ! outer medulla of kidney relationship: part_of UBERON:0001293 ! outer medulla of kidney [Term] id: CL:1000617 name: kidney inner medulla cell namespace: cell xref: KUPO:0001026 is_a: CL:1000504 ! kidney medulla cell intersection_of: CL:1000504 ! kidney medulla cell intersection_of: part_of UBERON:0001294 ! inner medulla of kidney relationship: part_of UBERON:0001294 ! inner medulla of kidney [Term] id: CL:1000618 name: juxtaglomerular complex cell namespace: cell xref: KUPO:0001028 is_a: CL:0002681 ! kidney cortical cell intersection_of: CL:0002681 ! kidney cortical cell intersection_of: part_of UBERON:0002303 ! juxtaglomerular apparatus relationship: part_of UBERON:0002303 ! juxtaglomerular apparatus [Term] id: CL:1000681 name: kidney cortex interstitial cell namespace: cell xref: KUPO:0001091 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000500 ! kidney interstitial cell intersection_of: CL:1000500 ! kidney interstitial cell intersection_of: part_of UBERON:0005270 ! renal cortex interstitium relationship: part_of UBERON:0005270 ! renal cortex interstitium [Term] id: CL:1000682 name: kidney medulla interstitial cell namespace: cell xref: KUPO:0001092 is_a: CL:1000500 ! kidney interstitial cell is_a: CL:1000504 ! kidney medulla cell intersection_of: CL:1000500 ! kidney interstitial cell intersection_of: part_of UBERON:0005211 ! renal medulla interstitium relationship: part_of UBERON:0005211 ! renal medulla interstitium [Term] id: CL:1000691 name: kidney interstitial myofibroblast namespace: cell xref: KUPO:0001101 is_a: CL:0000186 ! myofibroblast cell is_a: CL:1000500 ! kidney interstitial cell [Term] id: CL:1000692 name: kidney interstitial fibroblast namespace: cell xref: KUPO:0001102 is_a: CL:0002241 ! pulmonary interstitial fibroblast is_a: CL:1000500 ! kidney interstitial cell [Term] id: CL:1000693 name: kidney interstitial fibrocyte namespace: cell xref: KUPO:0001103 is_a: CL:0000135 ! fibrocyte is_a: CL:1000500 ! kidney interstitial cell [Term] id: CL:1000695 name: kidney interstitial alternatively activated macrophage namespace: cell xref: KUPO:0001106 is_a: CL:0000864 ! tissue-resident macrophage is_a: CL:0000890 ! alternatively activated macrophage is_a: CL:1000500 ! kidney interstitial cell [Term] id: CL:1000696 name: kidney interstitial inflammatory macrophage namespace: cell xref: KUPO:0001107 is_a: CL:0000863 ! inflammatory macrophage is_a: CL:0000864 ! tissue-resident macrophage is_a: CL:1000500 ! kidney interstitial cell [Term] id: CL:1000697 name: kidney interstitial suppressor macrophage namespace: cell xref: KUPO:0001108 is_a: CL:0000862 ! suppressor macrophage is_a: CL:0000864 ! tissue-resident macrophage is_a: CL:1000500 ! kidney interstitial cell [Term] id: CL:1000698 name: kidney resident macrophage namespace: cell xref: KUPO:0001109 is_a: CL:0000864 ! tissue-resident macrophage is_a: CL:1000500 ! kidney interstitial cell [Term] id: CL:1000699 name: kidney resident dendritic cell namespace: cell xref: KUPO:0001110 is_a: CL:0001007 ! interstitial dendritic cell is_a: CL:1000500 ! kidney interstitial cell [Term] id: CL:1000702 name: kidney pelvis smooth muscle cell namespace: cell xref: KUPO:0001113 is_a: CL:1000505 ! kidney pelvis cell is_a: CL:1000979 ! ureter smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0004227 ! kidney pelvis smooth muscle relationship: part_of UBERON:0004227 ! kidney pelvis smooth muscle [Term] id: CL:1000703 name: kidney pelvis urothelial cell namespace: cell xref: KUPO:0001114 is_a: CL:0002518 ! kidney epithelial cell is_a: CL:1000505 ! kidney pelvis cell is_a: CL:1000706 ! ureter urothelial cell intersection_of: CL:0002518 ! kidney epithelial cell intersection_of: part_of UBERON:0004788 ! kidney pelvis urothelium relationship: part_of UBERON:0004788 ! kidney pelvis urothelium [Term] id: CL:1000706 name: ureter urothelial cell namespace: cell xref: KUPO:0001117 is_a: CL:0000731 ! urothelial cell is_a: CL:1000601 ! ureteral cell intersection_of: CL:0000731 ! urothelial cell intersection_of: part_of UBERON:0001254 ! urothelium of ureter relationship: part_of UBERON:0001254 ! urothelium of ureter [Term] id: CL:1000708 name: ureter adventitial cell namespace: cell xref: KUPO:0001119 is_a: CL:0000115 ! endothelial cell is_a: CL:0000134 ! mesenchymal cell is_a: CL:0002503 ! adventitial cell is_a: CL:1000601 ! ureteral cell intersection_of: CL:1000601 ! ureteral cell intersection_of: part_of UBERON:0001252 ! adventitia of ureter relationship: part_of UBERON:0001252 ! adventitia of ureter [Term] id: CL:1000714 name: kidney cortex collecting duct principal cell namespace: cell xref: KUPO:0001130 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000549 ! kidney cortex collecting duct epithelial cell is_a: CL:1001431 ! kidney collecting duct principal cell intersection_of: CL:0005009 ! renal principal cell intersection_of: part_of UBERON:0005267 ! renal cortex collecting duct relationship: part_of UBERON:0005267 ! renal cortex collecting duct [Term] id: CL:1000715 name: kidney cortex collecting duct intercalated cell namespace: cell xref: KUPO:0001131 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000549 ! kidney cortex collecting duct epithelial cell is_a: CL:1001432 ! kidney collecting duct intercalated cell intersection_of: CL:0005010 ! renal intercalated cell intersection_of: part_of UBERON:0005267 ! renal cortex collecting duct relationship: part_of UBERON:0005267 ! renal cortex collecting duct [Term] id: CL:1000716 name: kidney outer medulla collecting duct principal cell namespace: cell xref: KUPO:0001132 is_a: CL:1000548 ! kidney outer medulla collecting duct epithelial cell is_a: CL:1001431 ! kidney collecting duct principal cell intersection_of: CL:0005009 ! renal principal cell intersection_of: part_of UBERON:0005186 ! outer renal medulla collecting duct relationship: part_of UBERON:0005186 ! outer renal medulla collecting duct [Term] id: CL:1000717 name: kidney outer medulla collecting duct intercalated cell namespace: cell xref: KUPO:0001133 is_a: CL:1000548 ! kidney outer medulla collecting duct epithelial cell is_a: CL:1001432 ! kidney collecting duct intercalated cell intersection_of: CL:0005010 ! renal intercalated cell intersection_of: part_of UBERON:0005186 ! outer renal medulla collecting duct relationship: part_of UBERON:0005186 ! outer renal medulla collecting duct [Term] id: CL:1000718 name: kidney inner medulla collecting duct principal cell namespace: cell xref: KUPO:0001134 is_a: CL:1000547 ! kidney inner medulla collecting duct epithelial cell is_a: CL:1001431 ! kidney collecting duct principal cell intersection_of: CL:0005009 ! renal principal cell intersection_of: part_of UBERON:0005187 ! inner renal medulla collecting duct relationship: part_of UBERON:0005187 ! inner renal medulla collecting duct [Term] id: CL:1000719 name: kidney inner medulla collecting duct intercalated cell namespace: cell xref: KUPO:0001135 is_a: CL:1000547 ! kidney inner medulla collecting duct epithelial cell is_a: CL:1001432 ! kidney collecting duct intercalated cell intersection_of: CL:0005010 ! renal intercalated cell intersection_of: part_of UBERON:0005187 ! inner renal medulla collecting duct relationship: part_of UBERON:0005187 ! inner renal medulla collecting duct [Term] id: CL:1000720 name: kidney papillary duct intercalated cell namespace: cell xref: KUPO:0001136 is_a: CL:1000550 ! kidney papillary duct principal epithelial cell is_a: CL:1001432 ! kidney collecting duct intercalated cell intersection_of: CL:0005010 ! renal intercalated cell intersection_of: part_of UBERON:0005167 ! papillary duct relationship: part_of UBERON:0005167 ! papillary duct [Term] id: CL:1000721 name: kidney papillary duct principal cell namespace: cell xref: KUPO:0001137 is_a: CL:1000550 ! kidney papillary duct principal epithelial cell is_a: CL:1001431 ! kidney collecting duct principal cell intersection_of: CL:0005009 ! renal principal cell intersection_of: part_of UBERON:0005167 ! papillary duct relationship: part_of UBERON:0005167 ! papillary duct [Term] id: CL:1000742 name: glomerular mesangial cell namespace: cell def: "Intraglomerular mesangial cells are specialized pericytes located among the glomerular capillaries within a renal corpuscle of a kidney." [Wikipedia:Intraglomerular_mesangial_cell] synonym: "intraglomerular mesangial cell" EXACT [CL:cjm] xref: KUPO:0001032 is_a: CL:0000650 ! mesangial cell is_a: CL:1000500 ! kidney interstitial cell is_a: CL:1000746 ! glomerular cell is_a: CL:1001318 ! renal interstitial pericyte intersection_of: CL:1000612 ! kidney corpuscule cell intersection_of: part_of UBERON:0002320 ! glomerular mesangium relationship: part_of UBERON:0002320 ! glomerular mesangium [Term] id: CL:1000746 name: glomerular cell namespace: cell xref: KUPO:0001036 is_a: CL:1000612 ! kidney corpuscule cell intersection_of: CL:1000612 ! kidney corpuscule cell intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0000074 ! renal glomerulus [Term] id: CL:1000768 name: kidney connecting tubule epithelial cell namespace: cell xref: KUPO:0001058 is_a: CL:1000615 ! kidney cortex tubule cell intersection_of: CL:1000494 ! epithelial cell of renal tubule intersection_of: part_of UBERON:0005097 ! renal connecting tubule relationship: part_of UBERON:0005097 ! renal connecting tubule [Term] id: CL:1000803 name: kidney inner medulla interstitial cell namespace: cell xref: KUPO:0001093 is_a: CL:1000617 ! kidney inner medulla cell is_a: CL:1000682 ! kidney medulla interstitial cell intersection_of: CL:1000682 ! kidney medulla interstitial cell intersection_of: part_of UBERON:0005214 ! inner renal medulla interstitium relationship: part_of UBERON:0005214 ! inner renal medulla interstitium [Term] id: CL:1000804 name: kidney outer medulla interstitial cell namespace: cell xref: KUPO:0001094 is_a: CL:1000616 ! kidney outer medulla cell is_a: CL:1000682 ! kidney medulla interstitial cell intersection_of: CL:1000682 ! kidney medulla interstitial cell intersection_of: part_of UBERON:0005213 ! outer renal medulla interstitium relationship: part_of UBERON:0005213 ! outer renal medulla interstitium [Term] id: CL:1000838 name: kidney proximal convoluted tubule epithelial cell namespace: cell xref: KUPO:0001045 is_a: CL:0002306 ! epithelial cell of proximal tubule intersection_of: CL:0002306 ! epithelial cell of proximal tubule intersection_of: part_of UBERON:0001287 ! proximal convoluted tubule relationship: part_of UBERON:0001287 ! proximal convoluted tubule [Term] id: CL:1000839 name: kidney proximal straight tubule epithelial cell namespace: cell xref: KUPO:0001046 is_a: CL:0002306 ! epithelial cell of proximal tubule is_a: CL:1000616 ! kidney outer medulla cell is_a: CL:1001021 ! kidney loop of henle descending limb epithelial cell intersection_of: CL:0002306 ! epithelial cell of proximal tubule intersection_of: part_of UBERON:0001290 ! proximal straight tubule relationship: part_of UBERON:0001290 ! proximal straight tubule [Term] id: CL:1000849 name: kidney distal convoluted tubule epithelial cell namespace: cell xref: KUPO:0001056 is_a: CL:0002305 ! epithelial cell of distal tubule intersection_of: CL:0002305 ! epithelial cell of distal tubule intersection_of: part_of UBERON:0001292 ! distal convoluted tubule relationship: part_of UBERON:0001292 ! distal convoluted tubule [Term] id: CL:1000850 name: macula densa epithelial cell namespace: cell xref: KUPO:0001057 is_a: CL:0002305 ! epithelial cell of distal tubule is_a: CL:1000618 ! juxtaglomerular complex cell intersection_of: CL:0002305 ! epithelial cell of distal tubule intersection_of: part_of UBERON:0002335 ! macula densa relationship: part_of UBERON:0002335 ! macula densa [Term] id: CL:1000854 name: kidney blood vessel cell namespace: cell xref: KUPO:0001014 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000504 ! kidney medulla cell intersection_of: CL:1000504 ! kidney medulla cell intersection_of: part_of UBERON:0003517 ! kidney blood vessel relationship: part_of UBERON:0003517 ! kidney blood vessel relationship: participates_in GO:0008015 ! blood circulation [Term] id: CL:1000891 name: kidney arterial blood vessel cell namespace: cell xref: KUPO:0001029 is_a: CL:1000854 ! kidney blood vessel cell intersection_of: CL:1000854 ! kidney blood vessel cell intersection_of: part_of UBERON:0003644 ! kidney arterial blood vessel relationship: part_of UBERON:0003644 ! kidney arterial blood vessel [Term] id: CL:1000892 name: kidney capillary endothelial cell namespace: cell xref: KUPO:0001030 is_a: CL:0000071 ! blood vessel endothelial cell is_a: CL:1000854 ! kidney blood vessel cell [Term] id: CL:1000893 name: kidney venous blood vessel cell namespace: cell xref: KUPO:0001031 is_a: CL:1000854 ! kidney blood vessel cell intersection_of: CL:1000854 ! kidney blood vessel cell intersection_of: part_of UBERON:0001140 ! renal vein relationship: part_of UBERON:0001140 ! renal vein [Term] id: CL:1000909 name: kidney loop of henle epithelial cell namespace: cell xref: KUPO:0001047 is_a: CL:1000494 ! epithelial cell of renal tubule intersection_of: CL:1000494 ! epithelial cell of renal tubule intersection_of: part_of UBERON:0001288 ! loop of Henle relationship: part_of UBERON:0001288 ! loop of Henle [Term] id: CL:1000979 name: ureter smooth muscle cell namespace: cell xref: KUPO:0001118 is_a: CL:0000192 ! smooth muscle cell is_a: CL:1000601 ! ureteral cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0006855 ! ureter muscle layer relationship: part_of UBERON:0006855 ! ureter muscle layer [Term] id: CL:1001005 name: glomerular capillary endothelial cell namespace: cell xref: KUPO:0001037 is_a: CL:0002144 ! capillary endothelial cell is_a: CL:0002188 ! glomerular endothelial cell is_a: CL:1000494 ! epithelial cell of renal tubule is_a: CL:1000510 ! kidney glomerular epithelial cell is_a: CL:1000892 ! kidney capillary endothelial cell intersection_of: CL:1000892 ! kidney capillary endothelial cell intersection_of: part_of UBERON:0004294 ! glomerular capillary endothelium relationship: part_of UBERON:0004294 ! glomerular capillary endothelium [Term] id: CL:1001006 name: kidney afferent arteriole cell namespace: cell xref: KUPO:0001038 is_a: CL:1000494 ! epithelial cell of renal tubule is_a: CL:1000612 ! kidney corpuscule cell is_a: CL:1000891 ! kidney arterial blood vessel cell intersection_of: CL:1000891 ! kidney arterial blood vessel cell intersection_of: part_of UBERON:0004639 ! afferent arteriole relationship: part_of UBERON:0004639 ! afferent arteriole [Term] id: CL:1001009 name: kidney efferent arteriole cell namespace: cell xref: KUPO:0001041 is_a: CL:1000494 ! epithelial cell of renal tubule is_a: CL:1000612 ! kidney corpuscule cell is_a: CL:1000891 ! kidney arterial blood vessel cell intersection_of: CL:1000891 ! kidney arterial blood vessel cell intersection_of: part_of UBERON:0004640 ! efferent arteriole relationship: part_of UBERON:0004640 ! efferent arteriole [Term] id: CL:1001016 name: kidney loop of henle ascending limb epithelial cell namespace: cell xref: KUPO:0001048 is_a: CL:0002305 ! epithelial cell of distal tubule is_a: CL:1000909 ! kidney loop of henle epithelial cell intersection_of: CL:1000909 ! kidney loop of henle epithelial cell intersection_of: part_of UBERON:0005164 ! ascending limb of loop of Henle relationship: part_of UBERON:0005164 ! ascending limb of loop of Henle [Term] id: CL:1001021 name: kidney loop of henle descending limb epithelial cell namespace: cell xref: KUPO:0001053 is_a: CL:1000909 ! kidney loop of henle epithelial cell intersection_of: CL:1000909 ! kidney loop of henle epithelial cell intersection_of: part_of UBERON:0001289 ! descending limb of loop of Henle relationship: part_of UBERON:0001289 ! descending limb of loop of Henle [Term] id: CL:1001033 name: peritubular capillary endothelial cell namespace: cell xref: KUPO:0001065 is_a: CL:1000892 ! kidney capillary endothelial cell intersection_of: CL:1000892 ! kidney capillary endothelial cell intersection_of: part_of UBERON:0005272 ! peritubular capillary relationship: part_of UBERON:0005272 ! peritubular capillary [Term] id: CL:1001036 name: vasa recta cell namespace: cell xref: KUPO:0001068 is_a: CL:0002543 ! vein endothelial cell is_a: CL:1000892 ! kidney capillary endothelial cell is_a: CL:1000893 ! kidney venous blood vessel cell intersection_of: CL:1000892 ! kidney capillary endothelial cell intersection_of: part_of UBERON:0004726 ! vasa recta relationship: part_of UBERON:0004726 ! vasa recta [Term] id: CL:1001045 name: kidney cortex artery cell namespace: cell xref: KUPO:0001077 is_a: CL:1000891 ! kidney arterial blood vessel cell intersection_of: CL:1000891 ! kidney arterial blood vessel cell intersection_of: part_of UBERON:0005268 ! renal cortex artery relationship: part_of UBERON:0005268 ! renal cortex artery [Term] id: CL:1001052 name: kidney cortex vein cell namespace: cell xref: KUPO:0001084 is_a: CL:1000893 ! kidney venous blood vessel cell intersection_of: CL:1000893 ! kidney venous blood vessel cell intersection_of: part_of UBERON:0005269 ! renal cortex vein relationship: part_of UBERON:0005269 ! renal cortex vein [Term] id: CL:1001064 name: kidney artery smooth muscle cell namespace: cell comment: Note that the source of this term is KUPO:0001096 (artery smooth muscle cell), which we believe actually denotes the kidney specific structure. xref: KUPO:0001096 is_a: CL:0000359 ! vascular associated smooth muscle cell is_a: CL:1000891 ! kidney arterial blood vessel cell [Term] id: CL:1001066 name: kidney arteriole smooth muscle cell namespace: cell comment: Note that the source of this term is KUPO:0001098 (arteriole smooth muscle cell), which we believe actually denotes the kidney specific structure. xref: KUPO:0001098 is_a: CL:0000359 ! vascular associated smooth muscle cell is_a: CL:1000891 ! kidney arterial blood vessel cell [Term] id: CL:1001068 name: kidney venous system smooth muscle cell namespace: cell comment: Note that the source of this term is KUPO:0001068 (venous system smooth muscle cell), which we believe actually denotes the kidney specific structure. xref: KUPO:0001100 is_a: CL:0000359 ! vascular associated smooth muscle cell is_a: CL:1000893 ! kidney venous blood vessel cell [Term] id: CL:1001096 name: kidney afferent arteriole endothelial cell namespace: cell xref: KUPO:0001039 is_a: CL:1000412 ! endothelial cell of arteriole is_a: CL:1001006 ! kidney afferent arteriole cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0004639 ! afferent arteriole relationship: part_of UBERON:0004639 ! afferent arteriole [Term] id: CL:1001097 name: kidney afferent arteriole smooth muscle cell namespace: cell xref: KUPO:0001040 is_a: CL:1001006 ! kidney afferent arteriole cell is_a: CL:1001066 ! kidney arteriole smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0004639 ! afferent arteriole relationship: part_of UBERON:0004639 ! afferent arteriole [Term] id: CL:1001099 name: kidney efferent arteriole endothelial cell namespace: cell xref: KUPO:0001042 is_a: CL:1000412 ! endothelial cell of arteriole is_a: CL:1001009 ! kidney efferent arteriole cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0004640 ! efferent arteriole relationship: part_of UBERON:0004640 ! efferent arteriole [Term] id: CL:1001100 name: kidney efferent arteriole smooth muscle cell namespace: cell xref: KUPO:0001043 is_a: CL:1001009 ! kidney efferent arteriole cell is_a: CL:1001066 ! kidney arteriole smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0004640 ! efferent arteriole relationship: part_of UBERON:0004640 ! efferent arteriole [Term] id: CL:1001106 name: kidney loop of henle thick ascending limb epithelial cell namespace: cell xref: KUPO:0001049 is_a: CL:1000504 ! kidney medulla cell is_a: CL:1001016 ! kidney loop of henle ascending limb epithelial cell intersection_of: CL:1001016 ! kidney loop of henle ascending limb epithelial cell intersection_of: part_of UBERON:0001291 ! thick ascending limb of loop of Henle relationship: part_of UBERON:0001291 ! thick ascending limb of loop of Henle [Term] id: CL:1001107 name: kidney loop of henle thin ascending limb epithelial cell namespace: cell xref: KUPO:0001050 is_a: CL:1000617 ! kidney inner medulla cell is_a: CL:1001016 ! kidney loop of henle ascending limb epithelial cell intersection_of: CL:1001016 ! kidney loop of henle ascending limb epithelial cell intersection_of: part_of UBERON:0004193 ! loop of Henle ascending limb thin segment relationship: part_of UBERON:0004193 ! loop of Henle ascending limb thin segment [Term] id: CL:1001108 name: kidney loop of henle medullary thick ascending limb epithelial cell namespace: cell xref: KUPO:0001051 is_a: CL:1000616 ! kidney outer medulla cell is_a: CL:1001106 ! kidney loop of henle thick ascending limb epithelial cell intersection_of: CL:1001016 ! kidney loop of henle ascending limb epithelial cell intersection_of: part_of UBERON:0006376 ! premacula segment of distal straight tubule relationship: part_of UBERON:0006376 ! premacula segment of distal straight tubule [Term] id: CL:1001109 name: kidney loop of henle cortical thick ascending limb epithelial cell namespace: cell xref: KUPO:0001052 is_a: CL:1001106 ! kidney loop of henle thick ascending limb epithelial cell intersection_of: CL:1001016 ! kidney loop of henle ascending limb epithelial cell intersection_of: part_of UBERON:0006854 ! distal straight tubule postmacula segment relationship: part_of UBERON:0006854 ! distal straight tubule postmacula segment [Term] id: CL:1001111 name: kidney loop of henle thin descending limb epithelial cell namespace: cell xref: KUPO:0001054 is_a: CL:1000453 ! epithelial cell of intermediate tubule is_a: CL:1000616 ! kidney outer medulla cell is_a: CL:1001021 ! kidney loop of henle descending limb epithelial cell intersection_of: CL:1001021 ! kidney loop of henle descending limb epithelial cell intersection_of: part_of UBERON:0005096 ! descending thin limb relationship: part_of UBERON:0005096 ! descending thin limb [Term] id: CL:1001123 name: kidney outer medulla peritubular capillary cell namespace: cell xref: KUPO:0001066 is_a: CL:1000616 ! kidney outer medulla cell is_a: CL:1001033 ! peritubular capillary endothelial cell intersection_of: CL:1001033 ! peritubular capillary endothelial cell intersection_of: part_of UBERON:0006341 ! outer renal medulla peritubular capillary relationship: part_of UBERON:0006341 ! outer renal medulla peritubular capillary [Term] id: CL:1001124 name: kidney cortex peritubular capillary cell namespace: cell xref: KUPO:0001067 is_a: CL:1001033 ! peritubular capillary endothelial cell intersection_of: CL:1001033 ! peritubular capillary endothelial cell intersection_of: part_of UBERON:0006851 ! renal cortex peritubular capillary relationship: part_of UBERON:0006851 ! renal cortex peritubular capillary [Term] id: CL:1001126 name: inner renal medulla vasa recta cell namespace: cell xref: KUPO:0001069 is_a: CL:1000617 ! kidney inner medulla cell is_a: CL:1001036 ! vasa recta cell intersection_of: CL:1001036 ! vasa recta cell intersection_of: part_of UBERON:0004776 ! inner renal medulla vasa recta relationship: part_of UBERON:0004776 ! inner renal medulla vasa recta [Term] id: CL:1001127 name: outer renal medulla vasa recta cell namespace: cell xref: KUPO:0001070 is_a: CL:1000616 ! kidney outer medulla cell is_a: CL:1001036 ! vasa recta cell intersection_of: CL:1001036 ! vasa recta cell intersection_of: part_of UBERON:0004775 ! outer renal medulla vasa recta relationship: part_of UBERON:0004775 ! outer renal medulla vasa recta [Term] id: CL:1001131 name: vasa recta ascending limb cell namespace: cell xref: KUPO:0001074 is_a: CL:1001036 ! vasa recta cell intersection_of: CL:1001036 ! vasa recta cell intersection_of: part_of UBERON:0009091 ! vasa recta ascending limb relationship: part_of UBERON:0009091 ! vasa recta ascending limb [Term] id: CL:1001135 name: arcuate artery cell namespace: cell xref: KUPO:0001078 is_a: CL:1001045 ! kidney cortex artery cell intersection_of: CL:1001045 ! kidney cortex artery cell intersection_of: part_of UBERON:0001552 ! arcuate artery relationship: part_of UBERON:0001552 ! arcuate artery [Term] id: CL:1001138 name: interlobular artery cell namespace: cell xref: KUPO:0001081 is_a: CL:1001045 ! kidney cortex artery cell intersection_of: CL:1001045 ! kidney cortex artery cell intersection_of: part_of UBERON:0004723 ! interlobular artery relationship: part_of UBERON:0004723 ! interlobular artery [Term] id: CL:1001142 name: arcuate vein cell namespace: cell xref: KUPO:0001085 is_a: CL:1001052 ! kidney cortex vein cell intersection_of: CL:1001052 ! kidney cortex vein cell intersection_of: part_of UBERON:0004719 ! arcuate vein relationship: part_of UBERON:0004719 ! arcuate vein [Term] id: CL:1001145 name: interlobular vein cell namespace: cell xref: KUPO:0001088 is_a: CL:1001052 ! kidney cortex vein cell intersection_of: CL:1001052 ! kidney cortex vein cell intersection_of: part_of UBERON:0005168 ! interlobular vein relationship: part_of UBERON:0005168 ! interlobular vein [Term] id: CL:1001209 name: inner medulla vasa recta ascending limb cell namespace: cell xref: KUPO:0001075 is_a: CL:1001126 ! inner renal medulla vasa recta cell is_a: CL:1001131 ! vasa recta ascending limb cell intersection_of: CL:1001131 ! vasa recta ascending limb cell intersection_of: part_of UBERON:0009092 ! inner medulla vasa recta ascending limb relationship: part_of UBERON:0009092 ! inner medulla vasa recta ascending limb [Term] id: CL:1001210 name: outer medulla vasa recta ascending limb cell namespace: cell xref: KUPO:0001076 is_a: CL:1001127 ! outer renal medulla vasa recta cell is_a: CL:1001131 ! vasa recta ascending limb cell intersection_of: CL:1001131 ! vasa recta ascending limb cell intersection_of: part_of UBERON:0009093 ! outer medulla vasa recta ascending limb relationship: part_of UBERON:0009093 ! outer medulla vasa recta ascending limb [Term] id: CL:1001213 name: arcuate artery endothelial cell namespace: cell xref: KUPO:0001079 is_a: CL:1000413 ! endothelial cell of artery is_a: CL:1001135 ! arcuate artery cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001552 ! arcuate artery relationship: part_of UBERON:0001552 ! arcuate artery [Term] id: CL:1001214 name: arcuate artery smooth muscle cell namespace: cell xref: KUPO:0001080 is_a: CL:1001064 ! kidney artery smooth muscle cell is_a: CL:1001135 ! arcuate artery cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001552 ! arcuate artery relationship: part_of UBERON:0001552 ! arcuate artery [Term] id: CL:1001216 name: interlobulary artery endothelial cell namespace: cell xref: KUPO:0001082 is_a: CL:1000413 ! endothelial cell of artery is_a: CL:1001138 ! interlobular artery cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0004723 ! interlobular artery relationship: part_of UBERON:0004723 ! interlobular artery [Term] id: CL:1001217 name: interlobulary artery smooth muscle cell namespace: cell xref: KUPO:0001083 is_a: CL:1001064 ! kidney artery smooth muscle cell is_a: CL:1001138 ! interlobular artery cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0004723 ! interlobular artery relationship: part_of UBERON:0004723 ! interlobular artery [Term] id: CL:1001220 name: arcuate vein endothelial cell namespace: cell xref: KUPO:0001086 is_a: CL:0002543 ! vein endothelial cell is_a: CL:1001142 ! arcuate vein cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0004719 ! arcuate vein relationship: part_of UBERON:0004719 ! arcuate vein [Term] id: CL:1001221 name: arcuate vein smooth muscle cell namespace: cell xref: KUPO:0001087 is_a: CL:1001068 ! kidney venous system smooth muscle cell is_a: CL:1001142 ! arcuate vein cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0004719 ! arcuate vein relationship: part_of UBERON:0004719 ! arcuate vein [Term] id: CL:1001223 name: interlobulary vein endothelial cell namespace: cell xref: KUPO:0001089 is_a: CL:0002543 ! vein endothelial cell is_a: CL:1001145 ! interlobular vein cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0005168 ! interlobular vein relationship: part_of UBERON:0005168 ! interlobular vein [Term] id: CL:1001224 name: interlobulary vein smooth muscle cell namespace: cell xref: KUPO:0001090 is_a: CL:1001068 ! kidney venous system smooth muscle cell is_a: CL:1001145 ! interlobular vein cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0005168 ! interlobular vein relationship: part_of UBERON:0005168 ! interlobular vein [Term] id: CL:1001225 name: kidney collecting duct cell namespace: cell xref: KUPO:0001012 xref: Wikipedia:Kidney_collecting_duct_cell is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule relationship: part_of UBERON:0001232 ! collecting duct of renal tubule [Term] id: CL:1001285 name: vasa recta descending limb cell namespace: cell xref: KUPO:0001071 is_a: CL:1001036 ! vasa recta cell intersection_of: CL:1001036 ! vasa recta cell intersection_of: part_of UBERON:0009202 ! vasa recta descending limb relationship: part_of UBERON:0009202 ! vasa recta descending limb [Term] id: CL:1001286 name: inner medulla vasa recta descending limb cell namespace: cell xref: KUPO:0001072 is_a: CL:1001126 ! inner renal medulla vasa recta cell is_a: CL:1001285 ! vasa recta descending limb cell intersection_of: CL:1001285 ! vasa recta descending limb cell intersection_of: part_of UBERON:0009089 ! inner medulla vasa recta descending limb relationship: part_of UBERON:0009089 ! inner medulla vasa recta descending limb [Term] id: CL:1001287 name: outer medulla vasa recta descending limb cell namespace: cell xref: KUPO:0001073 is_a: CL:1001127 ! outer renal medulla vasa recta cell is_a: CL:1001285 ! vasa recta descending limb cell intersection_of: CL:1001285 ! vasa recta descending limb cell intersection_of: part_of UBERON:0009090 ! outer medulla vasa recta descending limb relationship: part_of UBERON:0009090 ! outer medulla vasa recta descending limb [Term] id: CL:1001318 name: renal interstitial pericyte namespace: cell xref: KUPO:0001104 is_a: CL:0000669 ! pericyte cell is_a: CL:1000497 ! kidney cell intersection_of: CL:0000669 ! pericyte cell intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney [Term] id: CL:1001319 name: bladder cell namespace: cell xref: KUPO:0001120 is_a: CL:1000600 ! lower urinary tract cell intersection_of: CL:0000548 ! animal cell intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001255 ! urinary bladder [Term] id: CL:1001320 name: urethra cell namespace: cell xref: KUPO:0001123 is_a: CL:1000600 ! lower urinary tract cell intersection_of: CL:0000548 ! animal cell intersection_of: part_of UBERON:0000057 ! urethra relationship: part_of UBERON:0000057 ! urethra [Term] id: CL:1001428 name: bladder urothelial cell namespace: cell xref: KUPO:0001121 is_a: CL:0000731 ! urothelial cell is_a: CL:1001319 ! bladder cell intersection_of: CL:0000731 ! urothelial cell intersection_of: part_of UBERON:0004645 ! urinary bladder urothelium relationship: part_of UBERON:0004645 ! urinary bladder urothelium [Term] id: CL:1001430 name: urethra urothelial cell namespace: cell xref: KUPO:0001124 is_a: CL:0000731 ! urothelial cell is_a: CL:1000296 ! epithelial cell of urethra intersection_of: CL:0000731 ! urothelial cell intersection_of: part_of UBERON:0004787 ! urethra urothelium relationship: part_of UBERON:0004787 ! urethra urothelium [Term] id: CL:1001431 name: kidney collecting duct principal cell namespace: cell xref: KUPO:0001128 is_a: CL:0005009 ! renal principal cell is_a: CL:1000454 ! kidney collecting duct epithelial cell intersection_of: CL:0005009 ! renal principal cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule relationship: part_of UBERON:0001232 ! collecting duct of renal tubule [Term] id: CL:1001432 name: kidney collecting duct intercalated cell namespace: cell xref: http://en.wikipedia.org/wiki/Collecting_duct_system#Intercalated_cells xref: KUPO:0001129 is_a: CL:0005010 ! renal intercalated cell is_a: CL:1000454 ! kidney collecting duct epithelial cell intersection_of: CL:0005010 ! renal intercalated cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule relationship: part_of UBERON:0001232 ! collecting duct of renal tubule [Term] id: CL:1001433 name: epithelial cell of exocrine pancreas namespace: cell def: "An epithelial cell of the exocrine pancreas." [GOC:tfm] synonym: "exocrine pancreas cell" EXACT [] xref: FMA:70986 is_a: CL:0000083 ! epithelial cell of pancreas intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000017 ! exocrine pancreas relationship: part_of UBERON:0000017 ! exocrine pancreas [Term] id: CL:1001434 name: olfactory bulb interneuron def: "A neuron residing in the olfactory bulb that serve to process and refine signals arising from olfactory sensory neurons" [PMID:18603310] is_a: CL:0000101 ! sensory neuron relationship: part_of UBERON:0002264 ! olfactory bulb [Term] id: CL:1001435 name: periglomerular cell def: "the small neuron in the glomerular layer of the olfactory bulb whose dendrites arborize within a glomerulus, where it receives synaptic input from olfactory receptor cell axon terminals, and also engages in dendrodendritic interactions with mitral and tufted cell dendrites; uses both GABA and dopamine as a neurotransmitter" [MP:0009943] synonym: "glomerular layer cell" EXACT [NIF_Cell:nifext_122] synonym: "olfactory bulb (accessory) glomerular layer cell" EXACT [NIF_Cell:nifext_122] synonym: "olfactory bulb glomerular layer cell" EXACT [NIF_Cell:nifext_122] synonym: "olfactory bulb glomerularal cell" EXACT [MP:0009943] synonym: "periglomerular cell" EXACT [NIF_Cell:nifext_122] xref: BTO:0003796 xref: NIF_Cell:nifext_122 is_a: CL:1001434 ! olfactory bulb interneuron relationship: part_of UBERON:0005377 ! olfactory bulb glomerular layer [Term] id: CL:1001436 name: hair-tylotrich neuron def: "the subcutaneous mechanoreceptors that innervate tylotrich hair follicles" [MP:0000977] is_a: CL:0002487 ! cutaneous/subcutaneous mechanoreceptor cell [Term] id: CL:1001437 name: hair-down neuron def: "the subcutaneous mechanoreceptors that innervate vellus hairs" [MP:0000979] is_a: CL:0002487 ! cutaneous/subcutaneous mechanoreceptor cell [Term] id: CL:1001451 name: sensory neuron of dorsal root ganglion def: "A sensory neuron of the dorsal root ganglia that senses body position and sends information about how much the muscle is stretched to the spinal cord." [MP:0004297] synonym: "proprioceptive neuron" EXACT [MP:0004297] is_a: CL:0009000 ! sensory neuron of spinal nerve relationship: part_of UBERON:0000044 ! dorsal root ganglion [Term] id: CL:1001474 name: medium spiny neuron def: "the inhibitory projection neurons located in the striatum that integrate glutamatergic signals arising from the cerebral cortex and thalamus" [MP:0008462] synonym: "medium-sized densely spiny neuron" RELATED [BTO:0004778] xref: BTO:0004778 is_a: CL:0000540 ! neuron relationship: part_of UBERON:0000369 ! corpus striatum [Term] id: CL:1001502 name: mitral cell def: "the large glutaminergic nerve cells whose dendrites synapse with axons of the olfactory receptor neurons in the glomerular layer of the olfactory bulb, and whose axons pass centrally in the olfactory tract to the olfactory cortex" [MP:0009954] is_a: CL:1001434 ! olfactory bulb interneuron relationship: part_of UBERON:0004186 ! olfactory bulb mitral cell layer [Term] id: CL:1001503 name: olfactory bulb tufted cell def: "the principal glutaminergic neuron located in the outer third of the external plexiform layer of the olfactory bulb; a single short primary dendrite traverses the outer external plexiform layer and terminates within an olfactory glomerulus in a tuft of branches, where it receives the input from olfactory receptor neuron axon terminals; axons of the tufted cells transfer information to a number of areas in the brain, including the piriform cortex, entorhinal cortex, olfactory tubercle, and amygdala" [MP:0009955] is_a: CL:0000540 ! neuron relationship: part_of UBERON:0005376 ! olfactory bulb external plexiform layer [Term] id: CL:1001505 name: parvocellular neurosecretory cell def: "the secretory neurons of the paraventricular nucleus that synthesize and secrete vasopressin, corticotropin-releasing factor (CRF) and thyrotropin-releasing hormone (TRH) into blood vessels in the hypothalamo-pituitary portal system" [MP:0010125] is_a: CL:0000167 ! peptide hormone secreting cell is_a: CL:0000540 ! neuron relationship: capable_of GO:0030103 ! vasopressin secretion relationship: part_of UBERON:0001930 ! paraventricular nucleus of hypothalamus [Term] id: CL:1001509 name: glycinergic neuron def: "the neurons that utilize glycine as a neurotransmitter" [MP:0010385] is_a: CL:0000540 ! neuron relationship: capable_of GO:0006545 ! glycine biosynthetic process [Term] id: CL:1001516 name: intestinal enteroendocrine cell def: "the various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the intestinal tract" [MP:0010802] is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000510 ! paneth cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: part_of UBERON:0001242 ! intestinal mucosa relationship: part_of UBERON:0001242 ! intestinal mucosa [Term] id: CL:1001517 name: stomach enteroendocrine cell def: "the various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the stomach" [MP:0010803] is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0002659 ! glandular cell of stomach intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: part_of UBERON:0001160 ! fundus of stomach relationship: part_of UBERON:0001160 ! fundus of stomach [Term] id: CL:1001561 name: vomeronasal sensory neuron def: "chemosensitive cells that innervate the vomernasal organ epithelium and are responsible for receiving and transmitting pheromone signals" [MP:0011679] is_a: CL:0000101 ! sensory neuron relationship: part_of UBERON:0002255 ! vomeronasal organ [Term] id: CL:1001566 name: bronchioalveolar stem cells def: "a respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole, which gives rise to alveolar cell types and Clara cells in response to lung injury." [MP:0011691] is_a: CL:0000034 ! stem cell relationship: part_of UBERON:0000115 ! lung epithelium [Term] id: CL:1001567 name: lung endothelial cell synonym: "endothelial cell of lung" RELATED [] synonym: "pulmonary vessel endothelial cell" RELATED [] is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0002139 ! endothelial cell of vascular tree intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0000102 ! lung vasculature relationship: part_of UBERON:0002048 ! lung [Term] id: CL:1001568 name: pulmonary artery endothelial cell synonym: "PAEC cell" RELATED [BTO:0001141] xref: BTO:0001141 is_a: CL:1000413 ! endothelial cell of artery intersection_of: CL:0002139 ! endothelial cell of vascular tree intersection_of: part_of UBERON:0002012 ! pulmonary artery relationship: part_of UBERON:0002012 ! pulmonary artery relationship: part_of UBERON:0005317 ! pulmonary artery endothelium [Term] id: CL:1001569 name: hippocampal interneuron def: "An interneuron of the hippocampus." [GOC:pr] xref: FMA:84777 is_a: CL:0000099 ! interneuron intersection_of: CL:0000099 ! interneuron intersection_of: part_of UBERON:0001954 ! Ammon's horn relationship: part_of UBERON:0001954 ! Ammon's horn [Term] id: CL:1001571 name: hippocampal pyramidal neuron def: "A pyramidal cell of the hippocampus." [GOC:pr, PMID:19342486] synonym: "hippocampus (CA) pyramidal cell" EXACT [NIF_Cell:sao131261273] synonym: "hippocampus (CA) pyramidal neuron" EXACT [NIF_Cell:sao131261273] xref: NIF_Cell:sao131261273 xref: SAO:sao131261273 is_a: CL:0000598 ! pyramidal cell is_a: CL:0002608 ! hippocampal neuron intersection_of: CL:0000598 ! pyramidal cell intersection_of: part_of UBERON:0001954 ! Ammon's horn relationship: part_of UBERON:0001954 ! Ammon's horn relationship: part_of UBERON:0002313 ! hippocampus pyramidal layer [Term] id: CP:0000000 name: neutrophillic cytoplasm namespace: cell def: "Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions." [GOC:tfm] is_a: GO:0005737 ! cytoplasm created_by: tmeehan creation_date: 2010-05-25T01:36:34Z [Term] id: CP:0000025 name: lobed nucleus namespace: cell def: "Nucleus with two or more lobes connected by a thin filament that contains no internal chromatin." [GOC:tfm] is_a: GO:0005634 ! nucleus intersection_of: GO:0005634 ! nucleus intersection_of: has_quality PATO:0001979 ! lobed relationship: has_quality PATO:0001979 ! lobed created_by: tmeehan creation_date: 2009-12-22T03:54:43Z [Term] id: CP:0000027 name: acidophilic cytoplasm namespace: cell def: "Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions." [GOC:tfm] synonym: "eosinophilic" NARROW [] is_a: GO:0005737 ! cytoplasm created_by: tmeehan creation_date: 2009-12-22T04:23:25Z [Term] id: CP:0000028 name: basophilic cytoplasm namespace: cell def: "Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions." [GOC:tfm] is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: has_quality PATO:0002094 ! basophilic relationship: has_quality PATO:0002094 ! basophilic created_by: tmeehan creation_date: 2009-12-22T04:24:54Z [Term] id: CP:0000035 name: polychromatophilic cytoplasm namespace: cell def: "Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions." [GOC:tfm] is_a: GO:0005737 ! cytoplasm created_by: tmeehan creation_date: 2009-12-28T04:25:23Z [Term] id: CP:0000037 name: increased nucleus size namespace: cell def: "A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell." [GOC:tfm] is_a: GO:0005634 ! nucleus intersection_of: GO:0005634 ! nucleus intersection_of: has_quality PATO:0000586 ! increased size relationship: has_quality PATO:0000586 ! increased size created_by: tmeehan creation_date: 2009-12-23T10:53:24Z [Term] id: CP:0000039 name: banded nucleus namespace: cell def: "A concave nuclear shape where the nucleus is indented to more than half the distance to the farthest nuclear margin, but in no area is the chromatin condensed to a single filament." [GOC:tfm] is_a: GO:0005634 ! nucleus created_by: tmeehan creation_date: 2009-12-23T02:18:43Z [Term] id: CP:0000040 name: reniform nucleus namespace: cell def: "A concave nucleus shape where the indentation is smaller than half of the distance to the farthest nuclear margin." [GOC:tfm] is_a: GO:0005634 ! nucleus intersection_of: GO:0005634 ! nucleus intersection_of: has_quality PATO:0001871 ! reniform relationship: has_quality PATO:0001871 ! reniform created_by: tmeehan creation_date: 2009-12-23T02:31:25Z [Term] id: CP:0000043 name: cartwheel heterochromatin namespace: cell def: "Heterochromatin that is arranged in a carthwheel pattern." [GOC:tfm] is_a: GO:0000792 ! heterochromatin created_by: tmeehan creation_date: 2009-12-28T04:28:35Z [Term] id: GO:0000003 name: reproduction namespace: biological_process alt_id: GO:0019952 alt_id: GO:0050876 def: "The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism." [GOC:go_curators, GOC:isa_complete, ISBN:0198506732] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "reproductive physiological process" EXACT [] xref: Wikipedia:Reproduction is_a: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0000018 name: regulation of DNA recombination namespace: biological_process def: "Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents." [GOC:go_curators, ISBN:0198506732] subset: gosubset_prok is_a: GO:0051052 ! regulation of DNA metabolic process relationship: regulates GO:0006310 ! DNA recombination property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0000087 name: M phase of mitotic cell cycle namespace: biological_process def: "M phase occurring as part of the mitotic cell cycle. M phase is the part of the cell cycle during which nuclear division takes place. A mitotic cell cycle is one which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells." [GOC:dph, GOC:mah, ISBN:0815316194] synonym: "M-phase of mitotic cell cycle" EXACT [] xref: Reactome:REACT_105412 "M Phase, Mus musculus" xref: Reactome:REACT_107095 "M Phase, Dictyostelium discoideum" xref: Reactome:REACT_109059 "M Phase, Saccharomyces cerevisiae" xref: Reactome:REACT_29488 "M Phase, Canis familiaris" xref: Reactome:REACT_33490 "M Phase, Caenorhabditis elegans" xref: Reactome:REACT_82055 "M Phase, Rattus norvegicus" xref: Reactome:REACT_87132 "M Phase, Bos taurus" xref: Reactome:REACT_88263 "M Phase, Xenopus tropicalis" xref: Reactome:REACT_910 "M Phase, Homo sapiens" xref: Reactome:REACT_92998 "M Phase, Danio rerio" xref: Reactome:REACT_93131 "M Phase, Schizosaccharomyces pombe" xref: Reactome:REACT_93566 "M Phase, Gallus gallus" xref: Reactome:REACT_93720 "M Phase, Drosophila melanogaster" xref: Reactome:REACT_94536 "M Phase, Taeniopygia guttata" is_a: GO:0000279 ! M phase relationship: part_of GO:0000278 ! mitotic cell cycle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0000226 name: microtubule cytoskeleton organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins." [GOC:mah] synonym: "microtubule cytoskeleton organisation" EXACT [GOC:mah] synonym: "microtubule cytoskeleton organization and biogenesis" RELATED [GOC:mah] synonym: "microtubule dynamics" EXACT [GOC:dph, GOC:tb] is_a: GO:0007010 ! cytoskeleton organization is_a: GO:0007017 ! microtubule-based process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0000278 name: mitotic cell cycle namespace: biological_process def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194, Reactome:69278] subset: goslim_yeast xref: Reactome:REACT_100451 "Cell Cycle, Mitotic, Taeniopygia guttata" xref: Reactome:REACT_104035 "Cell Cycle, Mitotic, Sus scrofa" xref: Reactome:REACT_104195 "Cell Cycle, Mitotic, Canis familiaris" xref: Reactome:REACT_105856 "Cell Cycle, Mitotic, Danio rerio" xref: Reactome:REACT_108233 "Cell Cycle, Mitotic, Saccharomyces cerevisiae" xref: Reactome:REACT_152 "Cell Cycle, Mitotic, Homo sapiens" xref: Reactome:REACT_28464 "Cell Cycle, Mitotic, Xenopus tropicalis" xref: Reactome:REACT_28953 "Cell Cycle, Mitotic, Bos taurus" xref: Reactome:REACT_33388 "Cell Cycle, Mitotic, Rattus norvegicus" xref: Reactome:REACT_53493 "Cell Cycle, Mitotic, Plasmodium falciparum" xref: Reactome:REACT_79085 "Cell Cycle, Mitotic, Schizosaccharomyces pombe" xref: Reactome:REACT_84794 "Cell Cycle, Mitotic, Caenorhabditis elegans" xref: Reactome:REACT_85137 "Cell Cycle, Mitotic, Gallus gallus" xref: Reactome:REACT_85950 "Cell Cycle, Mitotic, Arabidopsis thaliana" xref: Reactome:REACT_90332 "Cell Cycle, Mitotic, Mus musculus" xref: Reactome:REACT_90846 "Cell Cycle, Mitotic, Oryza sativa" xref: Reactome:REACT_96281 "Cell Cycle, Mitotic, Drosophila melanogaster" xref: Reactome:REACT_97744 "Cell Cycle, Mitotic, Dictyostelium discoideum" xref: Reactome:REACT_98208 "Cell Cycle, Mitotic, Mycobacterium tuberculosis" is_a: GO:0007049 ! cell cycle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0000279 name: M phase namespace: biological_process def: "A cell cycle process comprising the steps by which a cell progresses through M phase, the part of the cell cycle comprising nuclear division." [GOC:dph, GOC:mah, ISBN:0815316194] synonym: "M-phase" EXACT [] xref: Wikipedia:M_phase is_a: GO:0022403 ! cell cycle phase property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0000280 name: nuclear division namespace: biological_process def: "The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei." [GOC:mah] subset: goslim_pir synonym: "karyokinesis" RELATED [] is_a: GO:0048285 ! organelle fission property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0000323 name: lytic vacuole namespace: cellular_component def: "A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases." [GOC:krc] is_a: GO:0005773 ! vacuole property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0000785 name: chromatin namespace: cellular_component alt_id: GO:0005717 def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." [GOC:elh, PMID:20404130] synonym: "chromosome scaffold" RELATED [] xref: NIF_Subcellular:sao1615953555 is_a: GO:0044427 ! chromosomal part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0000791 name: euchromatin namespace: cellular_component def: "A dispersed and relatively uncompacted form of chromatin." [GOC:elh] xref: NIF_Subcellular:sao445485807 xref: Wikipedia:Euchromatin is_a: GO:0000785 ! chromatin property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0000792 name: heterochromatin namespace: cellular_component def: "A compact and highly condensed form of chromatin." [GOC:elh] xref: NIF_Subcellular:sao581845896 xref: Wikipedia:Heterochromatin is_a: GO:0000785 ! chromatin property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001501 name: skeletal system development namespace: biological_process def: "The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton)." [GOC:dph, GOC:jid, GOC:tb, http://www.stedmans.com/] synonym: "skeletal development" EXACT [] is_a: GO:0048731 ! system development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001503 name: ossification namespace: biological_process def: "The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance." [GOC:mtg_mpo, PMID:17572649] comment: Note that this term does not have a 'developmental process' parent because ossification isn't necessarily developmental, can also occur as part of bone remodeling. Instead use 'ossification involved in bone maturation ; GO:0043931'. synonym: "bone biosynthesis" EXACT [] synonym: "bone formation" EXACT [] synonym: "osteogenesis" EXACT [] xref: Wikipedia:Ossification is_a: GO:0044707 ! single-multicellular organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001525 name: angiogenesis namespace: biological_process def: "Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels." [ISBN:0878932453] synonym: "blood vessel formation from pre-existing blood vessels" EXACT systematic_synonym [] xref: Wikipedia:Angiogenesis is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis relationship: part_of GO:0048514 ! blood vessel morphogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001553 name: luteinization namespace: biological_process def: "The set of processes resulting in differentiation of theca and granulosa cells into luteal cells and in the formation of a corpus luteum after ovulation." [http://ovary.stanford.edu] synonym: "luteal phase" RELATED [] xref: Wikipedia:Luteal_phase xref: Wikipedia:Luteinization is_a: GO:0022602 ! ovulation cycle process relationship: part_of GO:0008585 ! female gonad development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001568 name: blood vessel development namespace: biological_process def: "The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood." [GOC:hjd, UBERON:0001981] is_a: GO:0048856 ! anatomical structure development relationship: part_of GO:0001944 ! vasculature development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001578 name: microtubule bundle formation namespace: biological_process def: "A process that results in a parallel arrangement of microtubules." [GOC:dph] synonym: "microtubule bundling" EXACT [] is_a: GO:0000226 ! microtubule cytoskeleton organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001649 name: osteoblast differentiation namespace: biological_process def: "The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone." [CL:0000062, GO_REF:0000034, GOC:jid] synonym: "osteoblast cell differentiation" EXACT [] is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0001503 ! ossification property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001667 name: ameboidal cell migration namespace: biological_process def: "Cell migration that is accomplished by extension and retraction of a pseudopodium." [GOC:dph] synonym: "ameboid cell migration" EXACT [] synonym: "amoeboid cell migration" EXACT [] synonym: "amoeboidal cell migration" EXACT [] is_a: GO:0016477 ! cell migration property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001675 name: acrosome assembly namespace: biological_process def: "The formation of the acrosome from the spermatid Golgi." [GOC:dph, GOC:hjd, GOC:tb] synonym: "acrosome formation" EXACT [GOC:dph, GOC:tb] is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0010927 ! cellular component assembly involved in morphogenesis is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism relationship: part_of GO:0007286 ! spermatid development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001773 name: myeloid dendritic cell activation namespace: biological_process def: "The change in morphology and behavior of a dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." [GOC:mgi_curators, ISBN:0781735149] is_a: GO:0002274 ! myeloid leukocyte activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001775 name: cell activation namespace: biological_process def: "A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:mgi_curators] subset: goslim_pir is_a: GO:0044763 ! single-organism cellular process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001776 name: leukocyte homeostasis namespace: biological_process def: "The process of regulating the proliferation and elimination of cells of the immune system such that the total number of cells of a particular cell type within a whole or part of an organism is stable over time in the absence of an outside stimulus." [GOC:add, ISBN:0781735149] comment: Note that this term represents the return of immune system cell levels to stable numbers following an immune response as well as the proliferation and elimination of cells of the immune system required to maintain stable numbers in the absence of an outside stimulus. synonym: "immune cell homeostasis" EXACT [] synonym: "leucocyte homeostasis" EXACT [] is_a: GO:0002376 ! immune system process is_a: GO:0048872 ! homeostasis of number of cells property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001782 name: B cell homeostasis namespace: biological_process def: "The process of regulating the proliferation and elimination of B cells such that the total number of B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus." [GOC:add, ISBN:0781735149, PMID:12956429] comment: Note that this term represents the return of B cell levels to stable numbers following an immune response as well as the proliferation and elimination of B cells required to maintain stable numbers in the absence of an outside stimulus. synonym: "B lymphocyte homeostasis" EXACT [] synonym: "B-cell homeostasis" EXACT [] synonym: "B-lymphocyte homeostasis" EXACT [] is_a: GO:0002260 ! lymphocyte homeostasis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001783 name: B cell apoptotic process namespace: biological_process def: "Any apoptotic process in a B cell, a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity." [CL:0000236, GOC:add, GOC:mtg_apoptosis, ISBN:0781735149] synonym: "apoptosis of B cells" EXACT [] synonym: "apoptosis of B lymphocytes" EXACT [] synonym: "apoptosis of B-cells" EXACT [] synonym: "apoptosis of B-lymphocytes" EXACT [] synonym: "B cell apoptosis" NARROW [] synonym: "B cell programmed cell death by apoptosis" EXACT [] synonym: "B lymphocyte apoptosis" EXACT [] synonym: "B lymphocyte programmed cell death by apoptosis" EXACT [] synonym: "B-cell apoptosis" EXACT [] synonym: "B-cell programmed cell death by apoptosis" EXACT [] synonym: "B-lymphocyte apoptosis" EXACT [] synonym: "B-lymphocyte programmed cell death by apoptosis" EXACT [] synonym: "programmed cell death of B cells by apoptosis" EXACT [] synonym: "programmed cell death of B lymphocytes by apoptosis" EXACT [] synonym: "programmed cell death of B-cells by apoptosis" EXACT [] synonym: "programmed cell death of B-lymphocytes by apoptosis" EXACT [] synonym: "programmed cell death, B cells" EXACT [] synonym: "programmed cell death, B lymphocytes" EXACT [] synonym: "programmed cell death, B-cells" EXACT [] synonym: "programmed cell death, B-lymphocytes" EXACT [] is_a: GO:0070227 ! lymphocyte apoptotic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001816 name: cytokine production namespace: biological_process def: "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] comment: Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular cytokine levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting cytokine molecules, or increased conversion from precursor molecules. subset: goslim_pir synonym: "interferon production" NARROW [GOC:add, GOC:mah] synonym: "interleukin production" NARROW [GOC:add, GOC:mah] is_a: GO:0044707 ! single-multicellular organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001817 name: regulation of cytokine production namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of production of a cytokine." [GOC:add, ISBN:0781735149] is_a: GO:0051239 ! regulation of multicellular organismal process relationship: regulates GO:0001816 ! cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001818 name: negative regulation of cytokine production namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of production of a cytokine." [GOC:add, ISBN:0781735149] synonym: "down regulation of cytokine production" EXACT [] synonym: "down-regulation of cytokine production" EXACT [] synonym: "downregulation of cytokine production" EXACT [] synonym: "inhibition of cytokine production" NARROW [] is_a: GO:0001817 ! regulation of cytokine production is_a: GO:0051241 ! negative regulation of multicellular organismal process relationship: negatively_regulates GO:0001816 ! cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001820 name: serotonin secretion namespace: biological_process def: "The regulated release of serotonin by a cell or group of cells. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells." [GOC:ef, ISBN:0198506732, ISBN:0781735149] synonym: "5-HT secretion" EXACT [] synonym: "5-hydroxytryptamine secretion" EXACT [] synonym: "serotonin release" RELATED [GOC:tb] is_a: GO:0006837 ! serotonin transport is_a: GO:0023061 ! signal release is_a: GO:0032940 ! secretion by cell property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001894 name: tissue homeostasis namespace: biological_process def: "A homeostatic process involved in the maintenance of an internal steady state within a defined tissue of an organism, including control of cellular proliferation and death and control of metabolic function." [GOC:add, GOC:isa_complete] synonym: "tissue maintenance" NARROW [GOC:add] is_a: GO:0060249 ! anatomical structure homeostasis relationship: part_of GO:0048871 ! multicellular organismal homeostasis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001906 name: cell killing namespace: biological_process def: "Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions." [GOC:add] subset: goslim_pir subset: gosubset_prok synonym: "necrosis" RELATED [] is_a: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001909 name: leukocyte mediated cytotoxicity namespace: biological_process def: "The directed killing of a target cell by a leukocyte." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149, PMID:11911826] comment: This term was improved by GO_REF:0000022. It was moved. Note that this term and its children describe contact-dependent killing of target cells by lymphocytes and myeloid cells of the immune system. synonym: "immune cell mediated cell death" EXACT [] synonym: "immune cell mediated cell killing" EXACT [] synonym: "immune cell mediated cytotoxicity" EXACT [] synonym: "leucocyte mediated cytotoxicity" EXACT [] is_a: GO:0001906 ! cell killing is_a: GO:0002252 ! immune effector process is_a: GO:0044699 ! single-organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001913 name: T cell mediated cytotoxicity namespace: biological_process def: "The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors." [GOC:add, GOC:pr, ISBN:0781735149, PMID:11911826] comment: Note that either or both mechanisms mentioned in the definition may be used in this process. Note that both granule release and the engagement of death receptors on target cells result in the induction of apoptosis in the target cell. Note that both CD4 and CD8 positive T cells can mediate apoptosis of target cells, independently of their definition as 'helper' T cells or not. synonym: "T cell mediated apoptosis" EXACT [] synonym: "T cell mediated cell death" EXACT [] synonym: "T cell mediated cell killing" EXACT [] synonym: "T cell mediated cytolysis" RELATED [] synonym: "T lymphocyte mediated cytotoxicity" EXACT [] synonym: "T-cell mediated apoptosis" EXACT [] synonym: "T-cell mediated cell death" EXACT [] synonym: "T-cell mediated cell killing" EXACT [] synonym: "T-cell mediated cytotoxicity" EXACT [] synonym: "T-lymphocyte mediated cytotoxicity" EXACT [] is_a: GO:0001909 ! leukocyte mediated cytotoxicity is_a: GO:0002456 ! T cell mediated immunity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001942 name: hair follicle development namespace: biological_process alt_id: GO:0001943 def: "The process whose specific outcome is the progression of the hair follicle over time, from its formation to the mature structure. A hair follicle is a tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open." [GOC:dph, UBERON:0002073] is_a: GO:0008544 ! epidermis development is_a: GO:0022405 ! hair cycle process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001944 name: vasculature development namespace: biological_process def: "The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism." [GOC:dph, UBERON:0002409] synonym: "vascular system development" RELATED [GOC:curators] is_a: GO:0048731 ! system development relationship: part_of GO:0072358 ! cardiovascular system development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001974 name: blood vessel remodeling namespace: biological_process def: "The reorganization or renovation of existing blood vessels." [GOC:hjd] is_a: GO:0048771 ! tissue remodeling property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002200 name: somatic diversification of immune receptors namespace: biological_process def: "The somatic process allowing for the production of immune receptors whose specificity is not encoded in the germline genomic sequences." [GOC:add, ISBN:0781735149, PMID:16102575, PMID:16166509] comment: Note that this process covers somatic recombination, gene conversion, hypermutation, N-region addition, and alternate splicing processes of immune receptor diversification. is_a: GO:0002376 ! immune system process relationship: part_of GO:0002520 ! immune system development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002204 name: somatic recombination of immunoglobulin genes involved in immune response namespace: biological_process def: "The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, also known as immunoglobulin gene segments, within a single locus following the induction of and contributing to an immune response." [GOC:add, ISBN:0781735149] synonym: "somatic recombination of antibody genes during immune response" RELATED [] synonym: "somatic recombination of immunoglobulin genes during immune response" RELATED [GOC:dph] is_a: GO:0002208 ! somatic diversification of immunoglobulins involved in immune response is_a: GO:0016447 ! somatic recombination of immunoglobulin gene segments property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002208 name: somatic diversification of immunoglobulins involved in immune response namespace: biological_process def: "The somatic process that results in the generation of sequence diversity of immunoglobulins after induction, and contributes to an immune response." [GOC:add, ISBN:0781735149, PMID:14991701] synonym: "somatic diversification of antibodies during immune response" RELATED [] synonym: "somatic diversification of immunoglobulins during immune response" RELATED [GOC:dph] is_a: GO:0016445 ! somatic diversification of immunoglobulins relationship: part_of GO:0002381 ! immunoglobulin production involved in immunoglobulin mediated immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002215 name: defense response to nematode namespace: biological_process alt_id: GO:0002216 def: "A response to protect an organism from a directly detected or perceived external threat from a nematode or nematodes, which results in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack." [GOC:add, PMID:11516579, PMID:14506883] synonym: "physiological defense response to nematode" EXACT [] is_a: GO:0006952 ! defense response is_a: GO:0009624 ! response to nematode property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002227 name: innate immune response in mucosa namespace: biological_process def: "Any process of the innate immune response that takes place in the mucosal tissues." [GOC:add, PMID:10719665, PMID:15971105] is_a: GO:0002385 ! mucosal immune response is_a: GO:0045087 ! innate immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002228 name: natural killer cell mediated immunity namespace: biological_process def: "The promotion of an immune response by natural killer cells through direct recognition of target cells or through the release of cytokines." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was added by GO_REF:0000022. synonym: "NK cell mediated immunity" EXACT [] is_a: GO:0002449 ! lymphocyte mediated immunity is_a: GO:0045087 ! innate immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002244 name: hematopoietic progenitor cell differentiation namespace: biological_process def: "The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells." [GOC:add, GOC:rl, ISBN:0781735149, PMID:16551251] synonym: "haematopoietic progenitor cell differentiation" EXACT [] synonym: "haemopoietic progenitor cell differentiation" EXACT [] synonym: "hemopoietic progenitor cell differentiation" EXACT [] is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0030097 ! hemopoiesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002249 name: lymphocyte anergy namespace: biological_process def: "Any process contributing to lymphocyte anergy, a state of functional inactivation." [GOC:add] is_a: GO:0002507 ! tolerance induction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002250 name: adaptive immune response namespace: biological_process def: "An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory)." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was added by GO_REF:0000022. synonym: "acquired immune response" EXACT [ISBN:068340007X] xref: Wikipedia:Adaptive_immune_system is_a: GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002251 name: organ or tissue specific immune response namespace: biological_process def: "An immune response taking place in an organ or tissues such as the liver, brain, mucosa, or nervous system tissues." [GO_REF:0000022, GOC:jal, GOC:mtg_15nov05] comment: This term was added by GO_REF:0000022. synonym: "immune response in organ or tissue" EXACT [] is_a: GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002252 name: immune effector process namespace: biological_process def: "Any process of the immune system that can potentially contribute to an immune response." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was added by GO_REF:0000022. is_a: GO:0002376 ! immune system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002260 name: lymphocyte homeostasis namespace: biological_process def: "The process of regulating the proliferation and elimination of lymphocytes such that the total number of lymphocytes within a whole or part of an organism is stable over time in the absence of an outside stimulus." [GOC:add, PMID:15826826, PMID:16319493, PMID:16551252, PMID:16551262] is_a: GO:0001776 ! leukocyte homeostasis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002263 name: cell activation involved in immune response namespace: biological_process def: "A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was added by GO_REF:0000022. synonym: "cell activation during immune response" RELATED [GOC:tb] is_a: GO:0001775 ! cell activation is_a: GO:0002252 ! immune effector process relationship: part_of GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002274 name: myeloid leukocyte activation namespace: biological_process def: "A change in the morphology or behavior of a myeloid leukocyte resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:add, ISBN:0781735149] synonym: "myeloid leucocyte activation" EXACT [] is_a: GO:0045321 ! leukocyte activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002285 name: lymphocyte activation involved in immune response namespace: biological_process def: "A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response." [GOC:add, ISBN:0781735149] synonym: "lymphocyte activation during immune response" RELATED [GOC:tb] is_a: GO:0002366 ! leukocyte activation involved in immune response is_a: GO:0046649 ! lymphocyte activation relationship: part_of GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002286 name: T cell activation involved in immune response namespace: biological_process def: "The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response." [GOC:add, ISBN:0781735149] synonym: "T cell activation during immune response" RELATED [GOC:tb] synonym: "T lymphocyte activation during immune response" RELATED [] synonym: "T-cell activation during immune response" RELATED [] synonym: "T-lymphocyte activation during immune response" RELATED [] is_a: GO:0002285 ! lymphocyte activation involved in immune response is_a: GO:0042110 ! T cell activation relationship: part_of GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002287 name: alpha-beta T cell activation involved in immune response namespace: biological_process def: "The change in morphology and behavior of an alpha-beta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response." [GOC:add, ISBN:0781735149] synonym: "alpha-beta T cell activation during immune response" RELATED [GOC:tb] synonym: "alpha-beta T lymphocyte activation during immune response" RELATED [] synonym: "alpha-beta T-cell activation during immune response" RELATED [] synonym: "alpha-beta T-lymphocyte activation during immune response" RELATED [] is_a: GO:0002286 ! T cell activation involved in immune response is_a: GO:0046631 ! alpha-beta T cell activation relationship: part_of GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002288 name: NK T cell activation involved in immune response namespace: biological_process def: "The change in morphology and behavior of a mature or immature natural killer T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response." [GOC:add, PMID:15771592] synonym: "natural killer T lymphocyte activation during immune response" RELATED [] synonym: "natural killer T-cell activation during immune response" RELATED [] synonym: "natural killer T-lymphocyte activation during immune response" RELATED [] synonym: "NK T cell activation during immune response" RELATED [GOC:tb] synonym: "NK T lymphocyte activation during immune response" RELATED [] synonym: "NK T-cell activation during immune response" RELATED [] synonym: "NK T-lymphocyte activation during immune response" RELATED [] is_a: GO:0002287 ! alpha-beta T cell activation involved in immune response is_a: GO:0051132 ! NK T cell activation relationship: part_of GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002292 name: T cell differentiation involved in immune response namespace: biological_process def: "The process in which an antigenically naive T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells." [GOC:add, ISBN:0781735149] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "T cell development involved in immune response" RELATED [GOC:add] synonym: "T cell differentiation during immune response" RELATED [GOC:tb] synonym: "T lymphocyte differentiation during immune response" RELATED [] synonym: "T-cell differentiation during immune response" RELATED [] synonym: "T-lymphocyte differentiation during immune response" RELATED [] is_a: GO:0002286 ! T cell activation involved in immune response is_a: GO:0030217 ! T cell differentiation relationship: part_of GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002293 name: alpha-beta T cell differentiation involved in immune response namespace: biological_process def: "The process in which an antigenically naive alpha-beta T cell acquires the specialized features of an effector, regulatory, or memory T cell during an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells." [GOC:add, ISBN:0781735149] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "alpha-beta T cell development involved in immune response" RELATED [GOC:add] synonym: "alpha-beta T cell differentiation during immune response" RELATED [GOC:tb] synonym: "alpha-beta T lymphocyte differentiation during immune response" RELATED [] synonym: "alpha-beta T-cell differentiation during immune response" RELATED [] synonym: "alpha-beta T-lymphocyte differentiation during immune response" RELATED [] is_a: GO:0002287 ! alpha-beta T cell activation involved in immune response is_a: GO:0002292 ! T cell differentiation involved in immune response is_a: GO:0046632 ! alpha-beta T cell differentiation relationship: part_of GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002294 name: CD4-positive, alpha-beta T cell differentiation involved in immune response namespace: biological_process def: "The process in which an antigenically naive CD4-positive, alpha-beta T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells." [GOC:add, ISBN:0781735149] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "CD4-positive, alpha-beta T cell development involved in immune response" RELATED [GOC:add] synonym: "CD4-positive, alpha-beta T cell differentiation during immune response" RELATED [GOC:tb] synonym: "CD4-positive, alpha-beta T lymphocyte differentiation during immune response" RELATED [] synonym: "CD4-positive, alpha-beta T-cell differentiation during immune response" RELATED [] synonym: "CD4-positive, alpha-beta T-lymphocyte differentiation during immune response" RELATED [] is_a: GO:0002293 ! alpha-beta T cell differentiation involved in immune response is_a: GO:0043367 ! CD4-positive, alpha-beta T cell differentiation relationship: part_of GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002312 name: B cell activation involved in immune response namespace: biological_process def: "The change in morphology and behavior of a mature or immature B cell during an immune response, resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." [GOC:jal] synonym: "B cell activation during immune response" RELATED [GOC:tb] synonym: "B lymphocyte activation during immune response" RELATED [] synonym: "B-cell activation during immune response" RELATED [] synonym: "B-lymphocyte activation during immune response" RELATED [] is_a: GO:0002285 ! lymphocyte activation involved in immune response is_a: GO:0042113 ! B cell activation relationship: part_of GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002313 name: mature B cell differentiation involved in immune response namespace: biological_process def: "The process in which a naive B cell acquires the specialized features of a mature or memory B cell during an immune response." [GOC:jal] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "mature B cell development involved in immune response" RELATED [GOC:add] synonym: "mature B cell differentiation during immune response" RELATED [GOC:tb] synonym: "mature B lymphocyte differentiation during immune response" RELATED [] synonym: "mature B-cell differentiation during immune response" RELATED [] synonym: "mature B-lymphocyte differentiation during immune response" RELATED [] is_a: GO:0002312 ! B cell activation involved in immune response is_a: GO:0002335 ! mature B cell differentiation relationship: part_of GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002314 name: germinal center B cell differentiation namespace: biological_process def: "The process in which a B cell in the spleen acquires the specialized features of a germinal center B cell. Germinal center B cells are rapidly cycling B cells which have downregulated IgD expression and exhibit high levels of binding by peanut agglutinin (PNA)." [GOC:jal, ISBN:0781735149] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "germinal center B cell development" RELATED [GOC:add] synonym: "germinal center B lymphocyte differentiation" EXACT [] synonym: "germinal center B-cell differentiation" EXACT [] synonym: "germinal center B-lymphocyte differentiation" EXACT [] is_a: GO:0002313 ! mature B cell differentiation involved in immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002335 name: mature B cell differentiation namespace: biological_process def: "The process in which transitional stage B cells acquire the specialized features of mature B cells in the spleen." [GOC:jal, ISBN:0781735149] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "mature B lymphocyte differentiation" EXACT [] synonym: "mature B-cell differentiation" EXACT [] synonym: "mature B-lymphocyte differentiation" EXACT [] synonym: "mature cell development" RELATED [GOC:add] is_a: GO:0030183 ! B cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002339 name: B cell selection namespace: biological_process def: "The process dependent upon B cell antigen receptor signaling in response to self or foreign antigen through which B cells are selected for survival." [GOC:jal] synonym: "B lymphocyte selection" EXACT [] synonym: "B-cell selection" EXACT [] synonym: "B-lymphocyte selection" EXACT [] is_a: GO:0002376 ! immune system process relationship: part_of GO:0030183 ! B cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002343 name: peripheral B cell selection namespace: biological_process def: "Any B cell selection process that occurs in the periphery." [GOC:jal] synonym: "peripheral B lymphocyte selection" EXACT [] synonym: "peripheral B-cell selection" EXACT [] synonym: "peripheral B-lymphocyte selection" EXACT [] is_a: GO:0002339 ! B cell selection property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002344 name: B cell affinity maturation namespace: biological_process def: "The process in which B cells produce antibodies with increased antigen affinity. This is accomplished by somatic hypermutation and selection for B cells which produce higher affinity antibodies to antigen." [GO_REF:0000022, GOC:jal, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was added by GO_REF:0000022. synonym: "B lymphocyte affinity maturation" EXACT [] synonym: "B-cell affinity maturation" EXACT [] synonym: "B-lymphocyte affinity maturation" EXACT [] is_a: GO:0002343 ! peripheral B cell selection relationship: part_of GO:0002381 ! immunoglobulin production involved in immunoglobulin mediated immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002349 name: histamine production involved in inflammatory response namespace: biological_process def: "The synthesis or release of histamine following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149, PMID:16730260] synonym: "histamine production involved in acute inflammatory response" BROAD [] is_a: GO:0002532 ! production of molecular mediator involved in inflammatory response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002351 name: serotonin production involved in inflammatory response namespace: biological_process def: "The synthesis or release of serotonin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149, PMID:16730260] synonym: "serotonin production involved in acute inflammatory response" BROAD [] is_a: GO:0002532 ! production of molecular mediator involved in inflammatory response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002366 name: leukocyte activation involved in immune response namespace: biological_process def: "A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response." [GOC:add, ISBN:0781735149] synonym: "immune cell activation during immune response" RELATED [] synonym: "leucocyte activation during immune response" RELATED [] synonym: "leukocyte activation during immune response" RELATED [GOC:tb] is_a: GO:0002263 ! cell activation involved in immune response is_a: GO:0045321 ! leukocyte activation relationship: part_of GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002367 name: cytokine production involved in immune response namespace: biological_process def: "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was added by GO_REF:0000022. Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular cytokine levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting cytokine molecules, or increased conversion from precursor molecules. synonym: "cytokine production during immune response" RELATED [GOC:dph] is_a: GO:0001816 ! cytokine production is_a: GO:0002440 ! production of molecular mediator of immune response relationship: part_of GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002369 name: T cell cytokine production namespace: biological_process def: "Any process that contributes to cytokine production by a T cell." [GOC:add, ISBN:0781735149] synonym: "T lymphocyte cytokine production" EXACT [] synonym: "T-cell cytokine production" EXACT [] synonym: "T-lymphocyte cytokine production" EXACT [] is_a: GO:0002367 ! cytokine production involved in immune response is_a: GO:0002456 ! T cell mediated immunity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002376 name: immune system process namespace: biological_process def: "Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05] comment: Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). This term was added by GO_REF:0000022. subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir xref: Wikipedia:Immune_system is_a: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002377 name: immunoglobulin production namespace: biological_process def: "The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] synonym: "antibody production" EXACT [] is_a: GO:0002440 ! production of molecular mediator of immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002381 name: immunoglobulin production involved in immunoglobulin mediated immune response namespace: biological_process def: "The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] synonym: "antibody production during immune response" RELATED [] synonym: "immunoglobulin production during immune response" RELATED [GOC:dph] synonym: "immunoglobulin production involved in immune response" RELATED [GOC:dph] is_a: GO:0002377 ! immunoglobulin production relationship: part_of GO:0016064 ! immunoglobulin mediated immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002385 name: mucosal immune response namespace: biological_process def: "An immune response taking place in mucosal tissues, including those of the intestinal tract, nasal and upper respiratory tract, and genital tract." [GO_REF:0000022, GOC:jal, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was added by GO_REF:0000022. is_a: GO:0002251 ! organ or tissue specific immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002386 name: immune response in mucosal-associated lymphoid tissue namespace: biological_process def: "Immune response taking place in the mucosal-associated lymphoid tissue (MALT). Mucosal-associated lymphoid tissue is typically found as nodules associated with mucosal epithelia with distinct internal structures including B- and T-zones for the activation of lymphocytes." [GOC:jal, ISBN:0781735149] synonym: "immune response in MALT" EXACT [] is_a: GO:0002385 ! mucosal immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002387 name: immune response in gut-associated lymphoid tissue namespace: biological_process def: "Immune response taking place in the gut-associated lymphoid tissue (GALT). GALT includes Peyer's patches, appendix, and solitary lymph nodules." [GOC:jal, ISBN:0781735149] synonym: "immune response in GALT" EXACT [] is_a: GO:0002386 ! immune response in mucosal-associated lymphoid tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002395 name: immune response in nasopharyngeal-associated lymphoid tissue namespace: biological_process def: "An immune response taking place in the nasopharyngeal-associated lymphoid tissue (NALT). NALT includes the tonsils and adenoids." [GOC:jal, ISBN:0781735149] synonym: "immune response in NALT" EXACT [] is_a: GO:0002386 ! immune response in mucosal-associated lymphoid tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002432 name: granuloma formation namespace: biological_process def: "The formation of nodular inflammatory lesions, usually small or granular, firm, persistent, well-structured, and containing compactly grouped T lymphocytes and modified phagocytes such as epithelioid cells, giant cells, and other macrophages. Granuloma formation represents a chronic inflammatory response initiated by various infectious and noninfectious agents. The center of a granuloma consists of fused macrophages, which can become necrotic." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:068340007X, ISBN:0721601464, ISBN:081533642X] comment: This term was added by GO_REF:0000022. is_a: GO:0002252 ! immune effector process relationship: part_of GO:0002544 ! chronic inflammatory response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002440 name: production of molecular mediator of immune response namespace: biological_process def: "The synthesis or release of any molecular mediator of the immune response, resulting in an increase in its intracellular or extracellular levels." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was added by GO_REF:0000022. synonym: "production of cellular mediator of immune response" RELATED [] is_a: GO:0002376 ! immune system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002443 name: leukocyte mediated immunity namespace: biological_process alt_id: GO:0019723 alt_id: GO:0042087 def: "Any process involved in the carrying out of an immune response by a leukocyte." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was added by GO_REF:0000022. synonym: "cell-mediated immune response" RELATED [] synonym: "cellular immune response" RELATED [] synonym: "immune cell effector process" EXACT [] synonym: "immune cell mediated immunity" EXACT [] synonym: "leucocyte immune effector process" EXACT [] synonym: "leucocyte mediated immunity" EXACT [] synonym: "leukocyte immune effector process" EXACT [] is_a: GO:0002252 ! immune effector process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002449 name: lymphocyte mediated immunity namespace: biological_process def: "Any process involved in the carrying out of an immune response by a lymphocyte." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was added by GO_REF:0000022. synonym: "cell-mediated immunity" BROAD [] synonym: "cellular immune response" BROAD [] is_a: GO:0002443 ! leukocyte mediated immunity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002456 name: T cell mediated immunity namespace: biological_process def: "Any process involved in the carrying out of an immune response by a T cell." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was added by GO_REF:0000022. synonym: "cell-mediated immunity" BROAD [] synonym: "cellular immune response" BROAD [] synonym: "T lymphocyte mediated immunity" EXACT [] synonym: "T-cell mediated immunity" EXACT [] synonym: "T-lymphocyte mediated immunity" EXACT [] is_a: GO:0002449 ! lymphocyte mediated immunity is_a: GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002460 name: adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains namespace: biological_process def: "An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains, and allowing for enhanced responses upon subsequent exposures to the same antigen (immunological memory). Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies). An example of this is the adaptive immune response found in Mus musculus." [GOC:add, GOC:mtg_sensu, ISBN:0781735149] is_a: GO:0002250 ! adaptive immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002461 name: tolerance induction dependent upon immune response namespace: biological_process def: "Tolerance induction dependent upon an immune response, typically a response by a mature T or B cell in the periphery resulting tolerance towards an antigen via induction of anergy, cellular deletion, or regulatory T cell activation." [GO_REF:0000022, GOC:jal, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was added by GO_REF:0000022. synonym: "immune response-dependent tolerance induction" EXACT [] is_a: GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains is_a: GO:0002507 ! tolerance induction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002465 name: peripheral tolerance induction namespace: biological_process def: "Tolerance induction in the peripheral lymphoid tissues: blood, lymph nodes, spleen, and mucosal-associated lymphoid tissues." [GO_REF:0000022, GOC:jal, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was added by GO_REF:0000022. is_a: GO:0002461 ! tolerance induction dependent upon immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002467 name: germinal center formation namespace: biological_process def: "The process in which germinal centers form. A germinal center is a specialized microenvironment formed when activated B cells enter lymphoid follicles. Germinal centers are the foci for B cell proliferation and somatic hypermutation." [GO_REF:0000022, GOC:jal, GOC:mtg_15nov05, ISBN:081533642X] comment: This term was added by GO_REF:0000022. is_a: GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002474 name: antigen processing and presentation of peptide antigen via MHC class I namespace: biological_process def: "The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules." [GOC:add, ISBN:0781735149, PMID:15224092, PMID:15771591] synonym: "peptide antigen processing and presentation via MHC class I" EXACT [] xref: Reactome:REACT_110097 "Class I MHC mediated antigen processing & presentation, Sus scrofa" xref: Reactome:REACT_114442 "Class I MHC mediated antigen processing & presentation, Xenopus tropicalis" xref: Reactome:REACT_75820 "Class I MHC mediated antigen processing & presentation, Homo sapiens" xref: Reactome:REACT_77569 "Class I MHC mediated antigen processing & presentation, Rattus norvegicus" xref: Reactome:REACT_83138 "Class I MHC mediated antigen processing & presentation, Bos taurus" xref: Reactome:REACT_84092 "Class I MHC mediated antigen processing & presentation, Taeniopygia guttata" xref: Reactome:REACT_86224 "Class I MHC mediated antigen processing & presentation, Mus musculus" xref: Reactome:REACT_88020 "Class I MHC mediated antigen processing & presentation, Danio rerio" xref: Reactome:REACT_90151 "Class I MHC mediated antigen processing & presentation, Canis familiaris" xref: Reactome:REACT_94042 "Class I MHC mediated antigen processing & presentation, Gallus gallus" is_a: GO:0048002 ! antigen processing and presentation of peptide antigen property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002478 name: antigen processing and presentation of exogenous peptide antigen namespace: biological_process def: "The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC protein complex. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell." [GOC:add, ISBN:0781735149] synonym: "exogenous peptide antigen processing and presentation" EXACT [] is_a: GO:0019884 ! antigen processing and presentation of exogenous antigen is_a: GO:0048002 ! antigen processing and presentation of peptide antigen relationship: part_of GO:0042638 ! exogen property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002495 name: antigen processing and presentation of peptide antigen via MHC class II namespace: biological_process def: "The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein." [GOC:add, ISBN:0781735149, PMID:15531770, PMID:15771591] synonym: "peptide antigen processing and presentation via MHC class II" EXACT [] is_a: GO:0002504 ! antigen processing and presentation of peptide or polysaccharide antigen via MHC class II is_a: GO:0048002 ! antigen processing and presentation of peptide antigen property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002504 name: antigen processing and presentation of peptide or polysaccharide antigen via MHC class II namespace: biological_process def: "The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex." [GOC:add, ISBN:0781735149, PMID:15531770, PMID:15771591, PMID:16153240] synonym: "peptide or polysaccharide antigen processing and presentation of via MHC class II" EXACT [] is_a: GO:0019882 ! antigen processing and presentation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002507 name: tolerance induction namespace: biological_process def: "A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it." [GO_REF:0000022, GOC:jal, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was added by GO_REF:0000022. is_a: GO:0002376 ! immune system process relationship: part_of GO:0002520 ! immune system development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002514 name: B cell tolerance induction namespace: biological_process def: "A process involving any mechanism for tolerance induction in B cells." [GOC:jal, ISBN:0781735149, PMID:16460922] synonym: "B lymphocyte tolerance induction" EXACT [] synonym: "B-cell tolerance induction" EXACT [] synonym: "B-lymphocyte tolerance induction" EXACT [] is_a: GO:0002507 ! tolerance induction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002515 name: B cell anergy namespace: biological_process def: "Any process contributing to anergy in B cells, a state of functional inactivation which is part of B cell tolerance induction." [GOC:jal, ISBN:0781735149] synonym: "B lymphocyte anergy" EXACT [] synonym: "B-cell anergy" EXACT [] synonym: "B-lymphocyte anergy" EXACT [] is_a: GO:0002249 ! lymphocyte anergy is_a: GO:0002514 ! B cell tolerance induction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002520 name: immune system development namespace: biological_process def: "The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process." [GOC:add, GOC:dph] is_a: GO:0002376 ! immune system process is_a: GO:0048731 ! system development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002521 name: leukocyte differentiation namespace: biological_process def: "The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." [CL:0000738, GOC:add, PMID:16551264] synonym: "immune cell differentiation" EXACT [] synonym: "leucocyte differentiation" EXACT [] is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0030097 ! hemopoiesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002532 name: production of molecular mediator involved in inflammatory response namespace: biological_process def: "The synthesis or release of any molecular mediator of the inflammatory response following an inflammatory stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, GOC:dph, GOC:tb, ISBN:0781735149] synonym: "production of cellular mediator of acute inflammation" RELATED [] synonym: "production of molecular mediator involved in acute inflammatory response" BROAD [] is_a: GO:0044707 ! single-multicellular organism process relationship: part_of GO:0006954 ! inflammatory response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002536 name: respiratory burst involved in inflammatory response namespace: biological_process def: "A phase of elevated metabolic activity, during which oxygen consumption increases following a stimulus as part of an inflammatory response; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals, resulting in an increase in their intracellular or extracellular levels." [GOC:add, ISBN:0781735149] synonym: "oxidative burst during acute inflammatory response " BROAD [] synonym: "production of reactive oxygen species during acute inflammatory response" BROAD [] synonym: "respiratory burst involved in acute inflammatory response" BROAD [] is_a: GO:0002532 ! production of molecular mediator involved in inflammatory response is_a: GO:0002679 ! respiratory burst involved in defense response relationship: part_of GO:0006954 ! inflammatory response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002537 name: nitric oxide production involved in inflammatory response namespace: biological_process def: "The synthesis or release of nitric oxide following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] synonym: "nitric oxide production involved in acute inflammatory response" BROAD [GOC:mah] synonym: "production of nitric oxide involved in acute inflammatory response" BROAD [] synonym: "production of nitric oxide involved in inflammatory response" EXACT [GOC:curators] is_a: GO:0002532 ! production of molecular mediator involved in inflammatory response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002538 name: arachidonic acid metabolite production involved in inflammatory response namespace: biological_process def: "The synthesis or release of products of arachidonic acid metabolism following a stimulus as part of an inflammatory response, resulting in an increase in their intracellular or extracellular levels." [GOC:add, ISBN:0781735149] synonym: "arachidonic acid metabolite production involved in acute inflammatory response" BROAD [GOC:mah] synonym: "production of arachidonic acid metabolites involved in acute inflammatory response" BROAD [] synonym: "production of arachidonic acid metabolites involved in inflammatory response" EXACT [GOC:curators] is_a: GO:0002532 ! production of molecular mediator involved in inflammatory response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002539 name: prostaglandin production involved in inflammatory response namespace: biological_process def: "The synthesis or release of any prostaglandin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] synonym: "prostaglandin production involved in acute inflammatory response" BROAD [] is_a: GO:0002538 ! arachidonic acid metabolite production involved in inflammatory response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002540 name: leukotriene production involved in inflammatory response namespace: biological_process def: "The synthesis or release of any leukotriene following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] synonym: "leukotriene production involved in acute inflammatory response" BROAD [] is_a: GO:0002538 ! arachidonic acid metabolite production involved in inflammatory response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002544 name: chronic inflammatory response namespace: biological_process def: "Inflammation of prolonged duration (weeks or months) in which active inflammation, tissue destruction, and attempts at repair are proceeding simultaneously. Although it may follow acute inflammation, chronic inflammation frequently begins insidiously, as a low-grade, smoldering, often asymptomatic response." [GO_REF:0000022, GOC:jal, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was added by GO_REF:0000022. is_a: GO:0006954 ! inflammatory response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002548 name: monocyte chemotaxis namespace: biological_process def: "The movement of a monocyte in response to an external stimulus." [GOC:add, PMID:11696603, PMID:15173832] is_a: GO:0030595 ! leukocyte chemotaxis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002562 name: somatic diversification of immune receptors via germline recombination within a single locus namespace: biological_process def: "The process in which immune receptor genes are diversified through recombination of the germline genetic elements within a single genetic locus." [GOC:add, ISBN:0781735149, PMID:16102575, PMID:16166509] is_a: GO:0002200 ! somatic diversification of immune receptors is_a: GO:0016444 ! somatic cell DNA recombination property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002566 name: somatic diversification of immune receptors via somatic mutation namespace: biological_process def: "The process in which immune receptor genes are diversified through somatic mutation." [ISBN:0781735149, PMID:16102575] is_a: GO:0002200 ! somatic diversification of immune receptors property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002573 name: myeloid leukocyte differentiation namespace: biological_process def: "The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage." [GOC:add, PMID:16551251] synonym: "myeloid leucocyte differentiation" EXACT [] is_a: GO:0002521 ! leukocyte differentiation is_a: GO:0030099 ! myeloid cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002574 name: thrombocyte differentiation namespace: biological_process def: "The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a thrombocyte, a nucleated cell found in all vertebrates but mammals involved in hemostasis." [GOC:add] comment: Note that platelets are the non-nucleated mammalian functional equivalent of the nucleated thrombocytes of non-mammalian vertebrates and are sometimes also referred to as thrombocytes. Platelet formation in mammals is covered by the biological_process term platelet formation ; GO:0030220. is_a: GO:0030099 ! myeloid cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002634 name: regulation of germinal center formation namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of germinal center formation." [GOC:add] is_a: GO:0002822 ! regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains relationship: regulates GO:0002467 ! germinal center formation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002637 name: regulation of immunoglobulin production namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of immunoglobulin production." [GOC:add] is_a: GO:0002700 ! regulation of production of molecular mediator of immune response relationship: regulates GO:0002377 ! immunoglobulin production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002643 name: regulation of tolerance induction namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of tolerance induction." [GOC:add] is_a: GO:0002682 ! regulation of immune system process is_a: GO:2000026 ! regulation of multicellular organismal development relationship: regulates GO:0002507 ! tolerance induction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002645 name: positive regulation of tolerance induction namespace: biological_process def: "Any process that activates or increases the frequency, rate, or extent of tolerance induction." [GOC:add] synonym: "activation of tolerance induction" NARROW [] synonym: "stimulation of tolerance induction" NARROW [] synonym: "up regulation of tolerance induction" EXACT [] synonym: "up-regulation of tolerance induction" EXACT [] synonym: "upregulation of tolerance induction" EXACT [] is_a: GO:0002643 ! regulation of tolerance induction is_a: GO:0002684 ! positive regulation of immune system process relationship: positively_regulates GO:0002507 ! tolerance induction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002652 name: regulation of tolerance induction dependent upon immune response namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of tolerance induction dependent upon immune response." [GOC:add] synonym: "regulation of immune response-dependent tolerance induction" EXACT [] is_a: GO:0002643 ! regulation of tolerance induction is_a: GO:0002822 ! regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains relationship: regulates GO:0002461 ! tolerance induction dependent upon immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002654 name: positive regulation of tolerance induction dependent upon immune response namespace: biological_process def: "Any process that activates or increases the frequency, rate, or extent of tolerance induction dependent upon immune response." [GOC:add] synonym: "activation of tolerance induction dependent upon immune response" NARROW [] synonym: "positive regulation of immune response-dependent tolerance induction" EXACT [] synonym: "stimulation of tolerance induction dependent upon immune response" NARROW [] synonym: "up regulation of tolerance induction dependent upon immune response" EXACT [] synonym: "up-regulation of tolerance induction dependent upon immune response" EXACT [] synonym: "upregulation of tolerance induction dependent upon immune response" EXACT [] is_a: GO:0002645 ! positive regulation of tolerance induction is_a: GO:0002652 ! regulation of tolerance induction dependent upon immune response is_a: GO:0002824 ! positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains relationship: positively_regulates GO:0002461 ! tolerance induction dependent upon immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002658 name: regulation of peripheral tolerance induction namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of peripheral tolerance induction." [GOC:add] is_a: GO:0002652 ! regulation of tolerance induction dependent upon immune response relationship: regulates GO:0002465 ! peripheral tolerance induction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002660 name: positive regulation of peripheral tolerance induction namespace: biological_process def: "Any process that activates or increases the frequency, rate, or extent of peripheral tolerance induction." [GOC:add] synonym: "activation of peripheral tolerance induction" NARROW [] synonym: "stimulation of peripheral tolerance induction" NARROW [] synonym: "up regulation of peripheral tolerance induction" EXACT [] synonym: "up-regulation of peripheral tolerance induction" EXACT [] synonym: "upregulation of peripheral tolerance induction" EXACT [] is_a: GO:0002654 ! positive regulation of tolerance induction dependent upon immune response is_a: GO:0002658 ! regulation of peripheral tolerance induction relationship: positively_regulates GO:0002465 ! peripheral tolerance induction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002679 name: respiratory burst involved in defense response namespace: biological_process def: "A phase of elevated metabolic activity, during which oxygen consumption increases made as part of a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals." [GOC:add, ISBN:0781735149, PMID:12789499] is_a: GO:0002252 ! immune effector process is_a: GO:0045730 ! respiratory burst relationship: part_of GO:0006952 ! defense response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002682 name: regulation of immune system process namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of an immune system process." [GOC:add] is_a: GO:0050789 ! regulation of biological process relationship: regulates GO:0002376 ! immune system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002683 name: negative regulation of immune system process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process." [GOC:add] synonym: "down regulation of immune system process" EXACT [] synonym: "down-regulation of immune system process" EXACT [] synonym: "downregulation of immune system process" EXACT [] synonym: "inhibition of immune system process" NARROW [] is_a: GO:0002682 ! regulation of immune system process is_a: GO:0048519 ! negative regulation of biological process relationship: negatively_regulates GO:0002376 ! immune system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002684 name: positive regulation of immune system process namespace: biological_process def: "Any process that activates or increases the frequency, rate, or extent of an immune system process." [GOC:add] synonym: "activation of immune system process" NARROW [] synonym: "stimulation of immune system process" NARROW [] synonym: "up regulation of immune system process" EXACT [] synonym: "up-regulation of immune system process" EXACT [] synonym: "upregulation of immune system process" EXACT [] is_a: GO:0002682 ! regulation of immune system process is_a: GO:0048518 ! positive regulation of biological process relationship: positively_regulates GO:0002376 ! immune system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002685 name: regulation of leukocyte migration namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of leukocyte migration." [GOC:add] synonym: "regulation of immune cell migration" EXACT [] synonym: "regulation of leucocyte migration" EXACT [] is_a: GO:0002682 ! regulation of immune system process is_a: GO:0030334 ! regulation of cell migration relationship: regulates GO:0050900 ! leukocyte migration property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002687 name: positive regulation of leukocyte migration namespace: biological_process def: "Any process that activates or increases the frequency, rate, or extent of leukocyte migration." [GOC:add] synonym: "activation of leukocyte migration" NARROW [] synonym: "positive regulation of immune cell migration" EXACT [] synonym: "positive regulation of leucocyte migration" EXACT [] synonym: "stimulation of leukocyte migration" NARROW [] synonym: "up regulation of leukocyte migration" EXACT [] synonym: "up-regulation of leukocyte migration" EXACT [] synonym: "upregulation of leukocyte migration" EXACT [] is_a: GO:0002684 ! positive regulation of immune system process is_a: GO:0002685 ! regulation of leukocyte migration is_a: GO:0030335 ! positive regulation of cell migration relationship: positively_regulates GO:0050900 ! leukocyte migration property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002688 name: regulation of leukocyte chemotaxis namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of leukocyte chemotaxis." [GOC:add] synonym: "regulation of immune cell chemotaxis" EXACT [] synonym: "regulation of leucocyte chemotaxis" EXACT [] is_a: GO:0002685 ! regulation of leukocyte migration is_a: GO:0050920 ! regulation of chemotaxis relationship: regulates GO:0030595 ! leukocyte chemotaxis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002690 name: positive regulation of leukocyte chemotaxis namespace: biological_process def: "Any process that activates or increases the frequency, rate, or extent of leukocyte chemotaxis." [GOC:add] synonym: "activation of leukocyte chemotaxis" NARROW [] synonym: "positive regulation of immune cell chemotaxis" EXACT [] synonym: "positive regulation of leucocyte chemotaxis" EXACT [] synonym: "stimulation of leukocyte chemotaxis" NARROW [] synonym: "up regulation of leukocyte chemotaxis" EXACT [] synonym: "up-regulation of leukocyte chemotaxis" EXACT [] synonym: "upregulation of leukocyte chemotaxis" EXACT [] is_a: GO:0002687 ! positive regulation of leukocyte migration is_a: GO:0002688 ! regulation of leukocyte chemotaxis is_a: GO:0050921 ! positive regulation of chemotaxis relationship: positively_regulates GO:0030595 ! leukocyte chemotaxis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002694 name: regulation of leukocyte activation namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of leukocyte activation." [GOC:add] synonym: "regulation of immune cell activation" EXACT [] synonym: "regulation of leucocyte activation" EXACT [] is_a: GO:0002682 ! regulation of immune system process is_a: GO:0050865 ! regulation of cell activation relationship: regulates GO:0045321 ! leukocyte activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002695 name: negative regulation of leukocyte activation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte activation." [GOC:add] synonym: "down regulation of leukocyte activation" EXACT [] synonym: "down-regulation of leukocyte activation" EXACT [] synonym: "downregulation of leukocyte activation" EXACT [] synonym: "inhibition of leukocyte activation" NARROW [] synonym: "negative regulation of immune cell activation" EXACT [] synonym: "negative regulation of leucocyte activation" EXACT [] is_a: GO:0002683 ! negative regulation of immune system process is_a: GO:0002694 ! regulation of leukocyte activation is_a: GO:0050866 ! negative regulation of cell activation relationship: negatively_regulates GO:0045321 ! leukocyte activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002696 name: positive regulation of leukocyte activation namespace: biological_process def: "Any process that activates or increases the frequency, rate, or extent of leukocyte activation." [GOC:add] synonym: "activation of leukocyte activation" NARROW [] synonym: "positive regulation of immune cell activation" EXACT [] synonym: "positive regulation of leucocyte activation" EXACT [] synonym: "stimulation of leukocyte activation" NARROW [] synonym: "up regulation of leukocyte activation" EXACT [] synonym: "up-regulation of leukocyte activation" EXACT [] synonym: "upregulation of leukocyte activation" EXACT [] is_a: GO:0002684 ! positive regulation of immune system process is_a: GO:0002694 ! regulation of leukocyte activation is_a: GO:0050867 ! positive regulation of cell activation relationship: positively_regulates GO:0045321 ! leukocyte activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002697 name: regulation of immune effector process namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of an immune effector process." [GOC:add] is_a: GO:0002682 ! regulation of immune system process relationship: regulates GO:0002252 ! immune effector process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002699 name: positive regulation of immune effector process namespace: biological_process def: "Any process that activates or increases the frequency, rate, or extent of an immune effector process." [GOC:add] synonym: "activation of immune effector process" NARROW [] synonym: "stimulation of immune effector process" NARROW [] synonym: "up regulation of immune effector process" EXACT [] synonym: "up-regulation of immune effector process" EXACT [] synonym: "upregulation of immune effector process" EXACT [] is_a: GO:0002684 ! positive regulation of immune system process is_a: GO:0002697 ! regulation of immune effector process relationship: positively_regulates GO:0002252 ! immune effector process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002700 name: regulation of production of molecular mediator of immune response namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of the production of molecular mediator of immune response." [GOC:add] is_a: GO:0002697 ! regulation of immune effector process relationship: regulates GO:0002440 ! production of molecular mediator of immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002703 name: regulation of leukocyte mediated immunity namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of leukocyte mediated immunity." [GOC:add] synonym: "regulation of immune cell mediated immunity" EXACT [] synonym: "regulation of leucocyte mediated immunity" EXACT [] is_a: GO:0002697 ! regulation of immune effector process relationship: regulates GO:0002443 ! leukocyte mediated immunity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002706 name: regulation of lymphocyte mediated immunity namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of lymphocyte mediated immunity." [GOC:add] is_a: GO:0002703 ! regulation of leukocyte mediated immunity relationship: regulates GO:0002449 ! lymphocyte mediated immunity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002712 name: regulation of B cell mediated immunity namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of B cell mediated immunity." [GOC:add] synonym: "regulation of B lymphocyte mediated immunity" EXACT [] synonym: "regulation of B-cell mediated immunity" EXACT [] synonym: "regulation of B-lymphocyte mediated immunity" EXACT [] is_a: GO:0002706 ! regulation of lymphocyte mediated immunity is_a: GO:0002822 ! regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains relationship: regulates GO:0019724 ! B cell mediated immunity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002775 name: antimicrobial peptide production namespace: biological_process def: "The synthesis or release of an antimicrobial peptide during an immune response, resulting in an increase in intracellular or extracellular levels. Such peptides may have protective properties against bacteria, fungi, viruses, or protozoa." [GOC:add, ISBN:0781735149, PMID:11807545, PMID:15638771] is_a: GO:0002440 ! production of molecular mediator of immune response relationship: part_of GO:0019730 ! antimicrobial humoral response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002776 name: antimicrobial peptide secretion namespace: biological_process def: "The regulated release of an antimicrobial peptide from a cell or group of cells. Such peptides may have protective properties against bacteria, fungi, viruses, or protozoa." [GOC:add, ISBN:0781735149, PMID:11807545, PMID:15638771] is_a: GO:0002790 ! peptide secretion relationship: part_of GO:0002775 ! antimicrobial peptide production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002790 name: peptide secretion namespace: biological_process def: "The controlled release of a peptide from a cell or group of cells." [GOC:add] is_a: GO:0015833 ! peptide transport is_a: GO:0046903 ! secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002819 name: regulation of adaptive immune response namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of an adaptive immune response." [GOC:add] is_a: GO:0050776 ! regulation of immune response relationship: regulates GO:0002250 ! adaptive immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002821 name: positive regulation of adaptive immune response namespace: biological_process def: "Any process that activates or increases the frequency, rate, or extent of an adaptive immune response." [GOC:add] synonym: "activation of adaptive immune response" NARROW [] synonym: "stimulation of adaptive immune response" NARROW [] synonym: "up regulation of adaptive immune response" EXACT [] synonym: "up-regulation of adaptive immune response" EXACT [] synonym: "upregulation of adaptive immune response" EXACT [] is_a: GO:0002819 ! regulation of adaptive immune response is_a: GO:0050778 ! positive regulation of immune response relationship: positively_regulates GO:0002250 ! adaptive immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002822 name: regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata." [GOC:add, GOC:mtg_sensu] is_a: GO:0002819 ! regulation of adaptive immune response relationship: regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002824 name: positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains namespace: biological_process def: "Any process that activates or increases the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata." [GOC:add, GOC:mtg_sensu] is_a: GO:0002821 ! positive regulation of adaptive immune response is_a: GO:0002822 ! regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains relationship: positively_regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002825 name: regulation of T-helper 1 type immune response namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of a T-helper 1 type immune response." [GOC:add] is_a: GO:0002822 ! regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains relationship: regulates GO:0042088 ! T-helper 1 type immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002827 name: positive regulation of T-helper 1 type immune response namespace: biological_process def: "Any process that activates or increases the frequency, rate, or extent of a T-helper 1 type immune response." [GOC:add] synonym: "activation of T-helper 1 type immune response" NARROW [] synonym: "stimulation of T-helper 1 type immune response" NARROW [] synonym: "up regulation of T-helper 1 type immune response" EXACT [] synonym: "up-regulation of T-helper 1 type immune response" EXACT [] synonym: "upregulation of T-helper 1 type immune response" EXACT [] is_a: GO:0002824 ! positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains is_a: GO:0002825 ! regulation of T-helper 1 type immune response relationship: positively_regulates GO:0042088 ! T-helper 1 type immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002828 name: regulation of type 2 immune response namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of a type 2 immune response." [GOC:add] synonym: "regulation of T-helper 2 type immune response" NARROW [GOC:add] synonym: "regulation of Th2 immune response" NARROW [GOC:add] is_a: GO:0050776 ! regulation of immune response relationship: regulates GO:0042092 ! type 2 immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002830 name: positive regulation of type 2 immune response namespace: biological_process def: "Any process that activates or increases the frequency, rate, or extent of a type 2 immune response." [GOC:add] synonym: "activation of type 2 immune response" NARROW [] synonym: "positive regulation of T-helper 2 type immune response" NARROW [GOC:add] synonym: "positive regulation of Th2 immune response" NARROW [GOC:add] synonym: "stimulation of type 2 immune response" NARROW [] synonym: "up regulation of type 2 immune response" EXACT [] synonym: "up-regulation of type 2 immune response" EXACT [] synonym: "upregulation of type 2 immune response" EXACT [] is_a: GO:0002828 ! regulation of type 2 immune response is_a: GO:0050778 ! positive regulation of immune response relationship: positively_regulates GO:0042092 ! type 2 immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002889 name: regulation of immunoglobulin mediated immune response namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of an immunoglobulin mediated immune response." [GOC:add] is_a: GO:0002712 ! regulation of B cell mediated immunity relationship: regulates GO:0016064 ! immunoglobulin mediated immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002901 name: mature B cell apoptotic process namespace: biological_process def: "Any apoptotic process in a B cell that is mature, having left the bone marrow." [CL:0000785, GOC:add, GOC:mtg_apoptosis, ISBN:0781735149] synonym: "apoptosis of mature B cells" EXACT [] synonym: "apoptosis of mature B lymphocytes" EXACT [] synonym: "apoptosis of mature B-cells" EXACT [] synonym: "apoptosis of mature B-lymphocytes" EXACT [] synonym: "mature B cell apoptosis" NARROW [] synonym: "mature B cell programmed cell death by apoptosis" EXACT [] synonym: "mature B lymphocyte apoptosis" EXACT [] synonym: "mature B lymphocyte programmed cell death by apoptosis" EXACT [] synonym: "mature B-cell apoptosis" EXACT [] synonym: "mature B-cell programmed cell death by apoptosis" EXACT [] synonym: "mature B-lymphocyte apoptosis" EXACT [] synonym: "mature B-lymphocyte programmed cell death by apoptosis" EXACT [] synonym: "programmed cell death of mature B cells by apoptosis" EXACT [] synonym: "programmed cell death of mature B lymphocytes by apoptosis" EXACT [] synonym: "programmed cell death of mature B-cells by apoptosis" EXACT [] synonym: "programmed cell death of mature B-lymphocytes by apoptosis" EXACT [] synonym: "programmed cell death, mature B cells" EXACT [] synonym: "programmed cell death, mature B lymphocytes" EXACT [] synonym: "programmed cell death, mature B-cells" EXACT [] synonym: "programmed cell death, mature B-lymphocytes" EXACT [] is_a: GO:0001783 ! B cell apoptotic process relationship: part_of GO:0001782 ! B cell homeostasis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002902 name: regulation of B cell apoptotic process namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of B cell apoptotic process." [GOC:add, GOC:mtg_apoptosis] synonym: "regulation of B cell apoptosis" NARROW [] is_a: GO:0070228 ! regulation of lymphocyte apoptotic process relationship: regulates GO:0001783 ! B cell apoptotic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002905 name: regulation of mature B cell apoptotic process namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of mature B cell apoptotic process." [GOC:add, GOC:mtg_apoptosis] synonym: "regulation of mature B cell apoptosis" NARROW [] is_a: GO:0002682 ! regulation of immune system process is_a: GO:0002902 ! regulation of B cell apoptotic process is_a: GO:0032844 ! regulation of homeostatic process relationship: regulates GO:0002901 ! mature B cell apoptotic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0003001 name: generation of a signal involved in cell-cell signaling namespace: biological_process def: "The cellular process that creates a physical entity or change in state, i.e. a signal, that originates in one cell and is used to transfer information to another cell. This process begins with the initial formation of the signal and ends with the mature form and placement of the signal." [GOC:dph] synonym: "formation of a signal" BROAD [] synonym: "generation of a signal involved in cell-cell signalling" EXACT [] synonym: "signal generation" BROAD [] is_a: GO:0044763 ! single-organism cellular process relationship: part_of GO:0007267 ! cell-cell signaling property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0003006 name: developmental process involved in reproduction namespace: biological_process def: "A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring." [GOC:dph, GOC:isa_complete] synonym: "reproductive developmental process" RELATED [GOC:dph, GOC:tb] is_a: GO:0032502 ! developmental process is_a: GO:0044702 ! single organism reproductive process relationship: part_of GO:0000003 ! reproduction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0003008 name: system process namespace: biological_process def: "A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective." [GOC:mtg_cardio] synonym: "organ system process" EXACT [] is_a: GO:0044707 ! single-multicellular organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0003012 name: muscle system process namespace: biological_process def: "A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers." [GOC:mtg_cardio] synonym: "muscle physiological process" RELATED [] is_a: GO:0003008 ! system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0003013 name: circulatory system process namespace: biological_process def: "A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism." [GOC:mtg_cardio] subset: goslim_generic xref: Wikipedia:Circulatory_system is_a: GO:0003008 ! system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0003674 name: molecular_function namespace: molecular_function alt_id: GO:0005554 def: "Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions." [GOC:go_curators] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "molecular function" EXACT [] synonym: "molecular function unknown" NARROW [] disjoint_from: GO:0005575 ! cellular_component disjoint_from: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0004871 name: signal transducer activity namespace: molecular_function alt_id: GO:0005062 alt_id: GO:0009369 alt_id: GO:0009370 def: "Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." [GOC:go_curators] comment: Ligands do NOT have the molecular function 'signal transducer activity'. subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "hematopoietin/interferon-class (D200-domain) cytokine receptor signal transducer activity" NARROW [] synonym: "quorum sensing response regulator activity" NARROW [] synonym: "quorum sensing signal generator activity" NARROW [] is_a: GO:0060089 ! molecular transducer activity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0004872 name: receptor activity namespace: molecular_function alt_id: GO:0019041 def: "Combining with an extracellular or intracellular messenger to initiate a change in cell activity." [GOC:ceb, ISBN:0198506732] subset: goslim_metagenomics subset: goslim_plant subset: gosubset_prok synonym: "receptor guanylate cyclase activity" NARROW [] synonym: "viral antireceptor activity" NARROW [] is_a: GO:0003674 ! molecular_function property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0004888 name: transmembrane signaling receptor activity namespace: molecular_function alt_id: GO:0004926 def: "Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:go_curators, Wikipedia:Transmembrane_receptor] subset: gosubset_prok synonym: "non G protein coupled 7TM receptor activity" NARROW [] synonym: "non-G-protein coupled 7TM receptor activity" NARROW [] synonym: "non-G-protein-coupled 7TM receptor activity" NARROW [] synonym: "transmembrane receptor activity" BROAD [GOC:bf, GOC:signaling] synonym: "transmembrane signalling receptor activity" EXACT [GOC:mah] is_a: GO:0038023 ! signaling receptor activity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005044 name: scavenger receptor activity namespace: molecular_function def: "Combining with any modified low-density lipoprotein (LDL) or other polyanionic ligand and delivering the ligand into the cell via endocytosis. Ligands include acetylated and oxidized LDL, Gram-positive and Gram-negative bacteria, apoptotic cells, beta-amyloid fibrils, and advanced glycation end products (AGEs)." [GOC:bf, PMID:11790542, PMID:12379907, PMID:12621157, PMID:20981357] comment: Note that many gene products that are called scavenger receptors have a broad range of potential ligands and also can be annotated to 'pattern recognition receptor activity ; GO:0008329' or its child terms, or to 'lipoprotein receptor activity ; GO:0030228' or its child terms. For receptors that transduce a signal rather than endocytose their ligand, consider instead the terms 'signaling receptor activity ; GO:0038023' and its children. subset: gosubset_prok synonym: "macrophage receptor activity" NARROW [] is_a: GO:0038024 ! cargo receptor activity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005215 name: transporter activity namespace: molecular_function alt_id: GO:0005478 def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells." [GOC:ai, GOC:dgf] subset: goslim_aspergillus subset: goslim_candida subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "small-molecule carrier or transporter" RELATED [] xref: Reactome:REACT_6315 "Virion-associated M2 protein mediated ion infusion, Homo sapiens" is_a: GO:0003674 ! molecular_function property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005488 name: binding namespace: molecular_function def: "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732] comment: For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "ligand" NARROW [] xref: Wikipedia:Binding_(molecular) is_a: GO:0003674 ! molecular_function property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005575 name: cellular_component namespace: cellular_component alt_id: GO:0008372 def: "The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together." [GOC:go_curators] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "cellular component" EXACT [] synonym: "cellular component unknown" NARROW [] xref: NIF_Subcellular:sao1337158144 disjoint_from: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005576 name: extracellular region namespace: cellular_component def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:go_curators] comment: Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'. subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "extracellular" EXACT [] xref: Wikipedia:Extracellular is_a: GO:0005575 ! cellular_component property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005615 name: extracellular space namespace: cellular_component def: "That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid." [ISBN:0198547684] comment: Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term. subset: goslim_generic subset: goslim_plant synonym: "intercellular space" RELATED [] xref: NIF_Subcellular:sao1425028079 is_a: GO:0044421 ! extracellular region part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005622 name: intracellular namespace: cellular_component def: "The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "internal to cell" EXACT [] synonym: "nucleocytoplasm" RELATED [GOC:mah] synonym: "protoplasm" EXACT [] synonym: "protoplast" RELATED [GOC:mah] xref: Wikipedia:Intracellular is_a: GO:0044464 ! cell part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005623 name: cell namespace: cellular_component def: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:go_curators] subset: goslim_generic subset: goslim_plant subset: gosubset_prok xref: NIF_Subcellular:sao1813327414 xref: Wikipedia:Cell_(biology) is_a: GO:0005575 ! cellular_component property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005634 name: nucleus namespace: cellular_component def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "cell nucleus" EXACT [] xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus is_a: GO:0043231 ! intracellular membrane-bounded organelle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005694 name: chromosome namespace: cellular_component def: "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [ISBN:0198547684] subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_yeast subset: gosubset_prok synonym: "chromatid" RELATED [] synonym: "interphase chromosome" NARROW [] synonym: "prophase chromosome" NARROW [] xref: Wikipedia:Chromosome is_a: GO:0043232 ! intracellular non-membrane-bounded organelle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005730 name: nucleolus namespace: cellular_component def: "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN:0198506732] subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast xref: NIF_Subcellular:sao1820400233 xref: Wikipedia:Nucleolus is_a: GO:0043232 ! intracellular non-membrane-bounded organelle is_a: GO:0044428 ! nuclear part relationship: part_of GO:0031981 ! nuclear lumen property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005737 name: cytoplasm namespace: cellular_component def: "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684] subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_plant subset: goslim_yeast subset: gosubset_prok xref: Wikipedia:Cytoplasm is_a: GO:0044424 ! intracellular part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005764 name: lysosome namespace: cellular_component def: "A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions." [GOC:mah, ISBN:0198506732] subset: goslim_generic subset: goslim_plant xref: NIF_Subcellular:sao585356902 xref: Wikipedia:Lysosome is_a: GO:0000323 ! lytic vacuole property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005766 name: primary lysosome namespace: cellular_component def: "A lysosome before it has fused with a vesicle or vacuole." [GOC:jl, ISBN:0815316194] xref: NIF_Subcellular:sao1140587416 is_a: GO:0005764 ! lysosome property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005773 name: vacuole namespace: cellular_component def: "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol." [GOC:mtg_sensu, ISBN:0198506732] subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "vacuolar carboxypeptidase Y" RELATED [] xref: Wikipedia:Vacuole is_a: GO:0043231 ! intracellular membrane-bounded organelle is_a: GO:0044444 ! cytoplasmic part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005794 name: Golgi apparatus namespace: cellular_component def: "A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions." [ISBN:0198506732] comment: Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon. subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "Golgi" BROAD [] synonym: "Golgi complex" EXACT [] synonym: "Golgi ribbon" NARROW [] xref: NIF_Subcellular:sao451912436 xref: Wikipedia:Golgi_apparatus is_a: GO:0043231 ! intracellular membrane-bounded organelle is_a: GO:0044444 ! cytoplasmic part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005840 name: ribosome namespace: cellular_component alt_id: GO:0033279 def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732] subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "free ribosome" NARROW [NIF_Subcellular:sao1139385046] synonym: "membrane bound ribosome" NARROW [NIF_Subcellular:sao1291545653] synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome is_a: GO:0030529 ! ribonucleoprotein complex is_a: GO:0043232 ! intracellular non-membrane-bounded organelle is_a: GO:0044444 ! cytoplasmic part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005886 name: plasma membrane namespace: cellular_component alt_id: GO:0005904 def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_plant subset: goslim_yeast subset: gosubset_prok synonym: "bacterial inner membrane" NARROW [] synonym: "cell membrane" EXACT [] synonym: "cytoplasmic membrane" EXACT [] synonym: "inner endospore membrane" NARROW [] synonym: "juxtamembrane" BROAD [] synonym: "plasma membrane lipid bilayer" NARROW [GOC:mah] synonym: "plasmalemma" EXACT [] xref: NIF_Subcellular:sao1663586795 xref: Wikipedia:Cell_membrane is_a: GO:0016020 ! membrane is_a: GO:0044464 ! cell part relationship: part_of GO:0071944 ! cell periphery property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005887 name: integral to plasma membrane namespace: cellular_component def: "Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC:go_curators] subset: gosubset_prok is_a: GO:0016021 ! integral to membrane is_a: GO:0031226 ! intrinsic to plasma membrane property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005902 name: microvillus namespace: cellular_component def: "Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells." [ISBN:0813516194] comment: Note that this term refers to a projection from a single cell, and should not be confused with 'microvillus' as used to refer to a multicellular structure such as that found in the placenta. subset: goslim_pir xref: Wikipedia:Microvillus is_a: GO:0042995 ! cell projection property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005929 name: cilium namespace: cellular_component def: "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:kmv, ISBN:0198547684] subset: goslim_generic subset: goslim_pir xref: NIF_Subcellular:sao787716553 xref: Wikipedia:Cilium is_a: GO:0042995 ! cell projection is_a: GO:0043231 ! intracellular membrane-bounded organelle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006022 name: aminoglycan metabolic process namespace: biological_process def: "The chemical reactions and pathways involving aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages." [GOC:ai, ISBN:0198506732] subset: gosubset_prok synonym: "aminoglycan metabolism" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:1901135 ! carbohydrate derivative metabolic process is_a: GO:1901564 ! organonitrogen compound metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006023 name: aminoglycan biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages." [GOC:ai, ISBN:0198506732] subset: gosubset_prok synonym: "aminoglycan anabolism" EXACT [] synonym: "aminoglycan biosynthesis" EXACT [] synonym: "aminoglycan formation" EXACT [] synonym: "aminoglycan synthesis" EXACT [] is_a: GO:0006022 ! aminoglycan metabolic process is_a: GO:0009059 ! macromolecule biosynthetic process is_a: GO:1901137 ! carbohydrate derivative biosynthetic process is_a: GO:1901566 ! organonitrogen compound biosynthetic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006024 name: glycosaminoglycan biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars." [ISBN:0192800981] subset: gosubset_prok synonym: "glycosaminoglycan anabolism" EXACT [] synonym: "glycosaminoglycan biosynthesis" EXACT [] synonym: "glycosaminoglycan formation" EXACT [] synonym: "glycosaminoglycan synthesis" EXACT [] is_a: GO:0006023 ! aminoglycan biosynthetic process is_a: GO:0030203 ! glycosaminoglycan metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006082 name: organic acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732] subset: goslim_pir subset: gosubset_prok synonym: "organic acid metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process is_a: GO:0044281 ! small molecule metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006139 name: nucleobase-containing compound metabolic process namespace: biological_process alt_id: GO:0055134 def: "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai] subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED [] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] is_a: GO:0006725 ! cellular aromatic compound metabolic process is_a: GO:0034641 ! cellular nitrogen compound metabolic process is_a: GO:0044238 ! primary metabolic process is_a: GO:0046483 ! heterocycle metabolic process is_a: GO:1901360 ! organic cyclic compound metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006259 name: DNA metabolic process namespace: biological_process alt_id: GO:0055132 def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732] subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "cellular DNA metabolism" EXACT [] synonym: "DNA metabolism" EXACT [] is_a: GO:0044260 ! cellular macromolecule metabolic process is_a: GO:0090304 ! nucleic acid metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006310 name: DNA recombination namespace: biological_process def: "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN:0198506732] subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok is_a: GO:0006259 ! DNA metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006323 name: DNA packaging namespace: biological_process def: "Any process in which DNA and associated proteins are formed into a compact, orderly structure." [GOC:mah, ISBN:0815316194] subset: goslim_pir synonym: "DNA organisation" EXACT [GOC:curators] synonym: "DNA organization" EXACT [GOC:curators] is_a: GO:0016043 ! cellular component organization is_a: GO:0071103 ! DNA conformation change property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006520 name: cellular amino acid metabolic process namespace: biological_process alt_id: GO:0006519 def: "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells." [CHEBI:33709, GOC:curators, ISBN:0198506732] subset: goslim_aspergillus subset: goslim_generic subset: goslim_metagenomics subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "amino acid and derivative metabolism" EXACT [GOC:curators] synonym: "amino acid metabolic process" EXACT [GOC:curators] synonym: "cellular amino acid and derivative metabolic process" EXACT [] synonym: "cellular amino acid metabolism" EXACT [] xref: Reactome:REACT_116093 "Amino acid metabolism, Gallus gallus" is_a: GO:0019752 ! carboxylic acid metabolic process is_a: GO:0044238 ! primary metabolic process is_a: GO:1901564 ! organonitrogen compound metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006544 name: glycine metabolic process namespace: biological_process def: "The chemical reactions and pathways involving glycine, aminoethanoic acid." [GOC:go_curators] subset: gosubset_prok synonym: "glycine metabolism" EXACT [] is_a: GO:0009069 ! serine family amino acid metabolic process is_a: GO:1901605 ! alpha-amino acid metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006545 name: glycine biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid." [GOC:go_curators] subset: gosubset_prok synonym: "glycine anabolism" EXACT [] synonym: "glycine biosynthesis" EXACT [] synonym: "glycine formation" EXACT [] synonym: "glycine synthesis" EXACT [] xref: MetaCyc:GLYCINE-SYN2-PWY is_a: GO:0006544 ! glycine metabolic process is_a: GO:0009070 ! serine family amino acid biosynthetic process is_a: GO:1901607 ! alpha-amino acid biosynthetic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006725 name: cellular aromatic compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells." [GOC:ai, ISBN:0198506732] subset: goslim_pir subset: gosubset_prok synonym: "aromatic compound metabolism" EXACT [] synonym: "aromatic hydrocarbon metabolic process" NARROW [] synonym: "aromatic hydrocarbon metabolism" NARROW [] is_a: GO:0044237 ! cellular metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006790 name: sulfur compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione." [GOC:ai] subset: goslim_generic subset: goslim_metagenomics subset: gosubset_prok synonym: "sulfur metabolism" EXACT [] synonym: "sulphur metabolic process" EXACT [] synonym: "sulphur metabolism" EXACT [] xref: Reactome:REACT_27247 "Sulfur compound metabolism, Mycobacterium tuberculosis" xref: Wikipedia:Sulfur_metabolism is_a: GO:0044237 ! cellular metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006801 name: superoxide metabolic process namespace: biological_process def: "The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species." [CHEBI:18421, GOC:jl] subset: gosubset_prok synonym: "oxygen free radical metabolic process" EXACT [] synonym: "oxygen free radical metabolism" EXACT [] synonym: "superoxide free radical metabolic process" EXACT [] synonym: "superoxide free radical metabolism" EXACT [] synonym: "superoxide metabolism" EXACT [] is_a: GO:0072593 ! reactive oxygen species metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006807 name: nitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium." [CHEBI:51143, GOC:go_curators, GOC:jl, ISBN:0198506732] comment: Note that amino acid and derivative metabolism should not be annotated here. Instead use the 'amino acid and derivative metabolism' node. subset: goslim_metagenomics subset: goslim_pir subset: gosubset_prok synonym: "nitrogen compound metabolism" EXACT [] is_a: GO:0044710 ! single-organism metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006810 name: transport namespace: biological_process alt_id: GO:0015457 alt_id: GO:0015460 def: "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC:dph, GOC:jl, GOC:mah] subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "auxiliary transport protein activity" RELATED [GOC:mah] synonym: "small molecule transport" NARROW [] synonym: "solute:solute exchange" NARROW [] synonym: "transport accessory protein activity" RELATED [GOC:mah] is_a: GO:0051234 ! establishment of localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006811 name: ion transport namespace: biological_process def: "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_metagenomics subset: goslim_pir subset: goslim_yeast subset: gosubset_prok xref: Reactome:REACT_102356 "Transport of inorganic cations/anions and amino acids/oligopeptides, Xenopus tropicalis" xref: Reactome:REACT_102895 "Transport of inorganic cations/anions and amino acids/oligopeptides, Staphylococcus aureus N315" xref: Reactome:REACT_106972 "Transport of inorganic cations/anions and amino acids/oligopeptides, Sus scrofa" xref: Reactome:REACT_109067 "Transport of inorganic cations/anions and amino acids/oligopeptides, Saccharomyces cerevisiae" xref: Reactome:REACT_110862 "Transport of inorganic cations/anions and amino acids/oligopeptides, Arabidopsis thaliana" xref: Reactome:REACT_19397 "Transport of inorganic cations/anions and amino acids/oligopeptides, Homo sapiens" xref: Reactome:REACT_29110 "Transport of inorganic cations/anions and amino acids/oligopeptides, Oryza sativa" xref: Reactome:REACT_31978 "Transport of inorganic cations/anions and amino acids/oligopeptides, Mus musculus" xref: Reactome:REACT_33992 "Transport of inorganic cations/anions and amino acids/oligopeptides, Danio rerio" xref: Reactome:REACT_34201 "Transport of inorganic cations/anions and amino acids/oligopeptides, Gallus gallus" xref: Reactome:REACT_79109 "Transport of inorganic cations/anions and amino acids/oligopeptides, Caenorhabditis elegans" xref: Reactome:REACT_82618 "Transport of inorganic cations/anions and amino acids/oligopeptides, Escherichia coli" xref: Reactome:REACT_87822 "Transport of inorganic cations/anions and amino acids/oligopeptides, Bos taurus" xref: Reactome:REACT_91472 "Transport of inorganic cations/anions and amino acids/oligopeptides, Dictyostelium discoideum" xref: Reactome:REACT_91958 "Transport of inorganic cations/anions and amino acids/oligopeptides, Drosophila melanogaster" xref: Reactome:REACT_92903 "Transport of inorganic cations/anions and amino acids/oligopeptides, Mycobacterium tuberculosis" xref: Reactome:REACT_93485 "Transport of inorganic cations/anions and amino acids/oligopeptides, Canis familiaris" xref: Reactome:REACT_94357 "Transport of inorganic cations/anions and amino acids/oligopeptides, Rattus norvegicus" xref: Reactome:REACT_96078 "Transport of inorganic cations/anions and amino acids/oligopeptides, Plasmodium falciparum" xref: Reactome:REACT_96919 "Transport of inorganic cations/anions and amino acids/oligopeptides, Taeniopygia guttata" xref: Reactome:REACT_98077 "Transport of inorganic cations/anions and amino acids/oligopeptides, Schizosaccharomyces pombe" is_a: GO:0006810 ! transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006812 name: cation transport namespace: biological_process alt_id: GO:0006819 alt_id: GO:0015674 def: "The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: gosubset_prok synonym: "di-, tri-valent inorganic cation transport" NARROW [GOC:mah] is_a: GO:0006811 ! ion transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006837 name: serotonin transport namespace: biological_process def: "The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems." [GOC:ai] is_a: GO:0015695 ! organic cation transport is_a: GO:0015837 ! amine transport is_a: GO:0015844 ! monoamine transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006869 name: lipid transport namespace: biological_process def: "The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [ISBN:0198506732] subset: goslim_pir subset: goslim_yeast subset: gosubset_prok is_a: GO:0071702 ! organic substance transport relationship: part_of GO:0010876 ! lipid localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006897 name: endocytosis namespace: biological_process alt_id: GO:0016193 alt_id: GO:0016196 def: "A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle." [GOC:mah, ISBN:0198506732, ISBN:0716731363] subset: goslim_yeast subset: gosubset_prok synonym: "nonselective vesicle endocytosis" RELATED [] synonym: "plasma membrane invagination" EXACT [] synonym: "vesicle endocytosis" EXACT [] xref: Wikipedia:Endocytosis is_a: GO:0016192 ! vesicle-mediated transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006909 name: phagocytosis namespace: biological_process def: "An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles." [ISBN:0198506732] xref: Wikipedia:Phagocytosis is_a: GO:0006897 ! endocytosis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006915 name: apoptotic process namespace: biological_process alt_id: GO:0008632 def: "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathways) which typically lead to rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. The process ends when the cell has died. The process is divided into a signaling pathway phase, and an execution phase, which is triggered by the former." [GOC:dhl, GOC:ecd, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263] synonym: "apoptosis" NARROW [] synonym: "apoptotic cell death" EXACT [GOC:sl] synonym: "apoptotic program" NARROW [GOC:add] synonym: "apoptotic programmed cell death" EXACT [] synonym: "cell suicide" BROAD [] synonym: "cellular suicide" BROAD [] synonym: "programmed cell death by apoptosis" EXACT [] synonym: "signaling (initiator) caspase activity" RELATED [] synonym: "type I programmed cell death" NARROW [] xref: Reactome:REACT_100045 "Apoptosis, Drosophila melanogaster" xref: Reactome:REACT_100962 "Apoptosis, Mus musculus" xref: Reactome:REACT_101249 "NRIF signals cell death from the nucleus, Danio rerio" xref: Reactome:REACT_104187 "NRAGE signals death through JNK, Taeniopygia guttata" xref: Reactome:REACT_105149 "NADE modulates death signalling, Rattus norvegicus" xref: Reactome:REACT_106405 "NRAGE signals death through JNK, Xenopus tropicalis" xref: Reactome:REACT_106672 "NADE modulates death signalling, Sus scrofa" xref: Reactome:REACT_107264 "NRIF signals cell death from the nucleus, Xenopus tropicalis" xref: Reactome:REACT_108651 "NRAGE signals death through JNK, Mus musculus" xref: Reactome:REACT_109165 "NRAGE signals death through JNK, Arabidopsis thaliana" xref: Reactome:REACT_110081 "NRAGE signals death through JNK, Schizosaccharomyces pombe" xref: Reactome:REACT_111964 "NRAGE signals death through JNK, Dictyostelium discoideum" xref: Reactome:REACT_13526 "NADE modulates death signalling, Homo sapiens" xref: Reactome:REACT_13638 "NRAGE signals death through JNK, Homo sapiens" xref: Reactome:REACT_13643 "NRIF signals cell death from the nucleus, Homo sapiens" xref: Reactome:REACT_28087 "Apoptosis, Saccharomyces cerevisiae" xref: Reactome:REACT_28795 "Apoptosis, Oryza sativa" xref: Reactome:REACT_28816 "Apoptosis, Danio rerio" xref: Reactome:REACT_30266 "Apoptosis, Arabidopsis thaliana" xref: Reactome:REACT_30361 "Apoptosis, Canis familiaris" xref: Reactome:REACT_30371 "NRAGE signals death through JNK, Saccharomyces cerevisiae" xref: Reactome:REACT_30548 "NRAGE signals death through JNK, Caenorhabditis elegans" xref: Reactome:REACT_30763 "NRAGE signals death through JNK, Oryza sativa" xref: Reactome:REACT_31349 "NRAGE signals death through JNK, Canis familiaris" xref: Reactome:REACT_34139 "NRAGE signals death through JNK, Gallus gallus" xref: Reactome:REACT_578 "Apoptosis, Homo sapiens" xref: Reactome:REACT_77132 "NRAGE signals death through JNK, Drosophila melanogaster" xref: Reactome:REACT_77313 "NADE modulates death signalling, Bos taurus" xref: Reactome:REACT_77415 "NRIF signals cell death from the nucleus, Canis familiaris" xref: Reactome:REACT_78287 "Apoptosis, Gallus gallus" xref: Reactome:REACT_78802 "NADE modulates death signalling, Canis familiaris" xref: Reactome:REACT_79809 "Apoptosis, Schizosaccharomyces pombe" xref: Reactome:REACT_82724 "Apoptosis, Taeniopygia guttata" xref: Reactome:REACT_83328 "Apoptosis, Sus scrofa" xref: Reactome:REACT_85877 "NRAGE signals death through JNK, Rattus norvegicus" xref: Reactome:REACT_86749 "Apoptosis, Rattus norvegicus" xref: Reactome:REACT_86873 "NRIF signals cell death from the nucleus, Gallus gallus" xref: Reactome:REACT_87570 "NRIF signals cell death from the nucleus, Rattus norvegicus" xref: Reactome:REACT_88740 "NRIF signals cell death from the nucleus, Sus scrofa" xref: Reactome:REACT_88784 "NRIF signals cell death from the nucleus, Mus musculus" xref: Reactome:REACT_89196 "Apoptosis, Dictyostelium discoideum" xref: Reactome:REACT_90267 "NRIF signals cell death from the nucleus, Taeniopygia guttata" xref: Reactome:REACT_91011 "Apoptosis, Caenorhabditis elegans" xref: Reactome:REACT_91243 "NADE modulates death signalling, Mus musculus" xref: Reactome:REACT_93937 "Apoptosis, Bos taurus" xref: Reactome:REACT_94099 "NRAGE signals death through JNK, Danio rerio" xref: Reactome:REACT_95069 "Apoptosis, Xenopus tropicalis" xref: Reactome:REACT_95675 "Apoptosis, Plasmodium falciparum" xref: Reactome:REACT_97627 "NRIF signals cell death from the nucleus, Bos taurus" xref: Reactome:REACT_99784 "NRAGE signals death through JNK, Bos taurus" xref: Reactome:REACT_99799 "NRAGE signals death through JNK, Sus scrofa" xref: Wikipedia:Apoptosis is_a: GO:0012501 ! programmed cell death property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006921 name: cellular component disassembly involved in execution phase of apoptosis namespace: biological_process def: "The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis." [GOC:dph, GOC:mah, GOC:mtg_apoptosis, GOC:tb] synonym: "cellular component disassembly involved in apoptosis" NARROW [] synonym: "cellular component disassembly involved in apoptotic process" BROAD [] synonym: "disassembly of cell structures" BROAD [] xref: Reactome:REACT_100800 "Apoptotic execution phase, Danio rerio" xref: Reactome:REACT_108463 "Apoptotic execution phase, Taeniopygia guttata" xref: Reactome:REACT_29660 "Apoptotic execution phase, Oryza sativa" xref: Reactome:REACT_77151 "Apoptotic execution phase, Sus scrofa" xref: Reactome:REACT_78666 "Apoptotic execution phase, Saccharomyces cerevisiae" xref: Reactome:REACT_79472 "Apoptotic execution phase, Schizosaccharomyces pombe" xref: Reactome:REACT_79859 "Apoptotic execution phase, Rattus norvegicus" xref: Reactome:REACT_80493 "Apoptotic execution phase, Dictyostelium discoideum" xref: Reactome:REACT_81021 "Apoptotic execution phase, Drosophila melanogaster" xref: Reactome:REACT_81052 "Apoptotic execution phase, Canis familiaris" xref: Reactome:REACT_84120 "Apoptotic execution phase, Xenopus tropicalis" xref: Reactome:REACT_89424 "Apoptotic execution phase, Arabidopsis thaliana" xref: Reactome:REACT_90988 "Apoptotic execution phase, Plasmodium falciparum" xref: Reactome:REACT_92689 "Apoptotic execution phase, Caenorhabditis elegans" xref: Reactome:REACT_93576 "Apoptotic execution phase, Gallus gallus" xref: Reactome:REACT_94230 "Apoptotic execution phase, Bos taurus" xref: Reactome:REACT_97703 "Apoptotic execution phase, Mus musculus" xref: Reactome:REACT_995 "Apoptotic execution phase, Homo sapiens" is_a: GO:0022411 ! cellular component disassembly relationship: part_of GO:0097194 ! execution phase of apoptosis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006928 name: cellular component movement namespace: biological_process def: "The directed, self-propelled movement of a cellular component without the involvement of an external agent such as a transporter or a pore." [GOC:dgh, GOC:dph, GOC:jl, GOC:mlg] comment: Note that in GO cellular components include whole cells (cell is_a cellular component). subset: goslim_pir subset: gosubset_prok synonym: "cell movement" RELATED [] synonym: "cellular component motion" EXACT [GOC:dph, GOC:jl] is_a: GO:0044763 ! single-organism cellular process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006935 name: chemotaxis namespace: biological_process def: "The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." [ISBN:0198506732] subset: goslim_metagenomics subset: gosubset_prok synonym: "taxis in response to chemical stimulus" EXACT [] xref: Wikipedia:Chemotaxis is_a: GO:0042221 ! response to chemical stimulus is_a: GO:0042330 ! taxis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006936 name: muscle contraction namespace: biological_process def: "A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis." [GOC:ef, GOC:mtg_muscle, ISBN:0198506732] subset: goslim_pir xref: Reactome:REACT_100109 "Smooth Muscle Contraction, Canis familiaris" xref: Reactome:REACT_102067 "Smooth Muscle Contraction, Taeniopygia guttata" xref: Reactome:REACT_20558 "Smooth Muscle Contraction, Homo sapiens" xref: Reactome:REACT_29015 "Smooth Muscle Contraction, Danio rerio" xref: Reactome:REACT_77478 "Smooth Muscle Contraction, Xenopus tropicalis" xref: Reactome:REACT_81255 "Smooth Muscle Contraction, Mus musculus" xref: Reactome:REACT_83607 "Smooth Muscle Contraction, Bos taurus" xref: Reactome:REACT_85440 "Smooth Muscle Contraction, Gallus gallus" xref: Reactome:REACT_87764 "Smooth Muscle Contraction, Sus scrofa" xref: Reactome:REACT_88232 "Smooth Muscle Contraction, Rattus norvegicus" xref: Reactome:REACT_92442 "Smooth Muscle Contraction, Dictyostelium discoideum" xref: Wikipedia:Muscle_contraction is_a: GO:0003012 ! muscle system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006937 name: regulation of muscle contraction namespace: biological_process def: "Any process that modulates the frequency, rate or extent of muscle contraction." [GOC:go_curators] is_a: GO:0090257 ! regulation of muscle system process relationship: regulates GO:0006936 ! muscle contraction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006939 name: smooth muscle contraction namespace: biological_process def: "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length." [GOC:ef, GOC:jl, GOC:mtg_muscle, ISBN:0198506732] synonym: "visceral muscle contraction" EXACT [] is_a: GO:0006936 ! muscle contraction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006940 name: regulation of smooth muscle contraction namespace: biological_process def: "Any process that modulates the frequency, rate or extent of smooth muscle contraction." [GOC:go_curators] is_a: GO:0006937 ! regulation of muscle contraction relationship: regulates GO:0006939 ! smooth muscle contraction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006950 name: response to stress namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC. subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_plant subset: gosubset_prok subset: high_level_annotation_qc synonym: "response to abiotic stress" RELATED [] synonym: "response to biotic stress" RELATED [] is_a: GO:0050896 ! response to stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006952 name: defense response namespace: biological_process alt_id: GO:0002217 alt_id: GO:0042829 def: "Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack." [GOC:go_curators] subset: gosubset_prok synonym: "antimicrobial peptide activity" RELATED [] synonym: "defence response" EXACT [] synonym: "defense/immunity protein activity" RELATED [] synonym: "physiological defense response" EXACT [] is_a: GO:0006950 ! response to stress property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006954 name: inflammatory response namespace: biological_process def: "The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages." [GO_REF:0000022, GOC:mtg_15nov05, ISBN:0198506732] comment: This term was improved by GO_REF:0000022. It was moved. xref: Wikipedia:Inflammation is_a: GO:0006952 ! defense response is_a: GO:0009611 ! response to wounding property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006955 name: immune response namespace: biological_process def: "Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05] comment: This term was improved by GO_REF:0000022. It was redefined and moved. is_a: GO:0002376 ! immune system process is_a: GO:0050896 ! response to stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006959 name: humoral immune response namespace: biological_process def: "An immune response mediated through a body fluid." [GOC:hb, ISBN:0198506732] xref: Wikipedia:Humoral_immunity is_a: GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006996 name: organelle organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] subset: goslim_aspergillus subset: goslim_candida subset: goslim_pir subset: gosubset_prok synonym: "organelle organisation" EXACT [GOC:curators] synonym: "organelle organization and biogenesis" RELATED [GOC:dph, GOC:jl, GOC:mah] is_a: GO:0016043 ! cellular component organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006997 name: nucleus organization namespace: biological_process alt_id: GO:0048287 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus." [GOC:dph, GOC:ems, GOC:jl, GOC:mah] subset: goslim_aspergillus subset: goslim_candida subset: goslim_pir subset: goslim_yeast synonym: "nuclear morphology" RELATED [] synonym: "nuclear organisation" EXACT [GOC:curators] synonym: "nuclear organization" EXACT [GOC:curators] synonym: "nuclear organization and biogenesis" RELATED [GOC:mah] synonym: "nucleus organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007010 name: cytoskeleton organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures." [GOC:dph, GOC:jl, GOC:mah] subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "cytoskeletal organization and biogenesis" RELATED [GOC:mah] synonym: "cytoskeletal regulator activity" RELATED [] synonym: "cytoskeleton organisation" EXACT [GOC:curators] synonym: "cytoskeleton organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007017 name: microtubule-based process namespace: biological_process def: "Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins." [GOC:mah] is_a: GO:0044763 ! single-organism cellular process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007049 name: cell cycle namespace: biological_process def: "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." [GOC:go_curators] subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "cell-division cycle" EXACT [] xref: Wikipedia:Cell_cycle is_a: GO:0044763 ! single-organism cellular process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007067 name: mitosis namespace: biological_process def: "A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell." [GOC:dph, GOC:ma, GOC:mah, ISBN:0198547684] subset: goslim_generic xref: Wikipedia:Mitosis is_a: GO:0000280 ! nuclear division is_a: GO:0022403 ! cell cycle phase relationship: part_of GO:0000087 ! M phase of mitotic cell cycle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007113 name: endomitotic cell cycle namespace: biological_process def: "A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell." [GOC:curators, GOC:dos, GOC:expert_vm] comment: Note that this term should not be confused with 'abortive mitotic cell cycle ; GO:0033277'. Although abortive mitosis is sometimes called endomitosis, GO:0033277 refers to a process in which a mitotic spindle forms and chromosome separation begins. synonym: "endomitosis" RELATED [] xref: Wikipedia:Mitosis#Endomitosis is_a: GO:0000278 ! mitotic cell cycle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007126 name: meiosis namespace: biological_process def: "A cell cycle process comprising the steps by which a cell progresses through the nuclear division phase of a meiotic cell cycle. A meiotic cell cycle is the specialized nuclear and cell division in which a single diploid cell undergoes two nuclear divisions following a single round of DNA replication in order to produce four daughter cells that contain half the number of chromosomes as the diploid cell. Meiotic division occurs during the formation of gametes from diploid organisms and at the beginning of haplophase in those organisms that alternate between diploid and haploid generations." [GOC:dph, GOC:mah, PMID:9334324] subset: goslim_pombe xref: Wikipedia:Meiosis is_a: GO:0022403 ! cell cycle phase is_a: GO:0048610 ! cellular process involved in reproduction relationship: part_of GO:0051327 ! M phase of meiotic cell cycle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007135 name: meiosis II namespace: biological_process def: "A cell cycle process comprising the steps by which a cell progresses through the second phase of meiosis, in which cells divide and separate the two chromatids in each chromosome." [GOC:dph, GOC:mah, ISBN:0198547684] xref: Wikipedia:Meiosis#Meiosis_II is_a: GO:0022403 ! cell cycle phase is_a: GO:0048610 ! cellular process involved in reproduction relationship: part_of GO:0007126 ! meiosis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007140 name: male meiosis namespace: biological_process def: "A cell cycle process comprising the steps by which a cell progresses through the nuclear division phase of a meiotic cell cycle in the male germline." [GOC:dph, GOC:mah] is_a: GO:0007126 ! meiosis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007142 name: male meiosis II namespace: biological_process def: "A cell cycle process comprising the steps by which a cell progresses through male meiosis II, the second meiotic division in the male germline." [GOC:dph, GOC:mah] is_a: GO:0007135 ! meiosis II relationship: part_of GO:0007140 ! male meiosis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007143 name: female meiosis namespace: biological_process def: "A cell cycle process comprising the steps by which a cell progresses through the nuclear division phase of a meiotic cell cycle in the female germline." [GOC:dph, GOC:ems, GOC:mah] comment: Note that female germ lines can be found in female or hermaphroditic organisms, so this term can be used to annotate gene products from hermaphrodites such as those of C. elegans. See also the biological process term 'meiosis ; GO:0007126'. is_a: GO:0007126 ! meiosis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007147 name: female meiosis II namespace: biological_process def: "The cell cycle process in which the second meiotic division occurs in the female germline." [GOC:mah] is_a: GO:0007135 ! meiosis II relationship: part_of GO:0007143 ! female meiosis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007154 name: cell communication namespace: biological_process def: "Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:mah] subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: gosubset_prok xref: Wikipedia:Cell_signaling is_a: GO:0044763 ! single-organism cellular process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007267 name: cell-cell signaling namespace: biological_process def: "Any process that mediates the transfer of information from one cell to another." [GOC:mah] subset: goslim_generic subset: goslim_plant subset: gosubset_prok synonym: "cell-cell signalling" EXACT [] is_a: GO:0007154 ! cell communication is_a: GO:0044700 ! single organism signaling property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007275 name: multicellular organismal development namespace: biological_process def: "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb] comment: Note that this term was 'developmental process'. subset: goslim_plant is_a: GO:0032502 ! developmental process is_a: GO:0044707 ! single-multicellular organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007276 name: gamete generation namespace: biological_process alt_id: GO:0009552 def: "The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell." [GOC:ems, GOC:mtg_sensu] synonym: "gametogenesis" RELATED [] is_a: GO:0048609 ! multicellular organismal reproductive process relationship: part_of GO:0019953 ! sexual reproduction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007281 name: germ cell development namespace: biological_process def: "The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism." [GOC:go_curators] synonym: "germ-cell development" EXACT [] synonym: "primordial germ cell development" NARROW [] is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0048468 ! cell development is_a: GO:0048610 ! cellular process involved in reproduction relationship: part_of GO:0007276 ! gamete generation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007283 name: spermatogenesis namespace: biological_process def: "The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis." [GOC:jid, ISBN:9780878933846] synonym: "generation of spermatozoa" EXACT systematic_synonym [] xref: Wikipedia:Spermatogenesis is_a: GO:0048232 ! male gamete generation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007286 name: spermatid development namespace: biological_process def: "The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure." [GOC:dph, GOC:go_curators] synonym: "spermatid cell development" EXACT [] synonym: "spermiogenesis" EXACT [] xref: Wikipedia:Spermiogenesis is_a: GO:0007281 ! germ cell development relationship: part_of GO:0048515 ! spermatid differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007288 name: sperm axoneme assembly namespace: biological_process def: "The assembly and organization of the sperm flagellar axoneme, the bundle of microtubules and associated proteins that forms the core of the eukaryotic sperm flagellum, and is responsible for movement." [GOC:bf, ISBN:0198547684] is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0010927 ! cellular component assembly involved in morphogenesis is_a: GO:0035084 ! flagellar axoneme assembly is_a: GO:0048610 ! cellular process involved in reproduction relationship: part_of GO:0007286 ! spermatid development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007289 name: spermatid nucleus differentiation namespace: biological_process def: "The specialization of the spermatid nucleus during the development of a spermatid into a mature male gamete competent for fertilization." [GOC:bf, GOC:dph, GOC:jl, GOC:mah] comment: See also the Cell Ontology term 'spermatid ; CL:0000018'. synonym: "spermatid nuclear differentiation" EXACT [] is_a: GO:0006997 ! nucleus organization is_a: GO:0048610 ! cellular process involved in reproduction relationship: part_of GO:0007286 ! spermatid development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007292 name: female gamete generation namespace: biological_process def: "Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction." [GOC:dph, ISBN:0198506732] is_a: GO:0007276 ! gamete generation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007399 name: nervous system development namespace: biological_process def: "The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state." [GOC:dgh] synonym: "pan-neural process" RELATED [] is_a: GO:0048731 ! system development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007507 name: heart development namespace: biological_process alt_id: GO:0007511 def: "The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood." [GOC:jid, UBERON:0000948] synonym: "cardiac development" RELATED [] synonym: "dorsal vessel development" NARROW [] xref: Wikipedia:Heart_development is_a: GO:0048513 ! organ development relationship: part_of GO:0072358 ! cardiovascular system development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007548 name: sex differentiation namespace: biological_process def: "The establishment of the sex of an organism by physical differentiation." [GOC:ai] xref: Wikipedia:Sexual_differentiation is_a: GO:0003006 ! developmental process involved in reproduction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007585 name: respiratory gaseous exchange namespace: biological_process def: "The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms." [ISBN:0198506732] synonym: "breathing" BROAD [] synonym: "respiration" BROAD [] is_a: GO:0044707 ! single-multicellular organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007586 name: digestion namespace: biological_process def: "The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." [GOC:isa_complete, ISBN:0198506732] subset: goslim_pir xref: Wikipedia:Digestion is_a: GO:0044707 ! single-multicellular organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007589 name: body fluid secretion namespace: biological_process def: "The controlled release of a fluid by a cell or group of cells in an animal." [GOC:ai, GOC:dph, GOC:mah, GOC:tb] is_a: GO:0046903 ! secretion is_a: GO:0050878 ! regulation of body fluid levels property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007596 name: blood coagulation namespace: biological_process def: "The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers." [http://www.graylab.ac.uk/omd/, ISBN:0198506732] synonym: "blood clotting" EXACT [] xref: Reactome:REACT_101311 "Hemostasis, Plasmodium falciparum" xref: Reactome:REACT_101372 "Common Pathway, Danio rerio" xref: Reactome:REACT_102544 "Common Pathway, Rattus norvegicus" xref: Reactome:REACT_102650 "Common Pathway, Mus musculus" xref: Reactome:REACT_105166 "Common Pathway, Taeniopygia guttata" xref: Reactome:REACT_105212 "Common Pathway, Sus scrofa" xref: Reactome:REACT_107268 "Hemostasis, Saccharomyces cerevisiae" xref: Reactome:REACT_108583 "Hemostasis, Danio rerio" xref: Reactome:REACT_113650 "Common Pathway, Drosophila melanogaster" xref: Reactome:REACT_114152 "Formation of Fibrin Clot (Clotting Cascade), Drosophila melanogaster" xref: Reactome:REACT_118351 "Hemostasis, Escherichia coli" xref: Reactome:REACT_1439 "Common Pathway, Homo sapiens" xref: Reactome:REACT_2051 "Formation of Fibrin Clot (Clotting Cascade), Homo sapiens" xref: Reactome:REACT_32530 "Hemostasis, Xenopus tropicalis" xref: Reactome:REACT_32765 "Hemostasis, Mycobacterium tuberculosis" xref: Reactome:REACT_33270 "Hemostasis, Canis familiaris" xref: Reactome:REACT_34525 "Hemostasis, Arabidopsis thaliana" xref: Reactome:REACT_604 "Hemostasis, Homo sapiens" xref: Reactome:REACT_76944 "Common Pathway, Canis familiaris" xref: Reactome:REACT_78290 "Hemostasis, Staphylococcus aureus N315" xref: Reactome:REACT_81054 "Formation of Fibrin Clot (Clotting Cascade), Canis familiaris" xref: Reactome:REACT_81972 "Formation of Fibrin Clot (Clotting Cascade), Taeniopygia guttata" xref: Reactome:REACT_82283 "Formation of Fibrin Clot (Clotting Cascade), Mus musculus" xref: Reactome:REACT_82383 "Hemostasis, Oryza sativa" xref: Reactome:REACT_82403 "Hemostasis, Rattus norvegicus" xref: Reactome:REACT_82445 "Formation of Fibrin Clot (Clotting Cascade), Sus scrofa" xref: Reactome:REACT_82812 "Hemostasis, Bos taurus" xref: Reactome:REACT_82940 "Common Pathway, Xenopus tropicalis" xref: Reactome:REACT_83271 "Hemostasis, Dictyostelium discoideum" xref: Reactome:REACT_84055 "Formation of Fibrin Clot (Clotting Cascade), Danio rerio" xref: Reactome:REACT_84833 "Formation of Fibrin Clot (Clotting Cascade), Rattus norvegicus" xref: Reactome:REACT_85674 "Hemostasis, Sus scrofa" xref: Reactome:REACT_86354 "Common Pathway, Gallus gallus" xref: Reactome:REACT_89750 "Hemostasis, Mus musculus" xref: Reactome:REACT_89805 "Formation of Fibrin Clot (Clotting Cascade), Xenopus tropicalis" xref: Reactome:REACT_90236 "Hemostasis, Taeniopygia guttata" xref: Reactome:REACT_90805 "Hemostasis, Caenorhabditis elegans" xref: Reactome:REACT_92318 "Hemostasis, Drosophila melanogaster" xref: Reactome:REACT_94085 "Hemostasis, Schizosaccharomyces pombe" xref: Reactome:REACT_94213 "Common Pathway, Bos taurus" xref: Reactome:REACT_94315 "Formation of Fibrin Clot (Clotting Cascade), Bos taurus" xref: Reactome:REACT_94798 "Formation of Fibrin Clot (Clotting Cascade), Gallus gallus" xref: Reactome:REACT_96458 "Hemostasis, Gallus gallus" xref: Wikipedia:Coagulation is_a: GO:0007599 ! hemostasis is_a: GO:0050817 ! coagulation relationship: part_of GO:0042060 ! wound healing property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007599 name: hemostasis namespace: biological_process def: "The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part." [ISBN:0198506732] xref: Wikipedia:Hemostasis is_a: GO:0050878 ! regulation of body fluid levels property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007600 name: sensory perception namespace: biological_process def: "The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." [GOC:ai, GOC:dph] xref: Wikipedia:Perception is_a: GO:0050877 ! neurological system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007601 name: visual perception namespace: biological_process def: "The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image." [GOC:ai] synonym: "sense of sight" EXACT [] synonym: "sensory visual perception" EXACT [] synonym: "vision" EXACT [] xref: Wikipedia:Visual_perception is_a: GO:0050953 ! sensory perception of light stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007605 name: sensory perception of sound namespace: biological_process def: "The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound." [GOC:ai] synonym: "hearing" EXACT [] synonym: "perception of sound" EXACT [] xref: Wikipedia:Hearing_(sense) is_a: GO:0050954 ! sensory perception of mechanical stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007606 name: sensory perception of chemical stimulus namespace: biological_process def: "The series of events required for an organism to receive a sensory chemical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." [GOC:ai] synonym: "chemosensory perception" EXACT [] is_a: GO:0007600 ! sensory perception property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007608 name: sensory perception of smell namespace: biological_process def: "The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process." [GOC:ai, http://www.onelook.com/] synonym: "olfaction" EXACT [] synonym: "scent perception" EXACT [] synonym: "sense of smell" EXACT [] synonym: "smell perception" EXACT [] xref: Wikipedia:Olfaction is_a: GO:0007606 ! sensory perception of chemical stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0007610 name: behavior namespace: biological_process def: "The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions." [GOC:ems, ISBN:0395448956] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC. subset: goslim_plant subset: gosubset_prok subset: high_level_annotation_qc synonym: "behavioral response to stimulus" EXACT [] synonym: "behaviour" EXACT [] synonym: "behavioural response to stimulus" EXACT [] xref: Wikipedia:Behavior is_a: GO:0050896 ! response to stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008015 name: blood circulation namespace: biological_process alt_id: GO:0070261 def: "The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products." [GOC:mtg_heart, ISBN:0192800825] subset: goslim_pir synonym: "hemolymph circulation" RELATED [] is_a: GO:0003013 ! circulatory system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008104 name: protein localization namespace: biological_process def: "Any process in which a protein is transported to, or maintained in, a specific location." [GOC:ai] subset: gosubset_prok synonym: "establishment and maintenance of protein localization" EXACT [] synonym: "protein localisation" EXACT [GOC:mah] is_a: GO:0033036 ! macromolecule localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008150 name: biological_process namespace: biological_process alt_id: GO:0000004 alt_id: GO:0007582 def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: goslim_yeast subset: gosubset_prok synonym: "biological process" EXACT [] synonym: "biological process unknown" NARROW [] synonym: "physiological process" EXACT [] xref: Wikipedia:Biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008152 name: metabolic process namespace: biological_process def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] synonym: "metabolism resulting in cell growth" NARROW [] xref: Wikipedia:Metabolism is_a: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008219 name: cell death namespace: biological_process def: "Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as \"apoptotic bodies\"); and/or (3) its corpse (or its fragments) have been engulfed by an adjacent cell in vivo." [GOC:mah, GOC:mtg_apoptosis] subset: goslim_generic subset: goslim_plant subset: gosubset_prok synonym: "necrosis" RELATED [] is_a: GO:0016265 ! death is_a: GO:0044763 ! single-organism cellular process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008283 name: cell proliferation namespace: biological_process def: "The multiplication or reproduction of cells, resulting in the expansion of a cell population." [GOC:mah, GOC:mb] comment: This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. subset: goslim_generic subset: goslim_pir subset: gosubset_prok is_a: GO:0044699 ! single-organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008284 name: positive regulation of cell proliferation namespace: biological_process def: "Any process that activates or increases the rate or extent of cell proliferation." [GOC:go_curators] subset: gosubset_prok synonym: "activation of cell proliferation" NARROW [] synonym: "stimulation of cell proliferation" NARROW [] synonym: "up regulation of cell proliferation" EXACT [] synonym: "up-regulation of cell proliferation" EXACT [] synonym: "upregulation of cell proliferation" EXACT [] is_a: GO:0042127 ! regulation of cell proliferation is_a: GO:0048522 ! positive regulation of cellular process relationship: positively_regulates GO:0008283 ! cell proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008285 name: negative regulation of cell proliferation namespace: biological_process def: "Any process that stops, prevents or reduces the rate or extent of cell proliferation." [GOC:go_curators] synonym: "down regulation of cell proliferation" EXACT [] synonym: "down-regulation of cell proliferation" EXACT [] synonym: "downregulation of cell proliferation" EXACT [] synonym: "inhibition of cell proliferation" NARROW [] is_a: GO:0042127 ! regulation of cell proliferation is_a: GO:0048523 ! negative regulation of cellular process relationship: negatively_regulates GO:0008283 ! cell proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008289 name: lipid binding namespace: molecular_function def: "Interacting selectively and non-covalently with a lipid." [GOC:ai] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok is_a: GO:0005488 ! binding property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008406 name: gonad development namespace: biological_process def: "The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones." [GOC:ems, ISBN:0198506732] is_a: GO:0048513 ! organ development is_a: GO:0048608 ! reproductive structure development relationship: part_of GO:0045137 ! development of primary sexual characteristics property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008509 name: anion transmembrane transporter activity namespace: molecular_function def: "Catalysis of the transfer of a negatively charged ion from one side of a membrane to the other." [GOC:dgf, GOC:mtg_transport, ISBN:0815340729] subset: gosubset_prok synonym: "anion transporter activity" EXACT [] xref: Reactome:REACT_100348 "FA anion flip-flops to the opposite surface, Canis familiaris" xref: Reactome:REACT_102329 "FA anion flip-flops to the opposite surface, Gallus gallus" xref: Reactome:REACT_106026 "FA anion flip-flops to the opposite surface, Sus scrofa" xref: Reactome:REACT_6188 "FA anion flip-flops to the opposite surface, Homo sapiens" xref: Reactome:REACT_79542 "FA anion flip-flops to the opposite surface, Xenopus tropicalis" xref: Reactome:REACT_86643 "FA anion flip-flops to the opposite surface, Taeniopygia guttata" xref: Reactome:REACT_87003 "FA anion flip-flops to the opposite surface, Danio rerio" xref: Reactome:REACT_88207 "FA anion flip-flops to the opposite surface, Mus musculus" xref: Reactome:REACT_90836 "FA anion flip-flops to the opposite surface, Oryza sativa" xref: Reactome:REACT_93989 "FA anion flip-flops to the opposite surface, Bos taurus" xref: Reactome:REACT_96294 "FA anion flip-flops to the opposite surface, Rattus norvegicus" xref: Reactome:REACT_99908 "FA anion flip-flops to the opposite surface, Arabidopsis thaliana" is_a: GO:0015075 ! ion transmembrane transporter activity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008544 name: epidermis development namespace: biological_process def: "The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of a plant or animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species." [GOC:go_curators, UBERON:0001003] synonym: "hypodermis development" RELATED [GOC:kmv, GOC:rk] is_a: GO:0009888 ! tissue development relationship: part_of GO:0048513 ! organ development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008585 name: female gonad development namespace: biological_process alt_id: GO:0061039 def: "The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure." [GOC:dph, GOC:jid, GOC:tb] synonym: "ovarian development" RELATED [GOC:sl] synonym: "ovary development" RELATED [GOC:sl] is_a: GO:0008406 ! gonad development relationship: part_of GO:0046545 ! development of primary female sexual characteristics property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008652 name: cellular amino acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents." [ISBN:0198506732] subset: gosubset_prok synonym: "amino acid biosynthetic process" EXACT [GOC:curators] synonym: "cellular amino acid anabolism" EXACT [] synonym: "cellular amino acid biosynthesis" EXACT [] synonym: "cellular amino acid formation" EXACT [] synonym: "cellular amino acid synthesis" EXACT [] xref: Reactome:REACT_101745 "Amino acid synthesis and interconversion (transamination), Saccharomyces cerevisiae" xref: Reactome:REACT_106399 "Amino acid synthesis and interconversion (transamination), Schizosaccharomyces pombe" xref: Reactome:REACT_108419 "Amino acid synthesis and interconversion (transamination), Bos taurus" xref: Reactome:REACT_109330 "Amino acid synthesis and interconversion (transamination), Drosophila melanogaster" xref: Reactome:REACT_110509 "Amino acid synthesis and interconversion (transamination), Oryza sativa" xref: Reactome:REACT_112051 "Amino acid synthesis and interconversion (transamination), Staphylococcus aureus N315" xref: Reactome:REACT_238 "Amino acid synthesis and interconversion (transamination), Homo sapiens" xref: Reactome:REACT_30236 "Amino acid synthesis and interconversion (transamination), Rattus norvegicus" xref: Reactome:REACT_30845 "Amino acid synthesis and interconversion (transamination), Arabidopsis thaliana" xref: Reactome:REACT_31295 "Amino acid synthesis and interconversion (transamination), Sus scrofa" xref: Reactome:REACT_33022 "Amino acid synthesis and interconversion (transamination), Caenorhabditis elegans" xref: Reactome:REACT_77237 "Amino acid synthesis and interconversion (transamination), Dictyostelium discoideum" xref: Reactome:REACT_77379 "Amino acid synthesis and interconversion (transamination), Mus musculus" xref: Reactome:REACT_77480 "Amino acid synthesis and interconversion (transamination), Canis familiaris" xref: Reactome:REACT_77498 "Amino acid synthesis and interconversion (transamination), Plasmodium falciparum" xref: Reactome:REACT_79609 "Amino acid synthesis and interconversion (transamination), Escherichia coli" xref: Reactome:REACT_83815 "Amino acid synthesis and interconversion (transamination), Danio rerio" xref: Reactome:REACT_83995 "Amino acid synthesis and interconversion (transamination), Gallus gallus" xref: Reactome:REACT_89765 "Amino acid synthesis and interconversion (transamination), Xenopus tropicalis" xref: Reactome:REACT_92648 "Amino acid synthesis and interconversion (transamination), Mycobacterium tuberculosis" xref: Reactome:REACT_95114 "Amino acid synthesis and interconversion (transamination), Taeniopygia guttata" xref: Wikipedia:Amino_acid_synthesis is_a: GO:0006520 ! cellular amino acid metabolic process is_a: GO:0046394 ! carboxylic acid biosynthetic process is_a: GO:1901566 ! organonitrogen compound biosynthetic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009058 name: biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] subset: goslim_generic subset: goslim_metagenomics subset: goslim_plant subset: gosubset_prok synonym: "anabolism" EXACT [] synonym: "biosynthesis" EXACT [] synonym: "formation" EXACT [] synonym: "synthesis" EXACT [] xref: Wikipedia:Anabolism is_a: GO:0008152 ! metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009059 name: macromolecule biosynthetic process namespace: biological_process alt_id: GO:0043284 def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [CHEBI:33694, GOC:mah] subset: gosubset_prok synonym: "biopolymer biosynthetic process" EXACT [GOC:mtg_chebi_dec09] synonym: "macromolecule anabolism" EXACT [] synonym: "macromolecule biosynthesis" EXACT [] synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:1901576 ! organic substance biosynthetic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009069 name: serine family amino acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving amino acids of the serine family, comprising cysteine, glycine, homoserine, selenocysteine and serine." [GOC:ai] subset: gosubset_prok synonym: "serine family amino acid metabolism" EXACT [] is_a: GO:0006520 ! cellular amino acid metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009070 name: serine family amino acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of amino acids of the serine family, comprising cysteine, glycine, homoserine, selenocysteine and serine." [GOC:ai] subset: gosubset_prok synonym: "serine family amino acid anabolism" EXACT [] synonym: "serine family amino acid biosynthesis" EXACT [] synonym: "serine family amino acid formation" EXACT [] synonym: "serine family amino acid synthesis" EXACT [] is_a: GO:0008652 ! cellular amino acid biosynthetic process is_a: GO:0009069 ! serine family amino acid metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009266 name: response to temperature stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a temperature stimulus." [GOC:hb] subset: gosubset_prok synonym: "response to thermal stimulus" EXACT [] is_a: GO:0009628 ! response to abiotic stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009296 name: flagellum assembly namespace: biological_process def: "The assembly of a flagellum. In bacteria, this is a whiplike motility appendage present on the surface of some species; in eukaryotes, flagella are threadlike protoplasmic extensions used to propel flagellates and sperm. Flagella are composed of flagellin and have the same basic structure as cilia but are longer in proportion to the cell and present in much smaller numbers." [GOC:curators, ISBN:0815316194] subset: gosubset_prok synonym: "flagella assembly" EXACT [GOC:mah] synonym: "flagella biogenesis" RELATED [] synonym: "flagellum biogenesis" RELATED [GOC:mah] is_a: GO:0030031 ! cell projection assembly is_a: GO:0043064 ! flagellum organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009306 name: protein secretion namespace: biological_process alt_id: GO:0045166 alt_id: GO:0045731 def: "The controlled release of proteins from a cell or group of cells." [GOC:ai] subset: goslim_metagenomics subset: gosubset_prok synonym: "glycoprotein secretion" NARROW [] synonym: "protein secretion during cell fate commitment" NARROW [] synonym: "protein secretion resulting in cell fate commitment" NARROW [] is_a: GO:0015031 ! protein transport is_a: GO:0032940 ! secretion by cell property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009314 name: response to radiation namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation." [GOC:jl, Wikipedia:Electromagnetic_radiation] comment: Note that 'radiation' refers to electromagnetic radiation of any wavelength. subset: gosubset_prok synonym: "response to electromagnetic radiation stimulus" EXACT [] synonym: "response to radiation stimulus" EXACT [] is_a: GO:0009628 ! response to abiotic stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009416 name: response to light stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light." [GOC:go_curators, ISBN:0582227089] subset: gosubset_prok is_a: GO:0009314 ! response to radiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009566 name: fertilization namespace: biological_process def: "The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy)." [GOC:tb, ISBN:0198506732] synonym: "syngamy" EXACT [] xref: Wikipedia:Fertilisation is_a: GO:0044702 ! single organism reproductive process relationship: part_of GO:0019953 ! sexual reproduction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009581 name: detection of external stimulus namespace: biological_process def: "The series of events in which an external stimulus is received by a cell and converted into a molecular signal." [GOC:hb] subset: gosubset_prok synonym: "perception of external stimulus" RELATED [] is_a: GO:0009605 ! response to external stimulus is_a: GO:0051606 ! detection of stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009582 name: detection of abiotic stimulus namespace: biological_process def: "The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal." [GOC:hb] subset: gosubset_prok synonym: "perception of abiotic stimulus" RELATED [] is_a: GO:0009628 ! response to abiotic stimulus is_a: GO:0051606 ! detection of stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009583 name: detection of light stimulus namespace: biological_process def: "The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal." [GOC:go_curators] subset: gosubset_prok synonym: "detection of light" EXACT [] synonym: "perception of light" RELATED [] is_a: GO:0009416 ! response to light stimulus is_a: GO:0009581 ! detection of external stimulus is_a: GO:0009582 ! detection of abiotic stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009584 name: detection of visible light namespace: biological_process def: "The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm." [GOC:go_curators, ISBN:0198506732] synonym: "perception of visible light" RELATED [] is_a: GO:0009583 ! detection of light stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009590 name: detection of gravity namespace: biological_process def: "The series of events in which a gravitational stimulus is received by a cell and converted into a molecular signal." [GOC:hb] synonym: "perception of gravity" RELATED [] is_a: GO:0009581 ! detection of external stimulus is_a: GO:0009582 ! detection of abiotic stimulus is_a: GO:0009629 ! response to gravity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009593 name: detection of chemical stimulus namespace: biological_process def: "The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal." [GOC:jl] synonym: "chemoperception" EXACT [] synonym: "detection of chemical substance" EXACT [] synonym: "perception of chemical stimulus" RELATED [] synonym: "perception of chemical substance" RELATED [] is_a: GO:0042221 ! response to chemical stimulus is_a: GO:0051606 ! detection of stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009605 name: response to external stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus." [GOC:hb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC. subset: goslim_plant subset: gosubset_prok subset: high_level_annotation_qc synonym: "response to environmental stimulus" EXACT [] is_a: GO:0050896 ! response to stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009607 name: response to biotic stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism." [GOC:hb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC. subset: goslim_plant subset: gosubset_prok subset: high_level_annotation_qc synonym: "response to biotic stress" NARROW [] is_a: GO:0050896 ! response to stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009611 name: response to wounding namespace: biological_process alt_id: GO:0002245 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism." [GOC:go_curators] synonym: "physiological response to wounding" EXACT [] is_a: GO:0006950 ! response to stress property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009612 name: response to mechanical stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus." [GOC:hb] subset: gosubset_prok synonym: "chemi-mechanical coupling" RELATED [] synonym: "mechanical stimulus response" EXACT [] is_a: GO:0009605 ! response to external stimulus is_a: GO:0009628 ! response to abiotic stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009617 name: response to bacterium namespace: biological_process alt_id: GO:0009618 alt_id: GO:0009680 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium." [GOC:hb] subset: gosubset_prok synonym: "response to bacteria" EXACT [] is_a: GO:0051707 ! response to other organism property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009624 name: response to nematode namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a nematode." [GOC:hb] synonym: "response to nematodes" EXACT [] is_a: GO:0051707 ! response to other organism property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009628 name: response to abiotic stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus." [GOC:hb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC. subset: goslim_plant subset: gosubset_prok subset: high_level_annotation_qc synonym: "response to abiotic stress" NARROW [] is_a: GO:0050896 ! response to stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009629 name: response to gravity namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gravitational stimulus." [GOC:hb] synonym: "response to gravitational stimulus" EXACT [] is_a: GO:0009628 ! response to abiotic stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009653 name: anatomical structure morphogenesis namespace: biological_process def: "The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form." [GOC:go_curators, ISBN:0521436125] subset: goslim_plant subset: gosubset_prok synonym: "anatomical structure organization" EXACT [] synonym: "embryogenesis and morphogenesis" BROAD [] synonym: "morphogenesis" EXACT [] xref: Wikipedia:Morphogenesis is_a: GO:0032502 ! developmental process is_a: GO:0044699 ! single-organism process relationship: part_of GO:0048856 ! anatomical structure development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009887 name: organ morphogenesis namespace: biological_process def: "Morphogenesis of an organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC:dgh, GOC:go_curators, ISBN:0471245208, ISBN:0721662544] synonym: "histogenesis and organogenesis" BROAD [] is_a: GO:0009653 ! anatomical structure morphogenesis relationship: part_of GO:0048513 ! organ development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009888 name: tissue development namespace: biological_process def: "The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure." [ISBN:0471245208] synonym: "histogenesis" EXACT [] synonym: "histogenesis and organogenesis" BROAD [] xref: Wikipedia:Histogenesis is_a: GO:0048856 ! anatomical structure development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009893 name: positive regulation of metabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] subset: gosubset_prok synonym: "activation of metabolic process" NARROW [] synonym: "positive regulation of metabolism" EXACT [] synonym: "stimulation of metabolic process" NARROW [] synonym: "up regulation of metabolic process" EXACT [] synonym: "up-regulation of metabolic process" EXACT [] synonym: "upregulation of metabolic process" EXACT [] is_a: GO:0019222 ! regulation of metabolic process is_a: GO:0048518 ! positive regulation of biological process relationship: positively_regulates GO:0008152 ! metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009914 name: hormone transport namespace: biological_process def: "The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:tb] subset: goslim_pir is_a: GO:0006810 ! transport is_a: GO:0010817 ! regulation of hormone levels property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0009987 name: cellular process namespace: biological_process alt_id: GO:0008151 alt_id: GO:0050875 def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "cell growth and/or maintenance" NARROW [] synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] is_a: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0010604 name: positive regulation of macromolecule metabolic process namespace: biological_process def: "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] is_a: GO:0009893 ! positive regulation of metabolic process is_a: GO:0060255 ! regulation of macromolecule metabolic process relationship: positively_regulates GO:0043170 ! macromolecule metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0010817 name: regulation of hormone levels namespace: biological_process def: "Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action." [GOC:BHF, GOC:dph, GOC:tb] is_a: GO:0065008 ! regulation of biological quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0010876 name: lipid localization namespace: biological_process def: "Any process in which a lipid is transported to, or maintained in, a specific location." [GOC:BHF, GOC:dph, GOC:tb] synonym: "lipid localisation" EXACT [GOC:mah] is_a: GO:0033036 ! macromolecule localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0010927 name: cellular component assembly involved in morphogenesis namespace: biological_process def: "The cellular component assembly that is part of the initial shaping of the component during its developmental progression." [GOC:dph, GOC:tb] is_a: GO:0022607 ! cellular component assembly is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis relationship: part_of GO:0009653 ! anatomical structure morphogenesis relationship: part_of GO:0032989 ! cellular component morphogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0010941 name: regulation of cell death namespace: biological_process def: "Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [GOC:dph, GOC:tb] is_a: GO:0050794 ! regulation of cellular process relationship: regulates GO:0008219 ! cell death property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0012501 name: programmed cell death namespace: biological_process alt_id: GO:0016244 def: "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." [GOC:lr, GOC:mtg_apoptosis] comment: Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. synonym: "non-apoptotic programmed cell death" NARROW [] synonym: "nonapoptotic programmed cell death" NARROW [] synonym: "PCD" EXACT [] xref: Wikipedia:Programmed_cell_death is_a: GO:0008219 ! cell death property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0012505 name: endomembrane system namespace: cellular_component def: "A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles." [GOC:lh] subset: goslim_aspergillus subset: goslim_candida subset: goslim_yeast xref: Wikipedia:Endomembrane_system is_a: GO:0044464 ! cell part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0012506 name: vesicle membrane namespace: cellular_component def: "The lipid bilayer surrounding any membrane-bounded vesicle in the cell." [GOC:mah] xref: NIF_Subcellular:sao1153182838 is_a: GO:0031090 ! organelle membrane is_a: GO:0044464 ! cell part relationship: part_of GO:0012505 ! endomembrane system relationship: part_of GO:0031988 ! membrane-bounded vesicle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0014046 name: dopamine secretion namespace: biological_process def: "The regulated release of dopamine by a cell or group of cells. Dopamine is a catecholamine and a precursor of adrenaline and noradrenaline. It acts as a neurotransmitter in the central nervous system but it is also produced peripherally and acts as a hormone." [GOC:ef] is_a: GO:0015872 ! dopamine transport is_a: GO:0023061 ! signal release is_a: GO:0050432 ! catecholamine secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0014706 name: striated muscle tissue development namespace: biological_process def: "The process whose specific outcome is the progression of a striated muscle over time, from its formation to the mature structure. Striated muscle contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle. Skeletal muscle myoblasts fuse to form myotubes and eventually multinucleated muscle fibers. The fusion of cardiac cells is very rare and can only form binucleate cells." [CL:0000737, GOC:dph, GOC:mtg_muscle] is_a: GO:0060537 ! muscle tissue development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0015031 name: protein transport namespace: biological_process alt_id: GO:0015831 def: "The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir subset: gosubset_prok synonym: "enzyme transport" NARROW [] is_a: GO:0045184 ! establishment of protein localization is_a: GO:0071702 ! organic substance transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0015075 name: ion transmembrane transporter activity namespace: molecular_function def: "Catalysis of the transfer of an ion from one side of a membrane to the other." [GOC:dgf, GOC:mtg_transport, ISBN:0815340729] subset: gosubset_prok synonym: "ion transporter activity" EXACT [] is_a: GO:0022891 ! substrate-specific transmembrane transporter activity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0015103 name: inorganic anion transmembrane transporter activity namespace: molecular_function def: "Catalysis of the transfer of inorganic anions from one side of a membrane to the other. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage." [GOC:ai] subset: gosubset_prok is_a: GO:0008509 ! anion transmembrane transporter activity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0015106 name: bicarbonate transmembrane transporter activity namespace: molecular_function def: "Catalysis of the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-." [GOC:ai] is_a: GO:0015103 ! inorganic anion transmembrane transporter activity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0015669 name: gas transport namespace: biological_process def: "The directed movement of substances that are gaseous in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir subset: gosubset_prok is_a: GO:0006810 ! transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0015671 name: oxygen transport namespace: biological_process def: "The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: gosubset_prok is_a: GO:0015669 ! gas transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0015695 name: organic cation transport namespace: biological_process def: "The directed movement of organic cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic cations are atoms or small molecules with a positive charge which contain carbon in covalent linkage." [GOC:ai] subset: gosubset_prok is_a: GO:0006812 ! cation transport is_a: GO:0071702 ! organic substance transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0015833 name: peptide transport namespace: biological_process def: "The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir subset: gosubset_prok is_a: GO:0042886 ! amide transport is_a: GO:0071702 ! organic substance transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0015837 name: amine transport namespace: biological_process def: "The directed movement of amines, including polyamines, organic compounds containing one or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai, ISBN:0198506732] subset: goslim_pir subset: gosubset_prok synonym: "amine/polyamine transport" RELATED [] is_a: GO:0071702 ! organic substance transport is_a: GO:0071705 ! nitrogen compound transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0015844 name: monoamine transport namespace: biological_process alt_id: GO:0015873 def: "The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [CHEBI:25375, GOC:mah] subset: gosubset_prok is_a: GO:0071702 ! organic substance transport is_a: GO:0071705 ! nitrogen compound transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0015850 name: organic hydroxy compound transport namespace: biological_process def: "The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom." [CHEBI:33822, GOC:ai] subset: gosubset_prok synonym: "organic alcohol transport" EXACT [CHEBI:33822] is_a: GO:0071702 ! organic substance transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0015872 name: dopamine transport namespace: biological_process def: "The directed movement of dopamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Dopamine is a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline." [GOC:ai] is_a: GO:0006812 ! cation transport is_a: GO:0051937 ! catecholamine transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0015874 name: norepinephrine transport namespace: biological_process def: "The directed movement of norepinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine." [GOC:ai, ISBN:0198506732] synonym: "levarterenol transport" EXACT [] synonym: "noradrenaline transport" EXACT [] is_a: GO:0051937 ! catecholamine transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016020 name: membrane namespace: cellular_component def: "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:mah, ISBN:0815316194] subset: goslim_aspergillus subset: goslim_candida subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok xref: Wikipedia:Biological_membrane is_a: GO:0005575 ! cellular_component property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016021 name: integral to membrane namespace: cellular_component def: "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC:go_curators] subset: gosubset_prok synonym: "transmembrane" RELATED [GOC:mah] xref: Wikipedia:Transmembrane_protein is_a: GO:0031224 ! intrinsic to membrane property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016023 name: cytoplasmic membrane-bounded vesicle namespace: cellular_component def: "A membrane-bounded vesicle found in the cytoplasm of the cell." [GOC:ai, GOC:mah] subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_yeast subset: gosubset_prok synonym: "cytoplasmic membrane bounded vesicle" EXACT [] synonym: "cytoplasmic membrane-enclosed vesicle" EXACT [] is_a: GO:0031410 ! cytoplasmic vesicle is_a: GO:0031988 ! membrane-bounded vesicle is_a: GO:0043231 ! intracellular membrane-bounded organelle relationship: part_of GO:0005737 ! cytoplasm property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016043 name: cellular component organization namespace: biological_process alt_id: GO:0044235 alt_id: GO:0071842 def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "cell organisation" EXACT [] synonym: "cell organization and biogenesis" RELATED [GOC:mah] synonym: "cellular component organisation at cellular level" EXACT [GOC:mah] synonym: "cellular component organisation in other organism" EXACT [GOC:mah] synonym: "cellular component organization at cellular level" EXACT [] synonym: "cellular component organization in other organism" EXACT [] is_a: GO:0071840 ! cellular component organization or biogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016048 name: detection of temperature stimulus namespace: biological_process def: "The series of events in which a temperature stimulus (hot or cold) is received and converted into a molecular signal." [GOC:hb] synonym: "detection of temperature" EXACT [] synonym: "detection of thermal stimulus" EXACT [] synonym: "perception of temperature" RELATED [] is_a: GO:0009266 ! response to temperature stimulus is_a: GO:0009581 ! detection of external stimulus is_a: GO:0009582 ! detection of abiotic stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016050 name: vesicle organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle." [GOC:mah] subset: goslim_pir subset: goslim_yeast synonym: "vesicle organisation" EXACT [GOC:curators] synonym: "vesicle organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016053 name: organic acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732] subset: gosubset_prok synonym: "organic acid anabolism" EXACT [] synonym: "organic acid biosynthesis" EXACT [] synonym: "organic acid formation" EXACT [] synonym: "organic acid synthesis" EXACT [] is_a: GO:0006082 ! organic acid metabolic process is_a: GO:0044249 ! cellular biosynthetic process is_a: GO:0044283 ! small molecule biosynthetic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016064 name: immunoglobulin mediated immune response namespace: biological_process def: "An immune response mediated by immunoglobulins, whether cell-bound or in solution." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was improved by GO_REF:0000022. It was renamed and redefined. synonym: "antibody-mediated immune response" EXACT [] is_a: GO:0019724 ! B cell mediated immunity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016192 name: vesicle-mediated transport namespace: biological_process alt_id: GO:0006899 def: "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000] subset: goslim_aspergillus subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: gosubset_prok synonym: "nonselective vesicle transport" NARROW [] synonym: "protein sorting along secretory pathway" RELATED [] synonym: "vesicle trafficking" RELATED [] synonym: "vesicle transport" EXACT [] synonym: "vesicular transport" EXACT [GOC:mah] is_a: GO:0006810 ! transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016265 name: death namespace: biological_process def: "A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism." [GOC:mah, ISBN:0877797099] comment: See also the biological process term 'apoptosis ; GO:0006915'. subset: goslim_plant subset: gosubset_prok xref: Wikipedia:Death is_a: GO:0044699 ! single-organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016444 name: somatic cell DNA recombination namespace: biological_process def: "Recombination occurring within or between DNA molecules in somatic cells." [GOC:ma] is_a: GO:0006310 ! DNA recombination property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016445 name: somatic diversification of immunoglobulins namespace: biological_process def: "The somatic process that results in the generation of sequence diversity of immunoglobulins." [GOC:add, GOC:ma, ISBN:0781735149] synonym: "somatic diversification of antibodies" EXACT [] is_a: GO:0002200 ! somatic diversification of immune receptors relationship: part_of GO:0002377 ! immunoglobulin production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016446 name: somatic hypermutation of immunoglobulin genes namespace: biological_process def: "Mutations occurring somatically that result in amino acid changes in the rearranged V regions of immunoglobulins." [GOC:add, ISBN:0781735149, PMID:11205330, PMID:11205333, PMID:14975236, PMID:7813007] synonym: "somatic hypermutation of antibody genes" EXACT [] is_a: GO:0002566 ! somatic diversification of immune receptors via somatic mutation is_a: GO:0016445 ! somatic diversification of immunoglobulins property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016447 name: somatic recombination of immunoglobulin gene segments namespace: biological_process def: "The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, as known as immunoglobulin gene segments, within a single locus." [GOC:add, ISBN:0781735149] synonym: "somatic recombination of antibody gene segments" EXACT [] is_a: GO:0002562 ! somatic diversification of immune receptors via germline recombination within a single locus is_a: GO:0016445 ! somatic diversification of immunoglobulins property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0016477 name: cell migration namespace: biological_process def: "The orderly movement of a cell from one site to another, often during the development of a multicellular organism or multicellular structure." [GOC:ems, GOC:pf] xref: Wikipedia:Cell_migration is_a: GO:0048870 ! cell motility property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0017145 name: stem cell division namespace: biological_process def: "The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types." [GOC:jid, ISBN:0582227089] synonym: "stem cell renewal" EXACT [] is_a: GO:0051301 ! cell division property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0019219 name: regulation of nucleobase-containing compound metabolic process namespace: biological_process def: "Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators] subset: gosubset_prok synonym: "regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] synonym: "regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] is_a: GO:0031323 ! regulation of cellular metabolic process is_a: GO:0051171 ! regulation of nitrogen compound metabolic process is_a: GO:0080090 ! regulation of primary metabolic process relationship: regulates GO:0006139 ! nucleobase-containing compound metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0019222 name: regulation of metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] subset: gosubset_prok synonym: "regulation of metabolism" EXACT [] is_a: GO:0050789 ! regulation of biological process relationship: regulates GO:0008152 ! metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0019724 name: B cell mediated immunity namespace: biological_process def: "Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] comment: This term was improved by GO_REF:0000022. It was moved. synonym: "B lymphocyte mediated immune effector process" EXACT [] synonym: "B lymphocyte mediated immunity" EXACT [] synonym: "B-cell mediated immune effector process" EXACT [] synonym: "B-cell mediated immunity" EXACT [] synonym: "B-lymphocyte mediated immune effector process" EXACT [] synonym: "B-lymphocyte mediated immunity" EXACT [] is_a: GO:0002449 ! lymphocyte mediated immunity is_a: GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0019730 name: antimicrobial humoral response namespace: biological_process alt_id: GO:0006960 alt_id: GO:0019735 def: "An immune response against microbes mediated through a body fluid. Examples of this process are seen in the antimicrobial humoral response of Drosophila melanogaster and Mus musculus." [GOC:go_curators, GOC:mtg_sensu] is_a: GO:0006959 ! humoral immune response is_a: GO:0051707 ! response to other organism property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0019752 name: carboxylic acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-)." [ISBN:0198506732] subset: gosubset_prok synonym: "carboxylic acid metabolism" EXACT [] is_a: GO:0043436 ! oxoacid metabolic process is_a: GO:0071704 ! organic substance metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0019814 name: immunoglobulin complex namespace: cellular_component def: "A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, GOC:jl, ISBN:0781765196] comment: Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. subset: goslim_pir is_a: GO:0043234 ! protein complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0019815 name: B cell receptor complex namespace: cellular_component alt_id: GO:0042570 def: "An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." [GOC:add, ISBN:0781735149] comment: Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "antibody" RELATED [GOC:mah] synonym: "B cell receptor accessory molecule complex" RELATED [] synonym: "B lymphocyte receptor complex" EXACT [] synonym: "B-cell receptor complex" EXACT [] synonym: "B-lymphocyte receptor complex" EXACT [] synonym: "BCR complex" EXACT [] synonym: "immunoglobulin complex, membrane bound" EXACT [] is_a: GO:0019814 ! immunoglobulin complex is_a: GO:0043235 ! receptor complex is_a: GO:0044459 ! plasma membrane part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0019882 name: antigen processing and presentation namespace: biological_process alt_id: GO:0030333 def: "The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149, PMID:15771591, PMID:15928678] comment: This term was improved by GO_REF:0000022. It was renamed and redefined. synonym: "antigen presentation" EXACT [] synonym: "antigen processing" EXACT [] xref: Wikipedia:Antigen_presentation is_a: GO:0002376 ! immune system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0019884 name: antigen processing and presentation of exogenous antigen namespace: biological_process def: "The process in which an antigen-presenting cell expresses antigen (peptide or lipid) of exogenous origin on its cell surface in association with an MHC protein complex." [GOC:add, ISBN:0781735149, PMID:15771591, PMID:15928678] synonym: "antigen presentation, exogenous antigen" EXACT [] is_a: GO:0019882 ! antigen processing and presentation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0019953 name: sexual reproduction namespace: biological_process def: "The regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times." [ISBN:0387520546] xref: Wikipedia:Sexual_reproduction is_a: GO:0000003 ! reproduction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0021700 name: developmental maturation namespace: biological_process def: "A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] comment: This term was added by GO_REF:0000021. subset: goslim_generic is_a: GO:0032502 ! developmental process is_a: GO:0044699 ! single-organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022008 name: neurogenesis namespace: biological_process def: "Generation of cells within the nervous system." [GO_REF:0000021, GOC:cls, GOC:curators, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] comment: This term was added by GO_REF:0000021. synonym: "nervous system cell generation" EXACT systematic_synonym [] synonym: "neural cell differentiation" RELATED [GOC:BHF, GOC:dph] xref: Wikipedia:Neurogenesis is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0007399 ! nervous system development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022402 name: cell cycle process namespace: biological_process def: "A cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events." [GOC:isa_complete] subset: gosubset_prok is_a: GO:0044763 ! single-organism cellular process relationship: part_of GO:0007049 ! cell cycle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022403 name: cell cycle phase namespace: biological_process def: "A cell cycle process comprising the steps by which a cell progresses through one of the biochemical and morphological phases and events that occur during successive cell replication or nuclear replication events." [GOC:dph, GOC:isa_complete, GOC:tb] is_a: GO:0022402 ! cell cycle process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022404 name: molting cycle process namespace: biological_process def: "A multicellular organismal process involved in the periodic casting off and regeneration of an outer covering of cuticle, feathers, hair, horns, skin." [GOC:isa_complete] is_a: GO:0044707 ! single-multicellular organism process relationship: part_of GO:0042303 ! molting cycle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022405 name: hair cycle process namespace: biological_process def: "A multicellular organismal process involved in the cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body." [GOC:isa_complete] is_a: GO:0022404 ! molting cycle process relationship: part_of GO:0042633 ! hair cycle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022411 name: cellular component disassembly namespace: biological_process alt_id: GO:0071845 def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] subset: goslim_pir subset: gosubset_prok synonym: "cell structure disassembly" EXACT [] synonym: "cellular component disassembly at cellular level" EXACT [] is_a: GO:0016043 ! cellular component organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022412 name: cellular process involved in reproduction in multicellular organism namespace: biological_process def: "A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism." [GOC:isa_complete] synonym: "reproductive cellular process in multicellular organism" EXACT [GOC:curators] is_a: GO:0048610 ! cellular process involved in reproduction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022414 name: reproductive process namespace: biological_process def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete] subset: gosubset_prok is_a: GO:0008150 ! biological_process relationship: part_of GO:0000003 ! reproduction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022600 name: digestive system process namespace: biological_process def: "A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." [GOC:isa_complete, GOC:jid, GOC:mtg_cardio] is_a: GO:0003008 ! system process relationship: part_of GO:0007586 ! digestion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022602 name: ovulation cycle process namespace: biological_process def: "A process involved in the sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years." [GOC:isa_complete] synonym: "estrous cycle process" RELATED [] synonym: "menstrual cycle process" RELATED [] is_a: GO:0048511 ! rhythmic process relationship: part_of GO:0042698 ! ovulation cycle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022603 name: regulation of anatomical structure morphogenesis namespace: biological_process def: "Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis." [GOC:mah] subset: gosubset_prok synonym: "regulation of morphogenesis" EXACT [] is_a: GO:0050793 ! regulation of developmental process relationship: regulates GO:0009653 ! anatomical structure morphogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022607 name: cellular component assembly namespace: biological_process alt_id: GO:0071844 def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] subset: goslim_generic subset: goslim_pir subset: gosubset_prok synonym: "cell structure assembly" EXACT [] synonym: "cellular component assembly at cellular level" EXACT [] is_a: GO:0016043 ! cellular component organization relationship: part_of GO:0044085 ! cellular component biogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022857 name: transmembrane transporter activity namespace: molecular_function alt_id: GO:0005386 alt_id: GO:0015646 def: "Enables the transfer of a substance from one side of a membrane to the other." [GOC:mtg_transport, ISBN:0815340729] subset: goslim_generic subset: goslim_yeast subset: gosubset_prok xref: Reactome:REACT_100033 "GLUT9 transports glucose, fructose and urate, Gallus gallus" xref: Reactome:REACT_106735 "GLUT9 transports glucose, fructose and urate, Xenopus tropicalis" xref: Reactome:REACT_111088 "Egress of internalized antigen to the cytosol via sec61, Homo sapiens" xref: Reactome:REACT_111933 "GLUT9 transports glucose, fructose and urate, Plasmodium falciparum" xref: Reactome:REACT_113047 "GLUT9 transports glucose, fructose and urate, Dictyostelium discoideum" xref: Reactome:REACT_113116 "GLUT9 transports glucose, fructose and urate, Mycobacterium tuberculosis" xref: Reactome:REACT_113829 "GLUT9 transports glucose, fructose and urate, Arabidopsis thaliana" xref: Reactome:REACT_114161 "GLUT9 transports glucose, fructose and urate, Oryza sativa" xref: Reactome:REACT_19288 "GLUT9 transports glucose, fructose and urate, Homo sapiens" xref: Reactome:REACT_77235 "GLUT9 transports glucose, fructose and urate, Canis familiaris" xref: Reactome:REACT_81225 "GLUT9 transports glucose, fructose and urate, Bos taurus" xref: Reactome:REACT_88503 "GLUT9 transports glucose, fructose and urate, Taeniopygia guttata" xref: Reactome:REACT_91849 "GLUT9 transports glucose, fructose and urate, Mus musculus" xref: Reactome:REACT_94185 "GLUT9 transports glucose, fructose and urate, Rattus norvegicus" is_a: GO:0005215 ! transporter activity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022891 name: substrate-specific transmembrane transporter activity namespace: molecular_function def: "Enables the transfer of a specific substance or group of related substances from one side of a membrane to the other." [GOC:jid, GOC:mtg_transport, ISBN:0815340729] subset: gosubset_prok is_a: GO:0022857 ! transmembrane transporter activity is_a: GO:0022892 ! substrate-specific transporter activity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022892 name: substrate-specific transporter activity namespace: molecular_function def: "Enables the directed movement of a specific substance or group of related substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells." [GOC:mtg_transport] subset: gosubset_prok is_a: GO:0005215 ! transporter activity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0023052 name: signaling namespace: biological_process alt_id: GO:0023046 def: "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling] comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. subset: goslim_pombe subset: goslim_yeast synonym: "biological signaling" EXACT [] synonym: "signaling process" EXACT [] synonym: "signalling" EXACT [] synonym: "signalling process" RELATED [GOC:mah] is_a: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0023061 name: signal release namespace: biological_process def: "The process in which a signal is secreted or discharged into the extracellular medium from a cellular source." [GOC:mtg_signal] is_a: GO:0044763 ! single-organism cellular process relationship: part_of GO:0003001 ! generation of a signal involved in cell-cell signaling property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030030 name: cell projection organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] subset: gosubset_prok synonym: "cell projection organisation" EXACT [GOC:curators] synonym: "cell projection organization and biogenesis" RELATED [GOC:mah] synonym: "cell surface structure organization and biogenesis" RELATED [GOC:mah] is_a: GO:0016043 ! cellular component organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030031 name: cell projection assembly namespace: biological_process def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] subset: goslim_metagenomics subset: gosubset_prok synonym: "cell projection biogenesis" RELATED [GOC:mah] synonym: "formation of a cell surface projection" EXACT [] is_a: GO:0022607 ! cellular component assembly is_a: GO:0030030 ! cell projection organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030072 name: peptide hormone secretion namespace: biological_process def: "The regulated release of a peptide hormone from a cell or organ." [GOC:mah] is_a: GO:0002790 ! peptide secretion is_a: GO:0046879 ! hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030073 name: insulin secretion namespace: biological_process def: "The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin." [GOC:mah, ISBN:0198506732] is_a: GO:0030072 ! peptide hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030097 name: hemopoiesis namespace: biological_process def: "The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates." [GOC:dgh, ISBN:0198506732] synonym: "blood cell biosynthesis" EXACT [] synonym: "blood cell formation" EXACT [] synonym: "haemopoiesis" EXACT [] synonym: "hematopoiesis" EXACT [] xref: Wikipedia:Haematopoiesis is_a: GO:0048534 ! hematopoietic or lymphoid organ development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030098 name: lymphocyte differentiation namespace: biological_process alt_id: GO:0046650 def: "The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." [CL:0000542, GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "lymphocyte cell differentiation" EXACT [] synonym: "lymphocyte development" RELATED [GOC:add] synonym: "lymphocytic blood cell differentiation" EXACT [] is_a: GO:0002521 ! leukocyte differentiation is_a: GO:0046649 ! lymphocyte activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030099 name: myeloid cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages." [GOC:add, ISBN:0781735149] is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0030097 ! hemopoiesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030101 name: natural killer cell activation namespace: biological_process def: "The change in morphology and behavior of a natural killer cell in response to a cytokine, chemokine, cellular ligand, or soluble factor." [GOC:mgi_curators, ISBN:0781735140] synonym: "NK cell activation" EXACT [] is_a: GO:0046649 ! lymphocyte activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030103 name: vasopressin secretion namespace: biological_process def: "The regulated release of vasopressin from secretory granules into the blood." [GOC:mah] is_a: GO:0030072 ! peptide hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030141 name: secretory granule namespace: cellular_component def: "A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules." [GOC:mah, ISBN:0198596732] comment: Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'transport vesicle ; GO:0030133'. synonym: "secretory vesicle" BROAD [] is_a: GO:0016023 ! cytoplasmic membrane-bounded vesicle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030154 name: cell differentiation namespace: biological_process def: "The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [ISBN:0198506732] subset: goslim_generic subset: goslim_plant subset: gosubset_prok xref: Wikipedia:Cellular_differentiation is_a: GO:0048869 ! cellular developmental process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030182 name: neuron differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized features of a neuron." [GOC:mah] is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0048699 ! generation of neurons property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030183 name: B cell differentiation namespace: biological_process alt_id: GO:0042115 def: "The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity." [GO_REF:0000022, GOC:mah, GOC:mtg_15nov05] comment: This term was improved by GO_REF:0000022. It was moved. Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "B cell development" RELATED [GOC:add] synonym: "B lymphocyte differentiation" EXACT [] synonym: "B-cell differentiation" EXACT [] synonym: "B-lymphocyte differentiation" EXACT [] is_a: GO:0030098 ! lymphocyte differentiation is_a: GO:0042113 ! B cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030198 name: extracellular matrix organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix." [GOC:mah] subset: goslim_generic subset: gosubset_prok synonym: "extracellular matrix organisation" EXACT [GOC:curators] synonym: "extracellular matrix organization and biogenesis" RELATED [GOC:mah] is_a: GO:0043062 ! extracellular structure organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030202 name: heparin metabolic process namespace: biological_process def: "The chemical reactions and pathways involving heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells. They are similar to heparan sulfates but are of somewhat higher average Mr (6000-20000) and contain fewer N-acetyl groups and more N-sulfate and O-sulfate groups; they may be attached in the same manner to protein, forming proteoglycans. They consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues." [GOC:mah, ISBN:0198506732] subset: gosubset_prok synonym: "heparan sulfate metabolic process" RELATED [] synonym: "heparin metabolism" EXACT [] is_a: GO:0006790 ! sulfur compound metabolic process is_a: GO:0030203 ! glycosaminoglycan metabolic process is_a: GO:0043436 ! oxoacid metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030203 name: glycosaminoglycan metabolic process namespace: biological_process def: "The chemical reactions and pathways involving glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars. Formerly known as mucopolysaccharides, they include hyaluronic acid and chondroitin, which provide lubrication in joints and form part of the matrix of cartilage. The three-dimensional structure of these molecules enables them to trap water, which forms a gel and gives glycosaminoglycans their elastic properties." [ISBN:0192800981] subset: gosubset_prok synonym: "glycosaminoglycan metabolism" EXACT [] is_a: GO:0006022 ! aminoglycan metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030210 name: heparin biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of heparin, any member of a group of glycosaminoglycans of average Mr (6000-20000), consisting predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues." [GOC:mah, ISBN:0198506732] subset: gosubset_prok synonym: "heparan sulfate biosynthetic process" RELATED [] synonym: "heparin anabolism" EXACT [] synonym: "heparin biosynthesis" EXACT [] synonym: "heparin formation" EXACT [] synonym: "heparin synthesis" EXACT [] is_a: GO:0006024 ! glycosaminoglycan biosynthetic process is_a: GO:0030202 ! heparin metabolic process is_a: GO:0044272 ! sulfur compound biosynthetic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030217 name: T cell differentiation namespace: biological_process alt_id: GO:0042112 alt_id: GO:0046652 def: "The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex." [GO_REF:0000022, GOC:jid, GOC:mah, GOC:mtg_15nov05] comment: This term was improved by GO_REF:0000022. It was moved. Note that the term 'thymocyte differentiation' was merged into this term because thymocytes are T cells, and thus the term was essentially redundant. Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "T cell development" RELATED [GOC:add] synonym: "T lymphocyte differentiation" EXACT [] synonym: "T-cell differentiation" EXACT [] synonym: "T-lymphocyte differentiation" EXACT [] is_a: GO:0030098 ! lymphocyte differentiation is_a: GO:0042110 ! T cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030218 name: erythrocyte differentiation namespace: biological_process def: "The process in which a myeloid precursor cell acquires specializes features of an erythrocyte." [GOC:mah] synonym: "erythrocyte cell differentiation" EXACT [] synonym: "erythropoiesis" EXACT [GOC:add, GOC:dph] synonym: "RBC differentiation" EXACT [CL:0000232] synonym: "red blood cell differentiation" EXACT [CL:0000232] xref: Wikipedia:Erythropoiesis is_a: GO:0030099 ! myeloid cell differentiation relationship: part_of GO:0034101 ! erythrocyte homeostasis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030219 name: megakaryocyte differentiation namespace: biological_process def: "The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte." [GOC:mah] synonym: "megakaryocyte cell differentiation" EXACT [] is_a: GO:0030099 ! myeloid cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030221 name: basophil differentiation namespace: biological_process def: "The process in which a relatively unspecialized myeloid precursor cell acquires specialized features of a basophil cell." [GOC:jid, GOC:mah] synonym: "basophil cell differentiation" EXACT [] is_a: GO:0030851 ! granulocyte differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030222 name: eosinophil differentiation namespace: biological_process def: "The process in which a relatively unspecialized myeloid precursor cell acquires the specializes features of an eosinophil." [GOC:mah] synonym: "eosinophil cell differentiation" EXACT [] is_a: GO:0030851 ! granulocyte differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030223 name: neutrophil differentiation namespace: biological_process def: "The process in which a myeloid precursor cell acquires the specialized features of a neutrophil." [GOC:mah] synonym: "neutrophil cell differentiation" EXACT [] synonym: "neutrophil granulocyte differentiation" EXACT [GOC:yaf] synonym: "neutrophil granulocytopoiesis" EXACT [GOC:yaf] is_a: GO:0030851 ! granulocyte differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030224 name: monocyte differentiation namespace: biological_process def: "The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte." [GOC:mah] synonym: "monocyte cell differentiation" EXACT [] is_a: GO:0002573 ! myeloid leukocyte differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030225 name: macrophage differentiation namespace: biological_process def: "The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage." [GOC:add, ISBN:0781735149] synonym: "macrophage cell differentiation" EXACT [] is_a: GO:0002573 ! myeloid leukocyte differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030252 name: growth hormone secretion namespace: biological_process def: "The regulated release of growth hormone from secretory granules into the blood." [GOC:mah] synonym: "somatotropin secretion" EXACT [GOC:mah] is_a: GO:0030072 ! peptide hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030261 name: chromosome condensation namespace: biological_process alt_id: GO:0000068 def: "The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells." [GOC:mah, ISBN:0815316194] is_a: GO:0006323 ! DNA packaging is_a: GO:0051276 ! chromosome organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030262 name: apoptotic nuclear changes namespace: biological_process def: "Alterations undergone by nuclei at the molecular and morphological level and that contribute to the execution phase of apoptosis." [GOC:mah, GOC:mtg_apoptosis] synonym: "apoptotic nuclear change" NARROW [] is_a: GO:0006921 ! cellular component disassembly involved in execution phase of apoptosis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030263 name: apoptotic chromosome condensation namespace: biological_process def: "The compaction of chromatin during apoptosis." [GOC:mah] synonym: "pyknosis" EXACT [] xref: Wikipedia:Pyknosis is_a: GO:0030261 ! chromosome condensation relationship: part_of GO:0030262 ! apoptotic nuclear changes property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030316 name: osteoclast differentiation namespace: biological_process def: "The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue." [CL:0000092, GOC:add, ISBN:0781735149, PMID:12161749] synonym: "osteoclast cell differentiation" EXACT [] is_a: GO:0002573 ! myeloid leukocyte differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030317 name: sperm motility namespace: biological_process def: "Any process involved in the controlled movement of a sperm cell." [GOC:jl] synonym: "sperm movement" EXACT [] xref: Wikipedia:Sperm_motility is_a: GO:0048870 ! cell motility property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030334 name: regulation of cell migration namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cell migration." [GOC:go_curators] is_a: GO:2000145 ! regulation of cell motility relationship: regulates GO:0016477 ! cell migration property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030335 name: positive regulation of cell migration namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of cell migration." [GOC:go_curators] subset: gosubset_prok synonym: "activation of cell migration" NARROW [] synonym: "stimulation of cell migration" NARROW [] synonym: "up regulation of cell migration" EXACT [] synonym: "up-regulation of cell migration" EXACT [] synonym: "upregulation of cell migration" EXACT [] is_a: GO:0030334 ! regulation of cell migration is_a: GO:2000147 ! positive regulation of cell motility relationship: positively_regulates GO:0016477 ! cell migration property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030529 name: ribonucleoprotein complex namespace: cellular_component def: "A macromolecular complex containing both protein and RNA molecules." [GOC:krc] subset: goslim_pir subset: gosubset_prok synonym: "protein-RNA complex" EXACT [] synonym: "ribonucleoprotein" EXACT [] synonym: "RNA-protein complex" EXACT [] synonym: "RNP" EXACT [] xref: Wikipedia:Ribonucleoprotein is_a: GO:0032991 ! macromolecular complex is_a: GO:0044424 ! intracellular part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030593 name: neutrophil chemotaxis namespace: biological_process def: "The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding." [GOC:jl, ISBN:0198506732] is_a: GO:0030595 ! leukocyte chemotaxis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030595 name: leukocyte chemotaxis namespace: biological_process def: "The movement of a leukocyte in response to an external stimulus." [GOC:add, GOC:jl] synonym: "immune cell chemotaxis" EXACT [] synonym: "leucocyte chemotaxis" EXACT [] is_a: GO:0050900 ! leukocyte migration is_a: GO:0060326 ! cell chemotaxis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030659 name: cytoplasmic vesicle membrane namespace: cellular_component def: "The lipid bilayer surrounding a cytoplasmic vesicle." [GOC:mah] subset: gosubset_prok is_a: GO:0012506 ! vesicle membrane is_a: GO:0044433 ! cytoplasmic vesicle part relationship: part_of GO:0016023 ! cytoplasmic membrane-bounded vesicle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030667 name: secretory granule membrane namespace: cellular_component def: "The lipid bilayer surrounding a secretory granule." [GOC:mah] synonym: "secretory vesicle membrane" BROAD [] is_a: GO:0030659 ! cytoplasmic vesicle membrane relationship: part_of GO:0030141 ! secretory granule property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030851 name: granulocyte differentiation namespace: biological_process def: "The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils." [GOC:ecd, http://life.nthu.edu.tw/~g864204/dict-search1.htm] synonym: "granulocyte cell differentiation" EXACT [] is_a: GO:0002573 ! myeloid leukocyte differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030855 name: epithelial cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium." [GOC:ecd, PMID:11839751] is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0060429 ! epithelium development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0031090 name: organelle membrane namespace: cellular_component def: "The lipid bilayer surrounding an organelle." [GOC:mah] subset: gosubset_prok is_a: GO:0016020 ! membrane is_a: GO:0044422 ! organelle part relationship: part_of GO:0043227 ! membrane-bounded organelle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0031224 name: intrinsic to membrane namespace: cellular_component def: "Located in a membrane such that some covalently attached portion of the gene product, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, spans or is embedded in one or both leaflets of the membrane." [GOC:mah] comment: Note that proteins intrinsic to membranes cannot be removed without disrupting the membrane, e.g. by detergent. subset: gosubset_prok is_a: GO:0044425 ! membrane part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0031226 name: intrinsic to plasma membrane namespace: cellular_component def: "Located in the plasma membrane such that some covalently attached portion of the gene product, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, spans or is embedded in one or both leaflets of the membrane." [GOC:mah] subset: gosubset_prok is_a: GO:0031224 ! intrinsic to membrane is_a: GO:0044459 ! plasma membrane part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0031268 name: pseudopodium organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pseudopodium, a temporary protrusion or retractile process of a cell, associated with cellular movement." [GOC:pg] synonym: "pseudopodium organisation" EXACT [GOC:curators] synonym: "pseudopodium organization and biogenesis" RELATED [GOC:mah] is_a: GO:0030030 ! cell projection organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0031294 name: lymphocyte costimulation namespace: biological_process def: "The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the B- or T cell receptor to augment B- or T cell activation." [ISBN:0781735149] synonym: "lymphocyte co-stimulation" EXACT [] is_a: GO:0002376 ! immune system process is_a: GO:0051251 ! positive regulation of lymphocyte activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0031323 name: regulation of cellular metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] subset: gosubset_prok synonym: "regulation of cellular metabolism" EXACT [] is_a: GO:0019222 ! regulation of metabolic process is_a: GO:0050794 ! regulation of cellular process relationship: regulates GO:0044237 ! cellular metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0031325 name: positive regulation of cellular metabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] subset: gosubset_prok synonym: "activation of cellular metabolic process" NARROW [] synonym: "positive regulation of cellular metabolism" EXACT [] synonym: "stimulation of cellular metabolic process" NARROW [] synonym: "up regulation of cellular metabolic process" EXACT [] synonym: "up-regulation of cellular metabolic process" EXACT [] synonym: "upregulation of cellular metabolic process" EXACT [] xref: Reactome:REACT_101225 "ChREBP activates metabolic gene expression, Mus musculus" xref: Reactome:REACT_102187 "ChREBP activates metabolic gene expression, Escherichia coli" xref: Reactome:REACT_102331 "ChREBP activates metabolic gene expression, Caenorhabditis elegans" xref: Reactome:REACT_105293 "ChREBP activates metabolic gene expression, Plasmodium falciparum" xref: Reactome:REACT_108571 "ChREBP activates metabolic gene expression, Drosophila melanogaster" xref: Reactome:REACT_109170 "ChREBP activates metabolic gene expression, Xenopus tropicalis" xref: Reactome:REACT_2122 "ChREBP activates metabolic gene expression, Homo sapiens" xref: Reactome:REACT_28360 "ChREBP activates metabolic gene expression, Arabidopsis thaliana" xref: Reactome:REACT_31270 "ChREBP activates metabolic gene expression, Mycobacterium tuberculosis" xref: Reactome:REACT_79603 "ChREBP activates metabolic gene expression, Canis familiaris" xref: Reactome:REACT_80902 "ChREBP activates metabolic gene expression, Saccharomyces cerevisiae" xref: Reactome:REACT_83058 "ChREBP activates metabolic gene expression, Taeniopygia guttata" xref: Reactome:REACT_84314 "ChREBP activates metabolic gene expression, Oryza sativa" xref: Reactome:REACT_86633 "ChREBP activates metabolic gene expression, Dictyostelium discoideum" xref: Reactome:REACT_87840 "ChREBP activates metabolic gene expression, Danio rerio" xref: Reactome:REACT_88060 "ChREBP activates metabolic gene expression, Rattus norvegicus" xref: Reactome:REACT_91293 "ChREBP activates metabolic gene expression, Staphylococcus aureus N315" xref: Reactome:REACT_91429 "ChREBP activates metabolic gene expression, Gallus gallus" xref: Reactome:REACT_91906 "ChREBP activates metabolic gene expression, Schizosaccharomyces pombe" xref: Reactome:REACT_92487 "ChREBP activates metabolic gene expression, Bos taurus" xref: Reactome:REACT_99393 "ChREBP activates metabolic gene expression, Sus scrofa" is_a: GO:0009893 ! positive regulation of metabolic process is_a: GO:0031323 ! regulation of cellular metabolic process is_a: GO:0048522 ! positive regulation of cellular process relationship: positively_regulates GO:0044237 ! cellular metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0031347 name: regulation of defense response namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a defense response." [GOC:mah] is_a: GO:0080134 ! regulation of response to stress relationship: regulates GO:0006952 ! defense response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0031348 name: negative regulation of defense response namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a defense response." [GOC:mah] synonym: "down regulation of defense response" EXACT [] synonym: "down-regulation of defense response" EXACT [] synonym: "downregulation of defense response" EXACT [] synonym: "inhibition of defense response" NARROW [] is_a: GO:0031347 ! regulation of defense response is_a: GO:0048585 ! negative regulation of response to stimulus relationship: negatively_regulates GO:0006952 ! defense response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0031349 name: positive regulation of defense response namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of a defense response." [GOC:mah] synonym: "activation of defense response" NARROW [] synonym: "stimulation of defense response" NARROW [] synonym: "up regulation of defense response" EXACT [] synonym: "up-regulation of defense response" EXACT [] synonym: "upregulation of defense response" EXACT [] is_a: GO:0031347 ! regulation of defense response is_a: GO:0048584 ! positive regulation of response to stimulus relationship: positively_regulates GO:0006952 ! defense response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0031410 name: cytoplasmic vesicle namespace: cellular_component def: "A vesicle formed of membrane or protein, found in the cytoplasm of a cell." [GOC:mah] subset: gosubset_prok xref: NIF_Subcellular:sao180601769 is_a: GO:0031982 ! vesicle is_a: GO:0043229 ! intracellular organelle is_a: GO:0044444 ! cytoplasmic part relationship: part_of GO:0005737 ! cytoplasm property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0031974 name: membrane-enclosed lumen namespace: cellular_component def: "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen." [GOC:add, GOC:mah] is_a: GO:0005575 ! cellular_component property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0031981 name: nuclear lumen namespace: cellular_component def: "The volume enclosed by the nuclear inner membrane." [GOC:mah, GOC:pz] is_a: GO:0044428 ! nuclear part is_a: GO:0070013 ! intracellular organelle lumen property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0031982 name: vesicle namespace: cellular_component def: "Any small, fluid-filled, spherical organelle enclosed by membrane or protein." [GOC:mah, GOC:pz] subset: goslim_metagenomics subset: goslim_pir subset: gosubset_prok xref: NIF_Subcellular:sao221389602 xref: Wikipedia:Vesicle_(biology) is_a: GO:0043226 ! organelle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0031988 name: membrane-bounded vesicle namespace: cellular_component def: "Any small, fluid-filled, spherical organelle enclosed by a lipid bilayer." [GOC:mah] subset: gosubset_prok synonym: "membrane-enclosed vesicle" EXACT [] is_a: GO:0031982 ! vesicle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032101 name: regulation of response to external stimulus namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a response to an external stimulus." [GOC:mah] is_a: GO:0048583 ! regulation of response to stimulus relationship: regulates GO:0009605 ! response to external stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032102 name: negative regulation of response to external stimulus namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus." [GOC:mah] synonym: "down regulation of response to external stimulus" EXACT [] synonym: "down-regulation of response to external stimulus" EXACT [] synonym: "downregulation of response to external stimulus" EXACT [] synonym: "inhibition of response to external stimulus" NARROW [] is_a: GO:0032101 ! regulation of response to external stimulus is_a: GO:0048585 ! negative regulation of response to stimulus relationship: negatively_regulates GO:0009605 ! response to external stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032103 name: positive regulation of response to external stimulus namespace: biological_process def: "Any process that activates, maintains or increases the rate of a response to an external stimulus." [GOC:mah] synonym: "activation of response to external stimulus" NARROW [] synonym: "stimulation of response to external stimulus" NARROW [] synonym: "up regulation of response to external stimulus" EXACT [] synonym: "up-regulation of response to external stimulus" EXACT [] synonym: "upregulation of response to external stimulus" EXACT [] is_a: GO:0032101 ! regulation of response to external stimulus is_a: GO:0048584 ! positive regulation of response to stimulus relationship: positively_regulates GO:0009605 ! response to external stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032274 name: gonadotropin secretion namespace: biological_process def: "The regulated release of a gonadotropin, any hormone that stimulates the gonads, especially follicle-stimulating hormone and luteinizing hormone." [GOC:mah, ISBN:0721662544] synonym: "gonadotrophin secretion" EXACT [] is_a: GO:0060986 ! endocrine hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032275 name: luteinizing hormone secretion namespace: biological_process def: "The regulated release of luteinizing hormone, a gonadotropic glycoprotein hormone secreted by the anterior pituitary." [ISBN:0198506732] is_a: GO:0032274 ! gonadotropin secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032394 name: MHC class Ib receptor activity namespace: molecular_function def: "Combining with an MHC class Ib protein complex and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. Class Ib here refers to non-classical class I molecules, such as those of the CD1 or HLA-E gene families." [GOC:add, GOC:signaling, ISBN:0781735149] comment: Note that this term is intended for annotation of gene products that act as receptors for MHC class Ib protein complexes, not for components of the MHC class Ib protein complexes themselves. synonym: "alpha-beta T cell receptor activity" RELATED [] synonym: "gamma-delta T cell receptor activity" RELATED [] synonym: "T cell receptor activity" RELATED [] is_a: GO:0004888 ! transmembrane signaling receptor activity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032501 name: multicellular organismal process namespace: biological_process alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] subset: goslim_pir synonym: "organismal physiological process" EXACT [] is_a: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032502 name: developmental process namespace: biological_process def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] subset: goslim_aspergillus subset: goslim_pir subset: gosubset_prok synonym: "development" NARROW [] is_a: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032504 name: multicellular organism reproduction namespace: biological_process def: "The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:isa_complete, GOC:jid] is_a: GO:0000003 ! reproduction is_a: GO:0032501 ! multicellular organismal process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032606 name: type I interferon production namespace: biological_process def: "The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." [GOC:add, ISBN:0126896631, PMID:15546383, PMID:16681834] synonym: "interferon type I production" EXACT [] synonym: "type I IFN production" EXACT [] is_a: GO:0001816 ! cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032609 name: interferon-gamma production namespace: biological_process def: "The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon." [GOC:add, GOC:mah] synonym: "IFNG production" EXACT [GOC:mah] synonym: "type II IFN production" EXACT [GOC:mah] synonym: "type II interferon production" EXACT [] is_a: GO:0001816 ! cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032611 name: interleukin-1 beta production namespace: biological_process def: "The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] synonym: "IL-1 beta production" EXACT [] is_a: GO:0032612 ! interleukin-1 production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032612 name: interleukin-1 production namespace: biological_process def: "The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] synonym: "IL-1 production" EXACT [] is_a: GO:0001816 ! cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032613 name: interleukin-10 production namespace: biological_process def: "The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] synonym: "IL-10 production" EXACT [] is_a: GO:0001816 ! cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032616 name: interleukin-13 production namespace: biological_process def: "The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] synonym: "IL-13 production" EXACT [] is_a: GO:0001816 ! cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032620 name: interleukin-17 production namespace: biological_process def: "The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah, GOC:rv, PR:000001092, Wikipedia:Interleukin_17] synonym: "IL-17 production" EXACT [] is_a: GO:0001816 ! cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032623 name: interleukin-2 production namespace: biological_process def: "The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] synonym: "IL-2 production" EXACT [] is_a: GO:0001816 ! cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032626 name: interleukin-22 production namespace: biological_process def: "The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] synonym: "IL-22 production" EXACT [] is_a: GO:0001816 ! cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032633 name: interleukin-4 production namespace: biological_process def: "The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] synonym: "IL-4 production" EXACT [] is_a: GO:0001816 ! cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032635 name: interleukin-6 production namespace: biological_process def: "The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] synonym: "IL-6 production" EXACT [] is_a: GO:0001816 ! cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032637 name: interleukin-8 production namespace: biological_process def: "The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] synonym: "IL-8 production" EXACT [] is_a: GO:0001816 ! cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032638 name: interleukin-9 production namespace: biological_process def: "The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] synonym: "IL-9 production" EXACT [] is_a: GO:0001816 ! cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032640 name: tumor necrosis factor production namespace: biological_process def: "The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah] comment: Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF'). synonym: "TNF production" EXACT [] synonym: "TNF-alpha production" EXACT [] synonym: "tumor necrosis factor-alpha production" EXACT [] is_a: GO:0071706 ! tumor necrosis factor superfamily cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032649 name: regulation of interferon-gamma production namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon." [GOC:add, GOC:mah] synonym: "regulation of type II interferon production" EXACT [] is_a: GO:0001817 ! regulation of cytokine production relationship: regulates GO:0032609 ! interferon-gamma production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032689 name: negative regulation of interferon-gamma production namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon." [GOC:add, GOC:mah] synonym: "down regulation of interferon-gamma production" EXACT [] synonym: "down-regulation of interferon-gamma production" EXACT [] synonym: "downregulation of interferon-gamma production" EXACT [] synonym: "inhibition of interferon-gamma production" NARROW [] synonym: "negative regulation of type II interferon production" EXACT [] is_a: GO:0001818 ! negative regulation of cytokine production is_a: GO:0032649 ! regulation of interferon-gamma production relationship: negatively_regulates GO:0032609 ! interferon-gamma production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032814 name: regulation of natural killer cell activation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of natural killer cell activation." [GOC:mah] synonym: "regulation of NK cell activation" EXACT [] is_a: GO:0051249 ! regulation of lymphocyte activation relationship: regulates GO:0030101 ! natural killer cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032816 name: positive regulation of natural killer cell activation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of natural killer cell activation." [GOC:mah] synonym: "activation of natural killer cell activation" NARROW [] synonym: "positive regulation of NK cell activation" EXACT [] synonym: "stimulation of natural killer cell activation" NARROW [] synonym: "up regulation of natural killer cell activation" EXACT [] synonym: "up-regulation of natural killer cell activation" EXACT [] synonym: "upregulation of natural killer cell activation" EXACT [] is_a: GO:0032814 ! regulation of natural killer cell activation is_a: GO:0051251 ! positive regulation of lymphocyte activation relationship: positively_regulates GO:0030101 ! natural killer cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032844 name: regulation of homeostatic process namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of a homeostatic process." [GOC:mah] subset: gosubset_prok is_a: GO:0050789 ! regulation of biological process relationship: regulates GO:0042592 ! homeostatic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032879 name: regulation of localization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location." [GOC:mah] subset: gosubset_prok synonym: "regulation of localisation" EXACT [GOC:mah] is_a: GO:0050789 ! regulation of biological process relationship: regulates GO:0051179 ! localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032880 name: regulation of protein localization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location." [GOC:dph, GOC:mah, GOC:tb] subset: gosubset_prok synonym: "regulation of protein localisation" EXACT [GOC:mah] is_a: GO:0032879 ! regulation of localization relationship: regulates GO:0008104 ! protein localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032940 name: secretion by cell namespace: biological_process def: "The controlled release of a substance by a cell." [GOC:mah] synonym: "cellular secretion" EXACT [] xref: Wikipedia:Secretion is_a: GO:0044763 ! single-organism cellular process is_a: GO:0046903 ! secretion is_a: GO:0051649 ! establishment of localization in cell property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032943 name: mononuclear cell proliferation namespace: biological_process def: "The expansion of a mononuclear cell population by cell division. A mononuclear cell is a leukocyte with a single non-segmented nucleus in the mature form." [GOC:add] synonym: "PBMC proliferation" NARROW [] synonym: "peripheral blood mononuclear cell proliferation" NARROW [] is_a: GO:0070661 ! leukocyte proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032944 name: regulation of mononuclear cell proliferation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of mononuclear cell proliferation." [GOC:add] synonym: "regulation of PBMC proliferation" NARROW [] synonym: "regulation of peripheral blood mononuclear cell proliferation" NARROW [] is_a: GO:0070663 ! regulation of leukocyte proliferation relationship: regulates GO:0032943 ! mononuclear cell proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032945 name: negative regulation of mononuclear cell proliferation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of mononuclear cell proliferation." [GOC:add] synonym: "negative regulation of PBMC proliferation" NARROW [] synonym: "negative regulation of peripheral blood mononuclear cell proliferation" NARROW [] is_a: GO:0032944 ! regulation of mononuclear cell proliferation is_a: GO:0070664 ! negative regulation of leukocyte proliferation relationship: negatively_regulates GO:0032943 ! mononuclear cell proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032989 name: cellular component morphogenesis namespace: biological_process def: "The process in which cellular structures, including whole cells or cell parts, are generated and organized." [GOC:dph, GOC:mah, GOC:tb] subset: goslim_pir subset: gosubset_prok synonym: "cellular structure morphogenesis" EXACT [GOC:dph, GOC:tb] is_a: GO:0009653 ! anatomical structure morphogenesis is_a: GO:0016043 ! cellular component organization is_a: GO:0048869 ! cellular developmental process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032991 name: macromolecular complex namespace: cellular_component def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together." [GOC:mah] subset: goslim_pir subset: gosubset_prok synonym: "macromolecule complex" EXACT [] is_a: GO:0005575 ! cellular_component property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0032997 name: Fc receptor complex namespace: cellular_component def: "A protein complex composed of a subunit or subunits capable of binding the Fc portion of an immunoglobulin with additional signaling components. The complex functions as a receptor for immunoglobulin." [GOC:add, ISBN:0781735149] subset: goslim_pir synonym: "Fc-receptor complex" EXACT [] synonym: "FcR complex" EXACT [] synonym: "immunoglobulin receptor complex" BROAD [] is_a: GO:0043234 ! protein complex is_a: GO:0044459 ! plasma membrane part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0033001 name: Fc-gamma receptor III complex namespace: cellular_component def: "A protein complex composed of an Fc-gamma RIII alpha chain and an Fc-epsilon RI gamma chain dimer with or without an Fc-epsilon RI beta chain and additional signaling components. The complex functions primarily as an activating receptor for IgG." [GOC:add, ISBN:0781735149, PMID:11244038, PMID:12413532] synonym: "FcgRIII complex" EXACT [] synonym: "IgG receptor complex" BROAD [] synonym: "immunoglobulin G receptor complex" BROAD [] is_a: GO:0032997 ! Fc receptor complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0033036 name: macromolecule localization namespace: biological_process def: "Any process in which a macromolecule is transported to, or maintained in, a specific location." [GOC:mah] subset: gosubset_prok synonym: "macromolecule localisation" EXACT [GOC:mah] is_a: GO:0051179 ! localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0033151 name: V(D)J recombination namespace: biological_process def: "The process in which immune receptor V, D, and J, or V and J gene segments, depending on the specific receptor, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS)." [GOC:add, ISBN:0781700221, ISBN:0781735149] synonym: "V(D)J joining" EXACT [] synonym: "V-D-J joining" EXACT [] synonym: "V-D-J recombination" EXACT [] synonym: "V-J joining" EXACT [] synonym: "V-J recombination" EXACT [] xref: Wikipedia:V(D)J_recombination is_a: GO:0002562 ! somatic diversification of immune receptors via germline recombination within a single locus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0033152 name: immunoglobulin V(D)J recombination namespace: biological_process def: "The process in which immunoglobulin gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). For immunoglobulin heavy chains V, D, and J gene segments are joined, and for immunoglobulin light chains V and J gene segments are joined." [GOC:add, ISBN:0781735149] synonym: "immunoglobulin V(D)J joining" EXACT [GOC:add] synonym: "immunoglobulin V-D-J joining" NARROW [GOC:add] synonym: "immunoglobulin V-D-J recombination" NARROW [GOC:add] synonym: "immunoglobulin V-J joining" NARROW [GOC:add] synonym: "immunoglobulin V-J recombination" NARROW [GOC:add] is_a: GO:0016447 ! somatic recombination of immunoglobulin gene segments is_a: GO:0033151 ! V(D)J recombination property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0033363 name: secretory granule organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion." [GOC:mah] synonym: "secretory granule organisation" EXACT [GOC:mah] synonym: "secretory granule organization and biogenesis" RELATED [GOC:mah] is_a: GO:0016050 ! vesicle organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0033365 name: protein localization to organelle namespace: biological_process def: "A process in which a protein is transported to, or maintained in, a location within an organelle." [GOC:mah] synonym: "protein localisation to organelle" EXACT [GOC:mah] synonym: "protein localization in organelle" EXACT [GOC:mah] is_a: GO:0034613 ! cellular protein localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0033366 name: protein localization to secretory granule namespace: biological_process def: "A process in which a protein is transported to, or maintained in, a location within a secretory granule." [GOC:mah] synonym: "protein localisation in secretory granule" EXACT [GOC:mah] synonym: "protein localization in secretory granule" EXACT [GOC:curators] is_a: GO:0033365 ! protein localization to organelle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0033371 name: T cell secretory granule organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule in a T cell. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion." [GOC:mah] synonym: "T cell secretory granule organisation" EXACT [GOC:mah] synonym: "T cell secretory granule organization and biogenesis" RELATED [GOC:mah] synonym: "T lymphocyte secretory granule organization" EXACT [] synonym: "T-cell secretory granule organization" EXACT [] synonym: "T-lymphocyte secretory granule maturation" RELATED [] synonym: "T-lymphocyte secretory granule organization" EXACT [] is_a: GO:0033363 ! secretory granule organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0033374 name: protein localization to T cell secretory granule namespace: biological_process def: "A process in which a protein is transported to, or maintained in, a location within a secretory granule in a T cell." [GOC:mah] synonym: "protein localisation in T cell secretory granule" EXACT [GOC:mah] synonym: "protein localization in T cell secretory granule" EXACT [GOC:curators] synonym: "protein localization in T lymphocyte secretory granule" EXACT [] synonym: "protein localization in T-cell secretory granule" EXACT [] synonym: "protein localization in T-lymphocyte secretory granule" EXACT [] is_a: GO:0033366 ! protein localization to secretory granule relationship: part_of GO:0033371 ! T cell secretory granule organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0033375 name: protease localization to T cell secretory granule namespace: biological_process def: "Any process in which a protease is transported to, or maintained in, a location within a secretory granule in a T cell." [GOC:mah] synonym: "protease localisation in T cell secretory granule" EXACT [GOC:mah] synonym: "protease localization in T cell secretory granule" EXACT [GOC:curators] synonym: "protease localization in T lymphocyte secretory granule" EXACT [] synonym: "protease localization in T-cell secretory granule" EXACT [] synonym: "protease localization in T-lymphocyte secretory granule" EXACT [] is_a: GO:0033374 ! protein localization to T cell secretory granule property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0033380 name: granzyme B localization to T cell secretory granule namespace: biological_process def: "Any process in which the protease granzyme B is transported to, or maintained in, a location within a secretory granule in a T cell." [GOC:mah] synonym: "granzyme B localisation in T cell secretory granule" EXACT [GOC:mah] synonym: "granzyme B localization in T cell secretory granule" EXACT [GOC:curators] synonym: "granzyme B localization in T lymphocyte secretory granule" EXACT [] synonym: "granzyme B localization in T-cell secretory granule" EXACT [] synonym: "granzyme B localization in T-lymphocyte secretory granule" EXACT [] is_a: GO:0033375 ! protease localization to T cell secretory granule property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0034101 name: erythrocyte homeostasis namespace: biological_process def: "Any process of regulating the production and elimination of erythrocytes within an organism." [GOC:add, PMID:10694114, PMID:14754397] synonym: "RBC homeostasis" EXACT [CL:0000232] synonym: "red blood cell homeostasis" EXACT [CL:0000232] is_a: GO:0048872 ! homeostasis of number of cells property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0034102 name: erythrocyte clearance namespace: biological_process def: "The selective elimination of erythrocytes from the body by autoregulatory mechanisms." [GOC:add, PMID:12905029, PMID:14754397] comment: Note that this term is intended for annotation of self-gene products that lead to elimination of erythrocytes without the involvement of a symbiont. synonym: "neocytolysis" NARROW [PMID:14754397] synonym: "RBC clearance" EXACT [CL:0000232] synonym: "red blood cell clearance" EXACT [CL:0000232] is_a: GO:0048771 ! tissue remodeling relationship: part_of GO:0034101 ! erythrocyte homeostasis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0034613 name: cellular protein localization namespace: biological_process alt_id: GO:0016249 def: "Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GOC:mah] synonym: "cellular protein localisation" EXACT [GOC:mah] synonym: "channel localizer activity" NARROW [GOC:mah] is_a: GO:0008104 ! protein localization is_a: GO:0070727 ! cellular macromolecule localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0034641 name: cellular nitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells." [GOC:mah] subset: goslim_generic subset: gosubset_prok synonym: "cellular nitrogen compound metabolism" EXACT [] xref: Reactome:REACT_102000 "Metabolism of amino acids and derivatives, Mycobacterium tuberculosis" xref: Reactome:REACT_103710 "Metabolism of amino acids and derivatives, Escherichia coli" xref: Reactome:REACT_107293 "Metabolism of amino acids and derivatives, Arabidopsis thaliana" xref: Reactome:REACT_108179 "Metabolism of amino acids and derivatives, Xenopus tropicalis" xref: Reactome:REACT_109042 "Metabolism of amino acids and derivatives, Sus scrofa" xref: Reactome:REACT_13 "Metabolism of amino acids and derivatives, Homo sapiens" xref: Reactome:REACT_28699 "Metabolism of amino acids and derivatives, Saccharomyces cerevisiae" xref: Reactome:REACT_29108 "Metabolism of amino acids and derivatives, Caenorhabditis elegans" xref: Reactome:REACT_32429 "Metabolism of amino acids and derivatives, Rattus norvegicus" xref: Reactome:REACT_33347 "Metabolism of amino acids and derivatives, Mus musculus" xref: Reactome:REACT_34326 "Metabolism of amino acids and derivatives, Staphylococcus aureus N315" xref: Reactome:REACT_55564 "Metabolism of amino acids and derivatives, Gallus gallus" xref: Reactome:REACT_77741 "Metabolism of amino acids and derivatives, Taeniopygia guttata" xref: Reactome:REACT_82379 "Metabolism of amino acids and derivatives, Bos taurus" xref: Reactome:REACT_86268 "Metabolism of amino acids and derivatives, Drosophila melanogaster" xref: Reactome:REACT_90299 "Metabolism of amino acids and derivatives, Oryza sativa" xref: Reactome:REACT_91959 "Metabolism of amino acids and derivatives, Plasmodium falciparum" xref: Reactome:REACT_93580 "Metabolism of amino acids and derivatives, Danio rerio" xref: Reactome:REACT_95666 "Metabolism of amino acids and derivatives, Canis familiaris" xref: Reactome:REACT_98086 "Metabolism of amino acids and derivatives, Dictyostelium discoideum" xref: Reactome:REACT_99241 "Metabolism of amino acids and derivatives, Schizosaccharomyces pombe" is_a: GO:0006807 ! nitrogen compound metabolic process is_a: GO:0044237 ! cellular metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035010 name: encapsulation of foreign target namespace: biological_process def: "Events resulting in the formation of a multilayered cellular sheath surrounding an invader and thus preventing its development. This defense mechanism is often seen in insects in response to nematodes or parasitoids, which are too large to be phagocytosed by individual hemocytes. In some organisms the capsule is blackened due to melanization." [GO_REF:0000022, GOC:bf, GOC:mtg_15nov05, PMID:11846478, PMID:12225920] comment: This term was improved by GO_REF:0000022. It was moved. is_a: GO:0002252 ! immune effector process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035051 name: cardiac cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell that will form part of the cardiac organ of an individual." [GOC:bf] synonym: "heart cell differentiation" RELATED [] is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0007507 ! heart development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035082 name: axoneme assembly namespace: biological_process def: "The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia and flagella in eukaryotic cells and is responsible for their movements." [GOC:bf, ISBN:0815316194] synonym: "axoneme biogenesis" RELATED [GOC:mah] is_a: GO:0001578 ! microtubule bundle formation is_a: GO:0030031 ! cell projection assembly property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035084 name: flagellar axoneme assembly namespace: biological_process def: "The assembly of the bundle of microtubules and associated proteins that forms the core of flagellar in eukaryotic cells and is responsible for their movements." [GOC:bf, ISBN:0815316194] synonym: "flagella axoneme assembly" EXACT [GOC:mah] synonym: "flagella axoneme biogenesis" RELATED [] synonym: "flagellar axoneme biogenesis" RELATED [] synonym: "flagellum axoneme assembly" EXACT [GOC:mah] synonym: "flagellum axoneme biogenesis" RELATED [] is_a: GO:0035082 ! axoneme assembly relationship: part_of GO:0009296 ! flagellum assembly property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035369 name: pre-B cell receptor complex namespace: cellular_component def: "An immunoglobulin-like complex that is present in at least the plasma membrane of pre-B cells, and that is composed of two identical immunoglobulin heavy chains and two surrogate light chains, each composed of the lambda-5 and VpreB proteins, and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." [GOC:add, ISBN:0781765196, PMID:16464608, PMID:17306522] comment: Despite its name, the pre-BCR is not a receptor complex, as it appears to provide a low level of signal not dependent on a ligand, but rather simply on correct assembly of the complex as a measure for correct Ig heavy chain recombination and folding. A significant proportion of pre-BCR complexes fail to reach the cell surface, and in some cases may provide their signaling function from the trans-Golgi network or lysosome. synonym: "pre-BCR" EXACT [] is_a: GO:0043234 ! protein complex is_a: GO:0044425 ! membrane part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035710 name: CD4-positive, alpha-beta T cell activation namespace: biological_process def: "The change in morphology and behavior of a CD4-positive, alpha-beta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." [CL:0000624, GOC:BHF] is_a: GO:0046631 ! alpha-beta T cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035929 name: steroid hormone secretion namespace: biological_process def: "The regulated release of any steroid that acts as a hormone into the circulatory system." [CHEBI:26764, GOC:sl] is_a: GO:0060986 ! endocrine hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035930 name: corticosteroid hormone secretion namespace: biological_process def: "The regulated release of any corticosteroid hormone into the circulatory system." [CHEBI:3669, GOC:sl] synonym: "corticosteroid secretion" BROAD [GOC:bf] is_a: GO:0035929 ! steroid hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035931 name: mineralocorticoid secretion namespace: biological_process def: "The regulated release of any mineralocorticoid into the circulatory system. Mineralocorticoids are a class of steroid hormones that regulate water and electrolyte metabolism." [CHEBI:25354, GOC:sl] is_a: GO:0006869 ! lipid transport is_a: GO:0035930 ! corticosteroid hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035933 name: glucocorticoid secretion namespace: biological_process def: "The regulated release of any glucocorticoid hormone into the circulatory system. Glucocorticoids are a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood." [CHEBI:24261, GOC:sl] is_a: GO:0006869 ! lipid transport is_a: GO:0035930 ! corticosteroid hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035935 name: androgen secretion namespace: biological_process def: "The regulated release of an androgen into the circulatory system. Androgens are steroid hormones that stimulate or control the development and maintenance of masculine characteristics in vertebrates." [CHEBI:50113, GOC:sl] is_a: GO:0006869 ! lipid transport is_a: GO:0035929 ! steroid hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035936 name: testosterone secretion namespace: biological_process def: "The regulated release of testosterone into the circulatory system. Testosterone is an androgen having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5." [CHEBI:17347, GOC:sl, PMID:12606499] is_a: GO:0015850 ! organic hydroxy compound transport is_a: GO:0035935 ! androgen secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035937 name: estrogen secretion namespace: biological_process def: "The regulated release of estrogen into the circulatory system. Estrogen is a steroid hormone that stimulates or controls the development and maintenance of female sex characteristics in mammals." [CHEBI:50114, GOC:sl] synonym: "oestrogen secretion" RELATED [CHEBI:50114] is_a: GO:0006869 ! lipid transport is_a: GO:0035929 ! steroid hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0035938 name: estradiol secretion namespace: biological_process def: "The regulated release of estradiol into the circulatory system." [CHEBI:23965, GOC:sl, PMID:21632818] synonym: "oestradiol secretion" EXACT [CHEBI:23965] is_a: GO:0015850 ! organic hydroxy compound transport is_a: GO:0035937 ! estrogen secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0036160 name: melanocyte-stimulating hormone secretion namespace: biological_process def: "The regulated release of a melanocyte-stimulating hormone, any of a group of peptide hormones that are produced by cells in the intermediate lobe of the pituitary gland, and stimulate the production of melanin to increase pigmentation." [GOC:cjm, Wikipedia:Melanocyte-stimulating_hormone] synonym: "MSH secretion" EXACT [GOC:cjm] is_a: GO:0030072 ! peptide hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0036161 name: calcitonin secretion namespace: biological_process def: "The regulated release of calcitonin, a peptide hormone that participates in calcium and phosphorus metabolism." [GOC:cjm, PR:000027222] is_a: GO:0030072 ! peptide hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0038023 name: signaling receptor activity namespace: molecular_function def: "Receiving a signal and transmitting the signal in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." [GOC:bf, GOC:signaling] comment: Note that this term and its child terms are intended for receptors that are directly coupled to a signal transduction pathway. This term should therefore not be used to annotate decoy receptors and other proteins that bind a signal but do not pass the signal on. This term can be used to annotate dependence receptors that transduce a signal when a ligand is withdrawn (in this case, signal withdrawal is considered to be the initiating signal), or receptors that signal at a basal level in the absence of a bound agonist. For receptors that mediate transport of a substance into the cell by receptor-mediated endocytosis, consider instead the term 'cargo receptor activity ; GO:0038024' and its children. synonym: "receptor activity involved in signal transduction" EXACT [GOC:bf] synonym: "signalling receptor activity" EXACT [GOC:mah] is_a: GO:0004871 ! signal transducer activity is_a: GO:0004872 ! receptor activity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0038024 name: cargo receptor activity namespace: molecular_function def: "Combining selectively with an extracellular macromolecule and delivering the macromolecule into the cell via endocytosis." [GOC:bf, GOC:signaling, PMID:15239958] comment: Note that this term and its child terms are intended for receptors that bind to and internalize molecules by receptor-mediated endocytosis. For receptors that are coupled to a signal transduction pathway, consider instead the term 'signaling receptor activity ; GO:0038023' and its children. synonym: "endocytic receptor activity" RELATED [GOC:signaling, ISBN:0123645387, PMID:12671190] synonym: "receptor activity involved in ligand uptake" EXACT [PMID:12671190] synonym: "receptor activity involved in receptor-mediated endocytosis" EXACT [GOC:bf] synonym: "transport receptor activity" RELATED [GOC:signaling] is_a: GO:0004872 ! receptor activity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0040011 name: locomotion namespace: biological_process def: "Self-propelled movement of a cell or organism from one location to another." [GOC:dgh] subset: goslim_generic subset: goslim_pir subset: gosubset_prok is_a: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0040012 name: regulation of locomotion namespace: biological_process def: "Any process that modulates the frequency, rate or extent of locomotion of a cell or organism." [GOC:ems] is_a: GO:0050789 ! regulation of biological process relationship: regulates GO:0040011 ! locomotion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0040017 name: positive regulation of locomotion namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism." [GOC:go_curators] synonym: "activation of locomotion" NARROW [] synonym: "stimulation of locomotion" NARROW [] synonym: "up regulation of locomotion" EXACT [] synonym: "up-regulation of locomotion" EXACT [] synonym: "upregulation of locomotion" EXACT [] is_a: GO:0040012 ! regulation of locomotion is_a: GO:0048518 ! positive regulation of biological process relationship: positively_regulates GO:0040011 ! locomotion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042060 name: wound healing namespace: biological_process def: "The series of events that restore integrity to a damaged tissue, following an injury." [GOC:bf, PMID:15269788] xref: Wikipedia:Wound_healing is_a: GO:0009611 ! response to wounding property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042088 name: T-helper 1 type immune response namespace: biological_process def: "An immune response which is associated with resistance to intracellular bacteria, fungi, and protozoa, and pathological conditions such as arthritis, and which is typically orchestrated by the production of particular cytokines by T-helper 1 cells, most notably interferon-gamma, IL-2, and lymphotoxin." [GOC:add, ISBN:0781735149] synonym: "Th1 immune response" EXACT [] is_a: GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042092 name: type 2 immune response namespace: biological_process def: "An immune response which is associated with resistance to extracellular organisms such as helminths and pathological conditions such as allergy, which is orchestrated by the production of particular cytokines, most notably IL-4, IL-5, IL-10, and IL-13, by any of a variety of cell types including T-helper 2 cells, eosinophils, basophils, mast cells, and nuocytes, resulting in enhanced production of certain antibody isotypes and other effects." [GOC:add, ISBN:0781735149, PMID:18000958, PMID:18007680, PMID:20065995, PMID:20200518] synonym: "T-helper 2 type immune response" NARROW [GOC:add] synonym: "Th2 immune response" NARROW [GOC:add] is_a: GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042093 name: T-helper cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized thymocyte acquires specialized features of a T-helper cell." [GOC:ebc] synonym: "helper T cell differentiation" EXACT [CL:0000912] synonym: "T-helper cell development" RELATED [GOC:add] is_a: GO:0002294 ! CD4-positive, alpha-beta T cell differentiation involved in immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042098 name: T cell proliferation namespace: biological_process alt_id: GO:0042111 def: "The expansion of a T cell population by cell division. Follows T cell activation." [GOC:jl] synonym: "T lymphocyte proliferation" EXACT [] synonym: "T-cell proliferation" EXACT [] synonym: "T-lymphocyte proliferation" EXACT [] is_a: GO:0042110 ! T cell activation is_a: GO:0046651 ! lymphocyte proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042101 name: T cell receptor complex namespace: cellular_component def: "A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains." [GOC:mah, ISBN:0781735149] synonym: "T lymphocyte receptor complex" EXACT [] synonym: "T-cell receptor complex" EXACT [] synonym: "T-lymphocyte receptor complex" EXACT [] synonym: "TCR" RELATED [] xref: Wikipedia:T_cell_receptor is_a: GO:0043235 ! receptor complex is_a: GO:0044459 ! plasma membrane part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042105 name: alpha-beta T cell receptor complex namespace: cellular_component def: "A T cell receptor complex in which the TCR heterodimer comprises alpha and beta chains, associated with the CD3 complex; recognizes a complex consisting of an antigen-derived peptide bound to a class I or class II MHC protein." [GOC:mah, ISBN:0781735149] synonym: "alpha-beta T lymphocyte receptor complex" EXACT [] synonym: "alpha-beta T-cell receptor complex" EXACT [] synonym: "alpha-beta T-lymphocyte receptor complex" EXACT [] synonym: "alpha-beta TCR complex" EXACT [] is_a: GO:0042101 ! T cell receptor complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042106 name: gamma-delta T cell receptor complex namespace: cellular_component def: "A T cell receptor complex in which the TCR heterodimer comprises gamma and delta chains, associated with the CD3 complex; recognizes antigen directly, without a requirement for processing and presentation by an MHC protein." [GOC:mah, ISBN:0781735149] synonym: "gamma-delta T lymphocyte receptor complex" EXACT [] synonym: "gamma-delta T-cell receptor complex" EXACT [] synonym: "gamma-delta T-lymphocyte receptor complex" EXACT [] synonym: "gamma-delta TCR complex" EXACT [] is_a: GO:0042101 ! T cell receptor complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042110 name: T cell activation namespace: biological_process def: "The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." [GOC:mgi_curators, ISBN:0781735140] synonym: "T lymphocyte activation" EXACT [] synonym: "T-cell activation" EXACT [] synonym: "T-lymphocyte activation" EXACT [] is_a: GO:0046649 ! lymphocyte activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042113 name: B cell activation namespace: biological_process def: "The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." [GOC:mgi_curators, ISBN:0781735140] synonym: "B lymphocyte activation" EXACT [] synonym: "B-cell activation" EXACT [] synonym: "B-lymphocyte activation" EXACT [] is_a: GO:0046649 ! lymphocyte activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042127 name: regulation of cell proliferation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cell proliferation." [GOC:jl] subset: gosubset_prok is_a: GO:0050794 ! regulation of cellular process relationship: regulates GO:0008283 ! cell proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042129 name: regulation of T cell proliferation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of T cell proliferation." [GOC:jl] synonym: "regulation of T lymphocyte proliferation" EXACT [] synonym: "regulation of T-cell proliferation" EXACT [] synonym: "regulation of T-lymphocyte proliferation" EXACT [] is_a: GO:0050670 ! regulation of lymphocyte proliferation is_a: GO:0050863 ! regulation of T cell activation relationship: regulates GO:0042098 ! T cell proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042130 name: negative regulation of T cell proliferation namespace: biological_process def: "Any process that stops, prevents or reduces the rate or extent of T cell proliferation." [GOC:jl] synonym: "down regulation of T cell proliferation" EXACT [] synonym: "down-regulation of T cell proliferation" EXACT [] synonym: "downregulation of T cell proliferation" EXACT [] synonym: "inhibition of T cell proliferation" NARROW [] synonym: "negative regulation of T lymphocyte proliferation" EXACT [] synonym: "negative regulation of T-cell proliferation" EXACT [] synonym: "negative regulation of T-lymphocyte proliferation" EXACT [] is_a: GO:0042129 ! regulation of T cell proliferation is_a: GO:0050672 ! negative regulation of lymphocyte proliferation is_a: GO:0050868 ! negative regulation of T cell activation relationship: negatively_regulates GO:0042098 ! T cell proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042221 name: response to chemical stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus." [GOC:jl] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC. subset: goslim_aspergillus subset: goslim_candida subset: goslim_yeast subset: gosubset_prok subset: high_level_annotation_qc synonym: "response to chemical substance" EXACT [] is_a: GO:0050896 ! response to stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042267 name: natural killer cell mediated cytotoxicity namespace: biological_process def: "The directed killing of a target cell by a natural killer cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors." [GOC:add, GOC:pr] comment: Note that either or both mechanisms mentioned in the definition may be used in this process. Note that both granule release and the engagement of death receptors on target cells result in induction of apoptosis in the target cell. synonym: "killer activity" RELATED [] synonym: "natural killer cell mediated cell death" EXACT [] synonym: "natural killer cell mediated cell killing" EXACT [] synonym: "natural killer cell mediated cytolysis" RELATED [] synonym: "natural killer-cell mediated cytolysis" RELATED [] synonym: "NK cell mediated cell death" EXACT [] synonym: "NK cell mediated cell killing" EXACT [] synonym: "NK cell mediated cytolysis" RELATED [] synonym: "NK cell mediated cytotoxicity" EXACT [] is_a: GO:0001909 ! leukocyte mediated cytotoxicity is_a: GO:0002228 ! natural killer cell mediated immunity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042303 name: molting cycle namespace: biological_process def: "The periodic casting off and regeneration of an outer covering of cuticle, feathers, hair, horns, skin, etc." [GOC:jl, ISBN:0198506732] subset: goslim_pir is_a: GO:0044707 ! single-multicellular organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042330 name: taxis namespace: biological_process def: "The directed movement of a motile cell or organism in response to an external stimulus." [GOC:jl, ISBN:0192801023] subset: gosubset_prok synonym: "directed movement in response to stimulus" EXACT [] xref: Wikipedia:Taxis is_a: GO:0009605 ! response to external stimulus is_a: GO:0040011 ! locomotion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042470 name: melanosome namespace: cellular_component def: "A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells." [GOC:jl, PMID:11584301] xref: Wikipedia:Melanosome is_a: GO:0048770 ! pigment granule property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042475 name: odontogenesis of dentin-containing tooth namespace: biological_process def: "The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel." [GOC:cjm, GOC:mah, GOC:mtg_sensu, PMID:10333884, PMID:15355794] comment: Note that placoid scales found in the cartilaginous fishes presumably develop through the same processes, but are found on the dermis, rather than in the mouth or pharynx. See http://en.wikipedia.org/wiki/Placoid_scale#Placoid_scales. synonym: "odontogenesis of dentine-containing teeth" EXACT [] synonym: "odontogenesis of dentine-containing tooth" EXACT [GOC:mah] synonym: "odontogeny" BROAD [] synonym: "odontosis" BROAD [] synonym: "tooth development" BROAD [] is_a: GO:0042476 ! odontogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042476 name: odontogenesis namespace: biological_process alt_id: GO:0042477 def: "The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food." [GOC:jl, GOC:mah] synonym: "odontogenesis of calcareous or chitinous tooth" NARROW [] synonym: "odontogeny" EXACT [] synonym: "odontosis" EXACT [] synonym: "tooth development" EXACT [] xref: Wikipedia:Odontogenesis is_a: GO:0009887 ! organ morphogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042481 name: regulation of odontogenesis namespace: biological_process alt_id: GO:0042484 def: "Any process that modulates the frequency, rate or extent of the formation and development of a tooth or teeth." [GOC:jl] synonym: "regulation of odontogenesis of calcareous or chitinous tooth" NARROW [] synonym: "regulation of tooth development" EXACT [] is_a: GO:2000027 ! regulation of organ morphogenesis relationship: regulates GO:0042476 ! odontogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042483 name: negative regulation of odontogenesis namespace: biological_process alt_id: GO:0042486 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the formation and development of a tooth or teeth." [GOC:jl] synonym: "down regulation of odontogenesis" EXACT [] synonym: "down-regulation of odontogenesis" EXACT [] synonym: "downregulation of odontogenesis" EXACT [] synonym: "inhibition of odontogenesis" NARROW [] synonym: "negative regulation of odontogenesis of calcareous or chitinous tooth" NARROW [] synonym: "negative regulation of tooth development" EXACT [] is_a: GO:0042481 ! regulation of odontogenesis is_a: GO:0051093 ! negative regulation of developmental process relationship: negatively_regulates GO:0042476 ! odontogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042492 name: gamma-delta T cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized hemopoietic cell acquires specialized features of a gamma-delta T cell. A gamma-delta T cell is a T cell that expresses a gamma-delta T cell receptor complex." [CL:0000798, GOC:jl] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "gamma-delta T cell development" RELATED [GOC:add] synonym: "gamma-delta T lymphocyte differentiation" EXACT [] synonym: "gamma-delta T-cell differentiation" EXACT [] synonym: "gamma-delta T-lymphocyte differentiation" EXACT [] is_a: GO:0030217 ! T cell differentiation is_a: GO:0046629 ! gamma-delta T cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042554 name: superoxide anion generation namespace: biological_process def: "The enzymatic generation of superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species, by a cell in response to environmental stress, thereby mediating the activation of various stress-inducible signaling pathways." [GOC:jl, PMID:12359750] subset: gosubset_prok synonym: "superoxide release" EXACT [GOC:hjd, GOC:mah] is_a: GO:0006801 ! superoxide metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042571 name: immunoglobulin complex, circulating namespace: cellular_component def: "An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component." [GOC:add, ISBN:0781735149] comment: Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "antibody" EXACT [GOC:add] xref: Wikipedia:Antibody is_a: GO:0019814 ! immunoglobulin complex is_a: GO:0044421 ! extracellular region part relationship: part_of GO:0005615 ! extracellular space property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042582 name: azurophil granule namespace: cellular_component def: "Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid." [GOC:jl, PMID:17152095] synonym: "primary granule" EXACT [] is_a: GO:0005766 ! primary lysosome is_a: GO:0030141 ! secretory granule property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042588 name: zymogen granule namespace: cellular_component def: "A membrane-bounded, cytoplasmic secretory granule found in enzyme-secreting cells and visible by light microscopy. Contain zymogen, an inactive enzyme precursor, often of a digestive enzyme." [GOC:jl, ISBN:0198506732] is_a: GO:0030141 ! secretory granule property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042589 name: zymogen granule membrane namespace: cellular_component def: "The lipid bilayer surrounding a zymogen granule." [GOC:jl] is_a: GO:0030667 ! secretory granule membrane relationship: part_of GO:0042588 ! zymogen granule property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042590 name: antigen processing and presentation of exogenous peptide antigen via MHC class I namespace: biological_process def: "The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex. The peptide antigen is typically, but not always, processed from a whole protein. Class I here refers to classical class I molecules." [GOC:add, ISBN:0781735149, PMID:15771591] synonym: "antigen presentation, exogenous antigen via major histocompatibility complex class I" EXACT [] synonym: "antigen presentation, exogenous antigen via MHC class I" EXACT [] synonym: "cross presentation" BROAD [] synonym: "cross priming" BROAD [] synonym: "cross-presentation" BROAD [] synonym: "cross-priming" BROAD [] synonym: "exogenous peptide antigen processing and presentation via MHC class I" EXACT [] xref: Reactome:REACT_111119 "Antigen processing-Cross presentation, Homo sapiens" is_a: GO:0002474 ! antigen processing and presentation of peptide antigen via MHC class I is_a: GO:0002478 ! antigen processing and presentation of exogenous peptide antigen relationship: part_of GO:0042638 ! exogen property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042592 name: homeostatic process namespace: biological_process def: "Any biological process involved in the maintenance of an internal steady state." [GOC:jl, ISBN:0395825172] subset: goslim_generic subset: goslim_metagenomics subset: gosubset_prok synonym: "homeostasis" RELATED [] is_a: GO:0065008 ! regulation of biological quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042611 name: MHC protein complex namespace: cellular_component def: "A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen." [GOC:add, GOC:jl, ISBN:0781735149, PMID:15928678, PMID:16153240] subset: goslim_pir is_a: GO:0043234 ! protein complex is_a: GO:0044459 ! plasma membrane part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042613 name: MHC class II protein complex namespace: cellular_component def: "A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen." [GOC:add, GOC:jl, ISBN:0120781859, PMID:15928678] is_a: GO:0042611 ! MHC protein complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042633 name: hair cycle namespace: biological_process def: "The cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body." [GOC:go_curators, PMID:12230507] is_a: GO:0042303 ! molting cycle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042638 name: exogen namespace: biological_process def: "The shedding phase of the hair cycle." [PMID:12230507] synonym: "hair shedding" NARROW [] is_a: GO:0022405 ! hair cycle process relationship: part_of GO:0048820 ! hair follicle maturation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042692 name: muscle cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized features of a muscle cell." [CL:0000187, GOC:go_curators] xref: Reactome:REACT_109683 "Myogenesis, Rattus norvegicus" xref: Reactome:REACT_113484 "Myogenesis, Caenorhabditis elegans" xref: Reactome:REACT_21303 "Myogenesis, Homo sapiens" xref: Reactome:REACT_32665 "Myogenesis, Danio rerio" xref: Reactome:REACT_34056 "Myogenesis, Canis familiaris" xref: Reactome:REACT_77596 "Myogenesis, Sus scrofa" xref: Reactome:REACT_84060 "Myogenesis, Gallus gallus" xref: Reactome:REACT_84715 "Myogenesis, Drosophila melanogaster" xref: Reactome:REACT_85310 "Myogenesis, Taeniopygia guttata" xref: Reactome:REACT_90630 "Myogenesis, Bos taurus" xref: Reactome:REACT_95727 "Myogenesis, Mus musculus" xref: Reactome:REACT_95839 "Myogenesis, Xenopus tropicalis" is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0061061 ! muscle structure development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042698 name: ovulation cycle namespace: biological_process def: "The type of sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years." [ISBN:0721662544] synonym: "estrous cycle" RELATED [] synonym: "menstrual cycle" RELATED [] is_a: GO:0048511 ! rhythmic process is_a: GO:0048609 ! multicellular organismal reproductive process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042701 name: progesterone secretion namespace: biological_process def: "The regulated release of progesterone, a steroid hormone, by the corpus luteum of the ovary and by the placenta." [GOC:jl, ISBN:0395825172] is_a: GO:0006869 ! lipid transport is_a: GO:0022602 ! ovulation cycle process is_a: GO:0035929 ! steroid hormone secretion is_a: GO:0048610 ! cellular process involved in reproduction relationship: part_of GO:0001553 ! luteinization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042742 name: defense response to bacterium namespace: biological_process alt_id: GO:0042830 def: "Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism." [GOC:jl] subset: gosubset_prok synonym: "antibacterial peptide activity" RELATED [] synonym: "defence response to bacteria" EXACT [] synonym: "defence response to bacterium" EXACT [] synonym: "defense response to bacteria" EXACT [] is_a: GO:0006952 ! defense response is_a: GO:0009617 ! response to bacterium property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042886 name: amide transport namespace: biological_process def: "The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, ISBN:0198506732] subset: goslim_pir subset: gosubset_prok is_a: GO:0071705 ! nitrogen compound transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042981 name: regulation of apoptotic process namespace: biological_process def: "Any process that modulates the occurrence or rate of cell death by apoptotic process." [GOC:jl, GOC:mtg_apoptosis] comment: This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. synonym: "apoptosis regulator activity" RELATED [] synonym: "regulation of apoptosis" NARROW [] xref: Reactome:REACT_106248 "Regulation of Apoptosis, Mus musculus" xref: Reactome:REACT_109234 "Regulation of Apoptosis, Rattus norvegicus" xref: Reactome:REACT_109339 "Regulation of Apoptosis, Sus scrofa" xref: Reactome:REACT_13648 "Regulation of Apoptosis, Homo sapiens" xref: Reactome:REACT_29911 "Regulation of Apoptosis, Danio rerio" xref: Reactome:REACT_30641 "Regulation of Apoptosis, Drosophila melanogaster" xref: Reactome:REACT_79698 "Regulation of Apoptosis, Taeniopygia guttata" xref: Reactome:REACT_85908 "Regulation of Apoptosis, Bos taurus" xref: Reactome:REACT_86575 "Regulation of Apoptosis, Xenopus tropicalis" xref: Reactome:REACT_95946 "Regulation of Apoptosis, Caenorhabditis elegans" xref: Reactome:REACT_96201 "Regulation of Apoptosis, Canis familiaris" xref: Reactome:REACT_99944 "Regulation of Apoptosis, Gallus gallus" is_a: GO:0043067 ! regulation of programmed cell death relationship: regulates GO:0006915 ! apoptotic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042995 name: cell projection namespace: cellular_component def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] subset: goslim_pir subset: gosubset_prok synonym: "cell process" BROAD [] synonym: "cellular process" BROAD [] synonym: "cellular projection" EXACT [] is_a: GO:0044464 ! cell part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043011 name: myeloid dendritic cell differentiation namespace: biological_process def: "The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin." [CL:0000782, GOC:jl] synonym: "Langerhans cell differentiation" EXACT [] xref: Wikipedia:Dendritic_cell is_a: GO:0001773 ! myeloid dendritic cell activation is_a: GO:0002573 ! myeloid leukocyte differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043062 name: extracellular structure organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_pir subset: gosubset_prok synonym: "extracellular structure organisation" EXACT [GOC:curators] synonym: "extracellular structure organization and biogenesis" EXACT [GOC:dph, GOC:jl, GOC:mah] is_a: GO:0016043 ! cellular component organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043064 name: flagellum organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a flagellum, a long thin projection from a cell, used in movement." [GOC:curators, ISBN:0815316194] subset: gosubset_prok synonym: "flagellum organisation" EXACT [GOC:curators] synonym: "flagellum organization and biogenesis" RELATED [GOC:mah] is_a: GO:0030030 ! cell projection organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043067 name: regulation of programmed cell death namespace: biological_process alt_id: GO:0043070 def: "Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." [GOC:jl] synonym: "regulation of non-apoptotic programmed cell death" NARROW [] is_a: GO:0010941 ! regulation of cell death relationship: regulates GO:0012501 ! programmed cell death property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043129 name: surfactant homeostasis namespace: biological_process def: "Any process involved in the maintenance of a steady-state level of the surface-active lipoprotein mixture which coats the alveoli." [PMID:9751757] is_a: GO:0048875 ! chemical homeostasis within a tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043133 name: hindgut contraction namespace: biological_process def: "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the hindgut. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The hindgut is the posterior part of the alimentary canal, including the rectum, and the large intestine." [GOC:jl, GOC:mtg_muscle, UBERON:0001046] is_a: GO:0006939 ! smooth muscle contraction is_a: GO:0022600 ! digestive system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043134 name: regulation of hindgut contraction namespace: biological_process def: "Any process that modulates the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine." [GOC:jl, UBERON:0001046] is_a: GO:0006940 ! regulation of smooth muscle contraction is_a: GO:0044058 ! regulation of digestive system process relationship: regulates GO:0043133 ! hindgut contraction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043170 name: macromolecule metabolic process namespace: biological_process alt_id: GO:0043283 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [CHEBI:33694, GOC:mah] subset: goslim_pir subset: gosubset_prok synonym: "biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09] synonym: "macromolecule metabolism" EXACT [] is_a: GO:0071704 ! organic substance metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043208 name: glycosphingolipid binding namespace: molecular_function def: "Interacting selectively and non-covalently with glycosphingolipid, a compound with residues of sphingoid and at least one monosaccharide." [GOC:jl] is_a: GO:0046625 ! sphingolipid binding is_a: GO:0051861 ! glycolipid binding property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043226 name: organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane." [GOC:go_curators] subset: goslim_generic subset: goslim_pir subset: gosubset_prok xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle is_a: GO:0005575 ! cellular_component property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043227 name: membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] subset: gosubset_prok synonym: "membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043228 name: non-membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: gosubset_prok synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043229 name: intracellular organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators] subset: goslim_pir subset: gosubset_prok is_a: GO:0043226 ! organelle is_a: GO:0044424 ! intracellular part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043231 name: intracellular membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] subset: goslim_pir subset: gosubset_prok synonym: "intracellular membrane-enclosed organelle" EXACT [] is_a: GO:0043227 ! membrane-bounded organelle is_a: GO:0043229 ! intracellular organelle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043232 name: intracellular non-membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] subset: goslim_pir subset: gosubset_prok synonym: "intracellular non-membrane-enclosed organelle" EXACT [] is_a: GO:0043228 ! non-membrane-bounded organelle is_a: GO:0043229 ! intracellular organelle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043233 name: organelle lumen namespace: cellular_component def: "The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen." [GOC:jl, GOC:mah] is_a: GO:0031974 ! membrane-enclosed lumen is_a: GO:0044422 ! organelle part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043234 name: protein complex namespace: cellular_component def: "Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules." [GOC:go_curators] subset: goslim_generic subset: goslim_pir subset: gosubset_prok synonym: "protein-protein complex" EXACT [] xref: Wikipedia:Protein_complex is_a: GO:0032991 ! macromolecular complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043235 name: receptor complex namespace: cellular_component def: "Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:go_curators] subset: goslim_pir subset: gosubset_prok is_a: GO:0043234 ! protein complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043277 name: apoptotic cell clearance namespace: biological_process def: "The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte." [GOC:rk, PMID:14685684] comment: Note that unlike mammals or Drosophila, C. elegans (and many lower organisms) do not have professional macrophages/phagocytes, instead cell corpses are engulfed by neighboring cells. Cell types that can function as engulfing cells include hypodermal cells, gonadal sheath cells, pharyngeal muscle cells, and intestinal cells. synonym: "apoptotic cell removal" EXACT [] synonym: "efferocytosis" EXACT [PMID:17548650] synonym: "programmed cell clearance" EXACT [] is_a: GO:0006909 ! phagocytosis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043367 name: CD4-positive, alpha-beta T cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized T cell acquires specialized features of a mature CD4-positive, alpha-beta T cell." [CL:0000624, ISBN:0781735149] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "CD4-positive, alpha beta T cell development" RELATED [GOC:add] synonym: "CD4-positive, alpha beta T cell differentiation" EXACT [GOC:bf] synonym: "CD4-positive, alpha-beta T lymphocyte differentiation" EXACT [] synonym: "CD4-positive, alpha-beta T-cell differentiation" EXACT [] synonym: "CD4-positive, alpha-beta T-lymphocyte differentiation" EXACT [] is_a: GO:0035710 ! CD4-positive, alpha-beta T cell activation is_a: GO:0046632 ! alpha-beta T cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043368 name: positive T cell selection namespace: biological_process def: "The process of sparing immature T cells which react with self-MHC protein complexes with low affinity levels from apoptotic death." [ISBN:0781735149, PMID:12414722] synonym: "positive T lymphocyte selection" EXACT [] synonym: "positive T-cell selection" EXACT [] synonym: "positive T-lymphocyte selection" EXACT [] is_a: GO:0045058 ! T cell selection property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043370 name: regulation of CD4-positive, alpha-beta T cell differentiation namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of CD4-positive, alpha beta T cell differentiation." [GOC:add, ISBN:0781735149] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "regulation of CD4-positive T lymphocyte differentiation" EXACT [] synonym: "regulation of CD4-positive T-cell differentiation" EXACT [] synonym: "regulation of CD4-positive T-lymphocyte differentiation" EXACT [] synonym: "regulation of CD4-positive, alpha beta T cell development" RELATED [GOC:add] synonym: "regulation of CD4-positive, alpha beta T cell differentiation" EXACT [GOC:bf] synonym: "regulation of CD4-positive, alpha beta T lymphocyte differentiation" EXACT [] synonym: "regulation of CD4-positive, alpha beta T-cell differentiation" EXACT [] synonym: "regulation of CD4-positive, alpha beta T-lymphocyte differentiation" EXACT [] is_a: GO:0046637 ! regulation of alpha-beta T cell differentiation is_a: GO:2000514 ! regulation of CD4-positive, alpha-beta T cell activation relationship: regulates GO:0043367 ! CD4-positive, alpha-beta T cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043372 name: positive regulation of CD4-positive, alpha-beta T cell differentiation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha beta T cell differentiation." [GOC:add, ISBN:0781735149] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "activation of CD4-positive, alpha beta T cell differentiation" NARROW [] synonym: "positive regulation of CD4-positive T lymphocyte differentiation" EXACT [] synonym: "positive regulation of CD4-positive T-cell differentiation" EXACT [] synonym: "positive regulation of CD4-positive T-lymphocyte differentiation" EXACT [] synonym: "positive regulation of CD4-positive, alpha beta T cell development" RELATED [GOC:add] synonym: "positive regulation of CD4-positive, alpha beta T cell differentiation" EXACT [GOC:bf] synonym: "positive regulation of CD4-positive, alpha beta T lymphocyte differentiation" EXACT [] synonym: "positive regulation of CD4-positive, alpha beta T-cell differentiation" EXACT [] synonym: "positive regulation of CD4-positive, alpha beta T-lymphocyte differentiation" EXACT [] synonym: "stimulation of CD4-positive, alpha beta T cell differentiation" NARROW [] synonym: "up regulation of CD4-positive, alpha beta T cell differentiation" EXACT [] synonym: "up-regulation of CD4-positive, alpha beta T cell differentiation" EXACT [] synonym: "upregulation of CD4-positive, alpha beta T cell differentiation" EXACT [] is_a: GO:0043370 ! regulation of CD4-positive, alpha-beta T cell differentiation is_a: GO:0046638 ! positive regulation of alpha-beta T cell differentiation is_a: GO:2000516 ! positive regulation of CD4-positive, alpha-beta T cell activation relationship: positively_regulates GO:0043367 ! CD4-positive, alpha-beta T cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043384 name: pre-T cell receptor complex namespace: cellular_component def: "A receptor complex found on immature T cells consisting of a T cell receptor beta chain and the pre-TCR-alpha chain, along with additional signaling components including CD3 family members and additional signaling proteins." [ISBN:0781735149, PMID:12220932] synonym: "pre-T lymphocyte receptor complex" EXACT [] synonym: "pre-T-cell receptor complex" EXACT [] synonym: "pre-T-lymphocyte receptor complex" EXACT [] synonym: "pre-TCR complex" EXACT [] is_a: GO:0043235 ! receptor complex is_a: GO:0044459 ! plasma membrane part relationship: part_of GO:0005887 ! integral to plasma membrane property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043436 name: oxoacid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons)." [CHEBI:24833] subset: gosubset_prok synonym: "keto acid metabolic process" EXACT [] synonym: "keto acid metabolism" EXACT [] synonym: "ketoacid metabolic process" EXACT [] synonym: "ketoacid metabolism" EXACT [] synonym: "oxo acid metabolic process" EXACT [] synonym: "oxo acid metabolism" EXACT [] synonym: "oxoacid metabolism" EXACT [] is_a: GO:0006082 ! organic acid metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044057 name: regulation of system process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system." [GOC:jl] is_a: GO:0051239 ! regulation of multicellular organismal process relationship: regulates GO:0003008 ! system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044058 name: regulation of digestive system process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." [GOC:jl] is_a: GO:0044057 ! regulation of system process relationship: regulates GO:0022600 ! digestive system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044085 name: cellular component biogenesis namespace: biological_process alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] subset: gosubset_prok synonym: "cellular component biogenesis at cellular level" EXACT [] is_a: GO:0071840 ! cellular component organization or biogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044237 name: cellular metabolic process namespace: biological_process def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] subset: goslim_pir subset: gosubset_prok synonym: "cellular metabolism" EXACT [] synonym: "intermediary metabolism" RELATED [GOC:mah] is_a: GO:0008152 ! metabolic process is_a: GO:0044763 ! single-organism cellular process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044238 name: primary metabolic process namespace: biological_process def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org] subset: goslim_pir subset: gosubset_prok synonym: "primary metabolism" EXACT [] is_a: GO:0008152 ! metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044249 name: cellular biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:jl] subset: gosubset_prok synonym: "cellular anabolism" EXACT [] synonym: "cellular biosynthesis" EXACT [] synonym: "cellular formation" EXACT [] synonym: "cellular synthesis" EXACT [] is_a: GO:0009058 ! biosynthetic process is_a: GO:0044237 ! cellular metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044260 name: cellular macromolecule metabolic process namespace: biological_process alt_id: GO:0034960 def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells." [CHEBI:33694, GOC:mah] subset: gosubset_prok synonym: "cellular biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09] synonym: "cellular macromolecule metabolism" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:0044237 ! cellular metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044272 name: sulfur compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione." [GOC:jl] subset: gosubset_prok synonym: "sulfur biosynthesis" NARROW [] synonym: "sulfur biosynthetic process" NARROW [] synonym: "sulfur compound anabolism" EXACT [] synonym: "sulfur compound biosynthesis" EXACT [] synonym: "sulfur compound formation" EXACT [] synonym: "sulfur compound synthesis" EXACT [] is_a: GO:0006790 ! sulfur compound metabolic process is_a: GO:0044249 ! cellular biosynthetic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044281 name: small molecule metabolic process namespace: biological_process def: "The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw] comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. subset: goslim_generic subset: goslim_metagenomics synonym: "small molecule metabolism" EXACT [] xref: Reactome:REACT_111217 "Metabolism, Homo sapiens" xref: Reactome:REACT_112077 "Metabolism, Xenopus tropicalis" xref: Reactome:REACT_112140 "Metabolism, Dictyostelium discoideum" xref: Reactome:REACT_112621 "Metabolism, Mus musculus" xref: Reactome:REACT_112912 "Metabolism, Arabidopsis thaliana" xref: Reactome:REACT_113131 "Metabolism, Schizosaccharomyces pombe" xref: Reactome:REACT_113305 "Metabolism, Canis familiaris" xref: Reactome:REACT_113457 "Metabolism, Mycobacterium tuberculosis" xref: Reactome:REACT_113568 "Metabolism, Rattus norvegicus" xref: Reactome:REACT_113610 "Metabolism, Caenorhabditis elegans" xref: Reactome:REACT_113934 "Metabolism, Escherichia coli" xref: Reactome:REACT_114081 "Metabolism, Gallus gallus" xref: Reactome:REACT_114137 "Metabolism, Sus scrofa" xref: Reactome:REACT_114421 "Metabolism, Saccharomyces cerevisiae" xref: Reactome:REACT_114473 "Metabolism, Danio rerio" xref: Reactome:REACT_114495 "Metabolism, Staphylococcus aureus N315" xref: Reactome:REACT_114668 "Metabolism, Plasmodium falciparum" xref: Reactome:REACT_114983 "Metabolism, Drosophila melanogaster" xref: Reactome:REACT_115063 "Metabolism, Taeniopygia guttata" xref: Reactome:REACT_115388 "Metabolism, Oryza sativa" xref: Reactome:REACT_115420 "Metabolism, Bos taurus" xref: Reactome:REACT_115655 "Metabolism, Gallus gallus" is_a: GO:0044710 ! single-organism metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044283 name: small molecule biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw] comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. synonym: "small molecule biosynthesis" EXACT [] is_a: GO:0044281 ! small molecule metabolic process is_a: GO:0044711 ! single-organism biosynthetic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044421 name: extracellular region part namespace: cellular_component def: "Any constituent part of the extracellular region, the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers constituent parts of the host cell environment outside an intracellular parasite." [GOC:jl] subset: gosubset_prok subset: high_level_annotation_qc is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005576 ! extracellular region property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044422 name: organelle part namespace: cellular_component def: "Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane." [GOC:jl] subset: gosubset_prok subset: high_level_annotation_qc is_a: GO:0005575 ! cellular_component relationship: part_of GO:0043226 ! organelle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044424 name: intracellular part namespace: cellular_component def: "Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [GOC:jl] subset: gosubset_prok subset: high_level_annotation_qc is_a: GO:0044464 ! cell part relationship: part_of GO:0005622 ! intracellular property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044425 name: membrane part namespace: cellular_component def: "Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:jl] subset: gosubset_prok subset: high_level_annotation_qc is_a: GO:0005575 ! cellular_component relationship: part_of GO:0016020 ! membrane property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044427 name: chromosomal part namespace: cellular_component def: "Any constituent part of a chromosome, a structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [GOC:jl] subset: gosubset_prok subset: high_level_annotation_qc synonym: "chromosomal component" EXACT [] synonym: "chromosome component" EXACT [] synonym: "chromosome part" EXACT [] is_a: GO:0044446 ! intracellular organelle part relationship: part_of GO:0005694 ! chromosome property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044428 name: nuclear part namespace: cellular_component def: "Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated." [GOC:jl] subset: high_level_annotation_qc synonym: "nucleus component" EXACT [] is_a: GO:0044446 ! intracellular organelle part relationship: part_of GO:0005634 ! nucleus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044433 name: cytoplasmic vesicle part namespace: cellular_component def: "Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell." [GOC:jl] subset: gosubset_prok subset: high_level_annotation_qc is_a: GO:0044444 ! cytoplasmic part is_a: GO:0044446 ! intracellular organelle part relationship: part_of GO:0031410 ! cytoplasmic vesicle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044444 name: cytoplasmic part namespace: cellular_component def: "Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [GOC:jl] subset: gosubset_prok subset: high_level_annotation_qc synonym: "cytoplasm component" EXACT [] is_a: GO:0044424 ! intracellular part relationship: part_of GO:0005737 ! cytoplasm property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044446 name: intracellular organelle part namespace: cellular_component def: "A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane." [GOC:jl] subset: gosubset_prok subset: high_level_annotation_qc is_a: GO:0044422 ! organelle part is_a: GO:0044424 ! intracellular part relationship: part_of GO:0043229 ! intracellular organelle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044459 name: plasma membrane part namespace: cellular_component def: "Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [GOC:jl] subset: gosubset_prok subset: high_level_annotation_qc is_a: GO:0044425 ! membrane part is_a: GO:0044464 ! cell part relationship: part_of GO:0005886 ! plasma membrane property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044464 name: cell part namespace: cellular_component def: "Any constituent part of a cell, the basic structural and functional unit of all organisms." [GOC:jl] subset: goslim_pir subset: gosubset_prok subset: high_level_annotation_qc synonym: "protoplast" RELATED [GOC:mah] is_a: GO:0005575 ! cellular_component relationship: part_of GO:0005623 ! cell property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044699 name: single-organism process namespace: biological_process def: "A biological process that involves only one organism." [GOC:jl] synonym: "single organism process" EXACT [] is_a: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044700 name: single organism signaling namespace: biological_process def: "A signaling process occurring within a single organism." [GOC:jl] is_a: GO:0023052 ! signaling is_a: GO:0044699 ! single-organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044702 name: single organism reproductive process namespace: biological_process def: "A biological process that directly contributes to the process of producing new individuals, involving a single organism." [GOC:jl] is_a: GO:0022414 ! reproductive process is_a: GO:0044699 ! single-organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044707 name: single-multicellular organism process namespace: biological_process def: "A biological process occurring within a single, multicellular organism." [GOC:jl] is_a: GO:0032501 ! multicellular organismal process is_a: GO:0044699 ! single-organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044710 name: single-organism metabolic process namespace: biological_process def: "A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism." [GOC:jl] is_a: GO:0008152 ! metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044711 name: single-organism biosynthetic process namespace: biological_process def: "A biosynthetic process - chemical reactions and pathways resulting in the formation of substances - involving a single organism." [GOC:jl] is_a: GO:0009058 ! biosynthetic process is_a: GO:0044710 ! single-organism metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044763 name: single-organism cellular process namespace: biological_process def: "Any process that is carried out at the cellular level, occurring within a single organism." [GOC:jl] is_a: GO:0009987 ! cellular process is_a: GO:0044699 ! single-organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045058 name: T cell selection namespace: biological_process def: "The process in which T cells that express T cell receptors that are restricted by self MHC protein complexes and tolerant to self antigens are selected for further maturation." [ISBN:0781735149, PMID:12414722] synonym: "T lymphocyte selection" EXACT [] synonym: "T-cell selection" EXACT [] synonym: "T-lymphocyte selection" EXACT [] xref: Wikipedia:Thymocyte is_a: GO:0002376 ! immune system process relationship: part_of GO:0030217 ! T cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045063 name: T-helper 1 cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized T cell acquires the specialized features of a T-helper 1 (Th1) cell. A Th1 cell is a CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive and produces interferon-gamma." [CL:0000545, GOC:ebc] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "T-helper 1 cell development" RELATED [GOC:add] is_a: GO:0042093 ! T-helper cell differentiation relationship: part_of GO:0042088 ! T-helper 1 type immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045064 name: T-helper 2 cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized T cell acquires specialized features of a T-helper 2 (Th2) cell. A Th2 cell is a CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive and produces interleukin-4." [CL:0000546, GOC:ebc] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "T-helper 2 cell development" RELATED [GOC:add] is_a: GO:0042093 ! T-helper cell differentiation relationship: part_of GO:0042092 ! type 2 immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045087 name: innate immune response namespace: biological_process alt_id: GO:0002226 def: "Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens." [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_15nov05, GOC:mtg_sensu] comment: This term was improved by GO_REF:0000022. It was moved. synonym: "innate immunity" EXACT [GOC:pg] synonym: "nonspecific immune response" EXACT [] xref: Reactome:REACT_101086 "Innate Immune System, Bos taurus" xref: Reactome:REACT_108180 "Innate Immune System, Arabidopsis thaliana" xref: Reactome:REACT_110518 "Innate Immune System, Taeniopygia guttata" xref: Reactome:REACT_31297 "Innate Immune System, Xenopus tropicalis" xref: Reactome:REACT_32992 "Innate Immune System, Gallus gallus" xref: Reactome:REACT_6802 "Innate Immune System, Homo sapiens" xref: Reactome:REACT_78575 "Innate Immune System, Canis familiaris" xref: Reactome:REACT_81815 "Innate Immune System, Saccharomyces cerevisiae" xref: Reactome:REACT_81962 "Innate Immune System, Dictyostelium discoideum" xref: Reactome:REACT_86987 "Innate Immune System, Mus musculus" xref: Reactome:REACT_88681 "Innate Immune System, Drosophila melanogaster" xref: Reactome:REACT_90618 "Innate Immune System, Caenorhabditis elegans" xref: Reactome:REACT_90753 "Innate Immune System, Schizosaccharomyces pombe" xref: Reactome:REACT_94451 "Innate Immune System, Rattus norvegicus" xref: Reactome:REACT_95471 "Innate Immune System, Sus scrofa" xref: Reactome:REACT_95642 "Innate Immune System, Oryza sativa" xref: Reactome:REACT_99610 "Innate Immune System, Danio rerio" xref: Wikipedia:Innate_immune_system is_a: GO:0006952 ! defense response is_a: GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045137 name: development of primary sexual characteristics namespace: biological_process def: "The process whose specific outcome is the progression of the primary sexual characteristics over time, from their formation to the mature structures. The primary sexual characteristics are the testes in males and the ovaries in females and they develop in response to sex hormone secretion." [GOC:ai] is_a: GO:0003006 ! developmental process involved in reproduction relationship: part_of GO:0007275 ! multicellular organismal development relationship: part_of GO:0007548 ! sex differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045184 name: establishment of protein localization namespace: biological_process def: "The directed movement of a protein to a specific location." [GOC:bf] subset: gosubset_prok synonym: "establishment of protein localisation" EXACT [GOC:mah] synonym: "protein positioning" EXACT [] synonym: "protein recruitment" EXACT [] is_a: GO:0051234 ! establishment of localization relationship: part_of GO:0008104 ! protein localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045190 name: isotype switching namespace: biological_process def: "The switching of activated B cells from IgM biosynthesis to biosynthesis of other isotypes of immunoglobulin, accomplished through a recombination process involving an intrachromosomal deletion involving switch regions that reside 5' of each constant region gene segment in the immunoglobulin heavy chain locus." [ISBN:0781735149] comment: Note that IgM and IgD can be coexpressed by B cells via an alternate splicing mechanism, but true recombinational isotype switching to IgD has been demonstrated as well. Note that this term is best used to annotate gene products which are involved in the mechanism of DNA recombination used in isotype switching, like the B cell specific Swap70 factor in the mouse, rather than gene products which promote isotype switching such as cytokines or co-stimulatory molecules, which should instead be annotated to 'regulation of isotype switching ; GO:0045191'. synonym: "class switch recombination" EXACT [] synonym: "class switching" EXACT [] synonym: "isotype switch recombination" EXACT [] xref: Wikipedia:Immunoglobulin_class_switching is_a: GO:0002204 ! somatic recombination of immunoglobulin genes involved in immune response is_a: GO:0002312 ! B cell activation involved in immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045191 name: regulation of isotype switching namespace: biological_process def: "Any process that modulates the frequency, rate or extent of isotype switching." [GOC:ai] synonym: "regulation of class switch recombination" EXACT [] synonym: "regulation of class switching" EXACT [] synonym: "regulation of isotype switch recombination" EXACT [] is_a: GO:0000018 ! regulation of DNA recombination is_a: GO:0002637 ! regulation of immunoglobulin production is_a: GO:0002889 ! regulation of immunoglobulin mediated immune response is_a: GO:0050864 ! regulation of B cell activation is_a: GO:2000026 ! regulation of multicellular organismal development relationship: regulates GO:0045190 ! isotype switching property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045321 name: leukocyte activation namespace: biological_process def: "A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor." [GOC:add] synonym: "immune cell activation" EXACT [] synonym: "leucocyte activation" EXACT [] xref: Wikipedia:Immunologic_activation is_a: GO:0001775 ! cell activation is_a: GO:0002376 ! immune system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045443 name: juvenile hormone secretion namespace: biological_process def: "The regulated release of juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." [GOC:go_curators, ISBN:0198547684] is_a: GO:0046865 ! terpenoid transport is_a: GO:0060986 ! endocrine hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045444 name: fat cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat." [CL:0000136, GOC:go_curators] synonym: "adipocyte cell differentiation" EXACT [] synonym: "adipocyte differentiation" EXACT [] synonym: "adipogenesis" RELATED [] synonym: "adipose cell differentiation" EXACT [] is_a: GO:0030154 ! cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045453 name: bone resorption namespace: biological_process def: "The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products." [GOC:mah, PMID:10968780] xref: Wikipedia:Bone_resorption is_a: GO:0001894 ! tissue homeostasis relationship: part_of GO:0046849 ! bone remodeling property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045457 name: ecdysteroid secretion namespace: biological_process def: "The regulated release of ecdysteroids, a group of polyhydroxylated ketosteroids which initiate post-embryonic development." [GOC:go_curators] is_a: GO:0006869 ! lipid transport is_a: GO:0015850 ! organic hydroxy compound transport is_a: GO:0035929 ! steroid hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045580 name: regulation of T cell differentiation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of T cell differentiation." [GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "regulation of T cell development" RELATED [GOC:add] synonym: "regulation of T lymphocyte differentiation" EXACT [] synonym: "regulation of T-cell differentiation" EXACT [] synonym: "regulation of T-lymphocyte differentiation" EXACT [] is_a: GO:0045619 ! regulation of lymphocyte differentiation is_a: GO:0050863 ! regulation of T cell activation relationship: regulates GO:0030217 ! T cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045582 name: positive regulation of T cell differentiation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of T cell differentiation." [GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "activation of T cell differentiation" NARROW [] synonym: "positive regulation of T cell development" RELATED [GOC:add] synonym: "positive regulation of T lymphocyte differentiation" EXACT [] synonym: "positive regulation of T-cell differentiation" EXACT [] synonym: "positive regulation of T-lymphocyte differentiation" EXACT [] synonym: "stimulation of T cell differentiation" NARROW [] synonym: "up regulation of T cell differentiation" EXACT [] synonym: "up-regulation of T cell differentiation" EXACT [] synonym: "upregulation of T cell differentiation" EXACT [] is_a: GO:0045580 ! regulation of T cell differentiation is_a: GO:0045621 ! positive regulation of lymphocyte differentiation is_a: GO:0050870 ! positive regulation of T cell activation relationship: positively_regulates GO:0030217 ! T cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045595 name: regulation of cell differentiation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features." [GOC:go_curators] subset: gosubset_prok is_a: GO:0050793 ! regulation of developmental process is_a: GO:0050794 ! regulation of cellular process relationship: regulates GO:0030154 ! cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045597 name: positive regulation of cell differentiation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of cell differentiation." [GOC:go_curators] subset: gosubset_prok synonym: "activation of cell differentiation" NARROW [] synonym: "stimulation of cell differentiation" NARROW [] synonym: "up regulation of cell differentiation" EXACT [] synonym: "up-regulation of cell differentiation" EXACT [] synonym: "upregulation of cell differentiation" EXACT [] is_a: GO:0045595 ! regulation of cell differentiation is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0051094 ! positive regulation of developmental process relationship: positively_regulates GO:0030154 ! cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045619 name: regulation of lymphocyte differentiation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of lymphocyte differentiation." [GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "regulation of lymphocyte development" RELATED [GOC:add] is_a: GO:0045595 ! regulation of cell differentiation is_a: GO:0051249 ! regulation of lymphocyte activation is_a: GO:2000026 ! regulation of multicellular organismal development relationship: regulates GO:0030098 ! lymphocyte differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045621 name: positive regulation of lymphocyte differentiation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of lymphocyte differentiation." [GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "activation of lymphocyte differentiation" NARROW [] synonym: "positive regulation of lymphocyte development" RELATED [GOC:add] synonym: "stimulation of lymphocyte differentiation" NARROW [] synonym: "up regulation of lymphocyte differentiation" EXACT [] synonym: "up-regulation of lymphocyte differentiation" EXACT [] synonym: "upregulation of lymphocyte differentiation" EXACT [] is_a: GO:0045597 ! positive regulation of cell differentiation is_a: GO:0045619 ! regulation of lymphocyte differentiation is_a: GO:0051251 ! positive regulation of lymphocyte activation relationship: positively_regulates GO:0030098 ! lymphocyte differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045622 name: regulation of T-helper cell differentiation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of T-helper cell differentiation." [GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "regulation of T-helper cell development" RELATED [GOC:add] is_a: GO:0002697 ! regulation of immune effector process is_a: GO:0043370 ! regulation of CD4-positive, alpha-beta T cell differentiation is_a: GO:0050776 ! regulation of immune response relationship: regulates GO:0042093 ! T-helper cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045624 name: positive regulation of T-helper cell differentiation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of T-helper cell differentiation." [GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "activation of T-helper cell differentiation" NARROW [] synonym: "positive regulation of T-helper cell development" RELATED [GOC:add] synonym: "stimulation of T-helper cell differentiation" NARROW [] synonym: "up regulation of T-helper cell differentiation" EXACT [] synonym: "up-regulation of T-helper cell differentiation" EXACT [] synonym: "upregulation of T-helper cell differentiation" EXACT [] is_a: GO:0002699 ! positive regulation of immune effector process is_a: GO:0043372 ! positive regulation of CD4-positive, alpha-beta T cell differentiation is_a: GO:0045622 ! regulation of T-helper cell differentiation relationship: positively_regulates GO:0042093 ! T-helper cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045625 name: regulation of T-helper 1 cell differentiation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of T-helper 1 cell differentiation." [GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "regulation of T-helper 1 cell development" RELATED [GOC:add] is_a: GO:0002825 ! regulation of T-helper 1 type immune response is_a: GO:0045622 ! regulation of T-helper cell differentiation relationship: regulates GO:0045063 ! T-helper 1 cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045627 name: positive regulation of T-helper 1 cell differentiation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of T-helper 1 cell differentiation." [GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "activation of T-helper 1 cell differentiation" NARROW [] synonym: "positive regulation of T-helper 1 cell development" RELATED [GOC:add] synonym: "stimulation of T-helper 1 cell differentiation" NARROW [] synonym: "up regulation of T-helper 1 cell differentiation" EXACT [] synonym: "up-regulation of T-helper 1 cell differentiation" EXACT [] synonym: "upregulation of T-helper 1 cell differentiation" EXACT [] is_a: GO:0045624 ! positive regulation of T-helper cell differentiation is_a: GO:0045625 ! regulation of T-helper 1 cell differentiation relationship: positively_regulates GO:0045063 ! T-helper 1 cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045628 name: regulation of T-helper 2 cell differentiation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of T-helper 2 cell differentiation." [GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "regulation of T-helper 2 cell development" RELATED [GOC:add] is_a: GO:0002828 ! regulation of type 2 immune response is_a: GO:0045622 ! regulation of T-helper cell differentiation relationship: regulates GO:0045064 ! T-helper 2 cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045630 name: positive regulation of T-helper 2 cell differentiation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of T-helper 2 cell differentiation." [GOC:go_curators] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "activation of T-helper 2 cell differentiation" NARROW [] synonym: "positive regulation of T-helper 2 cell development" RELATED [GOC:add] synonym: "stimulation of T-helper 2 cell differentiation" NARROW [] synonym: "up regulation of T-helper 2 cell differentiation" EXACT [] synonym: "up-regulation of T-helper 2 cell differentiation" EXACT [] synonym: "upregulation of T-helper 2 cell differentiation" EXACT [] is_a: GO:0045624 ! positive regulation of T-helper cell differentiation is_a: GO:0045628 ! regulation of T-helper 2 cell differentiation relationship: positively_regulates GO:0045064 ! T-helper 2 cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045730 name: respiratory burst namespace: biological_process def: "A phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals." [ISBN:0198506732] synonym: "metabolic burst" EXACT [] synonym: "oxidative burst" EXACT [] xref: Wikipedia:Respiratory_burst is_a: GO:0044710 ! single-organism metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045765 name: regulation of angiogenesis namespace: biological_process def: "Any process that modulates the frequency, rate or extent of angiogenesis." [GOC:go_curators] is_a: GO:0022603 ! regulation of anatomical structure morphogenesis is_a: GO:1901342 ! regulation of vasculature development relationship: regulates GO:0001525 ! angiogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045766 name: positive regulation of angiogenesis namespace: biological_process def: "Any process that activates or increases angiogenesis." [GOC:go_curators] synonym: "activation of angiogenesis" NARROW [] synonym: "stimulation of angiogenesis" NARROW [] synonym: "up regulation of angiogenesis" EXACT [] synonym: "up-regulation of angiogenesis" EXACT [] synonym: "upregulation of angiogenesis" EXACT [] is_a: GO:0045765 ! regulation of angiogenesis is_a: GO:0051094 ! positive regulation of developmental process relationship: positively_regulates GO:0001525 ! angiogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045830 name: positive regulation of isotype switching namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of isotype switching." [GOC:go_curators] synonym: "activation of isotype switching" NARROW [] synonym: "positive regulation of class switch recombination" EXACT [] synonym: "positive regulation of class switching" EXACT [] synonym: "positive regulation of isotype switch recombination" EXACT [] synonym: "stimulation of isotype switching" NARROW [] synonym: "up regulation of isotype switching" EXACT [] synonym: "up-regulation of isotype switching" EXACT [] synonym: "upregulation of isotype switching" EXACT [] is_a: GO:0002699 ! positive regulation of immune effector process is_a: GO:0045191 ! regulation of isotype switching is_a: GO:0045911 ! positive regulation of DNA recombination is_a: GO:0050871 ! positive regulation of B cell activation relationship: positively_regulates GO:0045190 ! isotype switching property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045911 name: positive regulation of DNA recombination namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of DNA recombination." [GOC:go_curators] subset: gosubset_prok synonym: "activation of DNA recombination" NARROW [] synonym: "stimulation of DNA recombination" NARROW [] synonym: "up regulation of DNA recombination" EXACT [] synonym: "up-regulation of DNA recombination" EXACT [] synonym: "upregulation of DNA recombination" EXACT [] is_a: GO:0000018 ! regulation of DNA recombination is_a: GO:0051054 ! positive regulation of DNA metabolic process relationship: positively_regulates GO:0006310 ! DNA recombination property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0045935 name: positive regulation of nucleobase-containing compound metabolic process namespace: biological_process def: "Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators] subset: gosubset_prok synonym: "activation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" NARROW [] synonym: "positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] synonym: "positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] synonym: "stimulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" NARROW [] synonym: "up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process relationship: positively_regulates GO:0006139 ! nucleobase-containing compound metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046394 name: carboxylic acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups." [ISBN:0198506732] subset: gosubset_prok synonym: "carboxylic acid anabolism" EXACT [] synonym: "carboxylic acid biosynthesis" EXACT [] synonym: "carboxylic acid formation" EXACT [] synonym: "carboxylic acid synthesis" EXACT [] is_a: GO:0016053 ! organic acid biosynthetic process is_a: GO:0019752 ! carboxylic acid metabolic process is_a: GO:1901576 ! organic substance biosynthetic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046483 name: heterocycle metabolic process namespace: biological_process def: "The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [CHEBI:5686, ISBN:0198506732] subset: goslim_pir subset: gosubset_prok synonym: "heterocycle metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046545 name: development of primary female sexual characteristics namespace: biological_process def: "The process whose specific outcome is the progression of the primary female sexual characteristics over time, from their formation to the mature structure. The primary female sexual characteristics are the ovaries, and they develop in response to sex hormone secretion." [GOC:ai] is_a: GO:0045137 ! development of primary sexual characteristics relationship: part_of GO:0046660 ! female sex differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046625 name: sphingolipid binding namespace: molecular_function def: "Interacting selectively and non-covalently with sphingolipids, a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid)." [ISBN:0198506732] is_a: GO:0008289 ! lipid binding property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046629 name: gamma-delta T cell activation namespace: biological_process def: "The change in morphology and behavior of a gamma-delta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." [GOC:add] synonym: "gamma-delta T lymphocyte activation" EXACT [] synonym: "gamma-delta T-cell activation" EXACT [] synonym: "gamma-delta T-lymphocyte activation" EXACT [] is_a: GO:0042110 ! T cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046631 name: alpha-beta T cell activation namespace: biological_process def: "The change in morphology and behavior of an alpha-beta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." [GOC:add] synonym: "alpha-beta T lymphocyte activation" EXACT [] synonym: "alpha-beta T-cell activation" EXACT [] synonym: "alpha-beta T-lymphocyte activation" EXACT [] is_a: GO:0042110 ! T cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046632 name: alpha-beta T cell differentiation namespace: biological_process def: "The process in which a precursor cell type acquires the specialized features of an alpha-beta T cell. An alpha-beta T cell is a T cell that expresses an alpha-beta T cell receptor complex." [CL:0000789, GOC:ai] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "alpha-beta T cell development" RELATED [GOC:add] synonym: "alpha-beta T lymphocyte differentiation" EXACT [] synonym: "alpha-beta T-cell differentiation" EXACT [] synonym: "alpha-beta T-lymphocyte differentiation" EXACT [] is_a: GO:0030217 ! T cell differentiation is_a: GO:0046631 ! alpha-beta T cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046634 name: regulation of alpha-beta T cell activation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of alpha-beta T cell activation." [GOC:ai] synonym: "regulation of alpha-beta T lymphocyte activation" EXACT [] synonym: "regulation of alpha-beta T-cell activation" EXACT [] synonym: "regulation of alpha-beta T-lymphocyte activation" EXACT [] is_a: GO:0050863 ! regulation of T cell activation relationship: regulates GO:0046631 ! alpha-beta T cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046635 name: positive regulation of alpha-beta T cell activation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of alpha-beta T cell activation." [GOC:ai] synonym: "activation of alpha-beta T cell activation" NARROW [] synonym: "positive regulation of alpha-beta T lymphocyte activation" EXACT [] synonym: "positive regulation of alpha-beta T-cell activation" EXACT [] synonym: "positive regulation of alpha-beta T-lymphocyte activation" EXACT [] synonym: "stimulation of alpha-beta T cell activation" NARROW [] synonym: "up regulation of alpha-beta T cell activation" EXACT [] synonym: "up-regulation of alpha-beta T cell activation" EXACT [] synonym: "upregulation of alpha-beta T cell activation" EXACT [] is_a: GO:0046634 ! regulation of alpha-beta T cell activation is_a: GO:0050870 ! positive regulation of T cell activation relationship: positively_regulates GO:0046631 ! alpha-beta T cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046637 name: regulation of alpha-beta T cell differentiation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of alpha-beta T cell differentiation." [GOC:ai] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "regulation of alpha-beta T cell development" RELATED [GOC:add] synonym: "regulation of alpha-beta T lymphocyte differentiation" EXACT [] synonym: "regulation of alpha-beta T-cell differentiation" EXACT [] synonym: "regulation of alpha-beta T-lymphocyte differentiation" EXACT [] is_a: GO:0045580 ! regulation of T cell differentiation is_a: GO:0046634 ! regulation of alpha-beta T cell activation relationship: regulates GO:0046632 ! alpha-beta T cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046638 name: positive regulation of alpha-beta T cell differentiation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of alpha-beta T cell differentiation." [GOC:ai] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "activation of alpha-beta T cell differentiation" NARROW [] synonym: "positive regulation of alpha-beta T cell development" RELATED [GOC:add] synonym: "positive regulation of alpha-beta T lymphocyte differentiation" EXACT [] synonym: "positive regulation of alpha-beta T-cell differentiation" EXACT [] synonym: "positive regulation of alpha-beta T-lymphocyte differentiation" EXACT [] synonym: "stimulation of alpha-beta T cell differentiation" NARROW [] synonym: "up regulation of alpha-beta T cell differentiation" EXACT [] synonym: "up-regulation of alpha-beta T cell differentiation" EXACT [] synonym: "upregulation of alpha-beta T cell differentiation" EXACT [] is_a: GO:0045582 ! positive regulation of T cell differentiation is_a: GO:0046635 ! positive regulation of alpha-beta T cell activation is_a: GO:0046637 ! regulation of alpha-beta T cell differentiation relationship: positively_regulates GO:0046632 ! alpha-beta T cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046649 name: lymphocyte activation namespace: biological_process def: "A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor." [GOC:mgi_curators, ISBN:0781735140] is_a: GO:0045321 ! leukocyte activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046651 name: lymphocyte proliferation namespace: biological_process def: "The expansion of a lymphocyte population by cell division." [GOC:ai] is_a: GO:0032943 ! mononuclear cell proliferation is_a: GO:0046649 ! lymphocyte activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046660 name: female sex differentiation namespace: biological_process def: "The establishment of the sex of a female organism by physical differentiation." [GOC:bf] is_a: GO:0007548 ! sex differentiation relationship: part_of GO:0007275 ! multicellular organismal development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046849 name: bone remodeling namespace: biological_process def: "The continuous turnover of bone matrix and mineral that involves first, an increase in resorption (osteoclastic activity) and later, reactive bone formation (osteoblastic activity). The process of bone remodeling takes place in the adult skeleton at discrete foci. The process ensures the mechanical integrity of the skeleton throughout life and plays an important role in calcium homeostasis. An imbalance in the regulation of bone resorption and bone formation results in many of the metabolic bone diseases, such as osteoporosis." [GOC:curators] synonym: "bone remodelling" EXACT [] xref: Wikipedia:Bone_remodeling is_a: GO:0048771 ! tissue remodeling property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046864 name: isoprenoid transport namespace: biological_process def: "The directed movement of isoprenoids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Isoprenoids comprise a group of compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues." [GOC:ai] subset: goslim_pir is_a: GO:0006869 ! lipid transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046865 name: terpenoid transport namespace: biological_process def: "The directed movement of terpenoids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Terpenoids are a class of compounds characterized by an isoprenoid chemical structure and include derivatives with various functional groups." [GOC:ai] is_a: GO:0046864 ! isoprenoid transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046879 name: hormone secretion namespace: biological_process def: "The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells." [ISBN:0198506732] is_a: GO:0009914 ! hormone transport is_a: GO:0023061 ! signal release is_a: GO:0032940 ! secretion by cell property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0046903 name: secretion namespace: biological_process def: "The controlled release of a substance by a cell, a group of cells, or a tissue." [GOC:ai] subset: goslim_pir subset: gosubset_prok is_a: GO:0006810 ! transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048002 name: antigen processing and presentation of peptide antigen namespace: biological_process def: "The process in which an antigen-presenting cell expresses peptide antigen in association with an MHC protein complex on its cell surface, including proteolysis and transport steps for the peptide antigen both prior to and following assembly with the MHC protein complex. The peptide antigen is typically, but not always, processed from an endogenous or exogenous protein." [GOC:add, ISBN:0781735149, PMID:15771591] synonym: "antigen presentation, peptide antigen" EXACT [] synonym: "peptide antigen processing and presentation" EXACT [] is_a: GO:0019882 ! antigen processing and presentation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048103 name: somatic stem cell division namespace: biological_process def: "The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line." [GOC:jid, ISBN:0582227089] synonym: "somatic stem cell renewal" EXACT [] is_a: GO:0017145 ! stem cell division property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048134 name: germ-line cyst formation namespace: biological_process def: "Formation of a cluster of germ-line cells derived from a single founder cell." [GOC:jid, PMID:10370240] is_a: GO:0008283 ! cell proliferation is_a: GO:0048610 ! cellular process involved in reproduction relationship: part_of GO:0007281 ! germ cell development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048136 name: male germ-line cyst formation namespace: biological_process def: "Formation of a cluster of germ-line cells, in the male gonad of an insect, derived from a single founder cell (cystoblast)." [GOC:jid] is_a: GO:0048134 ! germ-line cyst formation relationship: part_of GO:0007283 ! spermatogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048137 name: spermatocyte division namespace: biological_process def: "The meiotic divisions undergone by the primary and secondary spermatocytes to produce a cyst of haploid spermatids." [GOC:jid, ISBN:0879694238] synonym: "spermatocyte cell division" EXACT [] is_a: GO:0048610 ! cellular process involved in reproduction is_a: GO:0051301 ! cell division relationship: part_of GO:0048136 ! male germ-line cyst formation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048232 name: male gamete generation namespace: biological_process def: "Generation of the male gamete; specialised haploid cells produced by meiosis and along with a female gamete takes part in sexual reproduction." [GOC:dph, GOC:jid] is_a: GO:0007276 ! gamete generation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048240 name: sperm capacitation namespace: biological_process def: "A process required for sperm to reach fertilization competence. Sperm undergo an incompletely understood series of morphological and molecular maturational processes, termed capacitation, involving, among other processes, protein tyrosine phosphorylation and increased intracellular calcium." [GOC:jid, PMID:11820818] synonym: "sperm activation" RELATED [PMID:23180860] is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0048469 ! cell maturation is_a: GO:0048610 ! cellular process involved in reproduction relationship: part_of GO:0007286 ! spermatid development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048241 name: epinephrine transport namespace: biological_process def: "The directed movement of epinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jid] synonym: "adrenaline transport" EXACT [] is_a: GO:0009914 ! hormone transport is_a: GO:0051937 ! catecholamine transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048242 name: epinephrine secretion namespace: biological_process def: "The regulated release of epinephrine by a cell or group of cells. Epinephrine is a catecholamine hormone secreted by the adrenal medulla and a neurotransmitter, released by certain neurons and active in the central nervous system." [GOC:ef, GOC:jid] synonym: "adrenaline secretion" EXACT [] is_a: GO:0048241 ! epinephrine transport is_a: GO:0050432 ! catecholamine secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048243 name: norepinephrine secretion namespace: biological_process def: "The regulated release of norepinephrine by a cell or group of cells. Norepinephrine is a catecholamine and it acts as a hormone and as a neurotransmitter of most of the sympathetic nervous system." [GOC:ef, GOC:jid] synonym: "noradrenaline secretion" EXACT [] is_a: GO:0015874 ! norepinephrine transport is_a: GO:0050432 ! catecholamine secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048285 name: organelle fission namespace: biological_process def: "The creation of two or more organelles by division of one organelle." [GOC:jid] subset: goslim_pir subset: goslim_yeast is_a: GO:0006996 ! organelle organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048289 name: isotype switching to IgE isotypes namespace: biological_process def: "The switching of activated B cells from IgM biosynthesis to IgE biosynthesis, accomplished through a recombination process involving an intrachromosomal deletion between switch regions that reside 5' of the IgM and IgE constant region gene segments in the immunoglobulin heavy chain locus." [ISBN:0781735149, PMID:12370374, PMID:2113175, PMID:9186655] synonym: "class switch recombination to IgE isotypes" EXACT [] synonym: "class switching to IgE isotypes" EXACT [] synonym: "isotype switch recombination to IgE isotypes" EXACT [] is_a: GO:0045190 ! isotype switching property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048293 name: regulation of isotype switching to IgE isotypes namespace: biological_process def: "Any process that modulates the frequency, rate or extent of isotype switching to IgE isotypes." [GOC:jid] synonym: "regulation of class switch recombination to IgE isotypes" EXACT [] synonym: "regulation of class switching to IgE isotypes" EXACT [] synonym: "regulation of isotype switch recombination to IgE isotypes" EXACT [] is_a: GO:0045191 ! regulation of isotype switching relationship: regulates GO:0048289 ! isotype switching to IgE isotypes property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048295 name: positive regulation of isotype switching to IgE isotypes namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of isotype switching to IgE isotypes." [GOC:jid] synonym: "activation of isotype switching to IgE isotypes" NARROW [] synonym: "positive regulation of class switch recombination to IgE isotypes" EXACT [] synonym: "positive regulation of class switching to IgE isotypes" EXACT [] synonym: "positive regulation of isotype switch recombination to IgE isotypes" EXACT [] synonym: "stimulation of isotype switching to IgE isotypes" NARROW [] synonym: "up regulation of isotype switching to IgE isotypes" EXACT [] synonym: "up-regulation of isotype switching to IgE isotypes" EXACT [] synonym: "upregulation of isotype switching to IgE isotypes" EXACT [] is_a: GO:0045830 ! positive regulation of isotype switching is_a: GO:0048293 ! regulation of isotype switching to IgE isotypes relationship: positively_regulates GO:0048289 ! isotype switching to IgE isotypes property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048305 name: immunoglobulin secretion namespace: biological_process def: "The regulated release of immunoglobulins from a B cell or plasma cell, whose mechanism includes the use of alternate polyadenylylation signals to favor the biosynthesis of secreted forms of immunoglobulin over membrane-bound immunoglobulin." [GOC:add, ISBN:0781735149, PMID:9185563] synonym: "antibody secretion" EXACT [] is_a: GO:0009306 ! protein secretion relationship: part_of GO:0002377 ! immunoglobulin production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048468 name: cell development namespace: biological_process def: "The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:go_curators] subset: goslim_candida subset: gosubset_prok synonym: "terminal differentiation" RELATED [GOC:dph, GOC:tb] is_a: GO:0048856 ! anatomical structure development is_a: GO:0048869 ! cellular developmental process relationship: part_of GO:0030154 ! cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048469 name: cell maturation namespace: biological_process def: "A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state." [GOC:go_curators] subset: goslim_pir subset: gosubset_prok synonym: "functional differentiation" RELATED [GOC:dph] is_a: GO:0021700 ! developmental maturation is_a: GO:0048869 ! cellular developmental process relationship: part_of GO:0048468 ! cell development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048477 name: oogenesis namespace: biological_process alt_id: GO:0009993 alt_id: GO:0048157 def: "The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster." [GOC:kmv, GOC:mtg_sensu] synonym: "ovum development" EXACT systematic_synonym [] xref: Wikipedia:Oogenesis is_a: GO:0007292 ! female gamete generation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048511 name: rhythmic process namespace: biological_process def: "Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism." [GOC:jid] subset: goslim_pir subset: gosubset_prok synonym: "rhythm" RELATED [] is_a: GO:0044699 ! single-organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048513 name: organ development namespace: biological_process def: "Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC:dph, GOC:jid] synonym: "development of an organ" EXACT [] synonym: "organogenesis" EXACT [] xref: Wikipedia:Organogenesis is_a: GO:0048856 ! anatomical structure development relationship: part_of GO:0048731 ! system development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048514 name: blood vessel morphogenesis namespace: biological_process def: "The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood." [GOC:jid] is_a: GO:0009653 ! anatomical structure morphogenesis relationship: part_of GO:0001568 ! blood vessel development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048515 name: spermatid differentiation namespace: biological_process def: "The process whose specific outcome is the progression of a spermatid over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." [GOC:dph, GOC:jid] synonym: "spermatid cell differentiation" EXACT [] is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0030154 ! cell differentiation is_a: GO:0048610 ! cellular process involved in reproduction relationship: part_of GO:0007283 ! spermatogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048518 name: positive regulation of biological process namespace: biological_process alt_id: GO:0043119 def: "Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] subset: gosubset_prok synonym: "activation of biological process" NARROW [] synonym: "positive regulation of physiological process" EXACT [] synonym: "stimulation of biological process" NARROW [] synonym: "up regulation of biological process" EXACT [] synonym: "up-regulation of biological process" EXACT [] synonym: "upregulation of biological process" EXACT [] is_a: GO:0050789 ! regulation of biological process relationship: positively_regulates GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048519 name: negative regulation of biological process namespace: biological_process alt_id: GO:0043118 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] subset: gosubset_prok synonym: "down regulation of biological process" EXACT [] synonym: "down-regulation of biological process" EXACT [] synonym: "downregulation of biological process" EXACT [] synonym: "inhibition of biological process" NARROW [] synonym: "negative regulation of physiological process" EXACT [] is_a: GO:0050789 ! regulation of biological process relationship: negatively_regulates GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048520 name: positive regulation of behavior namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli." [GOC:jid] synonym: "activation of behavior" NARROW [] synonym: "stimulation of behavior" NARROW [] synonym: "up regulation of behavior" EXACT [] synonym: "up-regulation of behavior" EXACT [] synonym: "upregulation of behavior" EXACT [] is_a: GO:0048584 ! positive regulation of response to stimulus is_a: GO:0050795 ! regulation of behavior relationship: positively_regulates GO:0007610 ! behavior property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048522 name: positive regulation of cellular process namespace: biological_process alt_id: GO:0051242 def: "Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:jid] subset: gosubset_prok synonym: "activation of cellular process" NARROW [] synonym: "positive regulation of cellular physiological process" EXACT [] synonym: "stimulation of cellular process" NARROW [] synonym: "up regulation of cellular process" EXACT [] synonym: "up-regulation of cellular process" EXACT [] synonym: "upregulation of cellular process" EXACT [] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0050794 ! regulation of cellular process relationship: positively_regulates GO:0009987 ! cellular process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048523 name: negative regulation of cellular process namespace: biological_process alt_id: GO:0051243 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:jid] subset: gosubset_prok synonym: "down regulation of cellular process" EXACT [] synonym: "down-regulation of cellular process" EXACT [] synonym: "downregulation of cellular process" EXACT [] synonym: "inhibition of cellular process" NARROW [] synonym: "negative regulation of cellular physiological process" EXACT [] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0050794 ! regulation of cellular process relationship: negatively_regulates GO:0009987 ! cellular process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048534 name: hematopoietic or lymphoid organ development namespace: biological_process def: "The process whose specific outcome is the progression of any organ involved in hematopoiesis (also known as hemopoiesis) or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation." [GOC:add, GOC:rl, ISBN:0781735149] synonym: "haematopoietic or lymphoid organ development" EXACT [] synonym: "haemopoietic or lymphoid organ development" EXACT [] synonym: "hemopoietic or lymphoid organ development" EXACT [] is_a: GO:0048513 ! organ development relationship: part_of GO:0002520 ! immune system development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048583 name: regulation of response to stimulus namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [GOC:jid] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC. subset: gosubset_prok subset: high_level_annotation_qc is_a: GO:0050789 ! regulation of biological process relationship: regulates GO:0050896 ! response to stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048584 name: positive regulation of response to stimulus namespace: biological_process def: "Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [GOC:jid] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC. subset: high_level_annotation_qc synonym: "activation of response to stimulus" NARROW [] synonym: "stimulation of response to stimulus" NARROW [] synonym: "up regulation of response to stimulus" EXACT [] synonym: "up-regulation of response to stimulus" EXACT [] synonym: "upregulation of response to stimulus" EXACT [] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0048583 ! regulation of response to stimulus relationship: positively_regulates GO:0050896 ! response to stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048585 name: negative regulation of response to stimulus namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [GOC:jid] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC. subset: high_level_annotation_qc synonym: "down regulation of response to stimulus" EXACT [] synonym: "down-regulation of response to stimulus" EXACT [] synonym: "downregulation of response to stimulus" EXACT [] synonym: "inhibition of response to stimulus" NARROW [] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0048583 ! regulation of response to stimulus relationship: negatively_regulates GO:0050896 ! response to stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048608 name: reproductive structure development namespace: biological_process def: "The reproductive developmental process whose specific outcome is the progression of structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures." [GOC:dph, GOC:isa_complete, GOC:jid] is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0048856 ! anatomical structure development relationship: part_of GO:0061458 ! reproductive system development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048609 name: multicellular organismal reproductive process namespace: biological_process def: "The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs." [GOC:dph, GOC:jid, GOC:tb] synonym: "organismal reproductive process" BROAD [GOC:curators] synonym: "reproductive process in a multicellular organism" EXACT [GOC:curators] is_a: GO:0044702 ! single organism reproductive process is_a: GO:0044707 ! single-multicellular organism process relationship: part_of GO:0032504 ! multicellular organism reproduction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048610 name: cellular process involved in reproduction namespace: biological_process def: "A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular or single-celled organism." [GOC:dph, GOC:jid] subset: gosubset_prok synonym: "reproductive cellular process" RELATED [GOC:dph, GOC:tb] is_a: GO:0044702 ! single organism reproductive process is_a: GO:0044763 ! single-organism cellular process relationship: part_of GO:0000003 ! reproduction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048646 name: anatomical structure formation involved in morphogenesis namespace: biological_process def: "The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:dph, GOC:jid, GOC:tb] comment: Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense. subset: goslim_generic synonym: "formation of an anatomical structure involved in morphogenesis" EXACT [GOC:dph, GOC:tb] is_a: GO:0032502 ! developmental process is_a: GO:0044699 ! single-organism process relationship: part_of GO:0009653 ! anatomical structure morphogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048699 name: generation of neurons namespace: biological_process def: "The process in which nerve cells are generated. This includes the production of neuroblasts and their differentiation into neurons." [GOC:nln] synonym: "neuron generation" EXACT [GOC:curators] is_a: GO:0022008 ! neurogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048731 name: system development namespace: biological_process def: "The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process." [GOC:dph, GOC:jid] is_a: GO:0048856 ! anatomical structure development relationship: part_of GO:0007275 ! multicellular organismal development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048738 name: cardiac muscle tissue development namespace: biological_process def: "The process whose specific outcome is the progression of cardiac muscle over time, from its formation to the mature structure." [GOC:dph, GOC:jid, GOC:lm] synonym: "heart muscle development" EXACT [] is_a: GO:0014706 ! striated muscle tissue development relationship: part_of GO:0007507 ! heart development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048770 name: pigment granule namespace: cellular_component def: "A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes." [GOC:jid, GOC:mh] is_a: GO:0016023 ! cytoplasmic membrane-bounded vesicle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048771 name: tissue remodeling namespace: biological_process def: "The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling." [GOC:ebc] subset: goslim_pir is_a: GO:0044707 ! single-multicellular organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048820 name: hair follicle maturation namespace: biological_process def: "A developmental process, independent of morphogenetic (shape) change, that is required for a hair follicle to attain its fully functional state." [GOC:devbiol] is_a: GO:0022405 ! hair cycle process is_a: GO:0071695 ! anatomical structure maturation relationship: part_of GO:0001942 ! hair follicle development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048856 name: anatomical structure development namespace: biological_process def: "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GO_REF:0000021, GOC:mtg_15jun06] comment: This term was added by GO_REF:0000021. subset: goslim_generic synonym: "development of an anatomical structure" EXACT [] is_a: GO:0032502 ! developmental process is_a: GO:0044699 ! single-organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048869 name: cellular developmental process namespace: biological_process def: "A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition." [GOC:isa_complete] subset: gosubset_prok is_a: GO:0032502 ! developmental process is_a: GO:0044763 ! single-organism cellular process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048870 name: cell motility namespace: biological_process def: "Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another." [GOC:dgh, GOC:dph, GOC:isa_complete, GOC:mlg] subset: goslim_generic subset: goslim_metagenomics subset: gosubset_prok synonym: "cell locomotion" EXACT [] synonym: "cell movement" RELATED [] synonym: "movement of a cell" EXACT [] is_a: GO:0006928 ! cellular component movement is_a: GO:0040011 ! locomotion relationship: part_of GO:0051674 ! localization of cell property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048871 name: multicellular organismal homeostasis namespace: biological_process def: "Any process involved in the maintenance of an internal steady state at the level of the multicellular organism." [GOC:isa_complete] is_a: GO:0042592 ! homeostatic process is_a: GO:0044707 ! single-multicellular organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048872 name: homeostasis of number of cells namespace: biological_process def: "Any biological process involved in the maintenance of the steady-state number of cells within a population of cells." [GOC:isa_complete] synonym: "cell population homeostasis" EXACT [] synonym: "homeostasis of cell number" EXACT [GOC:dph] is_a: GO:0042592 ! homeostatic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048875 name: chemical homeostasis within a tissue namespace: biological_process def: "Any process involved in the maintenance of the internal steady state of the amount of a chemical at the level of the tissue." [GOC:isa_complete] is_a: GO:0001894 ! tissue homeostasis is_a: GO:0048878 ! chemical homeostasis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0048878 name: chemical homeostasis namespace: biological_process def: "Any biological process involved in the maintenance of an internal steady state of a chemical." [GOC:isa_complete] subset: gosubset_prok is_a: GO:0042592 ! homeostatic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050432 name: catecholamine secretion namespace: biological_process def: "The regulated release of catecholamines by a cell or group of cells. The catecholamines are a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine." [GOC:ai, GOC:ef] is_a: GO:0032940 ! secretion by cell is_a: GO:0051937 ! catecholamine transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050670 name: regulation of lymphocyte proliferation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of lymphocyte proliferation." [GOC:ai] is_a: GO:0032944 ! regulation of mononuclear cell proliferation is_a: GO:0051249 ! regulation of lymphocyte activation relationship: regulates GO:0046651 ! lymphocyte proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050672 name: negative regulation of lymphocyte proliferation namespace: biological_process def: "Any process that stops, prevents or reduces the rate or extent of lymphocyte proliferation." [GOC:ai] synonym: "down regulation of lymphocyte proliferation" EXACT [] synonym: "down-regulation of lymphocyte proliferation" EXACT [] synonym: "downregulation of lymphocyte proliferation" EXACT [] synonym: "inhibition of lymphocyte proliferation" NARROW [] is_a: GO:0032945 ! negative regulation of mononuclear cell proliferation is_a: GO:0050670 ! regulation of lymphocyte proliferation is_a: GO:0051250 ! negative regulation of lymphocyte activation relationship: negatively_regulates GO:0046651 ! lymphocyte proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050673 name: epithelial cell proliferation namespace: biological_process def: "The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances." [ISBN:0721662544] is_a: GO:0008283 ! cell proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050678 name: regulation of epithelial cell proliferation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of epithelial cell proliferation." [GOC:ai] is_a: GO:0042127 ! regulation of cell proliferation relationship: regulates GO:0050673 ! epithelial cell proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050679 name: positive regulation of epithelial cell proliferation namespace: biological_process def: "Any process that activates or increases the rate or extent of epithelial cell proliferation." [GOC:ai] synonym: "activation of epithelial cell proliferation" NARROW [] synonym: "stimulation of epithelial cell proliferation" NARROW [] synonym: "up regulation of epithelial cell proliferation" EXACT [] synonym: "up-regulation of epithelial cell proliferation" EXACT [] synonym: "upregulation of epithelial cell proliferation" EXACT [] is_a: GO:0008284 ! positive regulation of cell proliferation is_a: GO:0050678 ! regulation of epithelial cell proliferation relationship: positively_regulates GO:0050673 ! epithelial cell proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050708 name: regulation of protein secretion namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell or group of cells." [GOC:ai] subset: gosubset_prok is_a: GO:0051046 ! regulation of secretion is_a: GO:0051223 ! regulation of protein transport is_a: GO:0060341 ! regulation of cellular localization relationship: regulates GO:0009306 ! protein secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050714 name: positive regulation of protein secretion namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell or group of cells." [GOC:ai] synonym: "activation of protein secretion" NARROW [] synonym: "stimulation of protein secretion" NARROW [] synonym: "up regulation of protein secretion" EXACT [] synonym: "up-regulation of protein secretion" EXACT [] synonym: "upregulation of protein secretion" EXACT [] is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0050708 ! regulation of protein secretion is_a: GO:0051047 ! positive regulation of secretion is_a: GO:0051222 ! positive regulation of protein transport relationship: positively_regulates GO:0009306 ! protein secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050727 name: regulation of inflammatory response namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents." [GOC:ai] is_a: GO:0031347 ! regulation of defense response is_a: GO:0032101 ! regulation of response to external stimulus relationship: regulates GO:0006954 ! inflammatory response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050728 name: negative regulation of inflammatory response namespace: biological_process alt_id: GO:0030236 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response." [GOC:ai] synonym: "anti-inflammatory response" EXACT [] synonym: "down regulation of inflammatory response" EXACT [] synonym: "down-regulation of inflammatory response" EXACT [] synonym: "downregulation of inflammatory response" EXACT [] synonym: "inhibition of inflammatory response" NARROW [] is_a: GO:0031348 ! negative regulation of defense response is_a: GO:0032102 ! negative regulation of response to external stimulus is_a: GO:0050727 ! regulation of inflammatory response relationship: negatively_regulates GO:0006954 ! inflammatory response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050729 name: positive regulation of inflammatory response namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the inflammatory response." [GOC:ai] synonym: "activation of inflammatory response" NARROW [] synonym: "stimulation of inflammatory response" NARROW [] synonym: "up regulation of inflammatory response" EXACT [] synonym: "up-regulation of inflammatory response" EXACT [] synonym: "upregulation of inflammatory response" EXACT [] is_a: GO:0031349 ! positive regulation of defense response is_a: GO:0032103 ! positive regulation of response to external stimulus is_a: GO:0050727 ! regulation of inflammatory response relationship: positively_regulates GO:0006954 ! inflammatory response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050776 name: regulation of immune response namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus." [GOC:ai] xref: Reactome:REACT_101484 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Gallus gallus" xref: Reactome:REACT_106667 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Rattus norvegicus" xref: Reactome:REACT_107426 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Mus musculus" xref: Reactome:REACT_11152 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Homo sapiens" xref: Reactome:REACT_81657 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Danio rerio" xref: Reactome:REACT_82803 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Canis familiaris" xref: Reactome:REACT_87475 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Bos taurus" xref: Reactome:REACT_94152 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Sus scrofa" xref: Reactome:REACT_95389 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Taeniopygia guttata" xref: Reactome:REACT_97860 "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, Xenopus tropicalis" is_a: GO:0002682 ! regulation of immune system process is_a: GO:0048583 ! regulation of response to stimulus relationship: regulates GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050777 name: negative regulation of immune response namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus." [GOC:ai] synonym: "down regulation of immune response" EXACT [] synonym: "down-regulation of immune response" EXACT [] synonym: "downregulation of immune response" EXACT [] synonym: "inhibition of immune response" NARROW [] is_a: GO:0002683 ! negative regulation of immune system process is_a: GO:0048585 ! negative regulation of response to stimulus is_a: GO:0050776 ! regulation of immune response relationship: negatively_regulates GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050778 name: positive regulation of immune response namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus." [GOC:ai] synonym: "stimulation of immune response" NARROW [] synonym: "up regulation of immune response" EXACT [] synonym: "up-regulation of immune response" EXACT [] synonym: "upregulation of immune response" EXACT [] is_a: GO:0002684 ! positive regulation of immune system process is_a: GO:0048584 ! positive regulation of response to stimulus is_a: GO:0050776 ! regulation of immune response relationship: positively_regulates GO:0006955 ! immune response property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050789 name: regulation of biological process namespace: biological_process alt_id: GO:0050791 def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators] subset: goslim_aspergillus subset: goslim_candida subset: gosubset_prok synonym: "regulation of physiological process" EXACT [] is_a: GO:0065007 ! biological regulation relationship: regulates GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050793 name: regulation of developmental process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:go_curators] subset: gosubset_prok is_a: GO:0050789 ! regulation of biological process relationship: regulates GO:0032502 ! developmental process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050794 name: regulation of cellular process namespace: biological_process alt_id: GO:0051244 def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators] subset: gosubset_prok synonym: "regulation of cellular physiological process" EXACT [] is_a: GO:0050789 ! regulation of biological process relationship: regulates GO:0009987 ! cellular process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050795 name: regulation of behavior namespace: biological_process def: "Any process that modulates the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli." [GOC:go_curators] subset: gosubset_prok synonym: "regulation of behaviour" EXACT [] is_a: GO:0048583 ! regulation of response to stimulus relationship: regulates GO:0007610 ! behavior property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050817 name: coagulation namespace: biological_process def: "The process in which a fluid solution, or part of it, changes into a solid or semisolid mass." [ISBN:0198506732] subset: goslim_pir synonym: "clotting" EXACT [] is_a: GO:0044707 ! single-multicellular organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050863 name: regulation of T cell activation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of T cell activation." [GOC:ai] synonym: "regulation of T lymphocyte activation" EXACT [] synonym: "regulation of T-cell activation" EXACT [] synonym: "regulation of T-lymphocyte activation" EXACT [] is_a: GO:0051249 ! regulation of lymphocyte activation relationship: regulates GO:0042110 ! T cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050864 name: regulation of B cell activation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of B cell activation." [GOC:ai] synonym: "regulation of B lymphocyte activation" EXACT [] synonym: "regulation of B-cell activation" EXACT [] synonym: "regulation of B-lymphocyte activation" EXACT [] is_a: GO:0051249 ! regulation of lymphocyte activation relationship: regulates GO:0042113 ! B cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050865 name: regulation of cell activation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cell activation, the change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:ai] is_a: GO:0050794 ! regulation of cellular process relationship: regulates GO:0001775 ! cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050866 name: negative regulation of cell activation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell activation." [GOC:ai] synonym: "down regulation of cell activation" EXACT [] synonym: "down-regulation of cell activation" EXACT [] synonym: "downregulation of cell activation" EXACT [] synonym: "inhibition of cell activation" NARROW [] is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0050865 ! regulation of cell activation relationship: negatively_regulates GO:0001775 ! cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050867 name: positive regulation of cell activation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of activation." [GOC:ai] synonym: "activation of cell activation" NARROW [] synonym: "stimulation of cell activation" NARROW [] synonym: "up regulation of cell activation" EXACT [] synonym: "up-regulation of cell activation" EXACT [] synonym: "upregulation of cell activation" EXACT [] is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0050865 ! regulation of cell activation relationship: positively_regulates GO:0001775 ! cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050868 name: negative regulation of T cell activation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of T cell activation." [GOC:ai] synonym: "down regulation of T cell activation" EXACT [] synonym: "down-regulation of T cell activation" EXACT [] synonym: "downregulation of T cell activation" EXACT [] synonym: "inhibition of T cell activation" NARROW [] synonym: "negative regulation of T lymphocyte activation" EXACT [] synonym: "negative regulation of T-cell activation" EXACT [] synonym: "negative regulation of T-lymphocyte activation" EXACT [] is_a: GO:0050863 ! regulation of T cell activation is_a: GO:0051250 ! negative regulation of lymphocyte activation relationship: negatively_regulates GO:0042110 ! T cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050870 name: positive regulation of T cell activation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of T cell activation." [GOC:ai] synonym: "activation of T cell activation" NARROW [] synonym: "positive regulation of T lymphocyte activation" EXACT [] synonym: "positive regulation of T-cell activation" EXACT [] synonym: "positive regulation of T-lymphocyte activation" EXACT [] synonym: "stimulation of T cell activation" NARROW [] synonym: "up regulation of T cell activation" EXACT [] synonym: "up-regulation of T cell activation" EXACT [] synonym: "upregulation of T cell activation" EXACT [] is_a: GO:0050863 ! regulation of T cell activation is_a: GO:0051251 ! positive regulation of lymphocyte activation relationship: positively_regulates GO:0042110 ! T cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050871 name: positive regulation of B cell activation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of B cell activation." [GOC:ai] synonym: "activation of B cell activation" NARROW [] synonym: "positive regulation of B lymphocyte activation" EXACT [] synonym: "positive regulation of B-cell activation" EXACT [] synonym: "positive regulation of B-lymphocyte activation" EXACT [] synonym: "stimulation of B cell activation" NARROW [] synonym: "up regulation of B cell activation" EXACT [] synonym: "up-regulation of B cell activation" EXACT [] synonym: "upregulation of B cell activation" EXACT [] is_a: GO:0050864 ! regulation of B cell activation is_a: GO:0051251 ! positive regulation of lymphocyte activation relationship: positively_regulates GO:0042113 ! B cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050877 name: neurological system process namespace: biological_process def: "A organ system process carried out by any of the organs or tissues of neurological system." [GOC:ai, GOC:mtg_cardio] subset: goslim_generic subset: goslim_pir synonym: "neurophysiological process" EXACT [] synonym: "pan-neural process" RELATED [] is_a: GO:0003008 ! system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050878 name: regulation of body fluid levels namespace: biological_process def: "Any process that modulates the levels of body fluids." [GOC:ai, GOC:dph, GOC:tb] subset: goslim_pir is_a: GO:0044707 ! single-multicellular organism process is_a: GO:0065008 ! regulation of biological quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050886 name: endocrine process namespace: biological_process def: "The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system." [ISBN:0721662544] subset: goslim_pir synonym: "endocrine physiological process" EXACT [] synonym: "endocrine physiology" EXACT [] is_a: GO:0003008 ! system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050896 name: response to stimulus namespace: biological_process alt_id: GO:0051869 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC. subset: goslim_pir subset: gosubset_prok subset: high_level_annotation_qc synonym: "physiological response to stimulus" EXACT [] is_a: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050900 name: leukocyte migration namespace: biological_process def: "The movement of a leukocyte within or between different tissues and organs of the body." [GOC:add, ISBN:0781735149, PMID:14680625, PMID:14708592, PMID:7507411, PMID:8600538] synonym: "immune cell migration" EXACT [] synonym: "immune cell trafficking" EXACT [] synonym: "leucocyte migration" EXACT [] synonym: "leucocyte trafficking" EXACT [] synonym: "leukocyte trafficking" EXACT [] xref: Reactome:REACT_100059 "Cell surface interactions at the vascular wall, Sus scrofa" xref: Reactome:REACT_12051 "Cell surface interactions at the vascular wall, Homo sapiens" xref: Reactome:REACT_28425 "Cell surface interactions at the vascular wall, Bos taurus" xref: Reactome:REACT_34071 "Cell surface interactions at the vascular wall, Xenopus tropicalis" xref: Reactome:REACT_77198 "Cell surface interactions at the vascular wall, Taeniopygia guttata" xref: Reactome:REACT_83057 "Cell surface interactions at the vascular wall, Danio rerio" xref: Reactome:REACT_86476 "Cell surface interactions at the vascular wall, Canis familiaris" xref: Reactome:REACT_86886 "Cell surface interactions at the vascular wall, Mus musculus" xref: Reactome:REACT_89386 "Cell surface interactions at the vascular wall, Gallus gallus" xref: Reactome:REACT_93252 "Cell surface interactions at the vascular wall, Rattus norvegicus" xref: Reactome:REACT_98799 "Cell surface interactions at the vascular wall, Drosophila melanogaster" is_a: GO:0002376 ! immune system process is_a: GO:0016477 ! cell migration property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050906 name: detection of stimulus involved in sensory perception namespace: biological_process def: "The series of events involved in sensory perception in which a sensory stimulus is received by a cell and converted into a molecular signal." [GOC:ai, GOC:dph] synonym: "sensory detection of stimulus" EXACT [] synonym: "sensory perception, sensory transduction of stimulus" EXACT [] synonym: "sensory perception, stimulus detection" EXACT [] synonym: "sensory transduction" EXACT [] xref: Wikipedia:Transduction_(physiology) is_a: GO:0051606 ! detection of stimulus relationship: part_of GO:0007600 ! sensory perception property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050907 name: detection of chemical stimulus involved in sensory perception namespace: biological_process def: "The series of events in which a sensory chemical stimulus is received by a cell and converted into a molecular signal." [GOC:ai] synonym: "sensory detection of chemical stimulus" EXACT [] synonym: "sensory detection of chemical stimulus during sensory perception" EXACT [] synonym: "sensory perception, sensory detection of chemical stimulus" EXACT [] synonym: "sensory perception, sensory transduction of chemical stimulus" EXACT [] synonym: "sensory transduction of chemical stimulus" EXACT [] synonym: "sensory transduction of chemical stimulus during sensory perception" EXACT [] is_a: GO:0009593 ! detection of chemical stimulus is_a: GO:0050906 ! detection of stimulus involved in sensory perception relationship: part_of GO:0007600 ! sensory perception relationship: part_of GO:0007606 ! sensory perception of chemical stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050908 name: detection of light stimulus involved in visual perception namespace: biological_process def: "The series of events involved in visual perception in which a sensory light stimulus is received by a cell and converted into a molecular signal." [GOC:ai] synonym: "sensory detection of light during visual perception" EXACT [] synonym: "sensory detection of light stimulus during visual perception" EXACT [] synonym: "sensory transduction of light during visual perception" EXACT [] synonym: "sensory transduction of light stimulus during visual perception" EXACT [] synonym: "visual perception, detection of light stimulus" EXACT [] synonym: "visual perception, sensory transduction during perception of light" EXACT [] synonym: "visual perception, sensory transduction of light stimulus" EXACT [] is_a: GO:0009584 ! detection of visible light is_a: GO:0050962 ! detection of light stimulus involved in sensory perception relationship: part_of GO:0007601 ! visual perception property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050909 name: sensory perception of taste namespace: biological_process def: "The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process." [GOC:ai, http://www.onelook.com/] synonym: "gustation" EXACT [] synonym: "sense of taste" EXACT [] synonym: "taste" EXACT [] synonym: "taste perception" EXACT [] xref: Wikipedia:Taste is_a: GO:0007606 ! sensory perception of chemical stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050910 name: detection of mechanical stimulus involved in sensory perception of sound namespace: biological_process alt_id: GO:0009592 alt_id: GO:0055128 def: "The series of events involved in the perception of sound vibration. The vibration is received by a cell and converted into a molecular signal." [GOC:ai] synonym: "detection of sound" EXACT [] synonym: "hearing, sensory transduction of sound" EXACT [] synonym: "perception of sound, detection of mechanical stimulus" EXACT [] synonym: "perception of sound, sensory detection of mechanical stimulus" EXACT [] synonym: "perception of sound, sensory transduction of mechanical stimulus" EXACT [] synonym: "sensory detection of mechanical stimulus during perception of sound" EXACT [] synonym: "sensory transduction of mechanical stimulus during perception of sound" EXACT [] synonym: "sensory transduction of sound" EXACT [] is_a: GO:0050877 ! neurological system process is_a: GO:0050974 ! detection of mechanical stimulus involved in sensory perception relationship: part_of GO:0007605 ! sensory perception of sound property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050911 name: detection of chemical stimulus involved in sensory perception of smell namespace: biological_process def: "The series of events involved in the perception of smell in which an olfactory chemical stimulus is received by a cell and converted into a molecular signal." [GOC:ai] synonym: "perception of smell, detection of chemical stimulus" EXACT [] synonym: "perception of smell, sensory detection of chemical stimulus" EXACT [] synonym: "perception of smell, sensory transduction of chemical stimulus" EXACT [] synonym: "sensory detection of chemical stimulus during perception of smell" EXACT [] synonym: "sensory detection of scent" EXACT [] synonym: "sensory detection of smell" EXACT [] synonym: "sensory transduction of chemical stimulus during perception of smell" EXACT [] synonym: "sensory transduction of scent" EXACT [] synonym: "sensory transduction of smell" EXACT [] is_a: GO:0050907 ! detection of chemical stimulus involved in sensory perception relationship: part_of GO:0007608 ! sensory perception of smell property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050912 name: detection of chemical stimulus involved in sensory perception of taste namespace: biological_process def: "The series of events involved in the perception of taste in which a gustatory chemical stimulus is received by a cell and converted into a molecular signal." [GOC:ai] synonym: "perception of taste, detection of chemical stimulus" EXACT [] synonym: "perception of taste, sensory detection of chemical stimulus" EXACT [] synonym: "perception of taste, sensory transduction of chemical stimulus" EXACT [] synonym: "sensory detection of chemical stimulus during perception of taste" EXACT [] synonym: "sensory detection of taste" EXACT [] synonym: "sensory transduction of chemical stimulus during perception of taste" EXACT [] synonym: "sensory transduction of taste" EXACT [] synonym: "taste perception" BROAD [] is_a: GO:0050907 ! detection of chemical stimulus involved in sensory perception relationship: part_of GO:0050909 ! sensory perception of taste property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050920 name: regulation of chemotaxis namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient." [GOC:ai] subset: gosubset_prok is_a: GO:0032101 ! regulation of response to external stimulus is_a: GO:0040012 ! regulation of locomotion is_a: GO:0050795 ! regulation of behavior relationship: regulates GO:0006935 ! chemotaxis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050921 name: positive regulation of chemotaxis namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient." [GOC:ai] subset: gosubset_prok synonym: "activation of chemotaxis" NARROW [] synonym: "stimulation of chemotaxis" NARROW [] synonym: "up regulation of chemotaxis" EXACT [] synonym: "up-regulation of chemotaxis" EXACT [] synonym: "upregulation of chemotaxis" EXACT [] is_a: GO:0032103 ! positive regulation of response to external stimulus is_a: GO:0040017 ! positive regulation of locomotion is_a: GO:0048520 ! positive regulation of behavior is_a: GO:0050920 ! regulation of chemotaxis relationship: positively_regulates GO:0006935 ! chemotaxis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050951 name: sensory perception of temperature stimulus namespace: biological_process def: "The series of events required for an organism to receive a sensory temperature stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." [GOC:ai] synonym: "sensory perception of thermal stimulus" EXACT [] is_a: GO:0007600 ! sensory perception property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050953 name: sensory perception of light stimulus namespace: biological_process def: "The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." [GOC:ai] is_a: GO:0007600 ! sensory perception property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050954 name: sensory perception of mechanical stimulus namespace: biological_process def: "The series of events required for an organism to receive a sensory mechanical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." [GOC:ai] synonym: "chemi-mechanical coupling" RELATED [] synonym: "mechanosensory perception" EXACT [] synonym: "perception of mechanical stimulus" EXACT [] is_a: GO:0007600 ! sensory perception property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050955 name: thermoception namespace: biological_process def: "The series of events required for an organism to receive a temperature stimulus, convert it to a molecular signal, and recognize and characterize the signal. Thermoception in larger animals is mainly done in the skin; mammals have at least two types of sensor, for detecting heat (temperatures above body temperature) and cold (temperatures below body temperature)." [GOC:ai, Wikipedia:Thermoception] synonym: "thermoreception" EXACT [] xref: Wikipedia:Thermoception is_a: GO:0050951 ! sensory perception of temperature stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050960 name: detection of temperature stimulus involved in thermoception namespace: biological_process def: "The series of events v thermoception in which a sensory temperature stimulus is received by a cell and converted into a molecular signal." [GOC:ai] synonym: "sensory detection of heat stimulus during thermoception" NARROW [] synonym: "sensory detection of temperature stimulus during thermoception" EXACT [] synonym: "sensory detection of thermal stimulus during thermoception" EXACT [] synonym: "sensory transduction of heat stimulus during thermoception" NARROW [] synonym: "sensory transduction of temperature stimulus during thermoception" EXACT [] synonym: "sensory transduction of thermal stimulus during thermoception" EXACT [] synonym: "thermoception, sensory detection of heat stimulus" NARROW [] synonym: "thermoception, sensory detection of temperature stimulus" EXACT [] synonym: "thermoception, sensory detection of thermal stimulus" EXACT [] synonym: "thermoception, sensory transduction of heat stimulus" NARROW [] synonym: "thermoception, sensory transduction of temperature stimulus" EXACT [] synonym: "thermoception, sensory transduction of thermal stimulus" EXACT [] is_a: GO:0050961 ! detection of temperature stimulus involved in sensory perception relationship: part_of GO:0050955 ! thermoception property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050961 name: detection of temperature stimulus involved in sensory perception namespace: biological_process def: "The series of events in which a sensory temperature stimulus is received by a cell and converted into a molecular signal." [GOC:ai] synonym: "sensory detection of heat stimulus during sensory perception" NARROW [] synonym: "sensory detection of temperature stimulus" EXACT [] synonym: "sensory detection of temperature stimulus during sensory perception" EXACT [] synonym: "sensory detection of thermal stimulus during sensory perception" EXACT [] synonym: "sensory perception, sensory detection of heat stimulus" NARROW [] synonym: "sensory perception, sensory detection of temperature stimulus" EXACT [] synonym: "sensory perception, sensory detection of thermal stimulus" EXACT [] synonym: "sensory perception, sensory transduction of heat stimulus" NARROW [] synonym: "sensory perception, sensory transduction of temperature stimulus" EXACT [] synonym: "sensory perception, sensory transduction of thermal stimulus" EXACT [] synonym: "sensory transduction of heat stimulus during sensory perception" NARROW [] synonym: "sensory transduction of temperature stimulus" EXACT [] synonym: "sensory transduction of temperature stimulus during sensory perception" EXACT [] synonym: "sensory transduction of thermal stimulus during sensory perception" EXACT [] is_a: GO:0016048 ! detection of temperature stimulus is_a: GO:0050906 ! detection of stimulus involved in sensory perception relationship: part_of GO:0007600 ! sensory perception relationship: part_of GO:0050951 ! sensory perception of temperature stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050962 name: detection of light stimulus involved in sensory perception namespace: biological_process def: "The series of events in which a sensory light stimulus is received by a cell and converted into a molecular signal." [GOC:ai] synonym: "sensory detection of light stimulus" EXACT [] synonym: "sensory detection of light stimulus during sensory perception" EXACT [] synonym: "sensory perception, sensory detection of light stimulus" EXACT [] synonym: "sensory perception, sensory transduction of light stimulus" EXACT [] synonym: "sensory transduction of light stimulus" EXACT [] synonym: "sensory transduction of light stimulus during sensory perception" EXACT [] is_a: GO:0009583 ! detection of light stimulus is_a: GO:0050906 ! detection of stimulus involved in sensory perception relationship: part_of GO:0007600 ! sensory perception relationship: part_of GO:0050953 ! sensory perception of light stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050974 name: detection of mechanical stimulus involved in sensory perception namespace: biological_process def: "The series of events in which a sensory mechanical stimulus is received by a cell and converted into a molecular signal." [GOC:ai] synonym: "sensory detection of mechanical stimulus" EXACT [] synonym: "sensory detection of mechanical stimulus during sensory perception" EXACT [] synonym: "sensory perception, sensory detection of mechanical stimulus" EXACT [] synonym: "sensory perception, sensory transduction of mechanical stimulus" EXACT [] synonym: "sensory transduction of mechanical stimulus" EXACT [] synonym: "sensory transduction of mechanical stimulus during sensory perception" EXACT [] is_a: GO:0050906 ! detection of stimulus involved in sensory perception is_a: GO:0050982 ! detection of mechanical stimulus relationship: part_of GO:0007600 ! sensory perception relationship: part_of GO:0050954 ! sensory perception of mechanical stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050975 name: sensory perception of touch namespace: biological_process def: "The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach)." [GOC:ai] synonym: "perception of touch" EXACT [] synonym: "tactile sense" EXACT [] synonym: "taction" EXACT [] synonym: "tactition" EXACT [] xref: Wikipedia:Touch is_a: GO:0050954 ! sensory perception of mechanical stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050976 name: detection of mechanical stimulus involved in sensory perception of touch namespace: biological_process def: "The series of events involved in the perception of touch in which a sensory mechanical stimulus is received by a cell and converted into a molecular signal." [GOC:ai] synonym: "perception of touch, detection of mechanical stimulus" EXACT [] synonym: "perception of touch, sensory detection of mechanical stimulus" EXACT [] synonym: "perception of touch, sensory transduction of mechanical stimulus" EXACT [] synonym: "sensory detection of mechanical stimulus during perception of touch" EXACT [] synonym: "sensory transduction of mechanical stimulus during perception of touch" EXACT [] synonym: "tactition, sensory detection of mechanical stimulus" EXACT [] is_a: GO:0050974 ! detection of mechanical stimulus involved in sensory perception relationship: part_of GO:0050975 ! sensory perception of touch property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050982 name: detection of mechanical stimulus namespace: biological_process def: "The series of events by which a mechanical stimulus is received by a cell and converted into a molecular signal." [GOC:ai] is_a: GO:0009581 ! detection of external stimulus is_a: GO:0009582 ! detection of abiotic stimulus is_a: GO:0009612 ! response to mechanical stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051023 name: regulation of immunoglobulin secretion namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the regulated release of immunoglobulins from a cell or group of cells." [GOC:ai] synonym: "regulation of antibody secretion" EXACT [] is_a: GO:0002637 ! regulation of immunoglobulin production is_a: GO:0050708 ! regulation of protein secretion relationship: regulates GO:0048305 ! immunoglobulin secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051024 name: positive regulation of immunoglobulin secretion namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the regulated release of immunoglobulins from a cell or group of cells." [GOC:ai] synonym: "activation of immunoglobulin secretion" NARROW [] synonym: "positive regulation of antibody secretion" EXACT [] synonym: "stimulation of immunoglobulin secretion" NARROW [] synonym: "up regulation of immunoglobulin secretion" EXACT [] synonym: "up-regulation of immunoglobulin secretion" EXACT [] synonym: "upregulation of immunoglobulin secretion" EXACT [] is_a: GO:0050714 ! positive regulation of protein secretion is_a: GO:0051023 ! regulation of immunoglobulin secretion relationship: positively_regulates GO:0048305 ! immunoglobulin secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051046 name: regulation of secretion namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or group of cells." [GOC:ai] subset: gosubset_prok is_a: GO:0051049 ! regulation of transport relationship: regulates GO:0046903 ! secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051047 name: positive regulation of secretion namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or group of cells." [GOC:ai] synonym: "activation of secretion" NARROW [] synonym: "stimulation of secretion" NARROW [] synonym: "up regulation of secretion" EXACT [] synonym: "up-regulation of secretion" EXACT [] synonym: "upregulation of secretion" EXACT [] is_a: GO:0051046 ! regulation of secretion is_a: GO:0051050 ! positive regulation of transport relationship: positively_regulates GO:0046903 ! secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051049 name: regulation of transport namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_yeast subset: gosubset_prok is_a: GO:0032879 ! regulation of localization relationship: regulates GO:0006810 ! transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051050 name: positive regulation of transport namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: gosubset_prok synonym: "activation of transport" NARROW [] synonym: "stimulation of transport" NARROW [] synonym: "up regulation of transport" EXACT [] synonym: "up-regulation of transport" EXACT [] synonym: "upregulation of transport" EXACT [] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0051049 ! regulation of transport relationship: positively_regulates GO:0006810 ! transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051052 name: regulation of DNA metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA." [GOC:ai] subset: goslim_yeast subset: gosubset_prok synonym: "regulation of DNA metabolism" EXACT [] is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process is_a: GO:0060255 ! regulation of macromolecule metabolic process relationship: regulates GO:0006259 ! DNA metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051054 name: positive regulation of DNA metabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA." [GOC:ai] subset: gosubset_prok synonym: "activation of DNA metabolic process" NARROW [] synonym: "positive regulation of DNA metabolism" EXACT [] synonym: "stimulation of DNA metabolic process" NARROW [] synonym: "up regulation of DNA metabolic process" EXACT [] synonym: "up-regulation of DNA metabolic process" EXACT [] synonym: "upregulation of DNA metabolic process" EXACT [] is_a: GO:0010604 ! positive regulation of macromolecule metabolic process is_a: GO:0045935 ! positive regulation of nucleobase-containing compound metabolic process is_a: GO:0051052 ! regulation of DNA metabolic process relationship: positively_regulates GO:0006259 ! DNA metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051093 name: negative regulation of developmental process namespace: biological_process def: "Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:ai] subset: gosubset_prok synonym: "down regulation of developmental process" EXACT [] synonym: "down-regulation of developmental process" EXACT [] synonym: "downregulation of developmental process" EXACT [] synonym: "inhibition of developmental process" NARROW [] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0050793 ! regulation of developmental process relationship: negatively_regulates GO:0032502 ! developmental process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051094 name: positive regulation of developmental process namespace: biological_process def: "Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:ai] subset: gosubset_prok synonym: "activation of developmental process" NARROW [] synonym: "stimulation of developmental process" NARROW [] synonym: "up regulation of developmental process" EXACT [] synonym: "up-regulation of developmental process" EXACT [] synonym: "upregulation of developmental process" EXACT [] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0050793 ! regulation of developmental process relationship: positively_regulates GO:0032502 ! developmental process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051132 name: NK T cell activation namespace: biological_process def: "The change in morphology and behavior of a mature or immature natural killer T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." [ISBN:0781735149, PMID:12154375, PMID:9133426] comment: Note that NK T cells are a distinct lineage of T cells expressing natural killer cell markers and having T cell receptors characterized by the usage of a restricted repetoire of variable region gene segments. synonym: "natural killer T cell activation" EXACT [] synonym: "natural T cell activation" EXACT [] synonym: "NK T lymphocyte activation" EXACT [] synonym: "NK T-cell activation" EXACT [] synonym: "NK T-lymphocyte activation" EXACT [] synonym: "NKT cell activation" EXACT [] synonym: "NT cell activation" EXACT [] is_a: GO:0046631 ! alpha-beta T cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051146 name: striated muscle cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized features of a striated muscle cell; striated muscle fibers are divided by transverse bands into striations, and cardiac and voluntary muscle are types of striated muscle." [CL:0000737, GOC:ai] synonym: "voluntary muscle cell differentiation" NARROW [] is_a: GO:0042692 ! muscle cell differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051171 name: regulation of nitrogen compound metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." [GOC:ai, GOC:tb] subset: gosubset_prok synonym: "regulation of nitrogen metabolic process" EXACT [GOC:tb] synonym: "regulation of nitrogen metabolism" EXACT [] is_a: GO:0019222 ! regulation of metabolic process relationship: regulates GO:0006807 ! nitrogen compound metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051173 name: positive regulation of nitrogen compound metabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." [GOC:ai, GOC:tb] synonym: "activation of nitrogen metabolic process" NARROW [] synonym: "positive regulation of nitrogen metabolic process" EXACT [GOC:tb] synonym: "positive regulation of nitrogen metabolism" EXACT [] synonym: "stimulation of nitrogen metabolic process" NARROW [] synonym: "up regulation of nitrogen metabolic process" EXACT [] synonym: "up-regulation of nitrogen metabolic process" EXACT [] synonym: "upregulation of nitrogen metabolic process" EXACT [] is_a: GO:0009893 ! positive regulation of metabolic process is_a: GO:0051171 ! regulation of nitrogen compound metabolic process relationship: positively_regulates GO:0006807 ! nitrogen compound metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051179 name: localization namespace: biological_process def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in a specific location." [GOC:ai] subset: goslim_pir subset: gosubset_prok synonym: "establishment and maintenance of cellular component location" NARROW [] synonym: "establishment and maintenance of localization" EXACT [] synonym: "establishment and maintenance of position" EXACT [] synonym: "establishment and maintenance of substance location" NARROW [] synonym: "establishment and maintenance of substrate location" NARROW [] synonym: "localisation" EXACT [GOC:mah] is_a: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051216 name: cartilage development namespace: biological_process def: "The process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate." [http://www.onelook.com] synonym: "cartilage biogenesis" EXACT [] synonym: "cartilage biosynthesis" EXACT [] synonym: "cartilage formation" EXACT [] synonym: "chondrogenesis" EXACT [] xref: Wikipedia:Chondrogenesis is_a: GO:0061448 ! connective tissue development relationship: part_of GO:0001501 ! skeletal system development relationship: part_of GO:0048513 ! organ development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051222 name: positive regulation of protein transport namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] synonym: "activation of protein transport" NARROW [] synonym: "stimulation of protein transport" NARROW [] synonym: "up regulation of protein transport" EXACT [] synonym: "up-regulation of protein transport" EXACT [] synonym: "upregulation of protein transport" EXACT [] is_a: GO:0051050 ! positive regulation of transport is_a: GO:0051223 ! regulation of protein transport relationship: positively_regulates GO:0015031 ! protein transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051223 name: regulation of protein transport namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] is_a: GO:0051049 ! regulation of transport is_a: GO:0070201 ! regulation of establishment of protein localization relationship: regulates GO:0015031 ! protein transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051234 name: establishment of localization namespace: biological_process def: "The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location." [GOC:ai] subset: goslim_pir subset: gosubset_prok synonym: "establishment of localisation" EXACT [GOC:mah] is_a: GO:0008150 ! biological_process relationship: part_of GO:0051179 ! localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051239 name: regulation of multicellular organismal process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai, GOC:dph, GOC:tb] is_a: GO:0050789 ! regulation of biological process relationship: regulates GO:0032501 ! multicellular organismal process relationship: regulates GO:0044707 ! single-multicellular organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051241 name: negative regulation of multicellular organismal process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai] synonym: "down regulation of multicellular organismal process" EXACT [] synonym: "down-regulation of multicellular organismal process" EXACT [] synonym: "downregulation of multicellular organismal process" EXACT [] synonym: "inhibition of multicellular organismal process" NARROW [] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0051239 ! regulation of multicellular organismal process relationship: negatively_regulates GO:0032501 ! multicellular organismal process relationship: negatively_regulates GO:0044707 ! single-multicellular organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051249 name: regulation of lymphocyte activation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of lymphocyte activation." [GOC:ai] is_a: GO:0002694 ! regulation of leukocyte activation relationship: regulates GO:0046649 ! lymphocyte activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051250 name: negative regulation of lymphocyte activation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte activation." [GOC:ai] synonym: "down regulation of lymphocyte activation" EXACT [] synonym: "down-regulation of lymphocyte activation" EXACT [] synonym: "downregulation of lymphocyte activation" EXACT [] synonym: "inhibition of lymphocyte activation" NARROW [] is_a: GO:0002695 ! negative regulation of leukocyte activation is_a: GO:0051249 ! regulation of lymphocyte activation relationship: negatively_regulates GO:0046649 ! lymphocyte activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051251 name: positive regulation of lymphocyte activation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of lymphocyte activation." [GOC:ai] synonym: "activation of lymphocyte activation" NARROW [] synonym: "stimulation of lymphocyte activation" NARROW [] synonym: "up regulation of lymphocyte activation" EXACT [] synonym: "up-regulation of lymphocyte activation" EXACT [] synonym: "upregulation of lymphocyte activation" EXACT [] is_a: GO:0002696 ! positive regulation of leukocyte activation is_a: GO:0051249 ! regulation of lymphocyte activation relationship: positively_regulates GO:0046649 ! lymphocyte activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051270 name: regulation of cellular component movement namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the movement of a cellular component." [GOC:ai, GOC:dph, GOC:jl] subset: gosubset_prok synonym: "regulation of cell movement" RELATED [] synonym: "regulation of cellular component motion" EXACT [GOC:mah] is_a: GO:0032879 ! regulation of localization is_a: GO:0050794 ! regulation of cellular process relationship: regulates GO:0006928 ! cellular component movement property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051272 name: positive regulation of cellular component movement namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the movement of a cellular component." [GOC:ai, GOC:dph, GOC:jl] subset: gosubset_prok synonym: "activation of cell motility" NARROW [] synonym: "positive regulation of cell movement" RELATED [] synonym: "positive regulation of cellular component motion" EXACT [GOC:mah] synonym: "stimulation of cell motility" NARROW [] synonym: "up regulation of cell motility" EXACT [] synonym: "up-regulation of cell motility" EXACT [] synonym: "upregulation of cell motility" EXACT [] is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0051270 ! regulation of cellular component movement relationship: positively_regulates GO:0006928 ! cellular component movement property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051276 name: chromosome organization namespace: biological_process alt_id: GO:0007001 alt_id: GO:0051277 def: "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_generic subset: goslim_pir subset: goslim_pombe subset: gosubset_prok synonym: "chromosome organisation" EXACT [] synonym: "chromosome organization and biogenesis" RELATED [GOC:mah] synonym: "maintenance of genome integrity" RELATED [] synonym: "nuclear genome maintenance" RELATED [] is_a: GO:0006996 ! organelle organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051301 name: cell division namespace: biological_process def: "The process resulting in the physical partitioning and separation of a cell into daughter cells." [GOC:go_curators] comment: Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis excludes nuclear division; in prokaryotes, there is little difference between cytokinesis and cell division. Note that there is no relationship between this term and 'nuclear division ; GO:0000280' because cell division can take place without nuclear division (as in prokaryotes) and vice versa (as in syncytium formation by mitosis without cytokinesis. subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: gosubset_prok xref: Wikipedia:Cell_division is_a: GO:0044763 ! single-organism cellular process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051321 name: meiotic cell cycle namespace: biological_process def: "Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell." [GOC:ai] subset: goslim_yeast is_a: GO:0007049 ! cell cycle is_a: GO:0048610 ! cellular process involved in reproduction property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051327 name: M phase of meiotic cell cycle namespace: biological_process def: "M phase occurring as part of the meiotic cell cycle. M phase is the part of the cell cycle during which nuclear division takes place. A meiotic cell cycle is one in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell." [GOC:ai, GOC:dph, GOC:mah] is_a: GO:0000279 ! M phase is_a: GO:0048610 ! cellular process involved in reproduction relationship: part_of GO:0051321 ! meiotic cell cycle property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051458 name: corticotropin secretion namespace: biological_process def: "The regulated release of corticotropin, by a cell or group of cells. Corticotropin hormone is a polypeptide hormone synthesized and secreted from corticotropes in the anterior lobe of the pituitary gland in response to corticotropin-releasing hormone (CRH) released by the hypothalamus." [CHEBI:3892, GOC:cjm, PMID:11027914] synonym: "ACTH secretion" EXACT [] synonym: "adrenocorticotropic hormone secretion" EXACT [] synonym: "adrenocorticotropin secretion" RELATED [GOC:dph, GOC:tb] synonym: "adrenotropic hormone secretion" EXACT [] synonym: "adrenotropin secretion" EXACT [] synonym: "corticotropic hormone secretion" EXACT [] is_a: GO:0030072 ! peptide hormone secretion is_a: GO:0060986 ! endocrine hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051606 name: detection of stimulus namespace: biological_process def: "The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal." [GOC:add, GOC:ai, GOC:dph, GOC:mah] subset: goslim_pir subset: gosubset_prok synonym: "perception of stimulus" RELATED [] synonym: "stimulus detection" EXACT [] synonym: "stimulus sensing" RELATED [] is_a: GO:0050896 ! response to stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051641 name: cellular localization namespace: biological_process def: "A localization process that takes place at the cellular level; as a result of a cellular localization process, a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within or in the membrane of a cell." [GOC:ai, GOC:mah] subset: goslim_pir subset: gosubset_prok synonym: "cellular localisation" EXACT [GOC:mah] synonym: "establishment and maintenance of cellular localization" EXACT [] synonym: "establishment and maintenance of localization in cell or cell membrane" EXACT [] synonym: "intracellular localization" NARROW [] synonym: "localization within cell" NARROW [] is_a: GO:0044763 ! single-organism cellular process is_a: GO:0051179 ! localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051649 name: establishment of localization in cell namespace: biological_process def: "The directed movement of a substance or cellular entity, such as a protein complex or organelle, to a specific location within, or in the membrane of, a cell." [GOC:ai, GOC:dph, GOC:tb] subset: gosubset_prok synonym: "establishment of cellular localization" RELATED [GOC:dph, GOC:tb] synonym: "establishment of intracellular localization" NARROW [] synonym: "establishment of localisation in cell" EXACT [GOC:mah] synonym: "establishment of localization within cell" NARROW [] synonym: "positioning within cell" NARROW [] is_a: GO:0051234 ! establishment of localization relationship: part_of GO:0051641 ! cellular localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051674 name: localization of cell namespace: biological_process def: "Any process in which a cell is transported to, and/or maintained in, a specific location." [GOC:ai] subset: gosubset_prok synonym: "cell localization" EXACT [] synonym: "establishment and maintenance of cell localization" EXACT [] synonym: "establishment and maintenance of localization of cell" EXACT [] synonym: "localisation of cell" EXACT [GOC:mah] is_a: GO:0051179 ! localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051704 name: multi-organism process namespace: biological_process alt_id: GO:0051706 def: "A biological process which involves another organism of the same or different species." [GOC:jl] subset: goslim_pir subset: gosubset_prok synonym: "interaction between organisms" EXACT [] synonym: "physiological interaction between organisms" EXACT [] synonym: "physiological interaction with other organism" EXACT [] is_a: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051707 name: response to other organism namespace: biological_process alt_id: GO:0009613 alt_id: GO:0042828 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism." [GOC:ai] subset: gosubset_prok is_a: GO:0009607 ! response to biotic stimulus is_a: GO:0051704 ! multi-organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051716 name: cellular response to stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell." [GOC:bf, GOC:jl] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Annotations to this term will be removed during annotation QC. subset: gosubset_prok subset: high_level_annotation_qc is_a: GO:0044763 ! single-organism cellular process is_a: GO:0050896 ! response to stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051768 name: nitric-oxide synthase 2 biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of nitric-oxide synthase 2, an enzyme which catalyzes the reaction L-arginine + n NADPH + n H+ + m O2 = citrulline + nitric oxide + n NADP+." [GOC:ai] synonym: "nitric-oxide synthase (type 2) biosynthesis" EXACT [] synonym: "nitric-oxide synthase (type 2) biosynthetic process" EXACT [] synonym: "nitric-oxide synthase (type II) biosynthesis" EXACT [] synonym: "nitric-oxide synthase (type II) biosynthetic process" EXACT [] synonym: "NOS2 synthase biosynthesis" EXACT [] synonym: "NOS2 synthase biosynthetic process" EXACT [] is_a: GO:0009059 ! macromolecule biosynthetic process [Term] id: GO:0051861 name: glycolipid binding namespace: molecular_function def: "Interacting selectively and non-covalently with a glycolipid, any compound containing one or more monosaccharide residues bound by a glycosidic linkage to a hydrophobic group such as an acylglycerol, a sphingoid, a ceramide (N-acylsphingoid) or a prenyl phosphate." [http://www.chem.qmul.ac.uk/iupac/misc/glylp.html#2.1] is_a: GO:0008289 ! lipid binding property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051937 name: catecholamine transport namespace: biological_process def: "The directed movement of catecholamines, a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine." [GOC:ai, ISBN:0198506732] subset: gosubset_prok is_a: GO:0015844 ! monoamine transport is_a: GO:0015850 ! organic hydroxy compound transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0055007 name: cardiac muscle cell differentiation namespace: biological_process def: "The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction." [GOC:devbiol, GOC:mtg_heart] synonym: "cardiomyocyte differentiation" EXACT [] synonym: "heart muscle cell differentiation" RELATED [] is_a: GO:0035051 ! cardiac cell differentiation is_a: GO:0051146 ! striated muscle cell differentiation relationship: part_of GO:0048738 ! cardiac muscle tissue development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0060054 name: positive regulation of epithelial cell proliferation involved in wound healing namespace: biological_process def: "Any process that activates or increases the rate or extent of epithelial cell proliferation, contributing to the restoration of integrity to a damaged tissue following an injury." [GOC:dph] is_a: GO:0050679 ! positive regulation of epithelial cell proliferation relationship: part_of GO:0042060 ! wound healing property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0060089 name: molecular transducer activity namespace: molecular_function def: "The molecular function that accepts an input of one form and creates an output of a different form." [GOC:mtg_MIT_16mar07] subset: goslim_pir subset: gosubset_prok is_a: GO:0003674 ! molecular_function property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0060249 name: anatomical structure homeostasis namespace: biological_process def: "A homeostatic process involved in the maintenance of an internal steady state within a defined anatomical structure of an organism, including control of cellular proliferation and death and control of metabolic function. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:dph] synonym: "anatomical structure maintenance" EXACT [GOC:dph] is_a: GO:0042592 ! homeostatic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0060255 name: regulation of macromolecule metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] subset: gosubset_prok is_a: GO:0019222 ! regulation of metabolic process relationship: regulates GO:0043170 ! macromolecule metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0060326 name: cell chemotaxis namespace: biological_process def: "The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." [GOC:dph] is_a: GO:0006935 ! chemotaxis is_a: GO:0016477 ! cell migration is_a: GO:0070887 ! cellular response to chemical stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0060341 name: regulation of cellular localization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell." [GOC:dph, GOC:tb] synonym: "regulation of cellular localisation" EXACT [GOC:mah] is_a: GO:0032879 ! regulation of localization is_a: GO:0050794 ! regulation of cellular process relationship: regulates GO:0051641 ! cellular localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0060374 name: mast cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation." [GOC:dph, GOC:tb] is_a: GO:0002573 ! myeloid leukocyte differentiation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0060429 name: epithelium development namespace: biological_process def: "The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure." [GOC:dph, GOC:mtg_lung] is_a: GO:0009888 ! tissue development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0060537 name: muscle tissue development namespace: biological_process def: "The progression of muscle tissue over time, from its initial formation to its mature state. Muscle tissue is a contractile tissue made up of actin and myosin fibers." [GOC:dph] is_a: GO:0009888 ! tissue development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0060591 name: chondroblast differentiation namespace: biological_process def: "The process in which a mesenchymal cell, acquires specialized structural and/or functional features of a chondroblast. Differentiation includes the processes involved in commitment of a cell to a chondroblast fate. A chondroblast is a precursor cell to chondrocytes." [GOC:dph] synonym: "chondrocyte progenitor cell differentiation" RELATED [GOC:dph] is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0051216 ! cartilage development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0060986 name: endocrine hormone secretion namespace: biological_process def: "The regulated release of a hormone into the circulatory system." [GOC:dph] is_a: GO:0046879 ! hormone secretion relationship: part_of GO:0050886 ! endocrine process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0061061 name: muscle structure development namespace: biological_process def: "The progression of a muscle structure over time, from its formation to its mature state. Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms." [GOC:dph] is_a: GO:0048856 ! anatomical structure development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0061448 name: connective tissue development namespace: biological_process def: "The progression of a connective tissue over time, from its formation to the mature structure." [GOC:BHF] is_a: GO:0009888 ! tissue development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0061458 name: reproductive system development namespace: biological_process def: "The progression of the reproductive system over time from its formation to the mature structure. The reproductive system consists of the organs that function in reproduction." [GOC:dph] is_a: GO:0048731 ! system development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0065007 name: biological regulation namespace: biological_process def: "Any process that modulates a measurable attribute of any biological process, quality or function." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw] subset: goslim_pir subset: gosubset_prok synonym: "regulation" BROAD [] is_a: GO:0008150 ! biological_process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0065008 name: regulation of biological quality namespace: biological_process def: "Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw] subset: gosubset_prok synonym: "regulation of biological attribute" EXACT [] synonym: "regulation of biological characteristic" EXACT [] is_a: GO:0065007 ! biological regulation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070013 name: intracellular organelle lumen namespace: cellular_component def: "An organelle lumen that is part of an intracellular organelle." [GOC:mah] is_a: GO:0043233 ! organelle lumen is_a: GO:0044446 ! intracellular organelle part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070091 name: glucagon secretion namespace: biological_process def: "The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans)." [GOC:BHF, GOC:rl] is_a: GO:0030072 ! peptide hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070201 name: regulation of establishment of protein localization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location." [GOC:BHF, GOC:mah] synonym: "regulation of establishment of protein localisation" EXACT [GOC:mah] is_a: GO:0032880 ! regulation of protein localization relationship: regulates GO:0045184 ! establishment of protein localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070227 name: lymphocyte apoptotic process namespace: biological_process def: "Any apoptotic process in a lymphocyte, a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." [CL:0000542, GOC:add, GOC:mtg_apoptosis, ISBN:0781765196] comment: Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542). synonym: "lymphocyte apoptosis" NARROW [] is_a: GO:0071887 ! leukocyte apoptotic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070228 name: regulation of lymphocyte apoptotic process namespace: biological_process def: "Any process that modulates the occurrence or rate of lymphocyte death by apoptotic process." [GOC:add, GOC:mtg_apoptosis, ISBN:0781765196] comment: Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542). synonym: "regulation of lymphocyte apoptosis" NARROW [] is_a: GO:2000106 ! regulation of leukocyte apoptotic process relationship: regulates GO:0070227 ! lymphocyte apoptotic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070253 name: somatostatin secretion namespace: biological_process def: "The regulated release of somatostatin from secretory granules in the D cells of the pancreas." [GOC:mah] is_a: GO:0030072 ! peptide hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070254 name: mucus secretion namespace: biological_process def: "The regulated release of mucus by the mucosa. Mucus is a viscous slimy secretion consisting of mucins and various inorganic salts dissolved in water, with suspended epithelial cells and leukocytes. The mucosa, or mucous membrane, is the membrane covered with epithelium that lines the tubular organs of the body. Mucins are carbohydrate-rich glycoproteins that have a lubricating and protective function." [GOC:add, ISBN:068340007X, ISBN:0721662544] synonym: "mucus production" EXACT [GOC:add] is_a: GO:0007589 ! body fluid secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070278 name: extracellular matrix constituent secretion namespace: biological_process def: "The controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells." [GOC:mah] synonym: "ECM constituent secretion" EXACT [GOC:mah] synonym: "ECM secretion" EXACT [GOC:mah] is_a: GO:0032940 ! secretion by cell relationship: part_of GO:0030198 ! extracellular matrix organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070459 name: prolactin secretion namespace: biological_process def: "The regulated release of prolactin, a peptide hormone that stimulates lactation, from secretory granules in the anterior pituitary." [GOC:mah, ISBN:0198506732] is_a: GO:0030072 ! peptide hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070460 name: thyroid-stimulating hormone secretion namespace: biological_process def: "The regulated release of thyroid-stimulating hormone, a peptide hormone that stimulates the activity of the thyroid gland, from secretory granules in the anterior pituitary." [GOC:mah, ISBN:0198506732] synonym: "thyroid stimulating hormone secretion" EXACT [GOC:mah] synonym: "TSH secretion" EXACT [] is_a: GO:0030072 ! peptide hormone secretion property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070661 name: leukocyte proliferation namespace: biological_process def: "The expansion of a leukocyte population by cell division." [GOC:add] is_a: GO:0008283 ! cell proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070663 name: regulation of leukocyte proliferation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of leukocyte proliferation." [GOC:add, GOC:mah] is_a: GO:0042127 ! regulation of cell proliferation relationship: regulates GO:0070661 ! leukocyte proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070664 name: negative regulation of leukocyte proliferation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte proliferation." [GOC:add, GOC:mah] synonym: "down regulation of leukocyte proliferation" EXACT [GOC:mah] synonym: "down-regulation of leukocyte proliferation" EXACT [GOC:mah] synonym: "downregulation of leukocyte proliferation" EXACT [GOC:mah] synonym: "inhibition of leukocyte proliferation" NARROW [GOC:mah] is_a: GO:0008285 ! negative regulation of cell proliferation is_a: GO:0070663 ! regulation of leukocyte proliferation relationship: negatively_regulates GO:0070661 ! leukocyte proliferation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070727 name: cellular macromolecule localization namespace: biological_process def: "Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GOC:mah] synonym: "cellular macromolecule localisation" EXACT [GOC:mah] is_a: GO:0033036 ! macromolecule localization is_a: GO:0051641 ! cellular localization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070820 name: tertiary granule namespace: cellular_component def: "A secretory granule that contains cathepsin and gelatinase and is readily exocytosed upon cell activation; found primarily in mature neutrophil cells." [GOC:BHF, GOC:mah, GOC:rl, PMID:12070036] is_a: GO:0030141 ! secretory granule property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070887 name: cellular response to chemical stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus." [GOC:mah] is_a: GO:0042221 ! response to chemical stimulus is_a: GO:0051716 ! cellular response to stimulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070925 name: organelle assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] subset: goslim_yeast is_a: GO:0022607 ! cellular component assembly relationship: part_of GO:0006996 ! organelle organization property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070998 name: sensory perception of gravity namespace: biological_process def: "The series of events required for an organism to receive a gravitational stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." [GOC:mah] is_a: GO:0007600 ! sensory perception property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0070999 name: detection of mechanical stimulus involved in sensory perception of gravity namespace: biological_process def: "The series of events involved in the perception of gravity in which a sensory mechanical stimulus is received by a cell and converted into a molecular signal." [GOC:mah] is_a: GO:0009590 ! detection of gravity is_a: GO:0050974 ! detection of mechanical stimulus involved in sensory perception relationship: part_of GO:0070998 ! sensory perception of gravity property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071103 name: DNA conformation change namespace: biological_process def: "A cellular process that results in a change in the spatial configuration of a DNA molecule. A conformation change can bend DNA, or alter the, twist, writhe, or linking number of a DNA molecule." [GOC:mah] subset: gosubset_prok synonym: "DNA conformation modification" EXACT [GOC:mah] is_a: GO:0006259 ! DNA metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071695 name: anatomical structure maturation namespace: biological_process def: "A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure to attain its fully functional state." [GOC:mah] is_a: GO:0021700 ! developmental maturation relationship: part_of GO:0048856 ! anatomical structure development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071702 name: organic substance transport namespace: biological_process def: "The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon." [CHEBI:50860, GOC:mah] is_a: GO:0006810 ! transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071704 name: organic substance metabolic process namespace: biological_process def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [CHEBI:50860, GOC:mah] synonym: "organic molecular entity metabolic process" EXACT [] synonym: "organic molecular entity metabolism" EXACT [] synonym: "organic substance metabolism" EXACT [] is_a: GO:0044710 ! single-organism metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071705 name: nitrogen compound transport namespace: biological_process def: "The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [CHEBI:51143, GOC:mah] is_a: GO:0006810 ! transport property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071706 name: tumor necrosis factor superfamily cytokine production namespace: biological_process def: "The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add] synonym: "TNF superfamily production" RELATED [GOC:rv] synonym: "TNFSF cytokine production" EXACT [GOC:add] is_a: GO:0001816 ! cytokine production property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071707 name: immunoglobulin heavy chain V-D-J recombination namespace: biological_process def: "The process in which immunoglobulin heavy chain V, D, and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS)." [GOC:add, ISBN:0781735149] synonym: "immunoglobulin V(D)J joining" BROAD [GOC:add] synonym: "immunoglobulin V(D)J recombination" BROAD [GOC:add] synonym: "immunoglobulin V-D-J joining" EXACT [GOC:add] is_a: GO:0033152 ! immunoglobulin V(D)J recombination property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071708 name: immunoglobulin light chain V-J recombination namespace: biological_process def: "The process in which immunoglobulin light chain V and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS)." [GOC:add, ISBN:0781735149] synonym: "immunoglobulin V(D)J joining" BROAD [GOC:add] synonym: "immunoglobulin V(D)J recombination" BROAD [GOC:add] synonym: "immunoglobulin V-J joining" EXACT [GOC:add] is_a: GO:0033152 ! immunoglobulin V(D)J recombination property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071735 name: IgG immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196] comment: Note that an IgG immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Also, IgG isotypes vary by species. synonym: "IgG1" NARROW [GOC:add] synonym: "IgG2" NARROW [GOC:add] synonym: "IgG2a" NARROW [GOC:add] synonym: "IgG2b" NARROW [GOC:add] synonym: "IgG2c" NARROW [GOC:add] synonym: "IgG3" NARROW [GOC:add] synonym: "IgG4" NARROW [GOC:add] is_a: GO:0019814 ! immunoglobulin complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071736 name: IgG immunoglobulin complex, circulating namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196] comment: Note that an IgG immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Also, IgG isotypes vary by species. synonym: "IgG antibody" NARROW [GOC:add] synonym: "IgG1 antibody" NARROW [GOC:add] synonym: "IgG2 antibody" NARROW [GOC:add] synonym: "IgG2a antibody" NARROW [GOC:add] synonym: "IgG2b antibody" NARROW [GOC:add] synonym: "IgG2c antibody" NARROW [GOC:add] synonym: "IgG3 antibody" NARROW [GOC:add] synonym: "IgG4 antibody" NARROW [GOC:add] is_a: GO:0042571 ! immunoglobulin complex, circulating is_a: GO:0071735 ! IgG immunoglobulin complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071738 name: IgD immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgD immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:11282392] comment: Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available. is_a: GO:0019814 ! immunoglobulin complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071739 name: IgD immunoglobulin complex, circulating namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:11282392] comment: Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "IgD antibody" EXACT [GOC:add] is_a: GO:0042571 ! immunoglobulin complex, circulating is_a: GO:0071738 ! IgD immunoglobulin complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071742 name: IgE immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgE immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196] comment: Note that an IgE immunoglobulin complex has the function of antigen binding if a suitable antigen is available. is_a: GO:0019814 ! immunoglobulin complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071743 name: IgE immunoglobulin complex, circulating namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196] comment: Note that an IgE immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "IgE antibody" EXACT [GOC:add] is_a: GO:0042571 ! immunoglobulin complex, circulating is_a: GO:0071742 ! IgE immunoglobulin complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071745 name: IgA immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:16362985] comment: Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "IgA1 antibody" NARROW [GOC:add] synonym: "IgA2 antibody" NARROW [GOC:add] is_a: GO:0019814 ! immunoglobulin complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071746 name: IgA immunoglobulin complex, circulating namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of an IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, sometimes complexed with J chain or J chain and secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:16362985] comment: Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "IgA antibody" EXACT [GOC:add] synonym: "IgA1 antibody" NARROW [GOC:add] synonym: "IgA2 antibody" NARROW [GOC:add] is_a: GO:0042571 ! immunoglobulin complex, circulating is_a: GO:0071745 ! IgA immunoglobulin complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071753 name: IgM immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:20176268] comment: Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available. is_a: GO:0019814 ! immunoglobulin complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071754 name: IgM immunoglobulin complex, circulating namespace: cellular_component def: "A polymer of five or six IgM core units each composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds; the individual IgM core units are held together via disulfide bonds with a single J chain polypeptide acting as a bridge between two of the polymeric units. Circulating IgM is present in the extracellular space, in mucosal areas or other tissues, or in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:20176268] comment: Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "IgM antibody" EXACT [GOC:add] is_a: GO:0042571 ! immunoglobulin complex, circulating is_a: GO:0071753 ! IgM immunoglobulin complex property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071840 name: cellular component organization or biogenesis namespace: biological_process alt_id: GO:0071841 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] synonym: "cellular component organisation or biogenesis" EXACT [GOC:mah] synonym: "cellular component organisation or biogenesis at cellular level" EXACT [GOC:mah] synonym: "cellular component organization or biogenesis at cellular level" EXACT [] is_a: GO:0044763 ! single-organism cellular process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071887 name: leukocyte apoptotic process namespace: biological_process def: "Any apoptotic process in a leukocyte, an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." [CL:0000738, GOC:BHF, GOC:mah, GOC:mtg_apoptosis] comment: Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542). synonym: "leukocyte apoptosis" NARROW [] is_a: GO:0097285 ! cell-type specific apoptotic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071944 name: cell periphery namespace: cellular_component def: "The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures." [GOC:mah] is_a: GO:0044464 ! cell part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0071971 name: extracellular vesicular exosome assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." [GOC:mah, GOC:tfm, PMID:19442504] is_a: GO:0070925 ! organelle assembly property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0072358 name: cardiovascular system development namespace: biological_process def: "The process whose specific outcome is the progression of the cardiovascular system over time, from its formation to the mature structure. The cardiovascular system is the anatomical system that has as its parts the heart and blood vessels." [GOC:mah, UBERON:0004535] is_a: GO:0048731 ! system development relationship: part_of GO:0072359 ! circulatory system development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0072359 name: circulatory system development namespace: biological_process def: "The process whose specific outcome is the progression of the circulatory system over time, from its formation to the mature structure. The circulatory system is the organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis." [GOC:mah, UBERON:0001009] is_a: GO:0048731 ! system development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0072593 name: reactive oxygen species metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers." [CHEBI:26523, GOC:mah] synonym: "reactive oxygen species metabolism" EXACT [GOC:mah] synonym: "ROS metabolic process" EXACT [CHEBI:26523, GOC:mah] is_a: GO:0044237 ! cellular metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0080090 name: regulation of primary metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [PMID:19211694] is_a: GO:0019222 ! regulation of metabolic process relationship: regulates GO:0044238 ! primary metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0080134 name: regulation of response to stress namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:dhl] is_a: GO:0048583 ! regulation of response to stimulus relationship: regulates GO:0006950 ! response to stress property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0090022 name: regulation of neutrophil chemotaxis namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding." [GOC:dph, GOC:tb] is_a: GO:0002688 ! regulation of leukocyte chemotaxis relationship: regulates GO:0030593 ! neutrophil chemotaxis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0090023 name: positive regulation of neutrophil chemotaxis namespace: biological_process def: "Any process that increases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding." [GOC:dph, GOC:tb] is_a: GO:0002690 ! positive regulation of leukocyte chemotaxis is_a: GO:0090022 ! regulation of neutrophil chemotaxis relationship: positively_regulates GO:0030593 ! neutrophil chemotaxis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0090257 name: regulation of muscle system process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a muscle system process, a multicellular organismal process carried out by any of the organs or tissues in a muscle system." [GOC:dph, GOC:tb] is_a: GO:0044057 ! regulation of system process relationship: regulates GO:0003012 ! muscle system process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0090304 name: nucleic acid metabolic process namespace: biological_process def: "Any cellular metabolic process involving nucleic acids." [GOC:dph, GOC:tb] is_a: GO:0006139 ! nucleobase-containing compound metabolic process is_a: GO:0043170 ! macromolecule metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0097186 name: amelogenesis namespace: biological_process def: "The process whose specific outcome is the formation of tooth enamel, occurring in two stages: secretory stage and maturation stage." [GOC:cjm, GOC:sl, PMID:10206335, PMID:21196346] synonym: "enamel development" EXACT [] is_a: GO:0042475 ! odontogenesis of dentin-containing tooth property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0097194 name: execution phase of apoptosis namespace: biological_process def: "A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. The execution phase ends when the cell has died." [GOC:mtg_apoptosis] synonym: "apoptosis" NARROW [] synonym: "execution phase of apoptotic process" EXACT [] is_a: GO:0044763 ! single-organism cellular process relationship: part_of GO:0006915 ! apoptotic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0097285 name: cell-type specific apoptotic process namespace: biological_process def: "Any apoptotic process in a specific cell type." [GOC:mtg_apoptosis] comment: This term was created as a generic parent to group terms indicating occurrences of apoptotic process in specific cell types. The process of apoptosis may not vary, but the cell type does. Please do not annotate to this term, and refer instead to its more granular children, or to its parent GO:0006915 apoptotic process. synonym: "cell-type specific apoptosis" NARROW [] is_a: GO:0006915 ! apoptotic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:1901135 name: carbohydrate derivative metabolic process namespace: biological_process def: "The chemical reactions and pathways involving carbohydrate derivative." [GOC:TermGenie] synonym: "carbohydrate derivative metabolism" EXACT [GOC:TermGenie] is_a: GO:0071704 ! organic substance metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:1901137 name: carbohydrate derivative biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of carbohydrate derivative." [GOC:TermGenie] synonym: "carbohydrate derivative anabolism" EXACT [GOC:TermGenie] synonym: "carbohydrate derivative biosynthesis" EXACT [GOC:TermGenie] synonym: "carbohydrate derivative formation" EXACT [GOC:TermGenie] synonym: "carbohydrate derivative synthesis" EXACT [GOC:TermGenie] is_a: GO:1901135 ! carbohydrate derivative metabolic process is_a: GO:1901576 ! organic substance biosynthetic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:1901342 name: regulation of vasculature development namespace: biological_process def: "Any process that modulates the frequency, rate or extent of vasculature development." [GOC:TermGenie] synonym: "regulation of vascular system development" RELATED [GOC:TermGenie] is_a: GO:2000026 ! regulation of multicellular organismal development relationship: regulates GO:0001944 ! vasculature development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:1901360 name: organic cyclic compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organic cyclic compound." [GOC:TermGenie] synonym: "organic cyclic compound metabolism" EXACT [GOC:TermGenie] is_a: GO:0071704 ! organic substance metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:1901564 name: organonitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organonitrogen compound." [GOC:pr, GOC:TermGenie] synonym: "organonitrogen compound metabolism" EXACT [GOC:TermGenie] is_a: GO:0006807 ! nitrogen compound metabolic process is_a: GO:0071704 ! organic substance metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:1901566 name: organonitrogen compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of organonitrogen compound." [GOC:pr, GOC:TermGenie] synonym: "organonitrogen compound anabolism" EXACT [GOC:TermGenie] synonym: "organonitrogen compound biosynthesis" EXACT [GOC:TermGenie] synonym: "organonitrogen compound formation" EXACT [GOC:TermGenie] synonym: "organonitrogen compound synthesis" EXACT [GOC:TermGenie] is_a: GO:1901564 ! organonitrogen compound metabolic process is_a: GO:1901576 ! organic substance biosynthetic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:1901576 name: organic substance biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] synonym: "organic molecular entity anabolism" EXACT [GOC:TermGenie] synonym: "organic molecular entity biosynthesis" EXACT [GOC:TermGenie] synonym: "organic molecular entity biosynthetic process" EXACT [] synonym: "organic molecular entity formation" EXACT [GOC:TermGenie] synonym: "organic molecular entity synthesis" EXACT [GOC:TermGenie] synonym: "organic substance anabolism" EXACT [] synonym: "organic substance biosynthesis" EXACT [] synonym: "organic substance formation" EXACT [] synonym: "organic substance synthesis" EXACT [] is_a: GO:0009058 ! biosynthetic process is_a: GO:0071704 ! organic substance metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:1901605 name: alpha-amino acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving an alpha-amino acid." [GOC:TermGenie] synonym: "alpha-amino acid metabolism" EXACT [GOC:TermGenie] is_a: GO:0006520 ! cellular amino acid metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:1901607 name: alpha-amino acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of an alpha-amino acid." [GOC:TermGenie] synonym: "alpha-amino acid anabolism" EXACT [GOC:TermGenie] synonym: "alpha-amino acid biosynthesis" EXACT [GOC:TermGenie] synonym: "alpha-amino acid formation" EXACT [GOC:TermGenie] synonym: "alpha-amino acid synthesis" EXACT [GOC:TermGenie] is_a: GO:0008652 ! cellular amino acid biosynthetic process is_a: GO:1901605 ! alpha-amino acid metabolic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:2000026 name: regulation of multicellular organismal development namespace: biological_process def: "Any process that modulates the frequency, rate or extent of multicellular organismal development." [GOC:obol] is_a: GO:0050793 ! regulation of developmental process is_a: GO:0051239 ! regulation of multicellular organismal process relationship: regulates GO:0007275 ! multicellular organismal development property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:2000027 name: regulation of organ morphogenesis namespace: biological_process def: "Any process that modulates the frequency, rate or extent of organ morphogenesis." [GOC:obol] synonym: "regulation of histogenesis and organogenesis" RELATED [GOC:obol] is_a: GO:0022603 ! regulation of anatomical structure morphogenesis is_a: GO:2000026 ! regulation of multicellular organismal development relationship: regulates GO:0009887 ! organ morphogenesis property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:2000106 name: regulation of leukocyte apoptotic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of leukocyte apoptotic process." [GOC:BHF, GOC:mtg_apoptosis] synonym: "regulation of leukocyte apoptosis" NARROW [] is_a: GO:0042981 ! regulation of apoptotic process relationship: regulates GO:0071887 ! leukocyte apoptotic process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:2000145 name: regulation of cell motility namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cell motility." [GOC:mah] synonym: "regulation of cell locomotion" EXACT [GOC:obol] synonym: "regulation of cell movement" RELATED [GOC:obol] synonym: "regulation of movement of a cell" EXACT [GOC:obol] is_a: GO:0040012 ! regulation of locomotion is_a: GO:0051270 ! regulation of cellular component movement relationship: regulates GO:0048870 ! cell motility property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:2000147 name: positive regulation of cell motility namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of cell motility." [GOC:mah] synonym: "positive regulation of cell locomotion" EXACT [GOC:obol] synonym: "positive regulation of cell movement" RELATED [GOC:obol] synonym: "positive regulation of movement of a cell" EXACT [GOC:obol] is_a: GO:0040017 ! positive regulation of locomotion is_a: GO:0051272 ! positive regulation of cellular component movement is_a: GO:2000145 ! regulation of cell motility relationship: positively_regulates GO:0048870 ! cell motility property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:2000514 name: regulation of CD4-positive, alpha-beta T cell activation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of CD4-positive, alpha-beta T cell activation." [GOC:obol] is_a: GO:0046634 ! regulation of alpha-beta T cell activation relationship: regulates GO:0035710 ! CD4-positive, alpha-beta T cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:2000516 name: positive regulation of CD4-positive, alpha-beta T cell activation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell activation." [GOC:obol] is_a: GO:0046635 ! positive regulation of alpha-beta T cell activation is_a: GO:2000514 ! regulation of CD4-positive, alpha-beta T cell activation relationship: positively_regulates GO:0035710 ! CD4-positive, alpha-beta T cell activation property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: PATO:0000001 name: quality namespace: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities." [PATOC:GVG] synonym: "trait" EXACT [] property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000050 name: life span namespace: quality def: "A time quality inhering in a bearer by virtue of the bearer's expected maximum age." [PATOC:GVG] subset: attribute_slim is_a: PATO:0000165 ! time property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000051 name: morphology namespace: quality def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001241 ! physical object quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000052 name: shape namespace: quality alt_id: PATO:0001647 def: "A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc)." [PATOC:GVG] comment: Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. subset: attribute_slim synonym: "relational shape quality" EXACT [] is_a: PATO:0000051 ! morphology property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000068 name: qualitative namespace: quality comment: TODO: define this or obsolete it and move children somewhere else. is_a: PATO:0000001 ! quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000069 name: deviation(from_normal) namespace: quality def: "A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average." [PATOC:GVG] subset: attribute_slim is_a: PATO:0000068 ! qualitative property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000117 name: size namespace: quality def: "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude." [WordNet:WordNet] subset: attribute_slim subset: scalar_slim is_a: PATO:0000051 ! morphology property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000165 name: time namespace: quality def: "A quality in which events occur in sequence." [PATOC:GVG] subset: attribute_slim subset: scalar_slim is_a: PATO:0001018 ! physical quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000261 name: maturity namespace: quality def: "A quality of a single physical entity which is held by a bearer when the latter exhibits complete growth, differentiation, or development." [Merriam-Webster:Merriam-Webster] subset: attribute_slim is_a: PATO:0001995 ! organismal quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000406 name: curved namespace: quality def: "A curvature quality inhering in a bearer by virtue of the bearer's having or being marked by a curve or smoothly rounded bend." [WordNet:WordNet] subset: cell_quality subset: value_slim synonym: "bowing" NARROW [] synonym: "curled" RELATED [] is_a: PATO:0001591 ! curvature property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000411 name: circular namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center." [thefreedictionary.com:thefreedictionary.com] subset: cell_quality subset: mpath_slim subset: value_slim synonym: "round" EXACT [] synonym: "rounded" EXACT [] is_a: PATO:0000947 ! elliptic property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000461 name: normal namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average." [PATOC:GVG] subset: abnormal_slim subset: mpath_slim subset: value_slim synonym: "average" RELATED [] is_a: PATO:0000069 ! deviation(from_normal) property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000586 name: increased size namespace: quality alt_id: PATO:0001202 def: "A size quality which is relatively high." [PATOC:GVG] subset: value_slim synonym: "big" RELATED [] synonym: "enlarged" RELATED [] synonym: "expanded" RELATED [] synonym: "great" RELATED [] synonym: "large" RELATED [] is_a: PATO:0000117 ! size is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0000117 ! size intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal relationship: increased_in_magnitude_relative_to PATO:0000461 ! normal property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000587 name: decreased size namespace: quality def: "A size quality which is relatively low." [PATOC:GVG] subset: value_slim synonym: "hypoplasia" NARROW [] synonym: "small" RELATED [] synonym: "tiny" RELATED [] synonym: "underdeveloped" NARROW [] is_a: PATO:0000117 ! size is_a: PATO:0002303 ! decreased object quality intersection_of: PATO:0000117 ! size intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal relationship: decreased_in_magnitude_relative_to PATO:0000461 ! normal property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0000947 name: elliptic namespace: quality def: "A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section." [PATOC:GVG] subset: cell_quality subset: mpath_slim subset: value_slim synonym: "ellipse-shaped" EXACT [] synonym: "ellipsoid" EXACT [] synonym: "elliptical" EXACT [] synonym: "oval" RELATED [] synonym: "ovoid" RELATED [] is_a: PATO:0002318 ! superelliptic property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001018 name: physical quality namespace: quality alt_id: PATO:0002079 def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] subset: attribute_slim synonym: "relational physical quality" EXACT [] xref: Wikipedia:Physical_property is_a: PATO:0001241 ! physical object quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001237 name: quality of a single physical entity namespace: cell def: "A physical object quality which inheres in a single-bearer." [PATOC:GVG] synonym: "monadic quality of a continuant" EXACT [] synonym: "monadic quality of a physical entity" EXACT [] synonym: "monadic quality of an object" NARROW [] synonym: "monadic quality of continuant" EXACT [] synonym: "single bearer quality of a physical entity" EXACT [] synonym: "singly inhering of a physical entity" EXACT [] is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0001238 name: quality of related physical entities namespace: cell def: "A physical entity quality which exists in relation towards some other entity." [PATOC:GVG] comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles\\nRelational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles subset: relational_slim synonym: "multiple bearer quality of a physical entity " EXACT [] synonym: "multiply inhering quality of a physical entity " EXACT [] synonym: "relational quality of a continuant" EXACT [] synonym: "relational quality of an object " EXACT [] synonym: "relational quality of continuant" EXACT [] is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0001241 name: physical object quality namespace: quality alt_id: PATO:0001237 alt_id: PATO:0001238 def: "A quality which inheres in a continuant." [PATOC:GVG] comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. synonym: "monadic quality of a continuant" EXACT [] synonym: "monadic quality of an object" NARROW [] synonym: "monadic quality of continuant" NARROW [] synonym: "multiply inhering quality of a physical entity " EXACT [] synonym: "quality of a continuant" EXACT [] synonym: "quality of a single physical entity" EXACT [] synonym: "quality of an object" EXACT [] synonym: "quality of continuant" EXACT [] xref: snap:Quality is_a: PATO:0000001 ! quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001374 name: ploidy namespace: quality def: "A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism." [Wikipedia:http\://en.wikipedia.org/wiki/Ploidy] subset: attribute_slim is_a: PATO:0001396 ! cellular quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001375 name: haploid namespace: quality def: "A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes." [Wikipedia:http\://en.wikipedia.org/wiki/Haploid] subset: cell_quality subset: value_slim is_a: PATO:0001393 ! euploid property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001393 name: euploid namespace: quality def: "A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes." [Wikipedia:http\://en.wikipedia.org/wiki/Euploid] subset: cell_quality subset: value_slim is_a: PATO:0001374 ! ploidy property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001394 name: diploid namespace: quality def: "A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father." [Wikipedia:http\://en.wikipedia.org/wiki/Diploid] comment: The exact number may be one or two different from the 2n number and still be classified as diploidy (although with aneuploidy). Nearly all mammals are diploid organisms, although all individuals have some small fracton of cells that are polyploidy. subset: cell_quality subset: value_slim is_a: PATO:0001393 ! euploid property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001396 name: cellular quality namespace: quality def: "A monadic quality of continuant that exists at the cellular level of organisation." [PATOC:GVG] is_a: PATO:0001241 ! physical object quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001397 name: cellular potency namespace: quality def: "A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types." [PATOC:GVG] subset: attribute_slim subset: disposition_slim is_a: PATO:0001396 ! cellular quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001400 name: unipotent namespace: quality def: "A cellular potency that is the capacity to produce only one differentiated cell type." [Wikipedia:http\://en.wikipedia.org/wiki/Unipotent] comment: Unipotent cells have the quality of self-renewal which distinguishes them from non-stem cells. subset: cell_quality subset: disposition_slim subset: value_slim is_a: PATO:0001397 ! cellular potency property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001401 name: oligopotent namespace: quality def: "A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity." [PATOC:MAH] comment: Less potent than multipotent, often thought of as precursor or progenitor cell status. subset: cell_quality subset: disposition_slim subset: value_slim is_a: PATO:0001397 ! cellular potency property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001402 name: multipotent namespace: quality def: "A cellular potency that is the capacity to form multiple differentiated cell types." [Wikipedia:http\://en.wikipedia.org/wiki/Multipotent] subset: cell_quality subset: disposition_slim subset: value_slim is_a: PATO:0001397 ! cellular potency property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001404 name: nucleate quality namespace: quality def: "A cellular quality inhering in a bearer by virtue of bearer's number of nuclei." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001396 ! cellular quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001405 name: anucleate namespace: quality def: "A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus." [Biology-online:Biology-online] subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001406 name: binucleate namespace: quality def: "A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei." [Biology-online:Biology-online] subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0001908 ! multinucleate property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001407 name: mononucleate namespace: quality def: "A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus." [Biology-online:Biology-online] subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001501 name: immature namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development." [Merriam-Webster:Merriam-Webster] subset: value_slim synonym: "underdeveloped" RELATED [] is_a: PATO:0000261 ! maturity property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001591 name: curvature namespace: quality def: "A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending." [WordNet:WordNet] subset: attribute_slim is_a: PATO:0000052 ! shape property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001604 name: decreased life span namespace: quality def: "A life span which is relatively low." [PATO:GVG] synonym: "low life span" EXACT [] is_a: PATO:0000050 ! life span is_a: PATO:0002303 ! decreased object quality intersection_of: PATO:0000050 ! life span intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal relationship: decreased_in_magnitude_relative_to PATO:0000461 ! normal property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001789 name: domed namespace: quality def: "A curvature quality inhering in a bearer by virtue of the bearer's having a shape resembling a dome." [PATOC:GVG] subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0000406 ! curved property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001857 name: concave namespace: quality def: "A shape quality in a bearer by virtue of the bearer's curving inward." [WordNet:WordNet] subset: cell_quality subset: value_slim is_a: PATO:0002005 ! concavity property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001871 name: reniform namespace: quality def: "A concave 3-D shape quality inhering in a bearer by virtue of the bearer's having the shape of a kidney." [ISBN:0881923214] subset: value_slim synonym: "bean shaped" RELATED [] synonym: "kidney-shaped" EXACT [] is_a: PATO:0002008 ! concave 3-D shape property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001873 name: cylindrical namespace: quality alt_id: PATO:0001203 def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section." [PATOC:MAH] subset: cell_quality subset: value_slim synonym: "rod-like" EXACT [] synonym: "rod-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0002007 ! convex 3-D shape relationship: has_cross_section PATO:0000411 ! circular property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001874 name: discoid namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter." [PATOC:cjm] subset: cell_quality subset: value_slim synonym: "disc-shaped" EXACT [] synonym: "disk-shaped" EXACT [] is_a: PATO:0001873 ! cylindrical property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001908 name: multinucleate namespace: quality def: "A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus." [PATOC:GVG] subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001979 name: lobed namespace: quality def: "A shape quality inhering in a bearer by virtue of the bearer's being partly divided into a determinate number of regions." [ISBN:0881923214] subset: mpath_slim subset: value_slim is_a: PATO:0000052 ! shape property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001995 name: organismal quality namespace: quality def: "A quality that inheres in an entire organism or part of an organism." [PATOC:CJM] is_a: PATO:0001241 ! physical object quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0002005 name: concavity namespace: quality def: "Surface shape that refers to the inward or outward curvature of the surface." [PATOC:MAH] subset: attribute_slim is_a: PATO:0000052 ! shape property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0002006 name: 2-D shape namespace: quality def: "A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity." [PATOC:CJM] subset: attribute_slim synonym: "2-D projection" RELATED [] synonym: "cross-sectional" RELATED [] is_a: PATO:0000052 ! shape property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0002007 name: convex 3-D shape namespace: quality def: "A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave." [PATOC:CJM] comment: Use this term or an is_a child of this term when the entire shape of the object is known. subset: attribute_slim xref: Image:http\://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png is_a: PATO:0002266 ! 3-D shape relationship: has_cross_section PATO:0002006 ! 2-D shape property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0002008 name: concave 3-D shape namespace: quality def: "A complete three dimensional shape in which there is a line connecting pair of points on the object that lies outside the object. Or: a shape with cavities. Contrast: concave." [PATOC:CJM] subset: attribute_slim xref: Image:http\://en.wikipedia.org/wiki/Image\:Convex_polygon_illustration2.png is_a: PATO:0002266 ! 3-D shape relationship: has_part PATO:0001857 ! concave property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0002039 name: biconcave namespace: quality def: "A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces." [PATOC:GVG] subset: value_slim is_a: PATO:0001857 ! concave property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0002061 name: relational molecular quality namespace: cell def: "An emergent molecular relational quality that arises from the molecular interaction exerted between two entities in contact." [PATOC:GVG] is_a: PATO:0001238 ! quality of related physical entities created_by: george creation_date: 2009-06-05T08:21:37Z [Term] id: PATO:0002070 name: affinity namespace: quality def: "A molecular quality that arises from the molecular attraction exerted between two atoms or compounds." [PATOC:GVG] subset: attribute_slim subset: disposition_slim subset: relational_slim subset: scalar_slim is_a: PATO:0002182 ! molecular quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl created_by: George Gkoutos creation_date: 2009-09-18T01:16:16Z [Term] id: PATO:0002094 name: basophilic namespace: quality def: "An affinity inhering in a tissue constituent by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific ph conditions." [PATOC:GVG] subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0002070 ! affinity property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl created_by: george creation_date: 2009-10-05T12:05:23Z [Term] id: PATO:0002182 name: molecular quality namespace: quality alt_id: PATO:0002061 def: "A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc." [PATOC:GVG] synonym: "relational molecular quality" EXACT [] is_a: PATO:0001241 ! physical object quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl created_by: George Gkoutos creation_date: 2010-03-10T03:18:15Z [Term] id: PATO:0002266 name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl created_by: george creation_date: 2010-10-05T12:31:16Z [Term] id: PATO:0002300 name: increased quality namespace: quality def: "A quality that has a value that is increased compared to normal or average." [PATOC:GVG] is_a: PATO:0000069 ! deviation(from_normal) intersection_of: PATO:0000001 ! quality intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal relationship: increased_in_magnitude_relative_to PATO:0000461 ! normal property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl created_by: George Gkoutos creation_date: 2011-06-16T06:39:43Z [Term] id: PATO:0002301 name: decreased quality namespace: quality def: "A quality that has a value that is decreased compared to normal or average." [PATOC:GVG] is_a: PATO:0000069 ! deviation(from_normal) intersection_of: PATO:0000001 ! quality intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal relationship: decreased_in_magnitude_relative_to PATO:0000461 ! normal property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl created_by: George Gkoutos creation_date: 2011-06-16T06:40:15Z [Term] id: PATO:0002303 name: decreased object quality namespace: quality def: "A quality of an object that has a value that is decreased compared to normal or average." [PATOC:GVG] is_a: PATO:0001241 ! physical object quality is_a: PATO:0002301 ! decreased quality intersection_of: PATO:0001241 ! physical object quality intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal relationship: decreased_in_magnitude_relative_to PATO:0000461 ! normal property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl created_by: George Gkoutos creation_date: 2011-06-16T06:51:54Z [Term] id: PATO:0002305 name: increased object quality namespace: quality def: "A quality of an object that has a value that is increased compared to normal or average." [PATOC:GVG] is_a: PATO:0001241 ! physical object quality is_a: PATO:0002300 ! increased quality intersection_of: PATO:0001241 ! physical object quality intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal relationship: increased_in_magnitude_relative_to PATO:0000461 ! normal property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl created_by: George Gkoutos creation_date: 2011-06-16T06:54:01Z [Term] id: PATO:0002318 name: superelliptic namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl created_by: George Gkoutos creation_date: 2011-10-12T12:45:16Z [Term] id: PR:000000001 name: protein namespace: protein def: "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA." [PRO:DAN, PRO:WCB] comment: Proteins descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. is_a: PR:000018263 ! amino acid chain property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001002 name: CD19 molecule namespace: protein def: "A protein that is a translation product of the CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction." [PMID:15778510] comment: Category=gene. synonym: "B-lymphocyte surface antigen B4" EXACT [] synonym: "CD19" EXACT PRO-short-label [] synonym: "differentiation antigen CD19" EXACT [] synonym: "T-cell surface antigen Leu-12" EXACT [] xref: PIRSF:PIRSF016630 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001003 name: CD34 molecule namespace: protein def: "A protein that is a translation product of the CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved." [PMID:16720896, PMID:8983065] comment: Category=gene. synonym: "CD34" EXACT PRO-short-label [] synonym: "hematopoietic progenitor cell antigen CD34" EXACT [] xref: PIRSF:PIRSF028749 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001004 name: CD4 molecule namespace: protein def: "A protein that is a translation product of the CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence." [PMID:15326605] comment: Category=gene. synonym: "CD4" EXACT PRO-short-label [] synonym: "T-cell differentiation antigen L3T4" EXACT [] synonym: "T-cell surface antigen T4/Leu-3" EXACT [] synonym: "T-cell surface glycoprotein CD4" EXACT [] xref: PIRSF:PIRSF001977 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001005 name: integrin alpha with A domain namespace: protein def: "An integrin alpha that contains an A domain. A hallmark of this class is the presence of a von Willebrand factor type A domain (PF00092) (I-domain) of approximately 200 amino acid residues at the N-terminus, which confers divalent cation binding properties. Unlike other integrin alpha proteins, they do not undergo proteolytic cleavage." [PIRSF:PIRSF002497] comment: Category=family. synonym: "integrin alpha with I domain" EXACT [] xref: PIRSF:PIRSF002497 is_a: PR:000025796 ! integrin alpha property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001006 name: receptor-type tyrosine-protein phosphatase C namespace: protein def: "A protein that is a translation product of the PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (PF00041) followed by two copies of the Protein-tyrosine phosphatase (PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule." [PMID:1351092, PRO:CNA] comment: Category=gene. synonym: "CD45" EXACT [] synonym: "L-CA" EXACT [] synonym: "leukocyte common antigen" EXACT [] synonym: "ly-5" EXACT [] synonym: "lymphocyte antigen 5" EXACT [] synonym: "PTPRC" EXACT PRO-short-label [] synonym: "T200" EXACT [] xref: PIRSF:PIRSF002004 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001008 name: integrin alpha-2 namespace: protein def: "An integrin alpha with A domain that is a translation product of the ITGA2 gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "CD49 antigen-like family member B" EXACT [] synonym: "CD49b" EXACT [] synonym: "collagen receptor" EXACT [] synonym: "GPIa" EXACT [] synonym: "ITGA2" EXACT PRO-short-label [] synonym: "platelet membrane glycoprotein Ia" EXACT [] synonym: "VLA-2 subunit alpha" EXACT [] is_a: PR:000001005 ! integrin alpha with A domain property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001010 name: integrin alpha-E namespace: protein def: "An integrin alpha with A domain that is a translation product of the ITGAE gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "CD103" EXACT [] synonym: "HML-1 antigen" EXACT [] synonym: "integrin alpha M290" EXACT [] synonym: "integrin alpha-IEL" EXACT [] synonym: "ITGAE" EXACT PRO-short-label [] synonym: "mucosal lymphocyte 1 antigen" EXACT [] is_a: PR:000001005 ! integrin alpha with A domain property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001012 name: integrin alpha-M namespace: protein def: "An integrin alpha with A domain that is a translation product of the ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1." [UniProtKB:P11215] comment: Category=gene. synonym: "CD11 antigen-like family member B" EXACT [] synonym: "CD11b" EXACT [] synonym: "cell surface glycoprotein MAC-1 subunit alpha" EXACT [] synonym: "CR-3 alpha chain" EXACT [] synonym: "CR3A" RELATED [] synonym: "ITGAM" EXACT PRO-short-label [] synonym: "leukocyte adhesion receptor MO1" EXACT [] synonym: "neutrophil adherence receptor" EXACT [] is_a: PR:000001005 ! integrin alpha with A domain property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001013 name: integrin alpha-X namespace: protein def: "An integrin alpha with A domain that is a translation product of the ITGAX gene or a 1:1 ortholog thereof. Integrin alpha-X complexed with beta-2 is a receptor for fibrinogen. It recognizes the sequence GPR in fibrinogen. It mediates cell-cell interaction during inflammatory responses. It is especially important in monocyte adhesion and chemotaxis." [UniProtKB:P20702] comment: Category=gene. synonym: "CD11 antigen-like family member C" EXACT [] synonym: "CD11c" EXACT [] synonym: "ITGAX" EXACT PRO-short-label [] synonym: "Leu M5" EXACT [DNx] synonym: "leukocyte adhesion glycoprotein p150,95 alpha chain" EXACT [] synonym: "leukocyte adhesion receptor p150,95" EXACT [] is_a: PR:000001005 ! integrin alpha with A domain property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001014 name: receptor-type tyrosine-protein phosphatase C isoform CD45R namespace: protein def: "A receptor-type tyrosine-protein phosphatase C that is a translation product of a mature transcript of the PTPRC gene, that includes the region encoded by the variable exons 4(A), 5(B), and 6(C). Represented by the sequence UniProtKB:P08575-1." [PMID:1351092, PRO:CNA] comment: Category=sequence. synonym: "B220" RELATED [] synonym: "CD45R" EXACT [] synonym: "CD45RABC" EXACT [] is_a: PR:000001006 ! receptor-type tyrosine-protein phosphatase C property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001015 name: receptor-type tyrosine-protein phosphatase C isoform CD45RA namespace: protein def: "A receptor-type tyrosine-protein phosphatase C that is a translation product of a mature transcript of the PTPRC gene, that includes the region encoded by the variable exon 4(A), and lacks the region encoded by exons 5(B) and 6(C)." [PMID:1351092, PRO:CNA] comment: Category=sequence. synonym: "CD45RA" EXACT [] is_a: PR:000001006 ! receptor-type tyrosine-protein phosphatase C property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001017 name: receptor-type tyrosine-protein phosphatase C isoform CD45RO namespace: protein def: "A receptor-type tyrosine-protein phosphatase C that is a translation product of a mature transcript of the PTPRC gene, that lacks the region encoded by the variable exons 4(A), 5(B), and 6(C). Represented by the sequence UniProtKB:P08575-2." [PMID:1351092, PRO:CNA] comment: Category=sequence. synonym: "180 kDa form" EXACT [] synonym: "T200" RELATED [] is_a: PR:000001006 ! receptor-type tyrosine-protein phosphatase C property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001018 name: CD3 subunit with immunoglobulin domain namespace: protein def: "A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response." [PMID:16473826, PMID:1724736] comment: Category=family. synonym: "CD3 subunit with Ig-like domain" EXACT [] xref: PIRSF:PIRSF001993 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001020 name: CD3 epsilon namespace: protein def: "A CD3 subunit that is a translation product of the CD3E gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "CD3E" EXACT PRO-short-label [] synonym: "CD3e" EXACT [] synonym: "T-cell surface antigen T3/Leu-4 epsilon chain" EXACT [] synonym: "T3E" RELATED [] is_a: PR:000001018 ! CD3 subunit with immunoglobulin domain property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001022 name: neural cell adhesion molecule namespace: protein def: "A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain." [PRO:CNA] comment: Category=family. xref: PIRSF:PIRSF002507 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001023 name: neural cell adhesion molecule NCAM namespace: protein def: "A neural cell adhesion molecule which is involved in neuronal development, synaptic plasticity, and regeneration." [PMID:17975827] comment: Category=family. xref: PIRSF:PIRSF501037 is_a: PR:000001022 ! neural cell adhesion molecule property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001024 name: neural cell adhesion molecule 1 namespace: protein def: "A neural cell adhesion molecule NCAM that is a translation product of the NCAM1 gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "CD56" EXACT [] synonym: "N-CAM-1" EXACT [] synonym: "NCAM" RELATED [] synonym: "NCAM-1" EXACT [] synonym: "NCAM1" EXACT PRO-short-label [] is_a: PR:000001023 ! neural cell adhesion molecule NCAM property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001025 name: C-type lectin with multiple lectin domains namespace: protein def: "A protein that is a type I transmembrane receptor with an N-terminal cysteine-rich domain, a single Fibronectin type II (FNII) domain (PF00040) and eight to ten copies of the Lectin C-type domain (PF00059) (CTLDs). The presence of multiple copies of the CTLD domain is a hallmark of this class." [PMID:12223280] comment: Category=family. xref: PIRSF:PIRSF002427 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001026 name: lymphocyte antigen 75 namespace: protein def: "A C-type lectin with multiple lectin domains that is a translation product of the LY75 gene or a 1:1 ortholog thereof. It consists of 12 extracellular domains (an N-terminal cysteine-rich domain, a fibronectin type II domain and 10 C-type carbohydrate recognition domains), a transmembrane region and a small cytoplasmic C terminus containing a single Tyr residue, but no obvious kinase domain. Acts as an endocytic receptor to direct captured antigens from the extracellular space to a specialized antigen-processing compartment." [PMID:9862343] comment: Category=gene. synonym: "C-type lectin domain family 13 member B" EXACT [] synonym: "CD205" EXACT [] synonym: "CLEC13B" RELATED [] synonym: "DEC-205" EXACT [] synonym: "gp200-MR6" EXACT [] synonym: "ly-75" EXACT [] synonym: "LY75" EXACT PRO-short-label [] is_a: PR:000001025 ! C-type lectin with multiple lectin domains property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001083 name: CD2 molecule namespace: protein def: "A protein that is a translation product of the CD2 gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "CD2" EXACT PRO-short-label [] synonym: "erythrocyte receptor" EXACT [] synonym: "LFA-2" EXACT [] synonym: "LFA-3 receptor" EXACT [] synonym: "ly-37" EXACT [] synonym: "lymphocyte antigen 37" EXACT [] synonym: "rosette receptor" EXACT [] synonym: "SRBC" RELATED [] synonym: "T-cell surface antigen CD2" EXACT [] synonym: "T-cell surface antigen T11/Leu-5" EXACT [] synonym: "T-cell surface glycoprotein CD2" EXACT [] xref: PIRSF:PIRSF001984 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001084 name: T-cell surface glycoprotein CD8 alpha chain namespace: protein def: "A protein that is a translation product of the CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain." [PMID:11114424, PRO:CNA, Wikipedia:CD8] comment: Category=gene. synonym: "CD8A" EXACT PRO-short-label [] synonym: "CD8a" EXACT [] synonym: "Lyt-2" RELATED [] synonym: "Lyt2" RELATED [] synonym: "MAL" RELATED [] synonym: "T-cell surface glycoprotein Lyt-2" EXACT [] synonym: "T-lymphocyte differentiation antigen T8/Leu-2" EXACT [] xref: PANTHER:PTHR10441\:SF1 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001094 name: rhodopsin-like G-protein coupled receptor namespace: protein def: "A protein that contains the 7 transmembrane receptor (rhodopsin family) domain (Pfam:PF00001), which includes 7 transmembrane helices (TMI-TM7) with 3 intracellular loops (IL1-IL3) and 3 extracellular loops (EL1-EL3) between the helices. The amino-terminal region is extracellular and the carboxyl-terminal region is intracellular. Rhodopsin-like G-protein coupled receptors (GPCRs) are unique among the several classes of GPCRs in that most have a very short amino-terminal segment and several characteristic sequence motifs, particularly NSxxNPxxY in TM7 and D/E-R-Y/F between TM3 and loop IL2. Most bind their ligands within a cavity between the TM regions." [PMID:12761335, PRO:WCB] comment: Category=family. synonym: "class 1 G-protein coupled receptor" EXACT [PMID:15914470] synonym: "class A G-protein coupled receptor" EXACT [IUPHAR:http\://www.iuphar-db.org/GPCR/ReceptorListForward] xref: PIRSF:PIRSF800006 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001128 name: chemokine receptor namespace: protein def: "A rhodopsin-like G protein coupled receptor whose active form binds one or more chemokines. Only those that have been unequivocally shown to activate a G-protein coupled signaling pathway appear on the official IUPHAR list." [PMID:12037138, PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038545 is_a: PR:000001094 ! rhodopsin-like G-protein coupled receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001197 name: chemokine receptor CCR1/3/1L namespace: protein def: "A rhodopsin-like G-protein coupled receptor that is a translation product of the CCR1, CCR3, or CCR1L1 genes (the last found so far only in mouse)." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF501024 is_a: PR:000001128 ! chemokine receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001199 name: C-C chemokine receptor type 2 namespace: protein def: "A chemokine receptor that is a translation product of the CCR2 gene or a 1:1 ortholog thereof. The preferred ligands include CCL2, CCL7, CCL8, CCL13." [PMID:12037138, PRO:WCB] comment: Category=gene. synonym: "C-C CKR-2" EXACT [] synonym: "CC-CKR-2" EXACT [] synonym: "CCR-2" EXACT [] synonym: "CCR2" EXACT PRO-short-label [] synonym: "CD192" EXACT [] synonym: "chemokine receptor CCR2" EXACT [] synonym: "CMKBR2" RELATED [] synonym: "JE/FIC receptor" EXACT [] synonym: "MCP-1 receptor" EXACT [] synonym: "MCP-1-R" EXACT [] synonym: "monocyte chemoattractant protein 1 receptor" EXACT [] is_a: PR:000001128 ! chemokine receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001201 name: C-C chemokine receptor type 5 namespace: protein def: "A chemokine receptor that is a translation product of the CCR5 gene or a 1:1 ortholog thereof. The preferred ligands include CCL3, CCL4, CCL5, CCL8, CCL14." [PMID:12037138, PRO:WCB] comment: Category=gene. synonym: "C-C CKR-5" EXACT [] synonym: "CC-CKR-5" EXACT [] synonym: "CCR-5" EXACT [] synonym: "CCR5" EXACT PRO-short-label [] synonym: "CD195" EXACT [] synonym: "chemokine receptor CCR5" EXACT [] synonym: "CHEMR13" EXACT [] synonym: "CMKBR5" RELATED [] synonym: "HIV-1 fusion coreceptor" EXACT [] synonym: "MIP-1 alpha receptor" EXACT [] is_a: PR:000001128 ! chemokine receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001202 name: C-C chemokine receptor type 6 namespace: protein def: "A chemokine receptor that is a translation product of the CCR6 gene or a 1:1 ortholog thereof. The preferred ligand is CCL20." [PMID:12037138, PRO:WCB] comment: Category=gene. synonym: "C-C CKR-6" EXACT [] synonym: "CC-CKR-6" EXACT [] synonym: "CCR-6" EXACT [] synonym: "CCR6" EXACT PRO-short-label [] synonym: "CD196" EXACT [] synonym: "chemokine receptor CCR6" EXACT [] synonym: "chemokine receptor-like 3" EXACT [] synonym: "CKR-L3" EXACT [] synonym: "CKRL3" RELATED [] synonym: "CMKBR6" RELATED [] synonym: "DRY6" EXACT [] synonym: "G-protein coupled receptor 29" EXACT [] synonym: "GPR-CY4" EXACT [] synonym: "GPR29" RELATED [] synonym: "GPRCY4" EXACT [] synonym: "KY411" EXACT [] synonym: "LARC receptor" EXACT [] synonym: "STRL22" RELATED [] is_a: PR:000001128 ! chemokine receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001203 name: C-C chemokine receptor type 7 namespace: protein def: "A chemokine receptor that is a translation product of the CCR7 gene or a 1:1 ortholog thereof. The preferred ligands are CCL19 and CCL21." [PMID:12037138, PRO:WCB] comment: Category=gene. synonym: "BLR2" EXACT [] synonym: "C-C CKR-7" EXACT [] synonym: "CC-CKR-7" EXACT [] synonym: "CCR-7" EXACT [] synonym: "CCR7" EXACT PRO-short-label [] synonym: "CD197" EXACT [] synonym: "CDw197" EXACT [] synonym: "chemokine receptor CCR7" EXACT [] synonym: "CMKBR7" RELATED [] synonym: "EBI1" EXACT [] synonym: "Ebi1h" RELATED [] synonym: "EBV-induced G-protein coupled receptor 1" EXACT [] synonym: "epstein-Barr virus-induced G-protein coupled receptor 1" EXACT [] synonym: "EVI1" RELATED [] synonym: "MIP-3 beta receptor" EXACT [] is_a: PR:000001128 ! chemokine receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001206 name: CX3C chemokine receptor 1 namespace: protein def: "A chemokine receptor that is a translation product of the CX3CR1 gene or a 1:1 ortholog thereof. The preferred ligand is CX3CL1." [PMID:12037138, PRO:WCB] comment: Category=gene. synonym: "beta chemokine receptor-like 1" EXACT [] synonym: "C-X3-C CKR-1" EXACT [] synonym: "chemokine receptor CX3CR1" EXACT [] synonym: "CMK-BRL-1" EXACT [] synonym: "CMK-BRL1" EXACT [] synonym: "CMKBRL1" RELATED [] synonym: "CX3CR1" EXACT PRO-short-label [] synonym: "fractalkine receptor" EXACT [] synonym: "G-protein coupled receptor 13" EXACT [] synonym: "GPR13" RELATED [] synonym: "V28" EXACT [] xref: PIRSF:PIRSF501025 is_a: PR:000001128 ! chemokine receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001207 name: C-X-C chemokine receptor type 3 namespace: protein def: "A chemokine receptor that is a translation product of the CXCR3 gene or a 1:1 ortholog thereof. The preferred ligands include CXCL9, CXCL10, CXCL11." [PMID:12037138, PRO:WCB] comment: Category=gene. synonym: "CD183" EXACT [] synonym: "chemokine receptor CXCR3" EXACT [] synonym: "CKR-L2" EXACT [] synonym: "Cmkar3" RELATED [] synonym: "CXC-R3" EXACT [] synonym: "CXCR-3" EXACT [] synonym: "CXCR3" EXACT PRO-short-label [] synonym: "G-protein coupled receptor 9" EXACT [] synonym: "GPR9" RELATED [] synonym: "interferon-inducible protein 10 receptor" EXACT [] synonym: "IP-10 receptor" EXACT [] xref: PIRSF:PIRSF501023 is_a: PR:000001128 ! chemokine receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001208 name: C-X-C chemokine receptor type 4 namespace: protein def: "A chemokine receptor that is a translation product of the CXCR4 gene or a 1:1 ortholog thereof. The preferred ligand is CXCL12." [PMID:12037138, PRO:WCB] comment: Category=gene. synonym: "CD184" EXACT [] synonym: "chemokine receptor CXCR4" EXACT [] synonym: "Cmkar4" RELATED [] synonym: "CXC-R4" EXACT [] synonym: "CXCR-4" EXACT [] synonym: "CXCR4" EXACT PRO-short-label [] synonym: "FB22" EXACT [] synonym: "fusin" EXACT [] synonym: "HM89" EXACT [] synonym: "LCR1" EXACT [] synonym: "LESTR" EXACT [] synonym: "leukocyte-derived seven transmembrane domain receptor" EXACT [] synonym: "NPYRL" EXACT [] synonym: "PB-CKR" EXACT [] synonym: "pre-B-cell-derived chemokine receptor" EXACT [] synonym: "SDF-1 receptor" EXACT [] synonym: "Sdf1r" RELATED [] synonym: "stromal cell-derived factor 1 receptor" EXACT [] xref: PIRSF:PIRSF501021 is_a: PR:000001128 ! chemokine receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001209 name: C-X-C chemokine receptor type 5 namespace: protein def: "A chemokine receptor that is a translation product of the CXCR5 gene or a 1:1 ortholog thereof. The preferred ligand is CXCL13." [PMID:12037138, PRO:WCB] comment: Category=gene. synonym: "BLR1" RELATED [] synonym: "burkitt lymphoma receptor 1" EXACT [] synonym: "burkitt lymphoma receptor 1 homolog" EXACT [] synonym: "CD185" EXACT [] synonym: "chemokine receptor CXCR5" EXACT [] synonym: "CXC-R5" EXACT [] synonym: "CXCR-5" EXACT [] synonym: "CXCR5" EXACT PRO-short-label [] synonym: "Gpcr6" RELATED [] synonym: "MDR-15" EXACT [] synonym: "MDR15" RELATED [] synonym: "monocyte-derived receptor 15" EXACT [] xref: PANTHER:PTHR24227\:SF213 is_a: PR:000001128 ! chemokine receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001226 name: high affinity interleukin-8 receptor namespace: protein def: "A chemokine receptor whose active form binds interleukin-8 with high affinity." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF501022 is_a: PR:000001128 ! chemokine receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001254 name: chemokine receptor CCR1 namespace: protein def: "A chemokine receptor CCR1/3/1L that is a translation product of the CCR1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "C-C CKR-1" EXACT [] synonym: "CC-CKR-1" EXACT [] synonym: "CCR-1" EXACT [] synonym: "CCR1" EXACT PRO-short-label [] synonym: "CD191" EXACT [] synonym: "CMKBR1" RELATED [] synonym: "CMKR1" RELATED [] synonym: "HM145" EXACT [] synonym: "LD78 receptor" EXACT [] synonym: "macrophage inflammatory protein 1-alpha receptor" EXACT [] synonym: "MIP-1alpha-R" EXACT [] synonym: "RANTES-R" EXACT [] synonym: "SCYAR1" RELATED [] is_a: PR:000001197 ! chemokine receptor CCR1/3/1L property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001255 name: chemokine receptor CCR3 namespace: protein def: "A chemokine receptor CCR1/3/1L that is a translation product of the CCR3 gene or a 1:1 ortholog thereof." [PMID:12037138, PRO:WCB] comment: Category=gene. synonym: "C-C CKR-3" EXACT [] synonym: "CC-CKR-3" EXACT [] synonym: "CCR-3" EXACT [] synonym: "CCR3" EXACT PRO-short-label [] synonym: "CD193" EXACT [] synonym: "CKR3" EXACT [] synonym: "Cmkbr1l2" RELATED [] synonym: "CMKBR3" RELATED [] synonym: "eosinophil eotaxin receptor" EXACT [] synonym: "macrophage inflammatory protein 1-alpha receptor-like 2" EXACT [] synonym: "MIP-1 alpha RL2" EXACT [] is_a: PR:000001197 ! chemokine receptor CCR1/3/1L property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001256 name: high affinity interleukin-8 receptor A namespace: protein def: "A high affinity interleukin-8 receptor that is a translation product of the IL8RA gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD181" EXACT [] synonym: "CDw128a" EXACT [] synonym: "CMKAR1" RELATED [] synonym: "CXC-R1" EXACT [] synonym: "CXCR-1" EXACT [] synonym: "CXCR1" RELATED [] synonym: "high affinity interleukin-8 receptor A" EXACT [] synonym: "IL-8 receptor type 1" EXACT [] synonym: "IL-8R A" EXACT [] synonym: "IL8RA" EXACT PRO-short-label [] is_a: PR:000001226 ! high affinity interleukin-8 receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001257 name: high affinity interleukin-8 receptor B namespace: protein def: "A high affinity interleukin-8 receptor that is a translation product of the IL8RB gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD182" EXACT [] synonym: "CDw128b" EXACT [] synonym: "Cmkar2" RELATED [] synonym: "CXC-R2" EXACT [] synonym: "CXCR-2" EXACT [] synonym: "CXCR2" RELATED [] synonym: "Gpcr16" RELATED [] synonym: "GRO/MGSA receptor" EXACT [] synonym: "high affinity interleukin-8 receptor B" EXACT [] synonym: "IL-8 receptor type 2" EXACT [] synonym: "IL-8R B" EXACT [] synonym: "IL8RB" EXACT PRO-short-label [] is_a: PR:000001226 ! high affinity interleukin-8 receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001281 name: ADP-ribosyl cyclase namespace: protein def: "A protein that contains the ADP-ribosyl cyclase domain (PF02267)." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF005736 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001288 name: B-cell receptor CD22 namespace: protein def: "A protein that is a translation product of the CD22 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "B-lymphocyte cell adhesion molecule" EXACT [] synonym: "BL-CAM" EXACT [] synonym: "CD22" EXACT PRO-short-label [] synonym: "Lyb-8" RELATED [] synonym: "sialic acid-binding Ig-like lectin 2" EXACT [] synonym: "siglec-2" EXACT [] synonym: "SIGLEC2" RELATED [] synonym: "T-cell surface antigen Leu-14" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001289 name: membrane-spanning 4-domains subfamily A member 1 namespace: protein def: "A protein that is a translation product of the MS4A1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "B-cell differentiation antigen Ly-44" EXACT [] synonym: "B-cell surface antigen CD20" EXACT [] synonym: "B-lymphocyte antigen CD20" EXACT [] synonym: "B-lymphocyte surface antigen B1" EXACT [] synonym: "Bp35" EXACT [DNx] synonym: "CD20" EXACT [] synonym: "leukocyte surface antigen Leu-16" EXACT [] synonym: "Ly-44" RELATED [] synonym: "lymphocyte antigen 44" EXACT [] synonym: "MS4A1" EXACT PRO-short-label [] synonym: "Ms4a2" RELATED [] xref: PIRSF:PIRSF001995 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001290 name: B7-related protein namespace: protein def: "A protein that is a member of a family that includes translation products of genes CD86, CD276, ICOSLG, and others. These are membrane-anchored proteins with a small intracellular domain and an extracellular domain with signal sequence, an Immunoglobulin V-set domain (PF07686), and a CD80-like C2-set immunoglobulin domain (PF08205)." [PRO:WCB] comment: Category=family. is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001292 name: C-type lectin domain family 4 member C namespace: protein def: "A protein that is a translation product of the CLEC4C gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "BDCA-2" EXACT [] synonym: "BDCA2" RELATED [] synonym: "blood dendritic cell antigen 2" EXACT [] synonym: "C-type lectin superfamily member 7" EXACT [] synonym: "CD303" EXACT [] synonym: "CLEC4C" EXACT PRO-short-label [] synonym: "CLECSF11" RELATED [] synonym: "CLECSF7" RELATED [] synonym: "dendritic lectin" EXACT [] synonym: "DLEC" RELATED [] synonym: "HECL" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001293 name: C-type lectin domain family 4 member K namespace: protein def: "A protein that is a translation product of the CD207 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD207" EXACT PRO-short-label [] synonym: "CLEC4K" RELATED [] synonym: "langerin" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001300 name: CD209 molecule namespace: protein def: "A protein that is a translation product of the CD209 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. This gene and CLEC4M are products of a recent gene duplication in the primate lineage. Independent duplications of an ancestral gene have given rise to several orthologs in rodents, including CD209A. synonym: "C-type lectin domain family 4 member L" EXACT [] synonym: "CD209" EXACT PRO-short-label [] synonym: "CD209 antigen" EXACT [] synonym: "CLEC4L" RELATED [] synonym: "DC-SIGN" RELATED [] synonym: "DC-SIGN1" EXACT [] synonym: "dendritic cell-specific ICAM-3-grabbing non-integrin 1" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001307 name: CD44 molecule namespace: protein def: "A protein that is a translation product of the CD44 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD44" EXACT PRO-short-label [] synonym: "CD44 antigen" EXACT [] synonym: "CDw44" EXACT [] synonym: "ECMR-III" EXACT [] synonym: "epican" EXACT [] synonym: "extracellular matrix receptor III" EXACT [] synonym: "GP90 lymphocyte homing/adhesion receptor" EXACT [] synonym: "heparan sulfate proteoglycan" EXACT [] synonym: "hermes antigen" EXACT [] synonym: "HUTCH-I" EXACT [] synonym: "hyaluronate receptor" EXACT [] synonym: "LHR" RELATED [] synonym: "ly-24" EXACT [] synonym: "lymphocyte antigen 24" EXACT [] synonym: "MDU2" RELATED [] synonym: "MDU3" RELATED [] synonym: "MIC4" RELATED [] synonym: "PGP-1" EXACT [] synonym: "PGP-I" RELATED [] synonym: "phagocytic glycoprotein 1" EXACT [] synonym: "phagocytic glycoprotein I" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001308 name: CD48 molecule namespace: protein def: "A protein that is a translation product of the CD48 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "B-lymphocyte activation marker BLAST-1" EXACT [] synonym: "Bcm-1" RELATED [] synonym: "BCM1" RELATED [] synonym: "BCM1 surface antigen" EXACT [] synonym: "BLAST-1" EXACT [] synonym: "BLAST1" RELATED [] synonym: "CD48" EXACT PRO-short-label [] synonym: "CD48 antigen" EXACT [] synonym: "HM48-1" EXACT [] synonym: "leukocyte antigen MEM-102" EXACT [] synonym: "MRC OX-45 surface antigen" EXACT [] synonym: "sgp-60" EXACT [] synonym: "TCT.1" EXACT [] xref: PANTHER:PTHR12080\:SF3 xref: PIRSF:PIRSF001973 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001310 name: CD83 molecule namespace: protein def: "A protein that is a translation product of the CD83 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "B-cell activation protein" EXACT [] synonym: "CD83" EXACT PRO-short-label [] synonym: "CD83 antigen" EXACT [] synonym: "cell surface protein HB15" EXACT [] synonym: "hCD83" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001318 name: L-selectin namespace: protein def: "A protein that is a translation product of the SELL gene or a 1:1 ortholog thereof. It is a leukocyte adhesion receptor that play an important role in regulating the inflammatory response by mediating leukocyte tethering and rolling on adherent leukocytes." [PMID:12403782, PRO:JAN] comment: Category=gene. synonym: "CD62 antigen-like family member L" EXACT [] synonym: "CD62L" EXACT [] synonym: "gp90-MEL" EXACT [] synonym: "LAM-1" EXACT [] synonym: "LECAM1" EXACT [] synonym: "leukocyte adhesion molecule 1" EXACT [] synonym: "leukocyte surface antigen Leu-8" EXACT [] synonym: "leukocyte-endothelial cell adhesion molecule 1" EXACT [] synonym: "LNHR" RELATED [] synonym: "ly-22" EXACT [] synonym: "Ly22" RELATED [] synonym: "LYAM1" RELATED [] synonym: "lymph node homing receptor" EXACT [] synonym: "lymphocyte antigen 22" EXACT [] synonym: "lymphocyte surface MEL-14 antigen" EXACT [] synonym: "SELL" EXACT PRO-short-label [] synonym: "TQ1" EXACT [] xref: PIRSF:PIRSF002421 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001319 name: SLAM family member 5 namespace: protein def: "A protein that is a translation product of the CD84 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD84" EXACT PRO-short-label [] synonym: "cell surface antigen MAX.3" EXACT [] synonym: "hly9-beta" EXACT [] synonym: "leukocyte differentiation antigen CD84" EXACT [] synonym: "signaling lymphocytic activation molecule 5" EXACT [] synonym: "SLAMF5" RELATED [] xref: PANTHER:PTHR12080\:SF6 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001320 name: alpha-(1,3)-fucosyltransferase namespace: protein def: "A protein that is a stand alone version of the Glycosyltransferase family 10 (fucosyltransferase) (PF00852) domain. Proteins in this class may catalyze alpha-1,3 glycosidic linkages." [PMID:9451017] comment: Category=family. xref: PIRSF:PIRSF005726 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001326 name: bone marrow stromal antigen 2 namespace: protein def: "A protein that is a translation product of the BST2 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "BST-2" EXACT [] synonym: "BST2" EXACT PRO-short-label [] synonym: "CD317" EXACT [] synonym: "HM1.24 antigen" EXACT [] synonym: "tetherin" EXACT [] xref: PIRSF:PIRSF023920 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001327 name: cadherin namespace: protein def: "A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (PF00028), a transmembrane region, and a Cadherin cytoplasmic region (PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF002504 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001332 name: carcinoembryonic antigen-related cell adhesion molecule 8 namespace: protein def: "A protein that is a translation product of the CEACAM8 gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "carcinoembryonic antigen CGM6" EXACT [] synonym: "CD66b" EXACT [] synonym: "CD67 antigen" EXACT [] synonym: "CEACAM8" EXACT PRO-short-label [] synonym: "CGM6" RELATED [] synonym: "non-specific cross-reacting antigen NCA-95" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001337 name: complement receptor type 1 namespace: protein def: "A protein that is a translation product of the CR1 gene or a 1:1 ortholog thereof. There is no counterpart in mouse." [PRO:WCB] comment: Category=gene. synonym: "C3b/C4b receptor" EXACT [] synonym: "C3BR" RELATED [] synonym: "CD35" EXACT [] synonym: "CR1" EXACT PRO-short-label [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001338 name: complement receptor type 2 namespace: protein def: "A protein that is a translation product of the CR2 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "C3DR" RELATED [] synonym: "CD21" EXACT [] synonym: "complement C3d receptor" EXACT [] synonym: "CR2" EXACT PRO-short-label [] synonym: "Cr2" EXACT [DNx] synonym: "EBV receptor" EXACT [] synonym: "epstein-Barr virus receptor" EXACT [] xref: PIRSF:PIRSF002484 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001343 name: CD69 molecule namespace: protein def: "A protein that is a translation product of the CD69 gene or a 1:1 ortholog thereof. A type II transmembrane protein with a C-type lectin binding domain in the extracellular portion of the molecule. Involved in lymphocyte proliferation and functions as a signal transmitting receptor in lymphocytes, natural killer (NK) cells, and platelets." [PMID:10466080, PRO:CNA, UniProtKB:Q07108] comment: Category=gene. synonym: "activation inducer molecule" EXACT [] synonym: "AIM" EXACT [] synonym: "BL-AC/P26" EXACT [] synonym: "C-type lectin domain family 2 member C" EXACT [] synonym: "CD69" EXACT PRO-short-label [] synonym: "CLEC2C" RELATED [] synonym: "EA1" EXACT [] synonym: "early activation antigen CD69" EXACT [] synonym: "early T-cell activation antigen p60" EXACT [] synonym: "GP32/28" EXACT [] synonym: "leukocyte surface antigen Leu-23" EXACT [] synonym: "MLR-3" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001344 name: ectonucleotide pyrophosphatase/phosphodiesterase family member 3 namespace: protein def: "A protein that is a translation product of the ENPP3 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD203c" EXACT [] synonym: "E-NPP 3" EXACT [] synonym: "ectonucleotide pyrophosphatase/phosphodiesterase 3" EXACT [] synonym: "ENPP3" EXACT PRO-short-label [] synonym: "PD-Ibeta" EXACT [] synonym: "PDNP3" RELATED [] synonym: "phosphodiesterase I beta" EXACT [] synonym: "phosphodiesterase I/nucleotide pyrophosphatase 3" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001345 name: endoglin namespace: protein def: "A protein that is a translation product of the ENG gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "CD105" EXACT [] synonym: "cell surface MJ7/18 antigen" EXACT [] synonym: "Edg" RELATED [] synonym: "END" RELATED [] synonym: "ENG" EXACT PRO-short-label [] xref: PIRSF:PIRSF038746 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001350 name: forkhead box protein P3 namespace: protein def: "A protein that is a translation product of the FOXP3 gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "FOXP3" EXACT PRO-short-label [] synonym: "IPEX" RELATED [] synonym: "scurfin" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001352 name: glycophorin namespace: protein def: "A protein that contains an extracellular Glycophorin A domain (PF01102), followed by a single-pass transmembrane region and a small intracellular domain. A protein that is an integral protein of the red cell membrane. Proteins in this class are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane." [InterPro:IPR001195, PRO:CNA] comment: Category=family. xref: PIRSF:PIRSF002466 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001355 name: immunoglobulin gamma Fc receptor II/III/IV namespace: protein def: "A protein with a core domain architecture consisting of an extracellular domain containing two copies of the Immunoglobulin domain (PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. Human II-a, II-b, and II-c represent a recent gene expansion and are equally related to mouse II, III, and IV. Human III-A and III-B are closely related and closer to mouse IV than to mouse III." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF001980 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001356 name: immunoglobulin gamma Fc receptor I namespace: protein def: "A protein with a core domain architecture consisting of an extracellular domain containing two or three copies of the Immunoglobulin domain (PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. It comprises the translation products of the FCGR1 gene (mouse) or one of the closely related FCGR1A, FCGR1B, or FCGR1C genes (human). FCGR1C may be a pseudogene in humans." [PRO:CNA] comment: Category=family. synonym: "Fc-gamma receptor" RELATED [] xref: PIRSF:PIRSF001981 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001380 name: interleukin-2 receptor subunit alpha namespace: protein def: "A protein that is a translation product of the IL2RA gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "CD25" EXACT [] synonym: "IL-2 receptor subunit alpha" EXACT [] synonym: "IL-2-RA" EXACT [] synonym: "IL-2R subunit alpha" EXACT [] synonym: "IL2-RA" EXACT [] synonym: "Il2r" RELATED [] synonym: "IL2RA" EXACT PRO-short-label [] synonym: "p55" RELATED [] synonym: "TAC antigen" EXACT [] xref: PIRSF:PIRSF001954 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001381 name: interleukin-2 receptor subunit beta namespace: protein def: "A protein that is a translation product of the IL2RB gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "CD122" EXACT [] synonym: "high affinity IL-2 receptor subunit beta" EXACT [] synonym: "IL-2 receptor subunit beta" EXACT [] synonym: "IL-2R subunit beta" EXACT [] synonym: "IL-2RB" EXACT [] synonym: "IL2RB" EXACT PRO-short-label [] synonym: "p70-75" EXACT [] synonym: "p75" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001398 name: leukocyte immunoglobulin-like receptor subfamily A member 4 namespace: protein def: "A protein that is a translation product of the LILRA4 gene or a 1:1 ortholog thereof. This gene is a member of a lineage-specific gene expansion in primates." [PRO:WCB] comment: Category=gene. synonym: "CD85 antigen-like family member G" EXACT [] synonym: "CD85g" EXACT [] synonym: "ILT-7" EXACT [] synonym: "ILT7" RELATED [] synonym: "immunoglobulin-like transcript 7" EXACT [] synonym: "LILRA4" EXACT PRO-short-label [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001402 name: killer cell lectin-like receptor subfamily D member 1 namespace: protein def: "A protein that is a translation product of the KLRD1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD94" EXACT [] synonym: "KLRD1" EXACT PRO-short-label [] synonym: "KP43" EXACT [] synonym: "natural killer cells antigen CD94" EXACT [] synonym: "NK cell receptor" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001403 name: tetraspanin namespace: protein def: "A protein with four transmembrane domains, small intracellular amino- and carboxyl-terminal regions, and two extracellular loops, a small one (EC1) and a larger one (EC2) of about 100 residues. The EC2 loop contains at least 4 cysteine residues, including a highly conserved 'CCG' motif." [PRO:WCB, Wikipedia:Tetraspanin] comment: Category=family. xref: PIRSF:PIRSF002419 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001408 name: ADP-ribosyl cyclase 1 namespace: protein def: "An ADP-ribosyl cyclase that is a translation product of the CD38 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "cADPr hydrolase 1" EXACT [] synonym: "CD38" EXACT PRO-short-label [] synonym: "cyclic ADP-ribose hydrolase 1" EXACT [] synonym: "I-19" EXACT [] synonym: "NIM-R5 antigen" EXACT [] synonym: "T10" EXACT [] is_a: PR:000001281 ! ADP-ribosyl cyclase property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001412 name: CD86 molecule namespace: protein def: "A B7-related protein that is a translation product of the CD86 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "activation B7-2 antigen" EXACT [] synonym: "B70" EXACT [] synonym: "BU63" EXACT [] synonym: "CD28LG2" RELATED [] synonym: "CD86" EXACT PRO-short-label [] synonym: "CD86 antigen" EXACT [] synonym: "CTLA-4 counter-receptor B7.2" EXACT [] synonym: "early T-cell costimulatory molecule 1" EXACT [] synonym: "ETC-1" EXACT [] synonym: "FUN-1" EXACT [] synonym: "T-lymphocyte activation antigen CD86" EXACT [] xref: PANTHER:PTHR25462\:SF45 is_a: PR:000001290 ! B7-related protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001431 name: N-formyl peptide receptor namespace: protein def: "A rhodopsin-like G-protein coupled receptor that is a translation product of the FPR1, FPR2, or FPR3 gene and whose active form binds N-formyl methionyl peptides." [InterPro:IPR000826, PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038561 is_a: PR:000001094 ! rhodopsin-like G-protein coupled receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001438 name: CD80 molecule namespace: protein def: "A B7-related protein that is a translation product of the CD80 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "activation B7-1 antigen" EXACT [] synonym: "B7" EXACT [] synonym: "BB1" EXACT [] synonym: "CD28LG" RELATED [] synonym: "CD28LG1" RELATED [] synonym: "CD80" EXACT PRO-short-label [] synonym: "CTLA-4 counter-receptor B7.1" EXACT [] synonym: "LAB7" RELATED [] synonym: "T-lymphocyte activation antigen CD80" EXACT [] is_a: PR:000001290 ! B7-related protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001444 name: cadherin-5 namespace: protein def: "A cadherin that is a translation product of the CDH5 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "7B4 antigen" EXACT [] synonym: "CD144" EXACT [] synonym: "CDH5" EXACT PRO-short-label [] synonym: "vascular endothelial cadherin" EXACT [] synonym: "VE-cadherin" EXACT [] is_a: PR:000001327 ! cadherin property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001447 name: epithelial cadherin namespace: protein def: "A cadherin that is a translation product of the CDH1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "ARC-1" EXACT [] synonym: "CAM 120/80" EXACT [] synonym: "CD324" EXACT [] synonym: "CDH1" EXACT PRO-short-label [] synonym: "CDHE" RELATED [] synonym: "E-cadherin" EXACT [] synonym: "epithelial cadherin" EXACT [] synonym: "UVO" RELATED [] synonym: "uvomorulin" EXACT [] is_a: PR:000001327 ! cadherin property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001456 name: alpha-(1,3)-fucosyltransferase FUT4 namespace: protein def: "A fucosyltransferase that is a translation product of the FUT4 gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "CD15" EXACT [] synonym: "ELAM-1 ligand fucosyltransferase" EXACT [] synonym: "ELFT" RELATED [] synonym: "FCT3A" RELATED [] synonym: "Fuc-TIV" EXACT [] synonym: "fucosyltransferase 4" EXACT [] synonym: "fucosyltransferase FUT4" EXACT [] synonym: "fucosyltransferase IV" EXACT [] synonym: "FucT-IV" EXACT [] synonym: "FUT4" EXACT PRO-short-label [] synonym: "galactoside 3-L-fucosyltransferase" EXACT [] is_a: PR:000001320 ! alpha-(1,3)-fucosyltransferase property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001460 name: glycophorin-A namespace: protein def: "A glycophorin that is a translation product of the GYPA gene or a 1:1 ortholog thereof. It is the major sialoglycoprotein of the erythrocyte membrane. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on Ser and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain." [InterPro:IPR001195, PRO:CNA] comment: Category=gene. synonym: "CD235a" EXACT [] synonym: "GPA" RELATED [] synonym: "GYPA" EXACT PRO-short-label [] synonym: "MN sialoglycoprotein" EXACT [] synonym: "PAS-2" EXACT [] synonym: "sialoglycoprotein alpha" EXACT [] is_a: PR:000001352 ! glycophorin property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001465 name: high affinity immunoglobulin gamma Fc receptor I namespace: protein def: "An immunoglobulin gamma Fc receptor I that is a translation product of the FCGR1A gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. The Fcgr1 gene in mouse is a 1:1 ortholog of FCGR1A, not FCGR1B. synonym: "CD64" EXACT [] synonym: "Fc-gamma RI" EXACT [] synonym: "FCG1" RELATED [] synonym: "FCGR1" RELATED [] synonym: "FCGR1A" EXACT PRO-short-label [] synonym: "FcRI" EXACT [] synonym: "IGFR1" RELATED [] synonym: "IgG Fc receptor I" EXACT [] is_a: PR:000001356 ! immunoglobulin gamma Fc receptor I property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001479 name: low affinity immunoglobulin gamma Fc region receptor II namespace: protein def: "An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the FCGR2 gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "CD32" BROAD [] synonym: "Fc gamma receptor IIB" EXACT [] synonym: "Fc-gamma RII" EXACT [] synonym: "Fc-gamma-RIIB" EXACT [] synonym: "FCGR2" EXACT PRO-short-label [] synonym: "Fcgr2" RELATED [] synonym: "Fcgr2b" RELATED [] synonym: "FcRII" EXACT [] synonym: "IgG Fc receptor II beta" EXACT [] synonym: "ly-17" EXACT [] synonym: "lymphocyte antigen 17" EXACT [] is_a: PR:000001355 ! immunoglobulin gamma Fc receptor II/III/IV property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001481 name: low affinity immunoglobulin gamma Fc region receptor II-b namespace: protein def: "An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the FCGR2B gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "CD32" BROAD [] synonym: "CDw32" BROAD [] synonym: "Fc-gamma RII-b" EXACT [] synonym: "Fc-gamma-RIIb" EXACT [] synonym: "FCG2" RELATED [] synonym: "FCGR2B" EXACT PRO-short-label [] synonym: "FcRII-b" EXACT [] synonym: "IGFR2" RELATED [] synonym: "IgG Fc receptor II-b" EXACT [] is_a: PR:000001355 ! immunoglobulin gamma Fc receptor II/III/IV property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001483 name: low affinity immunoglobulin gamma Fc region receptor III namespace: protein def: "An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the FCGR3 gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "CD16" EXACT [] synonym: "Fc-gamma RIII" EXACT [] synonym: "FCGR3" EXACT PRO-short-label [] synonym: "Fcgr3" RELATED [] synonym: "FcRIII" EXACT [] synonym: "IgG Fc receptor III" EXACT [] is_a: PR:000001355 ! immunoglobulin gamma Fc receptor II/III/IV property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001580 name: fMet-Leu-Phe receptor namespace: protein def: "An N-formyl peptide receptor that is a translation product of the FPR1 gene or a 1:1 ortholog thereof. The preferred ligand is the peptide fMet-Leu-Phe, a bacterial peptide that acts as a chemoattractant in various pathophysiological conditions." [InterPro:IPR000826, PRO:WCB] comment: Category=gene. synonym: "fMLP receptor" EXACT [] synonym: "FPR" EXACT [] synonym: "FPR1" EXACT PRO-short-label [] synonym: "N-formyl peptide receptor" BROAD [] synonym: "N-formylpeptide chemoattractant receptor" EXACT [] is_a: PR:000001431 ! N-formyl peptide receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001753 name: transcription factor NF-kappa-B namespace: protein def: "A protein with a core domain composition consisting of a Rel homology domain (RHD) (PF00554), an IPT/TIG domain (PF01833), six copies of the Ankyrin repeat (PF00023), a Death domain (PF00531) and a C-terminal PEST region." [PRO:JAN] comment: Category=family. xref: PIRSF:PIRSF036310 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001785 name: prominin namespace: protein def: "A protein with core architecture consisting of one Prominin (PF05478) domain. The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and Homo sapiens prominin and prominin-like 1 are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain." [InterPro:IPR008795, PMID:11467842] comment: Category=family. xref: PANTHER:PTHR22730 xref: PIRSF:PIRSF017831 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001786 name: prominin-1 namespace: protein def: "A prominin that is a translation product of the PROM1 gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "antigen AC133" EXACT [] synonym: "antigen AC133 homolog" EXACT [] synonym: "CD133" EXACT [] synonym: "Prom" RELATED [] synonym: "PROM1" EXACT PRO-short-label [] synonym: "prominin-like protein 1" EXACT [] synonym: "PROML1" RELATED [] is_a: PR:000001785 ! prominin property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001800 name: 5'-nucleotidase namespace: protein def: "A protein that is a translation product of the NT5E gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "5'-NT" EXACT [] synonym: "CD73" EXACT [] synonym: "ecto-5'-nucleotidase" EXACT [] synonym: "NT5" RELATED [] synonym: "NT5E" EXACT PRO-short-label [] synonym: "NTE" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001806 name: C-type lectin domain family 6 member A namespace: protein def: "A protein that is a translation product of the CLEC6A gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "C-type lectin superfamily member 10" EXACT [] synonym: "Clec4n" RELATED [] synonym: "CLEC6A" EXACT PRO-short-label [] synonym: "CLECSF10" RELATED [] synonym: "DC-associated C-type lectin 2" EXACT [] synonym: "dectin-2" EXACT [] synonym: "DECTIN2" RELATED [] synonym: "dendritic cell-associated C-type lectin 2" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001807 name: C-type lectin domain family 7 member A namespace: protein def: "A protein that is a translation product of the CLEC7A gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "beta-glucan receptor" EXACT [] synonym: "BGR" RELATED [] synonym: "C-type lectin superfamily member 12" EXACT [] synonym: "CLEC7A" EXACT PRO-short-label [] synonym: "CLECSF12" RELATED [] synonym: "DC-associated C-type lectin 1" EXACT [] synonym: "dectin-1" EXACT [] synonym: "DECTIN1" RELATED [] synonym: "dendritic cell-associated C-type lectin 1" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001809 name: CD59-like glycoprotein namespace: protein def: "A protein that is a translation product of the CD59 or closely related gene. This gene is present as a single copy in human and has undergone a lineage-specific duplication in mouse. CD59 antigen has a core architecture consisting of one UPAR/Ly-6 domain (PF00021), a small domain of about 70 amino acids and containing 5 conserved disulfide bonds. It is both N- and O-glycosylated and is a GPI-anchored protein that releases soluble forms in some tissues." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038782 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001810 name: CSF-1/PDGF receptor-type tyrosine-protein kinase namespace: protein def: "A protein with core architecture consisting of asignal sequence, 5 Ig-like domains, followed by a transmembrane sequence, followed by a Protein tyrosine kinase domain (PF07714). However, only 1-3 of the Ig domains are detected by the Pfam HMMs in most of the sequences. PF00047 is most common, but other members of the Ig domain clan, PF07679 and PF07686 can be identified instead. The fourth Ig domain lacks the disulfide-bonded cysteines." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF000615 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001813 name: EGF-like module-containing mucin-like hormone receptor-like 1 namespace: protein def: "A protein that is a translation product of the EMR1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "cell surface glycoprotein F4/80" EXACT [] synonym: "EGF-like module receptor 1" EXACT [] synonym: "EMR1" EXACT PRO-short-label [] synonym: "EMR1 hormone receptor" EXACT [] synonym: "Gpf480" RELATED [] synonym: "TM7LN3" RELATED [] xref: PIRSF:PIRSF038685 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001832 name: SIRP/SHPS-1 family protein namespace: protein def: "A protein with core architecture consisting of a signal sequence, one Immunoglobulin V-set domain (PF07686), two Immunoglobulin C1-set domains (PF07654), a single-pass transmembrane region and a very small cytoplasmic region." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038063 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001833 name: SLAM family member 1 namespace: protein def: "A protein that is a translation product of the SLAMF1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD150" EXACT [] synonym: "CDw150" EXACT [] synonym: "IPO-3" EXACT [] synonym: "SLAM" RELATED [] synonym: "SLAMF1" EXACT PRO-short-label [] xref: PANTHER:PTHR12080\:SF1 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001835 name: T-box transcription factor TBX21 namespace: protein def: "A protein that is a translation product of the TBX21 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "T-box protein 21" EXACT [] synonym: "T-cell-specific T-box transcription factor T-bet" EXACT [] synonym: "TBET" RELATED [] synonym: "TBLYM" RELATED [] synonym: "TBX21" EXACT PRO-short-label [] synonym: "transcription factor TBLYM" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001836 name: CD7 molecule namespace: protein def: "A protein that is a translation product of the CD7 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD7" EXACT PRO-short-label [] synonym: "GP40" EXACT [] synonym: "T-cell antigen CD7" EXACT [] synonym: "T-cell leukemia antigen" EXACT [] synonym: "T-cell surface antigen Leu-9" EXACT [] synonym: "TP41" EXACT [] xref: PIRSF:PIRSF038791 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001838 name: T-cell surface glycoprotein CD1 namespace: protein def: "A protein with core architecture consisting of a signal sequence, an extracellular region with Class I Histocompatibility antigen, domains alpha 1 and alpha two (PF00129) and an Immunoglobulin C1-set domain (PF07654), a single-pass transmembrane region, and a very short cytoplasmic region. Forms a heterodimer with beta-2 microglobulin." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038798 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001839 name: T-cell surface glycoprotein CD5 namespace: protein def: "A protein that is a translation product of the CD5 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD5" EXACT PRO-short-label [] synonym: "LEU1" RELATED [] synonym: "ly-1" EXACT [] synonym: "lymphocyte antigen 1" EXACT [] synonym: "lymphocyte antigen T1/Leu-1" EXACT [] synonym: "Lyt-1" EXACT [DNx] xref: PANTHER:PTHR19331\:SF6 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001841 name: T-cell-specific surface glycoprotein CD28 namespace: protein def: "A protein that is a translation product of the CD28 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD28" EXACT PRO-short-label [] synonym: "TP44" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001843 name: Thy-1 membrane glycoprotein namespace: protein def: "A protein that is a translation product of the THY1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD90" EXACT [] synonym: "CDw90" EXACT [] synonym: "Thy-1" RELATED [] synonym: "Thy-1 antigen" EXACT [DNx] synonym: "THY1" EXACT PRO-short-label [] xref: PIRSF:PIRSF038777 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001844 name: arginase-1 namespace: protein def: "A protein that is a translation product of the ARG1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "ARG1" EXACT PRO-short-label [] synonym: "liver-type arginase" EXACT [] synonym: "type I arginase" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001850 name: cathepsin K namespace: protein def: "A protein that is a translation product of the CTSK gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "cathepsin O" RELATED [] synonym: "cathepsin O2" EXACT [] synonym: "cathepsin X" RELATED [] synonym: "CTSK" EXACT PRO-short-label [] synonym: "CTSO" RELATED [] synonym: "CTSO2" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001852 name: cytotoxic T-lymphocyte protein 4 namespace: protein def: "A protein that is a translation product of the CTLA4 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD152" EXACT [] synonym: "CTLA-4" EXACT [] synonym: "CTLA4" EXACT PRO-short-label [] synonym: "cytotoxic T-lymphocyte-associated antigen 4" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001858 name: immunoglobulin iota chain namespace: protein def: "A protein that is a translation product of the VPREB1 gene or a 1:1 ortholog thereof. The gene is recently and independently duplicated in mouse and rabbit, giving rise to very closely related VPREB2 genes in those species. The protein associates with the Ig-mu chain to form a molecular complex that is expressed only on the surface of pre-B-cells." [PRO:WCB] comment: Category=gene. synonym: "CD179 antigen-like family member A" EXACT [] synonym: "CD179a" EXACT [] synonym: "protein VPreB1" EXACT [] synonym: "V(pre)B protein" EXACT [] synonym: "VPREB" RELATED [] synonym: "VpreB protein" EXACT [] synonym: "VPREB1" EXACT PRO-short-label [] xref: PIRSF:PIRSF038787 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001859 name: immunoglobulin lambda-like polypeptide 1 namespace: protein def: "A protein that is a translation product of the IGLL1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD179 antigen-like family member B" EXACT [] synonym: "CD179b" EXACT [] synonym: "Ig lambda-5" EXACT [] synonym: "Igl-5" RELATED [] synonym: "IGL1" RELATED [] synonym: "IGLL1" EXACT PRO-short-label [] synonym: "immunoglobulin omega polypeptide" EXACT [] synonym: "immunoglobulin-related protein 14.1" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001860 name: inducible T-cell costimulator namespace: protein def: "A protein that is a translation product of the ICOS gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "activation-inducible lymphocyte immunomediatory molecule" EXACT [] synonym: "AILIM" RELATED [] synonym: "CCLP" EXACT [] synonym: "CD278" EXACT [] synonym: "CD28 and CTLA-4-like protein" EXACT [] synonym: "CD28-related protein 1" EXACT [] synonym: "CRP-1" RELATED [] synonym: "ICOS" EXACT PRO-short-label [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001861 name: integrin beta namespace: protein def: "A protein with core architecture consisting of a large extracellular region containing one Integrin, beta chain domain (PF00362), up to four EGF-like domains (PF07974), and an Integrin beta tail domain (PF07965), followed by a single-pass transmembrane region and a small cytoplasmic region often containing an Integrin beta cytoplasmic domain (PF08725)." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF002512 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001865 name: interleukin-3 receptor class 2 alpha chain namespace: protein def: "A protein that is a translation product of the IL3RA gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD123" EXACT [] synonym: "IL-3 receptor subunit alpha" EXACT [] synonym: "IL-3R subunit alpha" EXACT [] synonym: "IL-3R-alpha" EXACT [] synonym: "IL-3RA" EXACT [] synonym: "IL3R" RELATED [] synonym: "IL3RA" EXACT PRO-short-label [] synonym: "interleukin-3 receptor class II alpha chain" EXACT [] synonym: "Sut-1" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001867 name: interleukin-5 receptor subunit alpha namespace: protein def: "A protein that is a translation product of the IL5RA gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD125" EXACT [] synonym: "CDw125" EXACT [] synonym: "IL-5 receptor subunit alpha" EXACT [] synonym: "IL-5R subunit alpha" EXACT [] synonym: "IL-5R-alpha" EXACT [] synonym: "IL-5RA" EXACT [] synonym: "IL5R" RELATED [] synonym: "IL5RA" EXACT PRO-short-label [] xref: PIRSF:PIRSF018419 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001869 name: interleukin-7 receptor subunit alpha namespace: protein def: "A protein that is a translation product of the IL7R gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD127" EXACT [] synonym: "CDw127" EXACT [] synonym: "IL-7 receptor subunit alpha" EXACT [] synonym: "IL-7R subunit alpha" EXACT [] synonym: "IL-7R-alpha" EXACT [] synonym: "IL-7RA" EXACT [] synonym: "IL7R" EXACT PRO-short-label [] xref: PIRSF:PIRSF001960 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001874 name: KLRB1-like protein namespace: protein def: "A protein that is a translation product of the KLRB1 gene or its closely related paralogs (KLRB1A-F). There are lineage-specific expansions in mouse and rat." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038804 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001879 name: leukosialin namespace: protein def: "A protein that is a translation product of the SPN gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "B-cell differentiation antigen LP-3" EXACT [] synonym: "CD43" EXACT [] synonym: "galactoglycoprotein" EXACT [] synonym: "GALGP" EXACT [] synonym: "leukocyte sialoglycoprotein" EXACT [] synonym: "ly-48" EXACT [] synonym: "lymphocyte antigen 48" EXACT [] synonym: "sialophorin" EXACT [] synonym: "SPN" EXACT PRO-short-label [] xref: PIRSF:PIRSF001994 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001880 name: low affinity immunoglobulin epsilon Fc receptor namespace: protein def: "A protein that is a translation product of the FCER2 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "BLAST-2" EXACT [] synonym: "C-type lectin domain family 4 member J" EXACT [] synonym: "CD23" EXACT [] synonym: "CD23A" RELATED [] synonym: "CLEC4J" RELATED [] synonym: "Fc-epsilon-RII" EXACT [] synonym: "FCE2" RELATED [] synonym: "FCER2" EXACT PRO-short-label [] synonym: "Fcer2a" RELATED [] synonym: "IGEBF" RELATED [] synonym: "immunoglobulin E-binding factor" EXACT [] synonym: "lymphocyte IgE receptor" EXACT [] xref: PIRSF:PIRSF002426 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001883 name: lysosome-associated membrane protein namespace: protein def: "A protein with core architecture consisting of a Lysosome-associated membrane glycoprotein (PF01299) domain. It is a single-pass type I membrane protein that shuttles between lysosomes, endosomes, and the plasma membrane." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF002462 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001884 name: macrophage receptor MARCO namespace: protein def: "A protein that is a translation product of the MARCO gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "macrophage receptor with collagenous structure" EXACT [] synonym: "MARCO" EXACT PRO-short-label [] synonym: "SCARA2" RELATED [] synonym: "scavenger receptor class A member 2" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001885 name: macrophage scavenger receptor types I and II namespace: protein def: "A protein that is a translation product of the MSR1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD204" EXACT [] synonym: "macrophage acetylated LDL receptor I and II" EXACT [] synonym: "MSR1" EXACT PRO-short-label [] synonym: "SCARA1" RELATED [] synonym: "scavenger receptor class A member 1" EXACT [] synonym: "scavenger receptor type A" EXACT [] synonym: "Scvr" RELATED [] synonym: "SR-A" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001888 name: membrane alanyl aminopeptidase-like metallopeptidase namespace: protein def: "A protein with core architecture consisting of a Peptidase family M1 domain (PF01433)." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF005502 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001889 name: CD14 molecule namespace: protein def: "A protein that is a translation product of the CD14 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD14" EXACT PRO-short-label [] synonym: "monocyte differentiation antigen CD14" EXACT [] synonym: "myeloid cell-specific leucine-rich glycoprotein" EXACT [] xref: PIRSF:PIRSF002017 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001892 name: CD33 molecule namespace: protein def: "A protein that is a translation product of the CD33 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD33" EXACT PRO-short-label [] synonym: "gp67" EXACT [] synonym: "myeloid cell surface antigen CD33" EXACT [] synonym: "sialic acid-binding Ig-like lectin 3" EXACT [] synonym: "siglec-3" EXACT [] synonym: "SIGLEC3" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001893 name: natural cytotoxicity triggering receptor 1 namespace: protein def: "A protein that is a translation product of the NCR1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "activating receptor 1" EXACT [] synonym: "CD335" EXACT [] synonym: "hNKp46" EXACT [] synonym: "LY94" RELATED [] synonym: "lymphocyte antigen 94" EXACT [] synonym: "lymphocyte antigen 94 homolog" EXACT [] synonym: "mAR-1" EXACT [] synonym: "mNKp46" EXACT [] synonym: "natural killer cell p46-related protein" EXACT [] synonym: "NCR1" EXACT PRO-short-label [] synonym: "NK cell-activating receptor" BROAD [] synonym: "NK-p46" EXACT [] synonym: "NKp46" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001896 name: natural killer cell receptor 2B4 namespace: protein def: "A protein that is a translation product of the CD244 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "2B4" RELATED [] synonym: "CD244" EXACT PRO-short-label [] synonym: "h2B4" EXACT [] synonym: "NAIL" EXACT [] synonym: "NK cell activation-inducing ligand" EXACT [] synonym: "NK cell type I receptor protein 2B4" EXACT [] synonym: "NKR2B4" EXACT [] synonym: "Nmrk" RELATED [] synonym: "non-MHC restricted killing associated" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001897 name: natural killer cell receptor NKG2 namespace: protein def: "A protein with core architecture consisting of an as yet unnamed domain in the amino-terminal half and a carboxyl-terminal Lectin C-type domain (PF00059)." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF005558 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001898 name: neprilysin namespace: protein def: "A protein that is a translation product of the MME gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "atriopeptidase" EXACT [] synonym: "CALLA" EXACT [] synonym: "CD10" EXACT [] synonym: "common acute lymphocytic leukemia antigen" EXACT [] synonym: "enkephalinase" EXACT [] synonym: "EPN" RELATED [] synonym: "MME" EXACT PRO-short-label [] synonym: "NEP" EXACT [] synonym: "neutral endopeptidase" EXACT [] synonym: "neutral endopeptidase 24.11" EXACT [] xref: PIRSF:PIRSF501074 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001902 name: nuclear receptor ROR-gamma namespace: protein def: "A protein that is a translation product of the RORC gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "NR1F3" RELATED [] synonym: "nuclear receptor RZR-gamma" EXACT [] synonym: "nuclear receptor subfamily 1 group F member 3" EXACT [] synonym: "retinoid-related orphan receptor-gamma" EXACT [] synonym: "RORC" EXACT PRO-short-label [] synonym: "RORG" RELATED [] synonym: "RZRG" RELATED [] synonym: "Thor" RELATED [] synonym: "thymus orphan receptor" EXACT [] synonym: "TOR" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001903 name: paired box protein PAX-5 namespace: protein def: "A protein that is a translation product of the PAX5 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "B-cell-specific transcription factor" EXACT [] synonym: "BSAP" EXACT [] synonym: "Pax-5" RELATED [] synonym: "PAX5" EXACT PRO-short-label [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001905 name: platelet glycoprotein 4 namespace: protein def: "A protein that is a translation product of the CD36 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD36" EXACT PRO-short-label [] synonym: "FAT" EXACT [] synonym: "fatty acid translocase" EXACT [] synonym: "glycoprotein IIIb" EXACT [] synonym: "GP3B" RELATED [] synonym: "GP4" RELATED [] synonym: "GPIIIB" EXACT [] synonym: "GPIV" EXACT [] synonym: "leukocyte differentiation antigen CD36" EXACT [] synonym: "PAS IV" EXACT [] synonym: "PAS-4" EXACT [] synonym: "platelet collagen receptor" EXACT [] synonym: "platelet glycoprotein IV" EXACT [] synonym: "thrombospondin receptor" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001907 name: platelet glycoprotein Ib alpha chain namespace: protein def: "A protein that is a translation product of the GP1BA gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "antigen CD42b-alpha" EXACT [] synonym: "CD42b" EXACT [] synonym: "glycoprotein Ibalpha" EXACT [] synonym: "GP-Ib alpha" EXACT [] synonym: "GP1BA" EXACT PRO-short-label [] synonym: "GPIb-alpha" EXACT [] synonym: "GPIbA" EXACT [] xref: PIRSF:PIRSF002493 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001919 name: programmed cell death protein 1 namespace: protein def: "A protein that is a translation product of the PDCD1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD279" EXACT [] synonym: "hPD-1" EXACT [] synonym: "mPD-1" EXACT [] synonym: "PD1" RELATED [] synonym: "PDCD1" EXACT PRO-short-label [] synonym: "protein PD-1" EXACT [] xref: PIRSF:PIRSF018380 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001925 name: scavenger receptor cysteine-rich type 1 protein M130 namespace: protein def: "A protein that is a translation product of the CD163 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD163" EXACT PRO-short-label [] synonym: "hemoglobin scavenger receptor" EXACT [] synonym: "M130" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001927 name: sialic acid-binding Ig-like lectin 5 namespace: protein def: "A protein that is a translation product of the SIGLEC5 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD170" EXACT [] synonym: "CD33 antigen-like 2" EXACT [] synonym: "CD33L2" RELATED [] synonym: "mSiglec-F" EXACT [] synonym: "OB-binding protein 2" EXACT [] synonym: "OB-BP2" EXACT [] synonym: "OBBP2" RELATED [] synonym: "obesity-binding protein 2" EXACT [] synonym: "sialic acid-binding Ig-like lectin F" EXACT [] synonym: "siglec-5" EXACT [] synonym: "siglec-F" EXACT [] synonym: "SIGLEC5" EXACT PRO-short-label [] synonym: "Siglecf" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001931 name: sialoadhesin namespace: protein def: "A protein that is a translation product of the SIGLEC1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD169" EXACT [] synonym: "Sa" RELATED [] synonym: "SER" EXACT [] synonym: "sheep erythrocyte receptor" EXACT [] synonym: "sialic acid-binding Ig-like lectin 1" EXACT [] synonym: "siglec-1" EXACT [] synonym: "SIGLEC1" EXACT PRO-short-label [] synonym: "SN" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001932 name: signal transducer CD24 namespace: protein def: "A protein that is a translation product of the CD24 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. The mouse ortholog is Cd24a. Mouse protein Cd24b likely also orthologous. Currently it is not in UniProt. synonym: "CD24" EXACT PRO-short-label [] synonym: "CD24A" RELATED [] synonym: "HSA" EXACT [] synonym: "ly-52" EXACT [] synonym: "lymphocyte antigen 52" EXACT [] synonym: "M1/69-J11D heat stable antigen" EXACT [] synonym: "nectadrin" EXACT [] synonym: "R13-Ag" EXACT [] synonym: "small cell lung carcinoma cluster 4 antigen" EXACT [] synonym: "X62 heat stable antigen" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001935 name: syndecan-1 namespace: protein def: "A protein that is a translation product of the SDC1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD138" EXACT [] synonym: "SDC" RELATED [] synonym: "SDC1" EXACT PRO-short-label [] synonym: "Synd-1" RELATED [] synonym: "SYND1" EXACT [] xref: PIRSF:PIRSF015854 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001937 name: tartrate-resistant acid phosphatase type 5 namespace: protein def: "A protein that is a translation product of the ACP5 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "ACP5" EXACT PRO-short-label [] synonym: "T5ap" RELATED [] synonym: "tartrate-resistant acid ATPase" EXACT [] synonym: "TR-AP" EXACT [] synonym: "Trap" RELATED [] synonym: "TrATPase" EXACT [DNx] synonym: "type 5 acid phosphatase" EXACT [] xref: PIRSF:PIRSF000898 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001938 name: thrombomodulin-like receptor namespace: protein def: "A protein with core architecture consisting of a signal sequence, a Lectin C-type domain (PF00059), 5 or 6 EGF-like domains (PF00008, PF09064, or PF07645), a transmembrane region, and a small cytoplasmic region (36-51 amino acids)." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF001775 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001941 name: trans-acting T-cell-specific transcription factor GATA-3 namespace: protein def: "A protein that is a translation product of the GATA3 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "Gata-3" RELATED [] synonym: "GATA-binding factor 3" EXACT [] synonym: "GATA3" EXACT PRO-short-label [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001944 name: transcription factor PU.1 namespace: protein def: "A protein that is a translation product of the SPI1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "31 kDa-transforming protein" EXACT [] synonym: "SFFV proviral integration 1 protein" EXACT [] synonym: "Sfpi-1" RELATED [] synonym: "Sfpi1" RELATED [] synonym: "SPI1" EXACT PRO-short-label [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001945 name: transferrin receptor protein 1 namespace: protein def: "A protein that is a translation product of the TFRC gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD71" EXACT [] synonym: "p90" RELATED [] synonym: "T9" EXACT [] synonym: "TfR" EXACT [] synonym: "TfR1" EXACT [] synonym: "TFRC" EXACT PRO-short-label [] synonym: "TR" RELATED [] synonym: "Trfr" EXACT [DNx] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001950 name: tumor necrosis factor ligand superfamily member 5 namespace: protein def: "A protein that is a translation product of the CD40LG gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD154" EXACT [] synonym: "CD40-L" EXACT [] synonym: "CD40L" RELATED [] synonym: "CD40LG" EXACT PRO-short-label [] synonym: "T-cell antigen Gp39" EXACT [] synonym: "TNF-related activation protein" EXACT [] synonym: "TNFSF5" RELATED [] synonym: "TRAP" EXACT [] synonym: "tumor necrosis factor ligand superfamily member 5" EXACT [] xref: PIRSF:PIRSF016527 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001954 name: tumor necrosis factor receptor superfamily member 11A namespace: protein def: "A protein that is a translation product of the TNFRSF11A gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD265" EXACT [] synonym: "ODFR" EXACT [] synonym: "osteoclast differentiation factor receptor" EXACT [] synonym: "RANK" RELATED [] synonym: "receptor activator of NF-KB" EXACT [] synonym: "TNFRSF11A" EXACT PRO-short-label [] xref: PIRSF:PIRSF038806 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001963 name: CD27 molecule namespace: protein def: "A protein that is a translation product of the CD27 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD27" EXACT PRO-short-label [] synonym: "CD27 molecule" EXACT [] synonym: "CD27L receptor" EXACT [] synonym: "T-cell activation antigen CD27" EXACT [] synonym: "T14" EXACT [] synonym: "TNFRSF7" RELATED [] xref: PIRSF:PIRSF001966 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001968 name: tyrosine-protein phosphatase non-receptor type substrate 1 namespace: protein def: "A SIRP/SHPS-1 family protein that is a translation product of the SIRPA gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "Bit" EXACT [DNx] synonym: "brain Ig-like molecule with tyrosine-based activation motifs" EXACT [] synonym: "CD172 antigen-like family member A" EXACT [] synonym: "CD172a" EXACT [] synonym: "inhibitory receptor SHPS-1" EXACT [] synonym: "macrophage fusion receptor" EXACT [] synonym: "MFR" RELATED [] synonym: "mSIRP-alpha1" EXACT [] synonym: "MyD-1 antigen" EXACT [] synonym: "MYD1" RELATED [] synonym: "p84" EXACT [] synonym: "PTPNS1" RELATED [] synonym: "SHP substrate 1" EXACT [] synonym: "SHPS-1" EXACT [] synonym: "SHPS1" RELATED [] synonym: "signal-regulatory protein alpha-1" EXACT [] synonym: "signal-regulatory protein alpha-2" EXACT [] synonym: "signal-regulatory protein alpha-3" EXACT [] synonym: "SIRP" RELATED [] synonym: "Sirp-alpha-1" EXACT [DNx] synonym: "Sirp-alpha-2" EXACT [DNx] synonym: "Sirp-alpha-3" EXACT [DNx] synonym: "SIRPA" EXACT PRO-short-label [] is_a: PR:000001832 ! SIRP/SHPS-1 family protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001969 name: urokinase plasminogen activator surface receptor namespace: protein def: "A protein that is a translation product of the PLAUR gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD87" EXACT [] synonym: "MO3" RELATED [] synonym: "monocyte activation antigen Mo3" EXACT [] synonym: "PLAUR" EXACT PRO-short-label [] synonym: "U-PAR" EXACT [] synonym: "uPAR" EXACT [] xref: PIRSF:PIRSF002022 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000001971 name: vascular endothelial growth factor receptor namespace: protein def: "A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (PF00047, PF07679, or PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain." [PRO:WCB] comment: Category=family. xref: PIRSF:PIRSF038502 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002001 name: FL cytokine receptor namespace: protein def: "A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the FLT3 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD135" EXACT [] synonym: "fetal liver kinase 2" EXACT [] synonym: "FLK-2" EXACT [] synonym: "FLT-3" EXACT [] synonym: "FLT3" EXACT PRO-short-label [] synonym: "Fms-like tyrosine kinase 3" EXACT [DNx] synonym: "stem cell tyrosine kinase 1" EXACT [] synonym: "STK-1" RELATED [] synonym: "STK1" RELATED [] synonym: "tyrosine-protein kinase FLT3" EXACT [] synonym: "tyrosine-protein kinase receptor flk-2" EXACT [] synonym: "tyrosine-protein kinase receptor FLT3" EXACT [] xref: PIRSF:PIRSF500949 is_a: PR:000001810 ! CSF-1/PDGF receptor-type tyrosine-protein kinase property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002023 name: NKG2-A/NKG2-B type II integral membrane protein namespace: protein def: "A natural killer cell receptor NKG2 that is a translation product of the KLRC1 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD159 antigen-like family member A" EXACT [] synonym: "CD159a" EXACT [] synonym: "KLRC1" EXACT PRO-short-label [] synonym: "NK cell receptor A" EXACT [] synonym: "NKG2-A/B-activating NK receptor" EXACT [] synonym: "NKG2A" RELATED [] is_a: PR:000001897 ! natural killer cell receptor NKG2 property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002025 name: T-cell surface glycoprotein CD1a namespace: protein def: "A T-cell surface glycoprotein CD1 that is a translation product of the CD1A gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD1A" EXACT PRO-short-label [] synonym: "CD1a" EXACT [] synonym: "hTa1 thymocyte antigen" EXACT [] synonym: "T-cell surface antigen T6/Leu-6" EXACT [] is_a: PR:000001838 ! T-cell surface glycoprotein CD1 property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002027 name: T-cell surface glycoprotein CD1c namespace: protein def: "A T-cell surface glycoprotein CD1 that is a translation product of the CD1C gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD1C" EXACT PRO-short-label [] synonym: "CD1c" EXACT [] is_a: PR:000001838 ! T-cell surface glycoprotein CD1 property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002028 name: T-cell surface glycoprotein CD1d namespace: protein def: "A T-cell surface glycoprotein CD1 that is a translation product of the CD1D gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "Cd1.1" RELATED [] synonym: "CD1D" EXACT PRO-short-label [] synonym: "CD1d" EXACT [] synonym: "CD1d.1" EXACT [] synonym: "Cd1d1" RELATED [] synonym: "R3G1" EXACT [] is_a: PR:000001838 ! T-cell surface glycoprotein CD1 property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002031 name: aminopeptidase N namespace: protein def: "A membrane alanyl aminopeptidase-like metallopeptidase that is a translation product of the ANPEP gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "alanyl aminopeptidase" EXACT [] synonym: "aminopeptidase M" EXACT [] synonym: "ANPEP" EXACT PRO-short-label [] synonym: "AP-M" EXACT [] synonym: "AP-N" EXACT [] synonym: "APN" RELATED [] synonym: "CD13" EXACT [] synonym: "gp150" EXACT [] synonym: "hAPN" EXACT [] synonym: "Lap-1" RELATED [] synonym: "Lap1" RELATED [] synonym: "mAPN" EXACT [] synonym: "membrane protein p161" EXACT [] synonym: "microsomal aminopeptidase" EXACT [] synonym: "myeloid plasma membrane glycoprotein CD13" EXACT [] synonym: "PEPN" RELATED [] is_a: PR:000001888 ! membrane alanyl aminopeptidase-like metallopeptidase property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002037 name: complement component C1q receptor namespace: protein def: "A thrombomodulin-like receptor that is a translation product of the CD93 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "Aa4" RELATED [] synonym: "C1q/MBL/SPA receptor" EXACT [] synonym: "C1qR" EXACT [] synonym: "C1qR(p)" EXACT [] synonym: "C1QR1" RELATED [] synonym: "C1qRp" EXACT [] synonym: "CD93" EXACT PRO-short-label [] synonym: "CDw93" EXACT [] synonym: "cell surface antigen AA4" EXACT [] synonym: "complement component 1 q subcomponent receptor 1" EXACT [] synonym: "ly-68" EXACT [] synonym: "Ly68" RELATED [] synonym: "lymphocyte antigen 68" EXACT [] synonym: "matrix-remodeling-associated protein 4" EXACT [] synonym: "MXRA4" RELATED [] is_a: PR:000001938 ! thrombomodulin-like receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002039 name: glutamyl aminopeptidase namespace: protein def: "A membrane alanyl aminopeptidase-like metallopeptidase that is a translation product of the ENPEP gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "aminopeptidase A" EXACT [] synonym: "AP-A" EXACT [] synonym: "BP-1/6C3 antigen" EXACT [] synonym: "CD249" EXACT [] synonym: "differentiation antigen gp160" EXACT [] synonym: "EAP" RELATED [] synonym: "ENPEP" EXACT PRO-short-label [] is_a: PR:000001888 ! membrane alanyl aminopeptidase-like metallopeptidase property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002062 name: macrophage colony-stimulating factor 1 receptor namespace: protein def: "A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the CSF1R gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD115" EXACT [] synonym: "CSF-1-R" EXACT [] synonym: "CSF1R" EXACT PRO-short-label [] synonym: "Csfmr" RELATED [] synonym: "FMS" RELATED [] synonym: "proto-oncogene c-Fms" EXACT [] xref: PIRSF:PIRSF500947 is_a: PR:000001810 ! CSF-1/PDGF receptor-type tyrosine-protein kinase property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002064 name: macrosialin namespace: protein def: "A lysosome-associated membrane protein that is a translation product of the CD68 gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD68" EXACT PRO-short-label [] synonym: "gp110" RELATED [] is_a: PR:000001883 ! lysosome-associated membrane protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002065 name: mast/stem cell growth factor receptor namespace: protein def: "A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the KIT gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD117" EXACT [] synonym: "KIT" EXACT PRO-short-label [] synonym: "proto-oncogene c-Kit" EXACT [] synonym: "SCFR" EXACT [] synonym: "Sl" RELATED [] synonym: "tyrosine-protein kinase Kit" EXACT [] xref: PIRSF:PIRSF500951 is_a: PR:000001810 ! CSF-1/PDGF receptor-type tyrosine-protein kinase property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002105 name: thrombomodulin namespace: protein def: "A thrombomodulin-like receptor that is a translation product of the THBD gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD141" EXACT [] synonym: "fetomodulin" EXACT [] synonym: "THBD" EXACT PRO-short-label [] synonym: "THRM" RELATED [] synonym: "TM" EXACT [] is_a: PR:000001938 ! thrombomodulin-like receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002112 name: vascular endothelial growth factor receptor 2 namespace: protein def: "A vascular endothelial growth factor receptor that is a translation product of the KDR gene or a 1:1 ortholog thereof." [PRO:WCB] comment: Category=gene. synonym: "CD309" EXACT [] synonym: "fetal liver kinase 1" EXACT [] synonym: "FLK-1" EXACT [] synonym: "FLK1" RELATED [] synonym: "KDR" EXACT PRO-short-label [] synonym: "kinase insert domain receptor" EXACT [] synonym: "kinase NYK" EXACT [] synonym: "protein-tyrosine kinase receptor flk-1" EXACT [] synonym: "VEGFR-2" EXACT [] is_a: PR:000001971 ! vascular endothelial growth factor receptor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002972 name: macrophage mannose receptor 1 namespace: protein def: "A C-type lectin with multiple lectin domains that is a translation product of the MRC1 gene or a 1:1 ortholog thereof." [PMID:8297379, PRO:CNA] comment: Category=gene. synonym: "C-type lectin domain family 13 member D" EXACT [] synonym: "CD206" EXACT [] synonym: "CLEC13D" RELATED [] synonym: "MMR" EXACT [] synonym: "MRC1" EXACT PRO-short-label [] is_a: PR:000001025 ! C-type lectin with multiple lectin domains property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002976 name: ly-6-like protein namespace: protein def: "A protein that is the translation product of any of the LY6 genes (LY6A-LY6I)." [PRO:CNA] comment: Category=family. xref: PIRSF:PIRSF002021 is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002977 name: killer cell lectin-like receptor subfamily B member 1C namespace: protein alt_id: PR:000009625 def: "A KLRB1-like protein that is a translation product of the mouse Klrb1c gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "CD161 antigen-like family member C" EXACT [] synonym: "CD161c" EXACT [] synonym: "Klrb1c" EXACT PRO-short-label [] synonym: "ly-55c" EXACT [] synonym: "Ly55c" RELATED [] synonym: "lymphocyte antigen 55c" EXACT [] synonym: "natural killer cell surface protein P1-40" EXACT [] synonym: "NK1.1" EXACT [] synonym: "NKR-P1 40" EXACT [] synonym: "NKR-P1.9" EXACT [] synonym: "NKR-P1C" EXACT [] synonym: "Nkrp1c" RELATED [] is_a: PR:000001874 ! KLRB1-like protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002978 name: lymphocyte antigen 6G namespace: protein def: "A ly-6-like protein that is a translation product of the LY6G gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "ly-6G" EXACT [] synonym: "ly-6G.1" EXACT [] synonym: "LY6G" EXACT PRO-short-label [] synonym: "Ly6g" RELATED [] is_a: PR:000002976 ! ly-6-like protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002979 name: lymphocyte antigen 6A-2/6E-1 namespace: protein def: "A ly-6-like protein that is a translation product of the LY6A gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "ly-6A.2/Ly-6E.1" EXACT [] synonym: "Ly6" RELATED [] synonym: "LY6A" EXACT PRO-short-label [] synonym: "Ly6a" RELATED [] synonym: "SCA-1" RELATED [] synonym: "stem cell antigen 1" EXACT [] synonym: "T-cell-activating protein" EXACT [] synonym: "TAP" RELATED [] is_a: PR:000002976 ! ly-6-like protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002980 name: lymphocyte antigen 6C namespace: protein def: "An ly-6-like protein that is a translation product of the LY6C2 gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "ly-6C2" EXACT [] synonym: "Ly6c" RELATED [] synonym: "LY6C2" EXACT PRO-short-label [] synonym: "Ly6c2" RELATED [] is_a: PR:000002976 ! ly-6-like protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000002981 name: lymphocyte antigen 76 namespace: protein def: "A protein that is a translation product of the LY76 gene or a 1:1 ortholog thereof." [MGI:106910, PMID:10848813] comment: Category=gene. synonym: "LY76" EXACT PRO-short-label [] synonym: "ly76" RELATED [] synonym: "ter-119" EXACT [] synonym: "ter119" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000003450 name: B-cell lymphoma 6 protein namespace: protein alt_id: PR:000004700 def: "A protein that is a translation product of the BCL6 gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "B-cell lymphoma 5 protein" EXACT [] synonym: "BCL-5" EXACT [] synonym: "BCL-6" EXACT [] synonym: "BCL5" RELATED [] synonym: "BCL6" EXACT PRO-short-label [] synonym: "LAZ3" RELATED [] synonym: "protein LAZ-3" EXACT [] synonym: "ZBTB27" RELATED [] synonym: "zinc finger and BTB domain-containing protein 27" EXACT [] synonym: "zinc finger protein 51" EXACT [] synonym: "ZNF51" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000003455 name: nuclear receptor ROR-gamma isoform 2 namespace: protein def: "A nuclear receptor ROR-gamma that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P51450-2 or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=sequence. is_a: PR:000001902 ! nuclear receptor ROR-gamma property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000003457 name: V(D)J recombination-activating protein 1 namespace: protein alt_id: PR:000013688 def: "A protein that is a translation product of the RAG1 gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "RAG-1" EXACT [] synonym: "RAG1" EXACT PRO-short-label [] synonym: "RING finger protein 74" EXACT [] synonym: "RNF74" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000003460 name: V(D)J recombination-activating protein 2 namespace: protein alt_id: PR:000013690 def: "A protein that is a translation product of the RAG2 gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "RAG-2" EXACT [] synonym: "RAG2" EXACT PRO-short-label [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000003463 name: eomesodermin namespace: protein alt_id: PR:000007101 def: "A T-brain transcription factor that is a translation product of the EOMES gene or a 1:1 ortholog thereof." [PMID:10407135, PRO:CNA] comment: Category=gene. synonym: "EOMES" EXACT PRO-short-label [] synonym: "T-box brain protein 2" EXACT [] synonym: "T-brain-2" EXACT [] synonym: "TBR-2" EXACT [] synonym: "TBR2" RELATED [] is_a: PR:000003506 ! T-brain transcription factor property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000003466 name: perforin-1 namespace: protein alt_id: PR:000013205 def: "A protein that is a translation product of the PRF1 gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "cytolysin" EXACT [] synonym: "lymphocyte pore-forming protein" EXACT [] synonym: "P1" RELATED [] synonym: "PFP" EXACT [] synonym: "PRF1" EXACT PRO-short-label [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000003469 name: early growth response protein 2 namespace: protein alt_id: PR:000006938 def: "A protein that is a translation product of the EGR2 gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "AT591" EXACT [] synonym: "EGR-2" EXACT [] synonym: "EGR2" EXACT PRO-short-label [] synonym: "Krox-20" RELATED [] synonym: "KROX20" RELATED [] synonym: "Zfp-25" RELATED [] synonym: "zinc finger protein Krox-20" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000003499 name: granzyme B namespace: protein def: "A leukocyte granule-associated proteinase that is a translation product of the human GZMB gene or a 1:1 ortholog thereof." [PRO:CNA] comment: Category=gene. synonym: "C11" EXACT [] synonym: "cathepsin G-like 1" EXACT [] synonym: "CGL1" RELATED [] synonym: "CSPB" RELATED [] synonym: "CTLA-1" EXACT [] synonym: "CTLA1" RELATED [] synonym: "CTSGL1" EXACT [] synonym: "cytotoxic T-lymphocyte proteinase 2" EXACT [] synonym: "fragmentin-2" EXACT [] synonym: "granzyme-2" EXACT [] synonym: "GRB" RELATED [] synonym: "GZMB" EXACT PRO-short-label [] synonym: "HLP" RELATED [] synonym: "human lymphocyte protein" EXACT [] synonym: "lymphocyte protease" EXACT [] synonym: "SECT" EXACT [] synonym: "T-cell serine protease 1-3E" EXACT [] is_a: PR:000003505 ! leukocyte granule-associated proteinase property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000003505 name: leukocyte granule-associated proteinase namespace: protein def: "A protein that is a serine protease of the granules from mast cells, cytotoxic T lymphocytes and/or natural killer cells. Leukocyte granule-associated proteinase is a component of the immune system that protect higher organisms against viral infection and cellular transformation. Members of this class have features that are strongly conserved including: consensus sequences at their N-termini and around the three catalytic residues, activation from zymogenic forms, and conserved disulphide bridges." [PMID:11790262, PMID:7952649, PMID:8929545] comment: Category=family. is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000003506 name: T-brain transcription factor namespace: protein def: "A protein that contains one copy of the T-box domain (PF00907) and it is involved in the anterior neural specification." [PMID:10750050, PMID:12210112] comment: Category=family. synonym: "Eomes/Tbr1/Tbx21 family protein" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000003516 name: lactosylceramide 4-alpha-galactosyltransferase namespace: protein def: "A protein that is a translation product of the A4GALT gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "A14GALT" RELATED [] synonym: "A4GALT" EXACT PRO-short-label [] synonym: "A4GALT1" RELATED [] synonym: "alpha-1,4-galactosyltransferase" EXACT [] synonym: "alpha-1,4-N-acetylglucosaminyltransferase" BROAD [] synonym: "alpha4Gal-T1" EXACT [] synonym: "CD77 synthase" EXACT [] synonym: "Gb3 synthase" EXACT [DNx] synonym: "globotriaosylceramide synthase" EXACT [] synonym: "P1/Pk synthase" EXACT [] synonym: "UDP-galactose:beta-D-galactosyl-beta1-R 4-alpha-D-galactosyltransferase" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000005178 name: CD9 molecule namespace: protein def: "A tetraspanin that is a translation product of the CD9 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "5H9 antigen" EXACT [] synonym: "CD9" EXACT PRO-short-label [] synonym: "CD9 antigen" EXACT [] synonym: "cell growth-inhibiting gene 2 protein" EXACT [] synonym: "leukocyte antigen MIC3" EXACT [] synonym: "MIC3" RELATED [] synonym: "motility-related protein" EXACT [] synonym: "MRP-1" EXACT [] synonym: "p24" RELATED [] synonym: "tetraspanin-29" EXACT [] synonym: "tspan-29" EXACT [] synonym: "TSPAN29" RELATED [] is_a: PR:000001403 ! tetraspanin property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000005307 name: CCAAT/enhancer-binding protein alpha namespace: protein def: "A protein that is a translation product of the CEBPA gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "C/EBP alpha" EXACT [] synonym: "CEBPA" EXACT PRO-short-label [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000005310 name: CCAAT/enhancer-binding protein epsilon namespace: protein def: "A protein that is a translation product of the CEBPE gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "C/EBP epsilon" EXACT [] synonym: "CEBPE" EXACT PRO-short-label [] synonym: "Gm294" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000006169 name: cell surface glycoprotein CD200 receptor 3 namespace: protein def: "A protein that is a translation product of the Cd200r3 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "CD200 cell surface glycoprotein receptor-like 3" EXACT [] synonym: "CD200 cell surface glycoprotein receptor-like b" EXACT [] synonym: "CD200 receptor-like 3" EXACT [] synonym: "Cd200r3" EXACT PRO-short-label [] synonym: "CD200RLb" EXACT [] synonym: "cell surface glycoprotein OX2 receptor 3" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000006172 name: CD209 molecule-like protein B namespace: protein def: "A protein that is a translation product of the Cd209b gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "Cd209b" EXACT PRO-short-label [] synonym: "DC-SIGN-related protein 1" EXACT [] synonym: "DC-SIGNR1" EXACT [] synonym: "OtB7" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000006611 name: DNA nucleotidylexotransferase namespace: protein def: "A protein that is a translation product of the DNTT gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "DNTT" EXACT PRO-short-label [] synonym: "TDT" EXACT [] synonym: "TDT" RELATED [] synonym: "terminal addition enzyme" EXACT [] synonym: "terminal deoxynucleotidyltransferase" EXACT [] synonym: "terminal transferase" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000007152 name: eosinophil peroxidase namespace: protein def: "A protein that is a translation product of the EPX gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "EPER" RELATED [] synonym: "EPO" EXACT [] synonym: "EPP" RELATED [] synonym: "EPX" EXACT PRO-short-label [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000007431 name: high affinity immunoglobulin epsilon receptor subunit alpha namespace: protein def: "An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the FCER1A gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "Fc-epsilon RI-alpha" EXACT [] synonym: "FCE1A" RELATED [] synonym: "FCER1A" EXACT PRO-short-label [] synonym: "FcERI" RELATED [] synonym: "IgE Fc receptor subunit alpha" EXACT [] is_a: PR:000001355 ! immunoglobulin gamma Fc receptor II/III/IV property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000007597 name: proto-oncogene c-Fos namespace: protein def: "A protein that is a translation product of the FOS gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "cellular oncogene fos" EXACT [] synonym: "FOS" EXACT PRO-short-label [] synonym: "G0/G1 switch regulatory protein 7" EXACT [] synonym: "G0S7" RELATED [] synonym: "proto-oncogene protein c-fos" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000007857 name: erythroid transcription factor namespace: protein def: "A protein that is a translation product of the GATA1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "Eryf1" EXACT [DNx] synonym: "GATA-1" EXACT [] synonym: "GATA-binding factor 1" EXACT [] synonym: "GATA1" EXACT PRO-short-label [] synonym: "GF-1" RELATED [] synonym: "GF1" RELATED [] synonym: "NF-E1 DNA-binding protein" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000007858 name: endothelial transcription factor GATA-2 namespace: protein def: "A protein that is a translation product of the GATA2 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "GATA-binding protein 2" EXACT [] synonym: "GATA2" EXACT PRO-short-label [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000007939 name: glial fibrillary acidic protein namespace: protein def: "A protein that is a translation product of the GFAP gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "GFAP" EXACT PRO-short-label [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000008467 name: hemoglobin subunit zeta namespace: protein def: "A protein that is a translation product of the HBZ gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "alpha-like embryonic globin chain x" EXACT [] synonym: "Hba-x" RELATED [] synonym: "HBAZ" EXACT [] synonym: "HBZ" EXACT PRO-short-label [] synonym: "Hbz1" RELATED [] synonym: "HBZ2" RELATED [] synonym: "hemoglobin zeta chain" EXACT [] synonym: "zeta-globin" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000008857 name: hemoglobin subunit beta-1 namespace: protein def: "A protein that is a translation product of the Hbb-b1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "beta-1-globin" EXACT [] synonym: "Hbb-b1" RELATED [] synonym: "Hbbb1" EXACT PRO-short-label [] synonym: "hemoglobin beta-1 chain" EXACT [] synonym: "hemoglobin beta-major chain" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000008982 name: interleukin-17 receptor B namespace: protein def: "A protein that is a translation product of the IL17RB gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "CRL4" RELATED [] synonym: "cytokine receptor-like 4" EXACT [] synonym: "EVI27" RELATED [] synonym: "IL-17 receptor B" EXACT [] synonym: "IL-17 receptor homolog 1" EXACT [] synonym: "IL-17B receptor" EXACT [] synonym: "IL-17ER" EXACT [] synonym: "IL-17RB" EXACT [] synonym: "IL-17Rh1" EXACT [] synonym: "IL17BR" RELATED [] synonym: "IL17RB" EXACT PRO-short-label [] synonym: "IL17Rh1" EXACT [] synonym: "interleukin-17B receptor" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000008994 name: interleukin-1 receptor-like 1 namespace: protein def: "A protein that is a translation product of the IL1RL1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "DER4" RELATED [] synonym: "IL1RL1" EXACT PRO-short-label [] synonym: "Ly84" RELATED [] synonym: "lymphocyte antigen 84" EXACT [] synonym: "protein ST2" EXACT [] synonym: "protein T1" EXACT [] synonym: "ST2" RELATED [] synonym: "Ste2" RELATED [] synonym: "T1" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000009127 name: integrin alpha-IIb namespace: protein def: "An integrin alpha lacking A domain that is a translation product of the ITGA2B gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "CD41" EXACT [] synonym: "GP2B" RELATED [] synonym: "GPalpha IIb" EXACT [] synonym: "GPIIb" EXACT [] synonym: "ITGA2B" EXACT PRO-short-label [] synonym: "ITGAB" RELATED [] synonym: "platelet membrane glycoprotein IIb" EXACT [] is_a: PR:000025797 ! integrin alpha lacking A domain property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000009129 name: integrin alpha-4 namespace: protein def: "An integrin alpha lacking A domain that is a translation product of the ITGA4 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "CD49 antigen-like family member D" EXACT [] synonym: "CD49d" EXACT [] synonym: "integrin alpha-IV" EXACT [] synonym: "ITGA4" EXACT PRO-short-label [] synonym: "LPAM subunit alpha" EXACT [] synonym: "lymphocyte Peyer patch adhesion molecules subunit alpha" EXACT [] synonym: "VLA-4 subunit alpha" EXACT [] is_a: PR:000025797 ! integrin alpha lacking A domain property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000009143 name: integrin beta-7 namespace: protein def: "An integrin beta that is a translation product of the ITGB7 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "Gut homing receptor beta subunit" EXACT [DNx] synonym: "integrin beta-P" EXACT [] synonym: "ITGB7" EXACT PRO-short-label [] synonym: "M290 IEL antigen" EXACT [] is_a: PR:000001861 ! integrin beta property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000009616 name: T-cell surface glycoprotein YE1/48 namespace: protein def: "A protein that is a translation product of the Klra1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "Klra1" EXACT PRO-short-label [] synonym: "Ly-49" RELATED [] synonym: "ly-49a" EXACT [] synonym: "Ly49" RELATED [] synonym: "Ly49A" RELATED [] synonym: "lymphocyte antigen 49a" EXACT [] synonym: "T lymphocyte antigen A1" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000009618 name: killer cell lectin-like receptor 3 namespace: protein def: "A protein that is a translation product of the Klra3 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "5E6" EXACT [] synonym: "Klra3" EXACT PRO-short-label [] synonym: "ly-49c" EXACT [] synonym: "Ly49C" RELATED [] synonym: "lymphocyte antigen 49c" EXACT [] synonym: "T-cell surface glycoprotein Ly-49C" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000009619 name: killer cell lectin-like receptor 4 namespace: protein def: "A protein that is a translation product of the Klra4 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "Klra4" EXACT PRO-short-label [] synonym: "ly-49d" EXACT [] synonym: "Ly49-d" RELATED [] synonym: "Ly49d" RELATED [] synonym: "lymphocyte antigen 49d" EXACT [] synonym: "T-cell surface glycoprotein Ly-49D" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000009623 name: killer cell lectin-like receptor 8 namespace: protein def: "A protein that is a translation product of the Klra8 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "Klra8" EXACT PRO-short-label [] synonym: "ly-49h" EXACT [] synonym: "Ly49-h" RELATED [] synonym: "Ly49H" RELATED [] synonym: "lymphocyte antigen 49h" EXACT [] synonym: "T-cell surface glycoprotein Ly-49H" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000009725 name: neutrophil gelatinase-associated lipocalin namespace: protein def: "A protein that is a translation product of the LCN2 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "25 kDa alpha-2-microglobulin-related subunit of MMP-9" EXACT [] synonym: "HNL" RELATED [] synonym: "LCN2" EXACT PRO-short-label [] synonym: "lipocalin-2" EXACT [] synonym: "NGAL" EXACT [] synonym: "oncogene 24p3" EXACT [] synonym: "p25" RELATED [] synonym: "SV-40-induced 24P3 protein" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000009766 name: galectin-1 namespace: protein def: "A protein that is a translation product of the LGALS1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "14 kDa laminin-binding protein" EXACT [] synonym: "14 kDa lectin" EXACT [] synonym: "beta-galactoside-binding lectin L-14-I" EXACT [] synonym: "gal-1" EXACT [] synonym: "galaptin" EXACT [] synonym: "Gbp" RELATED [] synonym: "HBL" EXACT [] synonym: "HLBP14" EXACT [] synonym: "HPL" EXACT [] synonym: "lactose-binding lectin 1" EXACT [] synonym: "lectin galactoside-binding soluble 1" EXACT [] synonym: "LGALS1" EXACT PRO-short-label [] synonym: "putative MAPK-activating protein PM12" EXACT [] synonym: "S-Lac lectin 1" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000009978 name: lactotransferrin namespace: protein def: "A protein that is a translation product of the LTF gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "lactoferrin" EXACT [] synonym: "LF" RELATED [] synonym: "LTF" EXACT PRO-short-label [] synonym: "talalactoferrin" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000010329 name: tyrosine-protein kinase Mer namespace: protein def: "A protein that is a translation product of the MERTK gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "MER" RELATED [] synonym: "MERTK" EXACT PRO-short-label [] synonym: "proto-oncogene c-Mer" EXACT [] synonym: "proto-oncogene tyrosine-protein kinase MER" EXACT [] synonym: "receptor tyrosine kinase MerTK" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000010543 name: myeloperoxidase namespace: protein def: "A protein that is a translation product of the MPO gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "MPO" EXACT PRO-short-label [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000010799 name: myb proto-oncogene protein namespace: protein def: "A protein that is a translation product of the MYB gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "MYB" EXACT PRO-short-label [] synonym: "proto-oncogene c-Myb" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000011178 name: nuclear factor NF-kappa-B p100 subunit namespace: protein def: "A transcription factor NF-kappa-B that is a translation product of the NFKB2 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "DNA-binding factor KBF2" EXACT [] synonym: "H2TF1" EXACT [] synonym: "lymphocyte translocation chromosome 10 protein" EXACT [] synonym: "lyt10" EXACT [] synonym: "NFKB2" EXACT PRO-short-label [] synonym: "nuclear factor of kappa light polypeptide gene enhancer in B-cells 2" EXACT [] synonym: "oncogene Lyt-10" EXACT [] is_a: PR:000001753 ! transcription factor NF-kappa-B property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000014046 name: non-secretory ribonuclease namespace: protein def: "A protein that is a translation product of the RNASE2 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "Ear4" RELATED [] synonym: "EDN" RELATED [] synonym: "eosinophil cationic-type ribonuclease 4" EXACT [] synonym: "eosinophil-derived neurotoxin" EXACT [] synonym: "MR-4" EXACT [] synonym: "ribonuclease 2" EXACT [] synonym: "ribonuclease US" EXACT [] synonym: "RNase 2" EXACT [] synonym: "RNase UpI-2" EXACT [] synonym: "RNASE2" EXACT PRO-short-label [] synonym: "RNS2" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000014047 name: eosinophil cationic protein namespace: protein def: "A protein that is a translation product of the RNASE3 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "ECP" EXACT [] synonym: "ribonuclease 3" RELATED [] synonym: "RNase 3" EXACT [] synonym: "RNASE3" EXACT PRO-short-label [] synonym: "RNS3" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000014362 name: runt-related transcription factor 1 namespace: protein def: "A protein that is a translation product of the RUNX1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "acute myeloid leukemia 1 protein" EXACT [] synonym: "AML1" RELATED [] synonym: "CBF-alpha-2" EXACT [] synonym: "CBFA2" RELATED [] synonym: "core-binding factor subunit alpha-2" EXACT [] synonym: "oncogene AML-1" EXACT [] synonym: "PEA2-alpha B" EXACT [] synonym: "PEBP2-alpha B" EXACT [] synonym: "Pebp2ab" RELATED [] synonym: "polyomavirus enhancer-binding protein 2 alpha B subunit" EXACT [] synonym: "RUNX1" EXACT PRO-short-label [] synonym: "SL3-3 enhancer factor 1 alpha B subunit" EXACT [] synonym: "SL3/AKV core-binding factor alpha B subunit" EXACT [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000016043 name: T-cell acute lymphocytic leukemia protein 1 namespace: protein def: "A protein that is a translation product of the TAL1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "bHLHa17" EXACT [] synonym: "class A basic helix-loop-helix protein 17" EXACT [] synonym: "SCL" RELATED [] synonym: "stem cell protein" EXACT [] synonym: "T-cell leukemia/lymphoma protein 5" EXACT [] synonym: "TAL-1" EXACT [] synonym: "TAL1" EXACT PRO-short-label [] synonym: "TCL5" RELATED [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000016401 name: transmembrane emp24 domain-containing protein 1 namespace: protein def: "A protein that is a translation product of the TMED1 gene or a 1:1 ortholog thereof." [PRO:DNx] comment: Category=gene. Flag=automatic. synonym: "IL1RL1L" RELATED [] synonym: "IL1RL1LG" RELATED [] synonym: "interleukin-1 receptor-like 1 ligand" EXACT [] synonym: "putative T1/ST2 receptor-binding protein" EXACT [] synonym: "TMED1" EXACT PRO-short-label [] is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000018263 name: amino acid chain namespace: protein def: "A polymer of amino acids linked by peptide bonds." [PRO:DAN] synonym: "peptide" NARROW [] synonym: "polypeptide" NARROW [] property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000018264 name: proteolytic cleavage product namespace: protein def: "An amino acid chain produced as the result of peptide bond cleavage of a longer amino acid chain." [PRO:DAN] synonym: "peptide" NARROW [] synonym: "polypeptide" NARROW [] is_a: PR:000018263 ! amino acid chain property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000021082 name: bone marrow proteoglycan proteolytic cleavage product namespace: protein def: "A proteolytic cleavage product that is derived from bone marrow proteoglycan." [PRO:DNx] comment: Category=modification. Flag=automatic. is_a: PR:000018264 ! proteolytic cleavage product property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000022006 name: eosinophil granule major basic protein namespace: protein def: "A bone marrow proteoglycan proteolytic cleavage product that derives from bone marrow proteoglycan isoform 1, signal peptide removed form that has had the acidic propeptide removed." [PMID:9657764] comment: Category=modification. is_a: PR:000021082 ! bone marrow proteoglycan proteolytic cleavage product property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000025402 name: T cell receptor co-receptor CD8 namespace: protein def: "A protein complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction." [PMID:18275828, PMID:3264320, PRO:DAN] comment: Category=complex. synonym: "CD8alphabeta" EXACT [] synonym: "TCR co-receptor CD8" EXACT [] property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000025403 name: T-cell surface glycoprotein CD8 alpha chain isoform 1 namespace: protein def: "A T-cell surface glycoprotein CD8 alpha chain that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P01732-1 or a 1:1 ortholog thereof. Having a single-pass transmembrane domain, this form is membrane bound." [PRO:DAN] comment: Category=sequence. synonym: "mCD8alpha" EXACT [] is_a: PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000025796 name: integrin alpha namespace: protein def: "A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif." [PMID:19693543] comment: Category=family. Integrins are heterodimeric complexes of an alpha and a beta subunit. They are a structurally elaborate family of adhesion molecules that transmit signals bidirectionally across the plasma membrane by undergoing large-scale structural rearrangements. By regulating cell-cell and cell-matrix contacts, integrins participate in a wide-range of biological interactions including development, tissue repair, angiogenesis, inflammation and hemostasis. [PMID:10402956, PMID:11988479, PMID:9676575]. is_a: PR:000000001 ! protein property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000025797 name: integrin alpha lacking A domain namespace: protein def: "An integrin alpha that lacks an A domain. This type of integrin is often cleaved into heavy and light chains." [PRO:DAN] comment: Category=family. xref: PIRSF:PIRSF005666 is_a: PR:000025796 ! integrin alpha property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: UBERON:0000002 name: uterine cervix namespace: uberon def: "Lower, narrow portion of the uterus where it joins with the top end of the vagina." [Wikipedia:Cervix] subset: uberon_slim synonym: "canalis cervicis uteri" EXACT LATIN [FMA:17740, FMA:TA] synonym: "canalis cervicis uteri" EXACT [FMA:TA] synonym: "caudal segment of uterus" EXACT [] synonym: "cervical canal" EXACT [FMA:17740] synonym: "cervical canal of uterus" EXACT [FMA:17740] synonym: "cervix" BROAD [EFO:0000979] synonym: "cervix uteri" EXACT LATIN [EMAPA:29927] synonym: "neck of uterus" EXACT [FMA:17740] synonym: "uterine cervix" EXACT [FMA:17740] xref: BTO:0001421 xref: BTO:0002249 xref: EFO:0000979 xref: EMAPA:29927 xref: EV:0100114 xref: FMA:17740 xref: GAID:376 xref: galen:CervixUteri xref: MA:0000392 xref: MAT:0000292 xref: MESH:A05.360.319.679.256 xref: ncithesaurus:Cervix xref: OpenCyc:Mx4rvVipEJwpEbGdrcN5Y29ycA xref: SCTID:245494008 xref: UMLS:C0007874 xref: VHOG:0001359 is_a: UBERON:0001560 {source="FMA"} ! neck of organ is_a: UBERON:0005156 ! reproductive structure relationship: part_of UBERON:0000995 ! uterus property_value: external_definition "The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001359", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/uterine+cervix"} property_value: has_relational_adjective "cervical" xsd:string property_value: homology_notes "The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001359", ontology="VHOG", source="DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000004 name: olfactory apparatus namespace: uberon def: "a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)." [Wikipedia:Nose] comment: TODO - distinguish generic olfactory apparatus from nose; we have olfactory organ for the generic organ - add new class 'olfactory structure'? subset: major_organ subset: uberon_slim subset: vertebrate_core synonym: "nasal sac" EXACT SENSU [ZFA:0000047] synonym: "Nasus" RELATED LATIN [Wikipedia:Nose] synonym: "nose" EXACT [] synonym: "peripheral olfactory organ" EXACT [] synonym: "proboscis" RELATED [] xref: BTO:0000840 xref: EFO:0000828 xref: EHDAA2:0001274 xref: EHDAA:1502 xref: EMAPA:16542 xref: EV:0100037 xref: EV:0100370 xref: FMA:46472 xref: GAID:77 xref: galen:Nose xref: http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg xref: MA:0000281 xref: MAT:0000139 xref: MESH:A01.456.505.733 xref: MIAA:0000139 xref: ncithesaurus:Nose xref: OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA xref: SCTID:181195007 xref: TAO:0000047 xref: UMLS:C0028429 xref: ZFA:0000047 is_a: UBERON:0002268 ! olfactory organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0003050 ! olfactory placode relationship: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0004089 ! midface property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000006 name: islet of Langerhans namespace: uberon def: "Regions of the pancreas that contain its endocrine (i.e., hormone-producing) cells." [Wikipedia:Islets_of_Langerhans] comment: A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986)[PMID:16417468] subset: uberon_slim synonym: "island of Langerhans" RELATED [BTO:0000991] synonym: "island of pancreas" RELATED [BTO:0000991] synonym: "islets of langerhans" RELATED [] synonym: "pancreatic insula" EXACT [] synonym: "pancreatic islet" EXACT [] xref: AAO:0010406 xref: BTO:0000991 xref: EFO:0000856 xref: EMAPA:19246 xref: EMAPA:19247 xref: EMAPA:19248 xref: EV:0100130 xref: FMA:16016 xref: GAID:324 xref: http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png xref: MA:0000127 xref: MAT:0000076 xref: MESH:A03.734.414 xref: MIAA:0000076 xref: ncithesaurus:Islet_of_Langerhans xref: UMLS:C0022131 xref: VHOG:0000646 xref: XAO:0000159 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0000016 ! endocrine pancreas property_value: external_definition "Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010406", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000646", ontology="VHOG", source="PMID:7600975 Slack JMW, Developmental biology of the pancreas. Development (1995)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000007 name: pituitary gland namespace: uberon def: "The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]." [Wikipedia:Pituitary_gland, ZFIN:curator] comment: Taxon notes: The lamprey possesses a distinct pituitary organ and hormones, the ascidian does not show distinct evidence of them [Sower S, Freamat M, Kavanaugh S. The origins of the vertebrate hypothalamic–pituitary–gonadal (HPG) and hypothalamic–pituitary–thyroid (HPT) endocrine systems: new insights from lampreys. Gen Comp Endocrinol 2009;161:20-9] subset: organ_slim subset: uberon_slim subset: vertebrate_core synonym: "glandula pituitaria" RELATED [BTO:0001073] synonym: "hypophysis" RELATED [ZFA:0000118] synonym: "hypophysis cerebri" RELATED [MA:0000176] synonym: "hypophysis, glandula pituitaria" RELATED LATIN [Wikipedia:Pituitary_gland] synonym: "pituitary" EXACT [BTO:0001073] synonym: "pituitary body" EXACT [BTO:0001073] xref: AAO:0010536 xref: BM:Die-Hy-HY xref: BTO:0001073 xref: EFO:0000857 xref: EHDAA2:0001471 xref: EHDAA:2183 xref: EHDAA:4477 xref: EMAPA:16647 xref: EMAPA:16898 xref: EV:0100132 xref: FMA:13889 xref: GAID:457 xref: http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/9/97/Gray1180.png/200px-Gray1180.png xref: MA:0000176 xref: MAT:0000077 xref: MESH:A06.407.747 xref: MIAA:0000077 xref: ncithesaurus:Pituitary_Gland xref: NIF_GrossAnatomy:birnlex_1353 xref: OpenCyc:Mx4rv6NQYJwpEbGdrcN5Y29ycA xref: SCTID:181125003 xref: TAO:0000118 xref: UMLS:C0032005 xref: VHOG:0000143 xref: XAO:0000017 xref: ZFA:0000118 is_a: UBERON:0003296 ! gland of diencephalon is_a: UBERON:0010133 ! neuroendocrine gland is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0000924 {source="Wikipedia"} ! ectoderm relationship: part_of UBERON:0001894 {source="ZFA"} ! diencephalon property_value: external_definition "An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010536", ontology="AAO", source="AAO:BJB"} property_value: external_definition "An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000118", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000143", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000009 name: submucosa namespace: uberon def: "A layer of dense irregular connective tissue in the gastrointestinal tract that supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle (fibers running circularly within layer of longitudinal muscle). [WP,unvetted]." [Wikipedia:Submucosa] subset: uberon_slim synonym: "organ submucosa" EXACT [FMA:85391] synonym: "region of submucosa" EXACT [FMA:85392] synonym: "submucosa of organ" EXACT [FMA:85391] synonym: "submucosa of region of organ" EXACT [FMA:85392] synonym: "submucous layer" RELATED [BTO:0002107] synonym: "tela submucosa" RELATED [BTO:0002107] synonym: "tunica submucosa" RELATED [] xref: BTO:0002107 xref: FMA:85391 xref: FMA:85392 xref: http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png xref: http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png xref: ncithesaurus:Submucosa xref: SCTID:68439008 xref: UMLS:C0225344 is_a: UBERON:0004923 ! organ component layer property_value: has_relational_adjective "submucosal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000010 name: peripheral nervous system namespace: uberon def: "Nervous structures including ganglia outside of the central nervous system. Divided into somatic nervous system and autonomic nervous system" [FB:gg, OMD:peripheral+nervous+system, Wikipedia:Peripheral_nervous_system, ZFIN:curator] subset: uberon_slim subset: vertebrate_core synonym: "pars peripherica; systema nervosum periphericum" RELATED LATIN [Wikipedia:Peripheral_nervous_system] synonym: "PNS" RELATED [] xref: AAO:0000429 xref: BILA:0000081 xref: BTO:0001028 xref: EFO:0000891 xref: EHDAA2:0001445 xref: EHDAA:2893 xref: EMAPA:16665 xref: EMAPA:18370 xref: EV:0100335 xref: FBbt:00005098 xref: FMA:9903 xref: GAID:715 xref: http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/b/ba/Nervous_system_diagram.png/200px-Nervous_system_diagram.png xref: MA:0000218 xref: MAT:0000338 xref: MESH:A08.800 xref: MIAA:0000338 xref: ncithesaurus:Peripheral_Nervous_System xref: NIF_GrossAnatomy:birnlex_1111 xref: SCTID:362292005 xref: TAO:0000142 xref: UMLS:C0206417 xref: VHOG:0000399 xref: XAO:0000178 xref: ZFA:0000142 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system property_value: external_definition "Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000142", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000429", ontology="AAO", source="AAO:BJB"} property_value: homology_notes " (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000399", ontology="VHOG", source="DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0001017 [Term] id: UBERON:0000015 name: anatomical boundary namespace: uberon def: "Structural anatomical relation which holds between each anatomical entity of one to three dimensions and some immaterial anatomical entity of one lower dimension such that the latter demarcates (delimits) the former from its neighborhood." [FMA:256502] subset: upper_level synonym: "anatomical boundary entity" EXACT [FMA:50705] xref: AEO:0000192 xref: FMA:50705 is_a: UBERON:0000466 ! immaterial anatomical entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000016 name: endocrine pancreas namespace: uberon def: "The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin[GO]." [GOC:GO, Wikipedia:Islets_of_Langerhans] comment: Editor notes - endocrine and exocrine pancrease are not co-associated in hagfishes or lampreys [PMID:20959416] - create a separate class for these? subset: organ_slim subset: uberon_slim subset: vertebrate_core synonym: "endocrine pancreas" EXACT [] synonym: "endocrine part of pancreas" RELATED [BTO:0000650] synonym: "islets of Langerhans part of pancreas" RELATED [] synonym: "pars endocrina pancreatis" EXACT [] xref: BTO:0000650 xref: EV:0100129 xref: FMA:16018 xref: MA:0001582 xref: ncithesaurus:Endocrine_Pancreas xref: SCTID:361339003 xref: TAO:0001260 xref: VHOG:0000049 xref: ZFA:0001260 is_a: UBERON:0002075 ! viscus is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0003923 ! dorsal pancreatic bud relationship: part_of UBERON:0001264 ! pancreas property_value: external_definition "The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000049", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/Pancreas"} property_value: external_definition "The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001260", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000049", ontology="VHOG", source="DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000017 name: exocrine pancreas namespace: uberon def: "The exocrine pancreas produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]. The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion." [GOC:GO, Wikipedia:Exocrine_component_of_pancreas] subset: organ_slim subset: uberon_slim subset: vertebrate_core synonym: "exocrine pancreas" EXACT [] synonym: "exocrine part of pancreas" RELATED [BTO:0000434] synonym: "pars exocrina pancreatis" EXACT [] xref: AAO:0010407 xref: BTO:0000434 xref: EV:0100093 xref: FMA:16017 xref: MA:0002415 xref: ncithesaurus:Exocrine_Pancreas xref: SCTID:248202004 xref: TAO:0001249 xref: UMLS:C0553695 xref: VHOG:0000048 xref: XAO:0000137 xref: ZFA:0001249 is_a: UBERON:0002075 ! viscus is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0003924 ! ventral pancreatic bud relationship: part_of UBERON:0001264 ! pancreas relationship: part_of UBERON:0002330 ! exocrine system property_value: external_definition "The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001249", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000048", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/Pancreas"} property_value: homology_notes "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000048", ontology="VHOG", source="DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000019 name: camera-type eye namespace: uberon def: "The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field[GO]. The eye contains the following parts (when they are present in the organism): the eyeball (eye proper), the lacrimal apparatus, the conjuctival, the eyelid." [GO:0043010, UBERON:cjm] comment: AO notes: FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ). MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this subset: uberon_slim subset: vertebrate_core synonym: "camera-type eye plus associated structures" RELATED [] synonym: "eye" BROAD [FMA:54448] synonym: "eyes" RELATED PLURAL [TAO:0000107] synonym: "orbital part of face" EXACT [FMA:54448] synonym: "orbital region" RELATED [FMA:54448] synonym: "regio orbitalis" EXACT LATIN [FMA:54448, FMA:TA] synonym: "vertebrate eye" NARROW [] xref: AAO:0010340 xref: BTO:0004688 xref: EHDAA2:0000484 xref: EHDAA:936 xref: EMAPA:16198 xref: FMA:54448 xref: MA:0000261 xref: ncithesaurus:Eye xref: NIF_GrossAnatomy:birnlex_1169 xref: OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvVil5pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycA xref: SCTID:181143004 xref: TAO:0000107 xref: UMLS:C0015392 xref: VHOG:0000275 xref: XAO:0000179 xref: ZFA:0000107 is_a: UBERON:0000047 ! simple eye is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0003072 {evidence="definitional"} ! optic cup relationship: part_of UBERON:0004088 ! ocular region property_value: external_definition "A cavitated compound organ that transduces light waves into neural signals.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000107", ontology="TAO", source="TAO:wd"} property_value: homology_notes "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000275", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000020 name: sense organ namespace: uberon def: "An organ that is capable of detection of chemical stimulus involved in sensory perception of smell." [UBERON:cjm] subset: uberon_slim synonym: "organ of sense organ system" EXACT [OBOL:accepted] synonym: "organ of sensory organ system" EXACT [OBOL:accepted] synonym: "organ of sensory system" EXACT [OBOL:accepted] synonym: "sense organ system organ" EXACT [OBOL:automatic] synonym: "sensillum" NARROW [WBbt:0006929] synonym: "sensor" RELATED [] synonym: "sensory organ" EXACT [] synonym: "sensory organ system organ" EXACT [OBOL:automatic] synonym: "sensory system organ" EXACT [OBOL:accepted] synonym: "Sinnesorgan" RELATED [BTO:0000202] xref: AEO:0000094 xref: BTO:0000202 xref: EHDAA2:0001824 xref: EHDAA:500 xref: EMAPA:16192 xref: FBbt:00005155 xref: GAID:63 xref: HAO:0000930 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/c0/Gray722.png/200px-Gray722.png xref: MA:0000017 xref: MESH:A09 xref: ncithesaurus:Organ_of_the_Special_Sense xref: SCTID:244485009 xref: UMLS:C0935626 xref: VHOG:0001407 xref: WBbt:0006929 is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0001032 ! sensory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000025 name: tube namespace: uberon def: "Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts. with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system" [GO:0035295, PMID:12526790] synonym: "epithelial or endothelial tube" EXACT [] xref: galen:Tube is_a: UBERON:0004111 ! anatomical conduit property_value: has_relational_adjective "tubular" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000029 name: lymph node namespace: uberon def: "Oval or bean shaped bodies (1 - 30 mm in diameter) located along the lymphatic system. Lymph nodes are garrisons of B, T, and other immune cells. Lymph nodes are found all through the body, and act as filters or traps for foreign particles. They contain white blood cells that use oxygen to process. Thus they are important in the proper functioning of the immune system. The lymph node is surrounded by a fibrous capsule, and inside the lymph node the fibrous capsule extends to form trabeculae. The substance of the lymph node is divided into the outer cortex and the inner medulla surrounded by the former all around except for at the hilum, where the medulla comes in direct contact with the surface. Thin reticular fibers, elastin and reticular fibers form a supporting meshwork called reticular network (RN) inside the node, within which the white blood cells (WBCs), most prominently, lymphocytes are tightly packed as follicles in the cortex. Elsewhere, there are only occasional WBCs. The RN provides not just the structural support, but also provide surface for adhesion of the dendritic cells, macrophages and lymphocytes. It allows for exchange of material with blood through the high endothelial venules and provides the growth and regulatory factors necessary for activation and maturation of immune cells[WP]." [GAID:947, Wikipedia:Lymph_node] subset: uberon_slim subset: vertebrate_core synonym: "lymph gland" RELATED [VHOG:0001273] synonym: "nodus lymphaticus" RELATED LATIN [Wikipedia:Lymph_node] xref: BTO:0000784 xref: EFO:0000872 xref: EV:0100050 xref: FMA:5034 xref: GAID:947 xref: galen:Lymphnode xref: http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png xref: MA:0000139 xref: MAT:0000442 xref: MESH:A15.382.520.604.412 xref: ncithesaurus:Lymph_Node xref: OpenCyc:Mx4rwLPqLpwpEbGdrcN5Y29ycA xref: SCTID:181756000 xref: TAO:0005318 xref: UMLS:C0024204 xref: VHOG:0001273 xref: ZFA:0005318 is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0002465 ! lymphoid system property_value: dubious_for_taxon NCBITaxon:32443 {source="ZFA", source="doie:10.1177/0192623311409597"} property_value: homology_notes "Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001273", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.630", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:8570 {source="Wikipedia"} [Term] id: UBERON:0000030 name: lamina propria namespace: uberon def: "A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions." [Wikipedia:Lamina_propria] comment: Editor notes: need to implement rules such that "lamina propria of X" is classified as part of some "mucosa of X" subset: uberon_slim synonym: "lamina propria mucosa" EXACT [] synonym: "lamina propria mucosae" EXACT [] synonym: "tunica propria" RELATED [BTO:0002330] xref: BTO:0002330 xref: FMA:62517 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/f/fb/GI_Organization.svg/250px-GI_Organization.svg.png xref: ncithesaurus:Lamina_Propria xref: SCTID:298225002 xref: UMLS:C1179187 is_a: UBERON:0004923 ! organ component layer relationship: part_of UBERON:0000344 ! mucosa property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000033 name: head namespace: uberon def: "The head is the anterior-most division of the body [GO]." [GO:0060322, Wikipedia:Head] subset: uberon_slim subset: vertebrate_core synonym: "adult head" NARROW [] synonym: "cephalic area" RELATED [SPD:0000016] synonym: "head (volume)" EXACT [FMA:7154] xref: AAO:0010335 xref: AEO:0000106 xref: BILA:0000115 xref: BTO:0000282 xref: EFO:0000964 xref: EHDAA2:0003106 xref: FBbt:00000004 xref: FMA:7154 xref: GAID:61 xref: galen:Head xref: HAO:0000397 xref: MA:0000023 xref: MAT:0000294 xref: MESH:A01.456 xref: MIAA:0000294 xref: ncithesaurus:Head xref: NIF_GrossAnatomy:birnlex_1230 xref: OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg xref: OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA xref: SCTID:302548004 xref: SPD:0000016 xref: TAO:0001114 xref: TGMA:0000002 xref: UMLS:C0018670 xref: VHOG:0001644 xref: WBbt:0005739 xref: XAO:0003024 xref: ZFA:0001114 is_a: UBERON:0011676 ! axial subdivision of organism relationship: part_of UBERON:0000153 ! anterior region of body relationship: part_of UBERON:0007811 ! craniocervical region property_value: external_definition "Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010335", ontology="AAO", source="AAO:BJB"} property_value: external_definition "Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001114", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001644", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0000948 property_value: spatially_disjoint_from UBERON:0002100 [Term] id: UBERON:0000042 name: serous membrane namespace: uberon def: "multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer." [http://purl.obolibrary.org/obo/uberon/tracker/86, Wikipedia:Serous_membrane] comment: in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. subset: uberon_slim subset: vertebrate_core synonym: "serosa" RELATED [Wikipedia:Serous_membrane] synonym: "tunica serosa" EXACT LATIN [FMA:9581] synonym: "wall of serous sac" EXACT [FMA:9581] xref: FMA:9581 xref: GAID:19 xref: http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png xref: http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png xref: MESH:A10.615.789 xref: ncithesaurus:Serosa xref: SCTID:362878009 xref: TAO:0005425 xref: UMLS:C0036760 xref: ZFA:0005425 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004457 ! cavity lining relationship: develops_from UBERON:0000926 {source="Wikipedia"} ! mesoderm relationship: part_of UBERON:0000060 ! anatomical wall property_value: external_definition "A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005425", ontology="TAO", source="http://en.wikipedia.org/wiki/Serous_membrane"} property_value: external_definition "a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]" xsd:string {source="http://en.wikipedia.org/wiki/Serous_membrane"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000043 name: tendon namespace: uberon def: "Dense regular connective tissue that connects muscle to bone[VSAO]." [VSAO:0000073, Wikipedia:Tendon] comment: AO notes: in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis subset: uberon_slim synonym: "sinew" RELATED [Wikipedia:Tendon] synonym: "tendo" RELATED LATIN [Wikipedia:Tendon] xref: AEO:0000091 xref: BTO:0001356 xref: EHDAA2:0003091 xref: EV:0100149 xref: FMA:9721 xref: GAID:276 xref: galen:Tendon xref: http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/3c/Achilles-tendon.jpg/200px-Achilles-tendon.jpg xref: MA:0000115 xref: MESH:A02.880 xref: ncithesaurus:Tendon xref: OpenCyc:Mx4rvVjefJwpEbGdrcN5Y29ycA xref: SCTID:256667004 xref: UMLS:C0039508 xref: VHOG:0001286 xref: VSAO:0000073 xref: XAO:0000173 xref: ZFA:0005647 is_a: UBERON:0007846 {source="VSAO"} ! dense regular connective tissue relationship: part_of UBERON:0002204 {source="OG"} ! musculoskeletal system property_value: external_definition "Dense regular connective tissue that connects muscle to bone.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000073", ontology="VSAO", source="PSPUB:0000170"} property_value: homology_notes "Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001286", ontology="VHOG", source="DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000044 name: dorsal root ganglion namespace: uberon def: "ganglion on the dorsal root of each spinal nerve that is one of a series of ganglia lodging cell bodies of sensory neurons[BTO]. Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves[..]. one on the posterior root of each spinal nerve, composed of unipolar nerve cell bodies of the sensory neurons of the nerve[TFD]." [Wikipedia:Dorsal_root_ganglion] comment: Development notes: The sensory ganglia of spinal nerves arise only from the neural crest, whereas many sensory ganglia of the “dorsal” cranial nerves arise from epibranchial placodes as well as the neural crest[doi: 10.1093/icb/icn065]. Other ontology notes: FMA treats dorsal root ganglion and spinal ganglion as equivalent labels. MA is the only ontology to introduce two classes here (also EHDAA2) subset: uberon_slim subset: vertebrate_core synonym: "dorsal root ganglia" RELATED PLURAL [] synonym: "dorsal root ganglion" EXACT [BTO:0001264] synonym: "DRG" RELATED [] synonym: "ganglion of dorsal root" EXACT [OBOL:automatic] synonym: "ganglion sensorium nervi spinalis" RELATED [BTO:0001264] synonym: "ganglion sensorium nervi spinalis" RELATED LATIN [Wikipedia:Dorsal_root_ganglion] synonym: "ganglion spinale" RELATED [BTO:0001264] synonym: "ganglion spinalis" EXACT [FMA:5888] synonym: "spinal ganglion" EXACT [FMA:5888] xref: AAO:0011032 xref: BTO:0001264 xref: EFO:0000900 xref: EHDAA2:0000418 xref: EHDAA2:0001897 xref: EHDAA:2899 xref: EMAPA:16668 xref: EMAPA:18372 xref: EV:0100373 xref: FMA:5888 xref: http://upload.wikimedia.org/wikipedia/commons/7/71/DRG_Chicken_e7.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/7/71/DRG_Chicken_e7.jpg/200px-DRG_Chicken_e7.jpg xref: MA:0000231 xref: MA:0000232 xref: MAT:0000162 xref: MIAA:0000162 xref: ncithesaurus:Dorsal_Root_Ganglion xref: NIF_GrossAnatomy:birnlex_2596 xref: SCTID:244455004 xref: TAO:0000200 xref: UMLS:C0017070 xref: VHOG:0000222 xref: XAO:0000210 xref: ZFA:0000200 is_a: UBERON:0001800 {source="MA"} ! sensory ganglion is_a: UBERON:0003338 ! ganglion of peripheral nervous system is_a: UBERON:0010313 ! neural crest-derived structure relationship: develops_from UBERON:0003083 {source="UBERONREF:0000002", source="ZFA"} ! trunk neural crest relationship: part_of UBERON:0002261 ! dorsal root of spinal cord property_value: external_definition "Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000200", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000222", ontology="VHOG", source="DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000045 name: ganglion namespace: uberon def: "A biological tissue mass, most commonly a mass of nerve cell bodies." [Wikipedia:Ganglion] comment: TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system. // Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com). subset: uberon_slim subset: vertebrate_core synonym: "ganglia" RELATED [] synonym: "neural ganglion" RELATED [BTO:0000497] xref: AAO:0010426 xref: AEO:0000135 xref: BTO:0000497 xref: EFO:0000899 xref: EHDAA2:0003135 xref: EHDAA:2897 xref: EHDAA:4662 xref: EHDAA:5621 xref: EHDAA:918 xref: EV:0100372 xref: FBbt:00005137 xref: FMA:5884 xref: MA:0002406 xref: MAT:0000207 xref: MAT:0000343 xref: MESH:A08.340 xref: MIAA:0000207 xref: MIAA:0000343 xref: ncithesaurus:Ganglion xref: NIF_GrossAnatomy:nlx_anat_100302 xref: TAO:0000190 xref: TGMA:0001016 xref: UMLS:C0017067 xref: VHOG:0000156 xref: WBbt:0005189 xref: XAO:0000209 xref: ZFA:0000190 is_a: UBERON:0003714 {source="EHDAA2"} ! neural tissue disjoint_from: UBERON:0002420 {inconsistent_with="BTO"} ! basal ganglion relationship: develops_from UBERON:0003869 {evidence="definitional"} ! presumptive ganglion relationship: part_of UBERON:0001016 ! nervous system property_value: external_definition "Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010426", ontology="AAO", source="AAO:EJS"} property_value: external_definition "Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000190", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "ganglionic" xsd:string property_value: homology_notes "Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000156", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000047 name: simple eye namespace: uberon def: "An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity." [Wikipedia:Eye#Simple_eyes] subset: grouping_class subset: uberon_slim xref: TGMA:0000729 is_a: UBERON:0000970 ! eye property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000054 name: macula namespace: uberon def: "Thickened areas of the saccule or utricle where the termination of the vestibular nerve occurs[MESH,modified]." [MESH:A09.246.631.909.625.125] comment: Usage notes: this refers to the inner ear structure, not the macula of the retina. We follow ZFA in including a grouping class for the macula of utricle and sacule subset: uberon_slim synonym: "acoustic macula" RELATED [MESH:A09.246.631.909.625.125] synonym: "acoustic maculae" RELATED PLURAL [MESH:A09.246.631.909.625.125] synonym: "macula" EXACT [] synonym: "maculae" EXACT PLURAL [] synonym: "sensory macula" EXACT [ZFA:0000386] synonym: "sensory patch" EXACT [ZFA:0000386] xref: GAID:777 xref: MESH:A09.246.631.909.625.125 xref: TAO:0000386 xref: ZFA:0000386 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001846 ! internal ear property_value: external_definition "Patches of thickened, pseudostratified epithelium of the inner ear, consisting of regular arrays of sensory hair cells interspersed with supporting cells. Each patch has its own charcteristic shape and polarity pattern. (See Anatomical Atlas entry for sensory patches of the ear by T. Whitfield.)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000386", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "macular" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000055 name: vessel namespace: uberon def: "A tubular structure that contains, conveys body fluid, such as blood or lymph." [UBERON:cjm] comment: compare with UBERON:0008782 subset: grouping_class is_a: UBERON:0004111 ! anatomical conduit property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000056 name: ureter namespace: uberon def: "Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. In humans, organ with organ cavity which connects the renal sinus to the urinary bladder. Examples: the right and the left ureters." [FMA:9704, GO:0090189, Wikipedia:Ureter] subset: major_organ subset: organ_slim subset: uberon_slim synonym: "metanephric duct" RELATED [ISBN10:0073040584, VHOG:0000605] xref: AAO:0010254 xref: BTO:0001409 xref: EFO:0000930 xref: EHDAA2:0002139 xref: EHDAA:9341 xref: EMAPA:17950 xref: EV:0100097 xref: FMA:9704 xref: GAID:438 xref: galen:Ureter xref: http://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/30/Urinary_system.svg/200px-Urinary_system.svg.png xref: MA:0000378 xref: MAT:0000120 xref: MESH:A05.810.776 xref: MIAA:0000120 xref: ncithesaurus:Ureter xref: OpenCyc:Mx4rvhmm6JwpEbGdrcN5Y29ycA xref: SCTID:302511008 xref: UMLS:C0041951 xref: VHOG:0000605 xref: XAO:0000144 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0005179 ! pelvis organ is_a: UBERON:0006555 ! excretory tube relationship: develops_from UBERON:0005081 {source="GO"} ! ureter ureteric bud relationship: part_of UBERON:0002355 {xref="MA:0000378"} ! pelvis relationship: part_of UBERON:0011143 {source="FMA"} ! upper urinary tract property_value: external_definition "Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010254", ontology="AAO", source="AAO:BJB"} property_value: external_definition "The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000605", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: has_relational_adjective "ureteral" xsd:string property_value: has_relational_adjective "ureteric" xsd:string property_value: homology_notes "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000605", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000057 name: urethra namespace: uberon def: "A tube which connects the urinary bladder to the outside of the body. In males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening. The external urethral sphincter is a striated muscle that allows voluntary control over urination." [Wikipedia:Urethra] subset: major_organ subset: organ_slim subset: uberon_slim xref: BTO:0001426 xref: EFO:0000931 xref: EMAPA:30901 xref: EV:0100099 xref: FMA:19667 xref: GAID:390 xref: galen:Urethra xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/cb/Female_anatomy.png/200px-Female_anatomy.png xref: MA:0000379 xref: MAT:0000121 xref: MESH:A05.360.444.492.726 xref: MIAA:0000121 xref: ncithesaurus:Urethra xref: OpenCyc:Mx4rvVjkypwpEbGdrcN5Y29ycA xref: SCTID:302513006 xref: UMLS:C0041967 xref: VHOG:0001264 xref: XAO:0000153 is_a: UBERON:0000062 ! organ is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0004111 ! anatomical conduit is_a: UBERON:0006554 ! urinary system structure relationship: develops_from UBERON:0000164 {notes="pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra", source="Wikipedia"} ! primitive urogenital sinus relationship: part_of UBERON:0001556 ! lower urinary tract property_value: has_relational_adjective "urethral" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000058 name: duct namespace: uberon def: "A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA]." [Wikipedia:Duct_(anatomy), ZFA:0005171] comment: TODO - make distinctions between duct and tube clearer. Single layer of cells vs multiples? Function (e.g. exocrine gland duct?). Different ontologies use it in different ways (e.g. isa epithelial tube in FBbt). Consider adding duct of gland subset: vertebrate_core synonym: "anatomical duct" EXACT [] synonym: "exocrine duct" NARROW [] synonym: "exocrine gland duct" NARROW [] xref: AAO:0011123 xref: FBbt:00100314 xref: FMA:30320 xref: galen:Duct xref: ncithesaurus:Duct xref: SCTID:91726008 xref: TAO:0005171 xref: UMLS:C0687028 xref: XAO:0004000 xref: ZFA:0005171 is_a: UBERON:0004111 ! anatomical conduit property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000059 name: large intestine namespace: uberon def: "A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]." [ISBN10:0073040584, Wikipedia:Large_intestine_(anatomy)] subset: major_organ subset: organ_slim synonym: "intestinum crassum" RELATED [BTO:0000706] xref: AAO:0010396 xref: BTO:0000706 xref: EFO:0000840 xref: EMAPA:19252 xref: EV:0100077 xref: FMA:7201 xref: GAID:306 xref: galen:LargeIntestine xref: MA:0000333 xref: MESH:A03.492.411.495 xref: MIAA:0000046 xref: ncithesaurus:Large_Intestine xref: OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA xref: SCTID:181254001 xref: UMLS:C0021851 xref: VHOG:0000054 xref: XAO:0000131 is_a: UBERON:0000062 ! organ is_a: UBERON:0004921 {order="2", source="cjm"} ! subdivision of digestive tract relationship: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0004907 ! lower digestive tract property_value: homology_notes "Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000054", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000060 name: anatomical wall namespace: uberon alt_id: UBERON:0009915 def: "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [FMA:82482] comment: AO notes: in FMA, serosa is a wall subset: upper_level synonym: "organ wall" RELATED [FMA:82482] synonym: "wall" EXACT [] synonym: "wall of organ" EXACT [FMA:82482] xref: EMAPA:25036 xref: FMA:82482 xref: galen:Wall is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000061 name: anatomical structure namespace: uberon def: "Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome." [CARO:0000003] subset: upper_level synonym: "biological structure" EXACT [] xref: AAO:0010825 xref: AEO:0000003 xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: FBbt:00007001 xref: FMA:67135 xref: GAID:781 xref: HAO:0000003 xref: MA:0003000 xref: MESH:A13 xref: SCTID:362889002 xref: TAO:0000037 xref: TGMA:0001823 xref: VHOG:0001759 xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000062 name: organ namespace: uberon def: "Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions[GO]." [Wikipedia:Organ_(anatomy)] comment: note that CARO does not include a generic 'organ' class, only simple and compound organ subset: upper_level synonym: "body organ" RELATED [] synonym: "element" RELATED [] xref: EFO:0000634 xref: FMA:67498 xref: MA:0003001 xref: ncithesaurus:Organ xref: NIF_GrossAnatomy:birnlex_4 xref: OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA xref: OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA xref: SCTID:272625005 xref: UMLS:C0178784 is_a: UBERON:0000061 ! anatomical structure relationship: part_of UBERON:0000467 ! anatomical system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} [Term] id: UBERON:0000063 name: organ segment namespace: uberon def: "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball[FMA]." [FMA:86140] subset: upper_level synonym: "organ region with fixed fiat boundary" EXACT [FMA:86140] synonym: "segment of organ" EXACT [FMA:86140] xref: FMA:86140 is_a: UBERON:0000064 ! organ part property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000064 name: organ part namespace: uberon def: "anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA]." [FMA:82472] subset: disjointness_axiom_removed subset: upper_level synonym: "cardinal organ part" EXACT [] xref: AAO:0011124 xref: EFO:0000635 xref: FMA:82472 xref: SCTID:113343008 xref: SCTID:91717005 is_a: UBERON:0000061 ! anatomical structure relationship: part_of UBERON:0000062 ! organ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000065 name: respiratory tract namespace: uberon def: "anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts" [UBERON:cjm] xref: EHDAA2:0001606 xref: EHDAA:1568 xref: EHDAA:2219 xref: EMAPA:16737 xref: OpenCyc:Mx4rvvM--pwpEbGdrcN5Y29ycA xref: SCTID:361110005 xref: VHOG:0000393 is_a: UBERON:0001005 ! respiratory airway is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0007026 {source="NBK10107"} ! primitive gut relationship: develops_from UBERON:0008947 ! respiratory primordium relationship: part_of UBERON:0001004 ! respiratory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000072 name: segment of respiratory tract namespace: uberon def: "An organ segment that is part of a respiratory tract [Obol]." [OBOL:automatic] comment: Note that MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole synonym: "respiratory tract" RELATED [MA:0000434] xref: MA:0000434 is_a: UBERON:0000063 ! organ segment is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0000065 ! respiratory tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000073 name: regional part of nervous system namespace: uberon def: "An anatomical structure that is part of a nervous system [Obol]." [OBOL:automatic] subset: non_informative subset: upper_level synonym: "part of nervous system" EXACT [NIF_GrossAnatomy:birnlex_1157] xref: ncithesaurus:Nervous_System_Part xref: NIF_GrossAnatomy:birnlex_1157 xref: SCTID:25087005 xref: UMLS:C1518256 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001016 ! nervous system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl created_by: Melissa Haendel creation_date: 2009-06-18T09:00:04Z [Term] id: UBERON:0000074 name: renal glomerulus namespace: uberon def: "A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO]." [MP:0005325, Wikipedia:Glomerulus] comment: ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. TODO - split glomerulus and glomerular tuft? DONE. GUDMAP: 'Together, the Bowman’s capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule? subset: vertebrate_core synonym: "glomerular capillary tuft" RELATED [ZFA:0001288] synonym: "glomerular tuft" RELATED INCONSISTENT [] synonym: "glomerulus" BROAD [] synonym: "glomerulus renis" RELATED LATIN [Wikipedia:Glomerulus] synonym: "malphigian glomerulus" RELATED [BTO:0000530] synonym: "renal corpuscle" RELATED INCONSISTENT [] synonym: "renal glomeruli" EXACT [TAO:0001288] xref: BTO:0000530 xref: EFO:0003667 xref: EV:0100386 xref: FMA:15624 xref: http://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg xref: http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/30/Gray1130.svg/200px-Gray1130.svg.png xref: MA:0001657 xref: MESH:A05.810.453.736.520 xref: ncithesaurus:Glomerulus xref: SCTID:362217000 xref: TAO:0001288 xref: UMLS:C0022663 xref: ZFA:0001288 is_a: UBERON:0000064 ! organ part is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0006554 ! urinary system structure relationship: develops_from UBERON:0005749 ! glomerular tuft relationship: part_of UBERON:0001229 {source="MA"} ! renal corpuscle property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl created_by: Melissa Haendel creation_date: 2009-06-18T09:26:37Z [Term] id: UBERON:0000075 name: subdivision of skeletal system namespace: uberon alt_id: UBERON:0010322 def: "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [UBERON:cjm, UBERONREF:0000003] subset: non_informative synonym: "skeletal system part" RELATED [] synonym: "skeletal system subdivision" EXACT [FMA:85544] xref: FMA:85544 xref: galen:ComplexSkeletalStructure xref: ncithesaurus:Skeletal_System_Part xref: SCTID:118966000 xref: UMLS:C1519343 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001434 ! skeletal system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000076 name: external ectoderm namespace: uberon def: "The surface ectoderm (or external ectoderm forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis [WP,unvetted]." [Wikipedia:External_ectoderm] comment: Editor note: merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube). synonym: "surface ectoderm" EXACT [] xref: EHDAA2:0001968 xref: EHDAA:1494 xref: EHDAA:350 xref: EHDAA:4784 xref: EHDAA:4790 xref: EHDAA:4796 xref: EHDAA:7860 xref: EMAPA:16096 xref: EMAPA:16539 xref: FMA:87656 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/1/1d/Ectoderm.png/200px-Ectoderm.png xref: ncithesaurus:Surface_Ectoderm xref: UMLS:C1515087 is_a: UBERON:0000923 ! germ layer relationship: part_of UBERON:0000924 ! ectoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000077 name: mixed endoderm/mesoderm-derived structure namespace: uberon def: "An anatomical structure that develops from the endoderm and the mesoderm." [UBERON:cjm] comment: Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple subset: grouping_class is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004120 ! mesoderm-derived structure relationship: develops_from UBERON:0000925 ! endoderm relationship: develops_from UBERON:0000926 ! mesoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000078 name: mixed ectoderm/mesoderm/endoderm-derived structure namespace: uberon def: "An anatomical structure that develops from the ectoderm, mesoderm and endoderm." [UBERON:cjm] comment: Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple subset: grouping_class is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0000924 ! ectoderm relationship: develops_from UBERON:0000925 ! endoderm relationship: develops_from UBERON:0000926 ! mesoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000079 name: male reproductive system namespace: uberon def: "the organs associated with producing offspring in the gender that produces spermatozoa." [MP:0001145] synonym: "genitalia of male organism" EXACT [OBOL:automatic] synonym: "male genital organ" RELATED [BTO:0000082] synonym: "male genital system" EXACT [FMA:45664] synonym: "male genitalia" EXACT [] synonym: "male genitals" EXACT [] synonym: "male organism genitalia" EXACT [OBOL:automatic] synonym: "male organism reproductive system" EXACT [OBOL:automatic] synonym: "male reproductive tract" RELATED [MA:0000396] synonym: "reproductive system of male organism" EXACT [OBOL:automatic] synonym: "systema genitale masculinum" RELATED [BTO:0000082] xref: BTO:0000082 xref: EFO:0000970 xref: EHDAA2:0001054 xref: EHDAA:8136 xref: EMAPA:17968 xref: EV:0100101 xref: FBbt:00004927 xref: FMA:45664 xref: GAID:386 xref: HAO:0000505 xref: MA:0000396 xref: MESH:A05.360.444 xref: ncithesaurus:Male_Genitalia xref: ncithesaurus:Male_Reproductive_System xref: OpenCyc:Mx4rvViCepwpEbGdrcN5Y29ycA xref: SCTID:361340001 xref: TGMA:0000634 xref: UMLS:C0017422 xref: UMLS:C1963704 xref: VHOG:0000725 xref: WBbt:0008423 xref: XAO:0000155 is_a: UBERON:0000990 ! reproductive system disjoint_from: UBERON:0000474 ! female reproductive system relationship: part_of UBERON:0003101 ! male organism property_value: homology_notes "By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000725", ontology="VHOG", source="ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000080 name: mesonephros namespace: uberon def: "In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the mesonephros will form the mature kidney[GO]. One of three excretory organs that develop in vertebrates. It serves as the main excretory organ of aquatic vertebrates and as a temporary kidney in higher vertebrates. composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo." [GO:0001823, Wikipedia:Mesonephros] comment: By contrast to the pronephros, the histological features of the mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP] comment: Taxon notes: The mesonephros persists and form the permanent kidneys in fishes and amphibians, but in reptiles, birds, and mammals, it atrophies and for the most part disappears rapidly as the permanent kidney (metanephros) begins to develop during the sixth or seventh week. By the beginning of the fifth month only the ducts and a few of the tubules of the mesonephros remain[WP] subset: organ_slim subset: vertebrate_core synonym: "mesonephric kidney" EXACT [XAO:0000141] synonym: "mesonephroi" EXACT PLURAL [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] synonym: "opisthonephros" RELATED [VHOG:0000038, XAO:0000141] synonym: "opisto nephros" RELATED [] synonym: "opistonephros" RELATED [http://www.usm.maine.edu/bio/courses/bio205/bio205_26_sex.html] synonym: "Wolffian body" EXACT [BTO:0001542, GOC:yaf, MESH:A16.254.500, Wikipedia:Mesonephros] xref: AAO:0010384 xref: BTO:0001542 xref: EFO:0000928 xref: EHDAA2:0001130 xref: EHDAA:1581 xref: EHDAA:5903 xref: EMAPA:16744 xref: EMAPA:17369 xref: EMAPA:27644 xref: FMA:72171 xref: GAID:1308 xref: http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/a/ad/Gray986.png/200px-Gray986.png xref: MESH:A16.254.500 xref: ncithesaurus:Mesonephros xref: SCTID:308799002 xref: TAO:0000529 xref: UMLS:C0025492 xref: VHOG:0000038 xref: XAO:0000141 xref: ZFA:0000529 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0002113 ! kidney relationship: develops_from UBERON:0002120 ! pronephros property_value: external_definition "A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000038", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: external_definition "Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010384", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "mesonephric" xsd:string property_value: homology_notes "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000038", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000083 name: mesonephric tubule namespace: uberon def: "A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]." [Wikipedia:Mesonephric_tubules] comment: TODO check synonym: "renal tubules" RELATED PLURAL [VHOG:0000500] synonym: "tubuli mesonephrici" RELATED LATIN [Wikipedia:Mesonephric_tubules] xref: AAO:0010389 xref: EHDAA2:0001134 xref: EMAPA:27588 xref: EMAPA:27659 xref: VHOG:0000500 xref: XAO:0000148 is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0005103 ! mesonephric epithelium is_a: UBERON:0006555 ! excretory tube relationship: part_of UBERON:0000080 ! mesonephros property_value: external_definition "Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000500", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/mesonephric+tubule"} property_value: homology_notes "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000500", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000084 name: ureteric bud namespace: uberon def: "a protrusion from the mesonephric duct during the development of the urinary and reproductive organs. It later develops into the adult kidney, except for the nephrons, which, in contrast, originate from the metanephric blastema[WP]. epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]" [https://sourceforge.net/tracker/?group_id=36855&atid=440764, MP:0010979, PMID:19828308, Wikipedia:Ureteric_bud] synonym: "diverticulum" RELATED [BTO:0001646] synonym: "diverticulum metanephricum" RELATED LATIN [Wikipedia:Ureteric_bud] synonym: "gemma ureterica" RELATED LATIN [Wikipedia:Ureteric_bud] synonym: "metanephric bud" RELATED [BTO:0001646] synonym: "metanephric diverticulum" RELATED [Wikipedia:Metanephros#Metanephros] synonym: "ureteric ampulla" RELATED [] synonym: "ureteric diverticulum" RELATED [VHOG:0000541] xref: BTO:0001646 xref: EHDAA2:0002140 xref: EHDAA:3091 xref: EHDAA:5917 xref: EMAPA:17209 xref: EMAPA:17376 xref: ncithesaurus:Metanephric_Diverticulum xref: SCTID:361528000 xref: UMLS:C1284058 xref: VHOG:0000541 is_a: UBERON:0000083 ! mesonephric tubule is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac relationship: develops_from UBERON:0003074 {source="EHDAA2"} ! mesonephric duct relationship: part_of UBERON:0003074 ! mesonephric duct property_value: external_definition "Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000541", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000541", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000085 name: morula namespace: uberon def: "An embryo at an early stage of embryonic development, consisting of cells (called blastomeres) in a solid ball contained within the zona pellucida[WP] The compacted embryo before cavity formation." [Wikipedia:Morula] comment: EHDAA2 has embryo starting later synonym: "morula (2-16 cells)" RELATED [EHDAA2:0000005] xref: BTO:0001508 xref: EHDAA2:0000005 xref: GAID:1295 xref: http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/c6/Blastulation.png/200px-Blastulation.png xref: MESH:A16.254.270.550 xref: ncithesaurus:Morula xref: SCTID:361474003 xref: UMLS:C0026573 xref: XAO:1000029 is_a: UBERON:0000922 ! embryo relationship: part_of UBERON:0004716 {source="EHDAA2"} ! conceptus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000087 name: inner cell mass namespace: uberon def: "Mass of cells inside the primordial embryo that will eventually give rise to the definitive structures of the fetus. This structure forms in the earliest steps of development, before implantation into the endometrium of the uterus has occurred. The ICM lies within the blastocoele (more correctly termed 'blastocyst cavity', as it is not strictly homologous to the blastocoele of anamniote vertebrates) and is entirely surrounded by the single layer of cells called trophoblast." [Wikipedia:Inner_cell_mass] subset: early_development synonym: "embryoblast" RELATED [] synonym: "embryoblastus; massa cellularis interna; pluriblastus senior" RELATED LATIN [Wikipedia:Inner_cell_mass] synonym: "ICM" RELATED [VHOG:0000742] synonym: "pluriblast" RELATED [] xref: EFO:0000547 xref: EHDAA2:0000830 xref: EHDAA:40 xref: EMAPA:16041 xref: FMA:86557 xref: http://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/7/72/Blastocyst_English.svg/200px-Blastocyst_English.svg.png xref: ncithesaurus:Inner_Cell_Mass xref: SCTID:361456007 xref: UMLS:C1283994 xref: VHOG:0000742 is_a: UBERON:0002050 ! embryonic structure relationship: develops_from UBERON:0000085 {source="EHDAA2"} ! morula relationship: develops_from UBERON:0000358 {source="Wikipedia"} ! blastocyst relationship: part_of UBERON:0000922 {source="EHDAA2"} ! embryo property_value: external_definition "A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000742", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000742", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000091 name: bilaminar disc namespace: uberon def: "the epiblast and the hypoblast, evolved from the embryoblast" [Wikipedia:Bilaminar_disc] subset: early_development synonym: "bilaminar disk" RELATED [Wikipedia:Bilaminar_disc] synonym: "bilaminary embryonic disc" EXACT [] synonym: "bilaminary germ disc" EXACT [ISBN:9780878932504] xref: http://upload.wikimedia.org/wikipedia/commons/thumb/e/e3/Gray21.png/200px-Gray21.png xref: ncithesaurus:Bilaminar_Embryonic_Disc xref: UMLS:C1283997 is_a: UBERON:0002050 ! embryonic structure relationship: develops_from UBERON:0000087 {source="Wikipedia"} ! inner cell mass property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000094 name: membrane organ namespace: uberon def: "Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]" [FMA:7145] synonym: "membrane of organ" EXACT [] xref: FMA:7145 is_a: UBERON:0000062 ! organ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl created_by: cjm creation_date: 2009-07-30T05:19:13Z [Term] id: UBERON:0000102 name: lung vasculature namespace: uberon def: "The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]." [GOC:GO] synonym: "lung vascular network" EXACT [OBOL:automatic] synonym: "pulmonary vasculature" EXACT [FMA:73750] synonym: "vascular network of lung" EXACT [OBOL:automatic] synonym: "vasculature of lung" EXACT [OBOL:automatic] xref: FMA:73750 is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0006876 ! vasculature of organ relationship: part_of UBERON:0002048 ! lung property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000115 name: lung epithelium namespace: uberon def: "the epithelial layer of the lung." [MP:0006382] synonym: "epithelial tissue of lung" EXACT [OBOL:automatic] synonym: "epithelium of lung" EXACT [OBOL:automatic] synonym: "lung epithelial tissue" EXACT [OBOL:automatic] synonym: "pulmonary epithelium" RELATED [BTO:0001653] xref: BTO:0001653 xref: MA:0001783 is_a: UBERON:0004815 ! lower respiratory tract epithelium relationship: develops_from UBERON:0001041 ! foregut relationship: part_of UBERON:0002048 ! lung property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000117 name: respiratory tube namespace: uberon def: "A tube in the respiratory tract." [GO:0030323] comment: Consider merging into respiratory tract synonym: "segment of tracheobronchial tree" NARROW [FMA:12224] synonym: "tracheobronchial tree segment" NARROW [FMA:12224] xref: FMA:12224 is_a: UBERON:0000025 ! tube is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0000065 ! respiratory tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000118 name: lung bud namespace: uberon def: "Structure derived from foregut that becomes a lung[GO]." [GO:0060431, Wikipedia:Respiratory_bud] comment: Editors note: clarify successors - include bronchi? synonym: "gemma pulmonalis" RELATED LATIN [Wikipedia:Lung_buds] synonym: "gemma respiratoria" RELATED LATIN [Wikipedia:Lung_buds] synonym: "lung bud" RELATED PLURAL [] synonym: "primary lung bud" RELATED [GO:0060572] synonym: "respiratory diverticulum" RELATED [Wikipedia:Lung_buds] xref: BTO:0001643 xref: EHDAA2:0004089 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/7/71/Gray948.png/200px-Gray948.png xref: ncithesaurus:Primary_Bronchial_Bud xref: ncithesaurus:Respiratory_Diverticulum xref: SCTID:361427007 xref: UMLS:C1514420 xref: UMLS:C1514897 is_a: UBERON:0005153 {source="GO:0060441"} ! epithelial bud is_a: UBERON:0005911 ! endo-epithelium relationship: develops_from UBERON:0005597 ! lung primordium relationship: develops_from UBERON:0008947 {source="EHDAA2"} ! respiratory primordium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000119 name: cell layer namespace: uberon def: "Portion of tissue, that consists of one or more layers of cells connected to each other by cell junctions" [UBERON:cjm] subset: upper_level synonym: "cell sheath" RELATED [] synonym: "layer of cells" EXACT [] is_a: UBERON:0000479 ! tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000121 name: perineurium namespace: uberon def: "Connective tissue surrounding a fascicle." [Wikipedia:Perineurium] comment: consider FBbt:00007090 (perineurium): The outer two layers of glial cells that cover the central nervous system and the nerves. The outer layer is the perineurial sheath (sometimes referred to as the perineurial sheath outer layer); the inner layer is the sub-perineural glial sheath (sometimes referred to as the perineurial sheath inner layer) xref: BTO:0003153 xref: FMA:52585 xref: http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray636.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/9/9c/Gray636.png/200px-Gray636.png xref: ncithesaurus:Perineurium xref: NIF_GrossAnatomy:nlx_anat_090205 xref: SCTID:362299001 xref: UMLS:C0205890 is_a: UBERON:0002384 ! connective tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000122 name: neuron projection bundle namespace: uberon alt_id: UBERON:0005163 def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [CARO:0001001, FBbt:00005099, FBC:DOS] synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] synonym: "neural fiber bundle" EXACT [] xref: CARO:0001001 xref: FBbt:00005099 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005162 ! multi cell component structure relationship: part_of UBERON:0001016 ! nervous system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000125 name: neural nucleus namespace: uberon def: "Anatomical structure consisting of a discrete aggregate of neuronal soma[GO]." [GO:0048857, GO_REF:0000021, Wikipedia:Nucleus_(neuroanatomy)] comment: do not include NIF_Subcellular:sao1702920020 Nucleus. Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in "subcortical" because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in "relatively compact" and "distiguishable by histology" because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate. synonym: "neuraxis nucleus" EXACT [FMA:83686] synonym: "neuronal nucleus" EXACT [AEO:0000136] synonym: "nucleus" BROAD [] synonym: "nucleus of neuraxis" RELATED [] xref: AEO:0000136 xref: FMA:83686 is_a: UBERON:0000073 ! regional part of nervous system relationship: part_of UBERON:0001016 ! nervous system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000153 name: anterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000158 name: membranous layer namespace: uberon synonym: "membranous organ component" EXACT [FMA:82500] xref: FMA:82500 is_a: UBERON:0004923 ! organ component layer property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000160 name: intestine namespace: uberon def: "Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine." [GOC:GO, Wikipedia:Intestine] comment: MA also has a class MA:0001524 bowel, not clear how this is different. Usage notes: this class is currently very general, encompassing the C elegans 'intestine', which is a tube of epithelial cells extending from the 'pharynx' to 'rectum'. Taxon notes: [in zebrafish] No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type. subset: uberon_slim subset: vertebrate_core synonym: "bowel" EXACT [] xref: AAO:0000246 xref: ANISEED:1235303 xref: BTO:0000648 xref: EFO:0000834 xref: EV:0100071 xref: FMA:7199 xref: GAID:295 xref: galen:Intestine xref: MA:0000328 xref: MA:0001524 xref: MESH:A03.492.411 xref: MIAA:0000043 xref: ncithesaurus:Intestine xref: SCTID:256876008 xref: TAO:0001338 xref: UMLS:C0021853 xref: VHOG:0000056 xref: WBbt:0005772 xref: XAO:0000129 xref: ZFA:0001338 is_a: UBERON:0004921 {source="cjm"} ! subdivision of digestive tract relationship: part_of UBERON:0005409 ! gastrointestinal system property_value: external_definition "Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000246", ontology="AAO", source="AAO:EJS"} property_value: external_definition "The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000056", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: has_relational_adjective "intestinal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000162 name: cloaca namespace: uberon def: "Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures" [ISBN10:0073040584, Wikipedia:Cloaca] comment: Development notes: hindgut endoderm and proctodeal ectoderm. Taxon notes: Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs[WP]. Editor notes: adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca synonym: "cloacal chamber" RELATED [AAO:0000095] synonym: "vent" RELATED [XAO:0000244] xref: AAO:0000095 xref: GAID:1206 xref: MESH:A13.223 xref: ncithesaurus:Cloaca xref: SCTID:362857006 xref: UMLS:C0008987 xref: VHOG:0001186 xref: XAO:0000244 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0004185 ! endodermal gut relationship: part_of UBERON:0001555 {source="ZFA"} ! digestive tract relationship: part_of UBERON:0004122 {source="AAO"} ! genitourinary system property_value: external_definition "A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001186", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/cloaca"} property_value: external_definition "Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000095", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "cloacal" xsd:string property_value: homology_notes "A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001186", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: present_in_taxon NCBITaxon:9369 {notes="most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults."} [Term] id: UBERON:0000163 name: embryonic cloaca namespace: uberon def: "endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]." [MP:0010115, Wikipedia:Cloaca_(embryology)] comment: compare UBERON:0000162 cloaca synonym: "cloaca" RELATED SENSU [] xref: EHDAA2:0000256 xref: EHDAA:4895 xref: EMAPA:27573 xref: EMAPA:27638 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0000162 ! cloaca is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004906 ! ectodermal gut is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0001008 {source="EHDAA2"} ! excretory system relationship: part_of UBERON:0012361 {source="EHDAA2"} ! internal anal region property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000164 name: primitive urogenital sinus namespace: uberon def: "Ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females[MP]." [Wikipedia:Definitive_urogenital_sinus] comment: Note that the term "urogenital sinus" may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal[MP] synonym: "fetal UGS" EXACT [PMID:18977204] synonym: "UGS" EXACT [MP:0010116] synonym: "urogenital sinus" BROAD [MP:0010116] xref: EHDAA2:0004060 xref: EHDAA:5029 xref: EHDAA:5919 xref: EMAPA:17211 xref: EMAPA:17379 xref: http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Gray1109.png/200px-Gray1109.png xref: ncithesaurus:Urogenital_Sinus xref: SCTID:50961009 xref: UMLS:C0231057 xref: VHOG:0000414 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0003064 ! intermediate mesoderm relationship: part_of UBERON:0000163 {source="MP-def"} ! embryonic cloaca relationship: part_of UBERON:0001008 {source="EHDAA2"} ! excretory system property_value: external_definition "The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000414", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/urogenital+sinus"} property_value: homology_notes "In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000414", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000165 name: mouth namespace: uberon def: "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes teeth, gums, lips, tongue and parts of the palate." [http://purl.obolibrary.org/obo/uberon/references/reference_0000034, Wikipedia:Mouth] comment: AO notes: in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. subset: major_organ subset: uberon_slim subset: vertebrate_core synonym: "adult mouth" EXACT [] synonym: "cavital oralis" RELATED LATIN [Wikipedia:Mouth] synonym: "cavitas oris" RELATED [BTO:0001090] synonym: "cavum oris" RELATED [BTO:0001090] synonym: "mouth cavity" RELATED [BTO:0001090] synonym: "oral region" RELATED [EHDAA2:0001326] synonym: "oral vestibule" RELATED [BTO:0001090] synonym: "regio oralis" EXACT [BTO:0004698] synonym: "regio oralis" EXACT LATIN [FMA:49184, FMA:TA] synonym: "rima oris" RELATED [BTO:0001090] synonym: "stoma" RELATED [] synonym: "stomatodaeum" RELATED [VHOG:0000812] synonym: "vestibule of mouth" RELATED [BTO:0001090] synonym: "vestibulum oris" RELATED [BTO:0001090] xref: AAO:0010355 xref: BTO:0001090 xref: BTO:0004698 xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 xref: FBbt:00003126 xref: FMA:49184 xref: GAID:75 xref: galen:Mouth xref: http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/0/06/Mouth_illustration-Otis_Archives.jpg/180px-Mouth_illustration-Otis_Archives.jpg xref: MA:0000341 xref: MA:0002474 xref: MAT:0000038 xref: MESH:A01.456.505.631 xref: MIAA:0000038 xref: OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA xref: SCTID:21082005 xref: TADS:0000040 xref: TAO:0000547 xref: TAO:0000590 xref: TGMA:0000131 xref: VHOG:0000280 xref: VHOG:0000812 xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004921 ! subdivision of digestive tract relationship: develops_from UBERON:0000930 ! stomodeum relationship: part_of UBERON:0000033 ! head property_value: external_definition "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010355", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "oral" xsd:string property_value: homology_notes "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000812", ontology="VHOG", source="DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000168 name: segment of colon namespace: uberon def: "An organ segment that is part of a colon [Obol]." [OBOL:automatic] xref: FMA:222905 is_a: UBERON:0000063 ! organ segment is_a: UBERON:0004921 {order="4", source="cjm"} ! subdivision of digestive tract relationship: part_of UBERON:0001155 ! colon property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000170 name: pair of lungs namespace: uberon synonym: "lungs" EXACT [] synonym: "lungs pair" EXACT [] synonym: "pulmones" EXACT LATIN [FMA:68877, FMA:TA] synonym: "set of lungs" EXACT [] xref: FMA:68877 xref: OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA is_a: UBERON:0000477 ! anatomical cluster is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0001558 {source="FMA-abduced"} ! lower respiratory tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000171 name: respiration organ namespace: uberon def: "Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms." [GO:0007585] subset: functional_classification subset: organ_slim synonym: "apparatus respiratorius organ" EXACT [OBOL:automatic] synonym: "breathing organ" EXACT [] synonym: "gas exchange organ" RELATED [] synonym: "organ of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "organ of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory organ" EXACT [] synonym: "respiratory system organ" EXACT [OBOL:automatic] xref: EMAPA:17607 xref: SCTID:272626006 xref: SPD:0000428 xref: TGMA:0001247 is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0001004 ! respiratory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000173 name: amniotic fluid namespace: uberon def: "Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided." [ENVO:02000021] synonym: "acqua amnii" RELATED [BTO:0000068] synonym: "liquor amnii" RELATED [BTO:0000068] xref: BTO:0000068 xref: ENVO:02000021 xref: EV:0100123 xref: GAID:1155 xref: MA:0002893 xref: MESH:A12.098 xref: ncithesaurus:Amniotic_Fluid xref: UMLS:C0002638 xref: VHOG:0001267 is_a: UBERON:0000463 ! portion of organism substance property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000178 name: blood namespace: uberon def: "Circulating body substance which consists of blood plasma and hemoglobin-carrying red blood cells. Excludes blood analogues (see UBERON:0000179 haemolymphatic fluid)." [FMA:9670, Wikipedia:Blood] subset: uberon_slim subset: vertebrate_core synonym: "portion of blood" EXACT [] synonym: "vertebrate blood" EXACT [] synonym: "whole blood" RELATED [BTO:0000089] xref: AAO:0000046 xref: BTO:0000089 xref: EFO:0000296 xref: EHDAA2:0000176 xref: EHDAA:418 xref: EMAPA:16332 xref: ENVO:02000027 xref: EV:0100047 xref: FMA:9670 xref: GAID:965 xref: galen:Blood xref: MA:0000059 xref: MESH:A12.207.152 xref: MIAA:0000315 xref: ncithesaurus:Blood xref: OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA xref: TAO:0000007 xref: UMLS:C0005767 xref: VHOG:0000224 xref: XAO:0000124 xref: ZFA:0000007 is_a: UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0002390 ! hematopoietic system relationship: part_of UBERON:0004535 ! cardiovascular system property_value: axiom_lost_from_external_ontology "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO"} property_value: external_definition "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000007", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO", source="AAO:LAP"} property_value: homology_notes "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000224", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) ", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000179 name: haemolymphatic fluid namespace: uberon def: "Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs." [] synonym: "blood or blood analog" RELATED [] is_a: UBERON:0000463 ! portion of organism substance relationship: part_of UBERON:0002390 ! hematopoietic system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl created_by: cjm creation_date: 2009-04-08T04:38:19Z [Term] id: UBERON:0000203 name: pallium namespace: uberon def: "Dorsal part (roof region) of the telencephalon[GO]." [GO:0021543, https://sourceforge.net/tracker/?func=detail&aid=3535324&group_id=76834&atid=994726, ISBN10:0471888893, Wikipedia:Pallium_(neuroanatomy)] comment: Taxon notes: In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus[WP] subset: developmental_classification synonym: "area dorsalis telencephali" EXACT [ZFA:0000505] synonym: "dorsal part of telencephalon" EXACT [ISBN10:0471888893] synonym: "dorsal telencephalic area" EXACT [ZFA:0000505] synonym: "dorsal telencephalon" EXACT [ZFA:0000505] xref: EFO:0003534 xref: SCTID:369224000 xref: TAO:0000505 xref: TAO:0007007 xref: ZFA:0000505 is_a: UBERON:0011300 ! gray matter of telencephalon relationship: part_of UBERON:0001893 ! telencephalon property_value: external_definition "The mantle of gray matter forming the cerebral cortex. http://www.thefreedictionary.com/pallium[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0007007", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl created_by: cjm creation_date: 2009-04-18T12:03:09Z [Term] id: UBERON:0000204 name: ventral part of telencephalon namespace: uberon def: "Dorsal part (base region) of the telencephalon." [GO:0021544, GO_REF:0000021, ISBN10:0471888893, PMID:12626695] comment: AO notes: BTO term refers specifically to the avian structure subset: developmental_classification synonym: "area ventralis telencephali" EXACT [ZFA:0000304] synonym: "subpallium" EXACT [GO:0021544, ZFA:0000304] synonym: "subpallium" NARROW [BTO:0003401] synonym: "ventral telencephalon" EXACT [ZFA:0000304] xref: BTO:0003401 xref: EFO:0003522 xref: TAO:0000304 xref: ZFA:0000304 is_a: UBERON:0002791 ! regional part of telencephalon relationship: part_of UBERON:0001893 ! telencephalon property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl created_by: cjm creation_date: 2009-04-18T12:12:27Z [Term] id: UBERON:0000211 name: ligament namespace: uberon def: "Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA]." [FMA:21496, Wikipedia:Ligament] comment: Note this groups both skeletal and non-skeletal ligaments. What is called a "ligament" in many AOs is actually a skeletal ligament subset: uberon_slim subset: vertebrate_core synonym: "ligament organ" EXACT [FMA:21496] xref: EFO:0001966 xref: FMA:21496 xref: galen:Ligament xref: http://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg xref: MA:0000113 xref: MESH:A02.513 xref: ncithesaurus:Ligament xref: OpenCyc:Mx4rvVjqpZwpEbGdrcN5Y29ycA xref: SCTID:182358004 xref: TAO:0001682 xref: UMLS:C0023685 xref: VHOG:0001272 xref: XAO:0004031 xref: ZFA:0001675 is_a: UBERON:0007846 {source="VSAO"} ! dense regular connective tissue property_value: external_definition "Portion of connective tissue that connects bone or cartilage.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001682", ontology="TAO", source="TAO:wd"} property_value: homology_notes "Compared with their Ediacarian predecessor, Cambrian animals in general were characterized by their much stouter bodies. The stoutness of the body is likely due to the formation of ligaments and tendons, which in turn requires the crosslinking of collagen triple helices.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001272", ontology="VHOG", source="PMID:8710894 Ohno S, The notion of the Cambrian pananimalia genome. PNAS (1996)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000305 name: amnion namespace: uberon def: "A membrane building the amniotic sac that surrounds and protects an embryo. It is developed in reptiles, birds, and mammals, which are hence called “Amniota”; but not in amphibians and fish (Ichthyopsida), which are consequently termed “Anamniota”. The primary function of this is the protection of the embryo for its development. It stems from parts of the mesoderm on the outer side and the ectoderm on the inner side[WP]." [Wikipedia:Amnion] xref: BTO:0000065 xref: EHDAA2:0000116 xref: EHDAA:136 xref: EMAPA:16109 xref: EV:0100122 xref: FMA:80223 xref: GAID:1298 xref: http://upload.wikimedia.org/wikipedia/commons/e/e7/Gray14.png xref: MESH:A16.254.403.277 xref: ncithesaurus:Amnion xref: SCTID:181457005 xref: UMLS:C0002630 xref: VHOG:0000721 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005631 ! extraembryonic membrane relationship: develops_from UBERON:0005971 {source="ISBN10:0073040584"} ! amniotic fold property_value: external_definition "A thin but tough extraembryonic membrane of reptiles, birds and mammals that lines the chorion and contains the fEtus and the amniotic fluid around it. [Biology_Online][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000721", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: has_relational_adjective "amniotic" xsd:string property_value: homology_notes "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000721", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000307 name: blastula namespace: uberon alt_id: UBERON:0007011 def: "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [Wikipedia:Blastula] comment: TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula subset: inconsistent_with_fma synonym: "blastosphere" RELATED [Wikipedia:Blastula] synonym: "blastula embryo" EXACT [BILA:0000059] xref: BILA:0000059 xref: BTO:0000128 xref: GAID:1294 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/c6/Blastulation.png/200px-Blastulation.png xref: MESH:A16.254.270.274 xref: OGEM:000006 xref: OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg is_a: UBERON:0000922 ! embryo relationship: develops_from UBERON:0007010 ! cleaving embryo property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000310 name: breast namespace: uberon def: "The breast is the upper ventral region of an animal's torso, particularly that of mammals, including human beings. The breasts of a female primate’s body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's. [WP,unvetted]." [Wikipedia:Breast] synonym: "mamma" RELATED LATIN [Wikipedia:Breast] synonym: "mammary part of chest" EXACT [FMA:9601] synonym: "mammary region" EXACT [FMA:9601] xref: BTO:0000149 xref: EV:0100124 xref: FMA:9601 xref: GAID:33 xref: galen:Breast xref: http://upload.wikimedia.org/wikipedia/commons/6/6e/Closeup_of_female_breast.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/6e/Closeup_of_female_breast.jpg/200px-Closeup_of_female_breast.jpg xref: MESH:A01.236 xref: ncithesaurus:Breast xref: OpenCyc:Mx4rvVjV7ZwpEbGdrcN5Y29ycA xref: SCTID:181131000 xref: UMLS:C0006141 is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0001443 ! chest property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000325 name: gastric gland namespace: uberon def: "any of the branched tubules in the inner lining of the stomach that secrete gastric juice and protective mucus." [] subset: grouping_class subset: organ_slim xref: BTO:0000503 xref: FMA:14919 is_a: UBERON:0002365 {source="cjm"} ! exocrine gland is_a: UBERON:0003294 ! gland of foregut relationship: part_of UBERON:0006924 {source="ISBN10:0073040584"} ! stomach glandular epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000333 name: intestinal gland namespace: uberon def: "A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]." [UBERON:cjm] comment: Note that some sources treat 'intestinal gland' as synonymous with subset: organ_slim synonym: "bowel mucosa gland" EXACT [OBOL:automatic] synonym: "bowel mucosa of organ gland" EXACT [OBOL:automatic] synonym: "bowel mucous membrane gland" EXACT [OBOL:automatic] synonym: "bowel organ mucosa gland" EXACT [OBOL:automatic] synonym: "crypt of Lieberkuehn" RELATED [BTO:0000640] synonym: "gland of bowel mucosa" EXACT [OBOL:automatic] synonym: "gland of bowel mucosa of organ" EXACT [OBOL:automatic] synonym: "gland of bowel mucous membrane" EXACT [OBOL:automatic] synonym: "gland of bowel organ mucosa" EXACT [OBOL:automatic] synonym: "gland of intestinal mucosa" EXACT [OBOL:automatic] synonym: "gland of intestine mucosa" EXACT [OBOL:automatic] synonym: "gland of intestine mucosa of organ" EXACT [OBOL:automatic] synonym: "gland of intestine mucous membrane" EXACT [OBOL:automatic] synonym: "gland of intestine organ mucosa" EXACT [OBOL:automatic] synonym: "gland of Lieberkuehn" RELATED [BTO:0000640] synonym: "gland of mucosa of bowel" EXACT [OBOL:automatic] synonym: "gland of mucosa of intestine" EXACT [OBOL:automatic] synonym: "gland of mucosa of organ of bowel" EXACT [OBOL:automatic] synonym: "gland of mucosa of organ of intestine" EXACT [OBOL:automatic] synonym: "gland of mucous membrane of bowel" EXACT [OBOL:automatic] synonym: "gland of mucous membrane of intestine" EXACT [OBOL:automatic] synonym: "gland of organ mucosa of bowel" EXACT [OBOL:automatic] synonym: "gland of organ mucosa of intestine" EXACT [OBOL:automatic] synonym: "glandula intestinalis" EXACT [FMA:15052] synonym: "glandulae intestinales" RELATED [] synonym: "intestinal mucosa gland" EXACT [OBOL:automatic] synonym: "intestine mucosa gland" EXACT [OBOL:automatic] synonym: "intestine mucosa of organ gland" EXACT [OBOL:automatic] synonym: "intestine mucous membrane gland" EXACT [OBOL:automatic] synonym: "intestine organ mucosa gland" EXACT [OBOL:automatic] synonym: "Lieberkuehn`s gland" RELATED [BTO:0000640] synonym: "mucosa of bowel gland" EXACT [OBOL:automatic] synonym: "mucosa of intestine gland" EXACT [OBOL:automatic] synonym: "mucosa of organ of bowel gland" EXACT [OBOL:automatic] synonym: "mucosa of organ of intestine gland" EXACT [OBOL:automatic] synonym: "mucous membrane of bowel gland" EXACT [OBOL:automatic] synonym: "mucous membrane of intestine gland" EXACT [OBOL:automatic] synonym: "organ mucosa of bowel gland" EXACT [OBOL:automatic] synonym: "organ mucosa of intestine gland" EXACT [OBOL:automatic] xref: BTO:0000640 xref: FMA:15052 xref: SCTID:266297002 is_a: UBERON:0003408 ! gland of gut relationship: part_of UBERON:0001242 ! intestinal mucosa property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000344 name: mucosa namespace: uberon def: "A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]" [Wikipedia:Mucous_membrane] comment: AO notes: FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately synonym: "mucosa of organ" EXACT [FMA:85355] synonym: "mucosa of organ part" EXACT [FMA:85358] synonym: "mucosal region" EXACT [FMA:85358] synonym: "mucous membrane" EXACT [FMA:85355] synonym: "organ mucosa" EXACT [FMA:85355] synonym: "region of mucosa" RELATED [FMA:85358] synonym: "tunica mucosa" RELATED LATIN [Wikipedia:Mucous_membrane] synonym: "tunica mucosa" RELATED [BTO:0000886] xref: AEO:0000199 xref: BTO:0000886 xref: EHDAA2:0003234 xref: EV:0100382 xref: FMA:85355 xref: FMA:85358 xref: GAID:297 xref: galen:Mucosa xref: http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png xref: http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png xref: MESH:A10.615.550 xref: ncithesaurus:Mucosa xref: OpenCyc:Mx4rvmKNOpwpEbGdrcN5Y29ycA xref: SCTID:361693009 xref: UMLS:C0026724 is_a: UBERON:0004923 ! organ component layer property_value: has_relational_adjective "mucosal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0000009 [Term] id: UBERON:0000349 name: limbic system namespace: uberon def: "A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]. including the hippocampus, amygdala, anterior thalamic nuclei, and limbic cortex, which support a variety of functions including emotion, behavior, long term memory, and olfaction [Wikipedia]." [BIRNLEX:Limbic_system, Wikipedia:Limbic_system] comment: obsoletion recommended. The current part_of children were chosen as the intersection of what is stated in wikipedia and in the FMA. NIF: We are including Limbic System because it is still used by neuroscientists and others, but as a data annotation term, it is very poor because it is not a clearly defined entity. xref: BTO:0000928 xref: FMA:242000 xref: GAID:615 xref: http://upload.wikimedia.org/wikipedia/commons/5/5c/Brain_limbicsystem.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/5c/Brain_limbicsystem.jpg/200px-Brain_limbicsystem.jpg xref: MESH:A08.186.211.577 xref: ncithesaurus:Limbic_System xref: OpenCyc:Mx4rwAeba5wpEbGdrcN5Y29ycA xref: SCTID:361342009 xref: UMLS:C0023715 is_a: UBERON:0000467 {source="GO"} ! anatomical system is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001890 ! forebrain property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000353 name: parenchyma namespace: uberon def: "functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin[WP]." [Wikipedia:Parenchyma] xref: EHDAA:3015 xref: EHDAA:3905 xref: EHDAA:3999 xref: EHDAA:4005 xref: EHDAA:6899 xref: EHDAA:6903 xref: EHDAA:6994 xref: EHDAA:8086 xref: EHDAA:9182 xref: EHDAA:9190 xref: EHDAA:9196 xref: EHDAA:9202 xref: FMA:45732 xref: ncithesaurus:Parenchyma xref: UMLS:C0933845 is_a: UBERON:0000064 ! organ part property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000358 name: blastocyst namespace: uberon def: "The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO]." [GO:0001824, Wikipedia:Blastocyst] comment: Editor's note: Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm) synonym: "blastocystis" RELATED LATIN [Wikipedia:Blastocyst] synonym: "blastula" RELATED [FMA:83041] xref: BTO:0001099 xref: EFO:0000295 xref: EV:0100394 xref: FMA:83041 xref: GAID:1153 xref: http://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/7/72/Blastocyst_English.svg/200px-Blastocyst_English.svg.png xref: MESH:A16.254.085 xref: ncithesaurus:Blastocyst xref: SCTID:308837009 xref: UMLS:C1281743 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000307 ! blastula property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000362 name: renal medulla namespace: uberon def: "The renal medulla is the innermost part of the kidney. The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla (latin renes medulla = kidney middle) contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water. [WP,unvetted]." [Wikipedia:Renal_medulla] synonym: "kidney medulla" EXACT [OBOL:automatic] synonym: "medulla of kidney" EXACT [OBOL:automatic] synonym: "medulla renalis" EXACT LATIN [FMA:74268, FMA:TA] synonym: "medullary pyramids" EXACT [FMA:74268] synonym: "pyramides renales" EXACT LATIN [FMA:74268, FMA:TA] synonym: "renal marrow" RELATED [BTO:0001167] synonym: "renal medullae" EXACT [FMA:86327] synonym: "renal medullae set" EXACT [FMA:86327] synonym: "renal pyramids" EXACT [FMA:74268] synonym: "renal pyramids set" EXACT [FMA:74268] synonym: "set of medullary pyramids" RELATED [FMA:74268] synonym: "set of renal pyramids" RELATED [FMA:74268] xref: BTO:0001167 xref: EMAPA:19279 xref: FMA:74268 xref: GAID:425 xref: galen:MedullaOfKidney xref: http://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/69/Illu_kidney.jpg/200px-Illu_kidney.jpg xref: MA:0000373 xref: MESH:A05.810.453.466 xref: ncithesaurus:Renal_Medulla xref: SCTID:30737000 xref: UMLS:C0022664 is_a: UBERON:0000958 ! medulla is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0002113 ! kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000365 name: urothelium namespace: uberon def: "The urothelium is the epithelial tissue layer that lines much of the urinary tract, including the renal pelvis, the ureters, the bladder, and parts of the urethra." [Wikipedia:Urothelium] comment: consider merging with transitional epithelium. MA uses the label 'urothelium' exclusively. FMA uses 'transitional epithelium' and has 'urothelium' as a sibling. FMA also lists 'urothelium' as the only example of 'transitional epithelium' synonym: "transitional epithelium" BROAD INCONSISTENT [] synonym: "uroepithelium" EXACT [FMA:67695] xref: BTO:0003906 xref: EMAPA:28089 xref: FMA:67695 xref: GAID:935 xref: http://upload.wikimedia.org/wikipedia/commons/9/91/Harnblase_Urothel.png xref: MESH:A10.272.850 xref: ncithesaurus:Urothelium xref: SCTID:57789003 xref: UMLS:C0227598 is_a: UBERON:0005910 ! transitional epithelium is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0001008 ! excretory system property_value: has_relational_adjective "urothelial" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000369 name: corpus striatum namespace: uberon def: "The corpus striatum (striated body) is a compound structure consisting of the caudate nucleus and the lentiform nucleus, which consists of the putamen and the globus pallidus[WP]." [Wikipedia:Corpus_striatum] comment: The term has been used in a few different ways: * It is a pair of nuclear masses which form the basal ganglia, along with the subthalamic nucleus and the substantia nigra. * It may also refer to both the basal ganglia and internal capsule collectively.[2] * According to the 1917 version of Gray's Anatomy, it is the combination of the lentiform nucleus (also known as the lenticular nucleus) and the caudate nucleus * According to BrainInfo it is a part of the basal ganglia comprising the globus pallidus and striatum synonym: "striate body" RELATED [BTO:0001311] synonym: "striated body" RELATED [BTO:0001311] xref: BTO:0001311 xref: CALOHA:TS-0183 xref: EFO:0000381 xref: EMAPA:17549 xref: EV:0100184 xref: FMA:77616 xref: GAID:667 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/b/b3/Gray656.png/200px-Gray656.png xref: MESH:A08.186.211.730.885.105.487 xref: ncithesaurus:Corpus_Striatum xref: SCTID:279318005 xref: UMLS:C0010097 xref: VHOG:0001175 is_a: UBERON:0002791 ! regional part of telencephalon relationship: part_of UBERON:0002420 {source="MA"} ! basal ganglion property_value: homology_notes "Thus, certain telencephalic characters - such as the presence of a pallium divided into lateral, dorsal, and medial formations and a subpallium divided into striatum and septum - appear to characterize all vertebrates. They are primitive characters and are homologous among all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001175", ontology="VHOG", source="DOI:10.1146/annurev.ne.04.030181.001505, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.487 Figure 14-10", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000379 name: tracheal mucosa namespace: uberon def: "A mucosa that is part of a respiratory airway." [OBOL:automatic] synonym: "mucosa of organ of trachea" EXACT [OBOL:automatic] synonym: "mucosa of organ of windpipe" EXACT [OBOL:automatic] synonym: "mucosa of trachea" EXACT [OBOL:automatic] synonym: "mucosa of windpipe" EXACT [OBOL:automatic] synonym: "Mucous membrane of trachea" EXACT [FMA:7471] synonym: "mucous membrane of trachea" EXACT [OBOL:automatic] synonym: "mucous membrane of windpipe" EXACT [OBOL:automatic] synonym: "organ mucosa of trachea" EXACT [OBOL:automatic] synonym: "organ mucosa of windpipe" EXACT [OBOL:automatic] synonym: "trachea mucosa" EXACT [OBOL:automatic] synonym: "trachea mucosa of organ" EXACT [OBOL:automatic] synonym: "trachea mucous membrane" EXACT [OBOL:automatic] synonym: "trachea organ mucosa" EXACT [OBOL:automatic] synonym: "Tracheal mucous membrane" EXACT [FMA:7471] synonym: "Tunica mucosa (tracheae)" EXACT [FMA:7471] synonym: "tunica mucosa tracheae" EXACT LATIN [FMA:7471, FMA:TA] synonym: "windpipe mucosa" EXACT [OBOL:automatic] synonym: "windpipe mucosa of organ" EXACT [OBOL:automatic] synonym: "windpipe mucous membrane" EXACT [OBOL:automatic] synonym: "windpipe organ mucosa" EXACT [OBOL:automatic] xref: BTO:0001390 xref: FMA:7471 xref: SCTID:660006 is_a: UBERON:0004785 ! respiratory system mucosa relationship: part_of UBERON:0001005 ! respiratory airway property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000383 name: musculature of body namespace: uberon def: "Anatomical system that consists of all the muscles of the body[VSAO, modified]." [VSAO:0000033] comment: AO notes: we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA synonym: "muscle system" EXACT [] synonym: "muscle system of body" EXACT [] synonym: "muscular system" EXACT [FMA:72954] synonym: "musculature system" EXACT [BILA:0000088] synonym: "muskelsystem" RELATED [BTO:0001485] synonym: "set of all muscles" EXACT [FMA:72954] synonym: "set of muscles of body" EXACT [FMA:72954] synonym: "vertebrate muscular system" EXACT [BTO:0001369] xref: AAO:0000307 xref: BILA:0000088 xref: BTO:0001369 xref: BTO:0001485 xref: EFO:0000801 xref: FBbt:00005069 xref: FMA:72954 xref: MA:0002888 xref: MAT:0000025 xref: MIAA:0000025 xref: VSAO:0000033 xref: XAO:0004042 is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0002204 ! musculoskeletal system property_value: external_definition "Anatomical system that consists of the muscles of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000033", ontology="VSAO", source="VSAO:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:6040 [Term] id: UBERON:0000397 name: colonic epithelium namespace: uberon def: "An epithelium that is part of a colon [Obol]." [OBOL:automatic] subset: vertebrate_core synonym: "colon epithelial tissue" EXACT [OBOL:automatic] synonym: "Colon epithelium" EXACT [FMA:17302] synonym: "colon epithelium" EXACT [OBOL:automatic] synonym: "epithelial tissue of colon" EXACT [OBOL:automatic] synonym: "epithelial tissue of large bowel" EXACT [OBOL:automatic] synonym: "epithelium of colon" EXACT [OBOL:automatic] synonym: "epithelium of large bowel" EXACT [OBOL:automatic] synonym: "large bowel epithelial tissue" EXACT [OBOL:automatic] synonym: "large bowel epithelium" EXACT [OBOL:automatic] synonym: "posterior intestine epithelium" EXACT [ZFA:0005128] xref: BTO:0001709 xref: FMA:17302 xref: SCTID:42978003 xref: TAO:0005128 xref: ZFA:0005128 is_a: UBERON:0001278 ! epithelium of large intestine relationship: part_of UBERON:0001155 ! colon property_value: external_definition "Intestinal epithelium which lines the lumen of the posterior intestine.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005128", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000410 name: bronchial mucosa namespace: uberon def: "A mucosa that is part of a bronchus [Obol]." [OBOL:automatic] synonym: "bronchi mucosa" EXACT [OBOL:automatic] synonym: "bronchi mucosa of organ" EXACT [OBOL:automatic] synonym: "bronchi mucous membrane" EXACT [OBOL:automatic] synonym: "bronchi organ mucosa" EXACT [OBOL:automatic] synonym: "bronchial trunk mucosa" EXACT [OBOL:automatic] synonym: "bronchial trunk mucosa of organ" EXACT [OBOL:automatic] synonym: "bronchial trunk mucous membrane" EXACT [OBOL:automatic] synonym: "bronchial trunk organ mucosa" EXACT [OBOL:automatic] synonym: "bronchus mucosa" EXACT [OBOL:automatic] synonym: "bronchus mucosa of organ" EXACT [OBOL:automatic] synonym: "bronchus mucous membrane" EXACT [OBOL:automatic] synonym: "bronchus organ mucosa" EXACT [OBOL:automatic] synonym: "mucosa of bronchi" EXACT [OBOL:automatic] synonym: "mucosa of bronchial trunk" EXACT [OBOL:automatic] synonym: "mucosa of bronchus" EXACT [OBOL:automatic] synonym: "mucosa of organ of bronchi" EXACT [OBOL:automatic] synonym: "mucosa of organ of bronchial trunk" EXACT [OBOL:automatic] synonym: "mucosa of organ of bronchus" EXACT [OBOL:automatic] synonym: "mucous membrane of bronchi" EXACT [OBOL:automatic] synonym: "mucous membrane of bronchial trunk" EXACT [OBOL:automatic] synonym: "Mucous membrane of bronchus" EXACT [FMA:62652] synonym: "mucous membrane of bronchus" EXACT [OBOL:automatic] synonym: "organ mucosa of bronchi" EXACT [OBOL:automatic] synonym: "organ mucosa of bronchial trunk" EXACT [OBOL:automatic] synonym: "organ mucosa of bronchus" EXACT [OBOL:automatic] synonym: "tunica mucosa bronchi" EXACT LATIN [FMA:62652, FMA:TA] xref: BTO:0001846 xref: FMA:62652 xref: SCTID:30802009 is_a: UBERON:0000379 ! tracheal mucosa is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0002185 ! bronchus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000412 name: dermal papilla namespace: uberon def: "small, nipple-like extensions (or interdigitations) of the dermis into the epidermis. They can be observed at the surface of the skin in hands and feet as epidermal or papillary ridges (colloquially known as fingerprints). The dermal papillae nourishes all hair follicles and bring food and oxygen to the lower layers of epidermal cells. The pattern of ridges they produce in hands and feet are inherited features that are developed before birth. They remain unaltered (except size) throughout life, and are therefore used for fingerprints. The dermal papillae are part of the uppermost layer of the dermis, the papillary dermis, and the ridges they form greatly increase the surface area between the dermis and epidermis. Because the dermis' main function is to support the epidermis, this greatly increases the exchange of oxygen, nutrients, and waste products between these two layers. Additionally, the increase in surface area prevent the dermal and epidermal layers from separating from each others by strengthening the junction between them. With age, the papillae tend to flatten and sometimes increase in numbers. Dermal papillae also play a pivotal role in hair formation, growth and, cycling" [Wikipedia:Dermal_papillae] comment: Consider adding grouping class for TAO:0001995 synonym: "dermal papilla cell" RELATED [BTO:0001858] synonym: "dermal papillae" EXACT PLURAL [] synonym: "DPC" RELATED [BTO:0001858] synonym: "follicular papilla" EXACT [FMA:70737] synonym: "hair follicle dermal papilla" RELATED [MP:0010687] synonym: "papilla corii" RELATED [BTO:0001858] synonym: "papilla dermatis" RELATED [BTO:0001858] synonym: "papilla dermis" RELATED [BTO:0001858] synonym: "papilla of corium" RELATED [BTO:0001858] synonym: "papillae dermis" RELATED LATIN [Wikipedia:Dermal_papillae] synonym: "skin papilla" RELATED [BTO:0001858] xref: BTO:0001858 xref: FMA:70737 xref: http://upload.wikimedia.org/wikipedia/commons/3/34/Skin.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/34/Skin.jpg/200px-Skin.jpg xref: ncithesaurus:Dermal_Papilla xref: SCTID:320101005 xref: UMLS:C0221931 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001992 ! papillary layer of dermis property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000414 name: mucous gland namespace: uberon def: "A gland that secretes mucus[cjm]. In humans, these are found in several different parts of the body, typically stain lighter than serous glands during standard histological preparation. Most are multicellular, but goblet cell are single-celled glands. [WP,modified]." [Wikipedia:Mucous_gland] subset: organ_slim synonym: "glandula mucosa" RELATED LATIN [Wikipedia:Mucous_gland] synonym: "glandula mucosa" RELATED [BTO:0001979] synonym: "muciparous gland" RELATED [BTO:0001979] synonym: "mucus gland" RELATED [] xref: AAO:0010601 xref: BTO:0001979 xref: FMA:62888 xref: http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/c0/Gray1021.png/200px-Gray1021.png is_a: UBERON:0002365 ! exocrine gland property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: taxon_notes "In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong]" xsd:string {scope="NCBITaxon:8292", source="Kardong"} [Term] id: UBERON:0000415 name: artery wall namespace: uberon def: "An anatomical wall that is part of an artery [Obol]." [OBOL:automatic] synonym: "Arterial wall" EXACT [FMA:14155] synonym: "wall of artery" EXACT [FMA:14155] xref: BTO:0002009 xref: FMA:14155 xref: galen:ArterialWall is_a: UBERON:0000060 ! anatomical wall is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0001637 ! artery property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000428 name: prostate epithelium namespace: uberon alt_id: UBERON:0002452 def: "the prostate epithelium." [MP:0001168] comment: TODO - check 2 FMA IDs synonym: "epithelial tissue of prostate" EXACT [OBOL:automatic] synonym: "epithelial tissue of prostate gland" EXACT [OBOL:automatic] synonym: "epithelium of prostate" EXACT [OBOL:automatic] synonym: "epithelium of prostate gland" EXACT [OBOL:automatic] synonym: "epithelium of prostatic gland" EXACT [FMA:79643] synonym: "prostate epithelial tissue" EXACT [OBOL:automatic] synonym: "prostate gland epithelial tissue" EXACT [OBOL:automatic] synonym: "prostate gland epithelium" EXACT [] synonym: "prostatic epithelium" EXACT [FMA:66812] synonym: "prostatic gland epithelium" EXACT [] xref: BTO:0002397 xref: FMA:66812 xref: FMA:79643 xref: MA:0001737 xref: ncithesaurus:Prostatic_Epithelium xref: UMLS:C1179826 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0000485 ! simple columnar epithelium is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0002367 ! prostate gland property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000444 name: lymphoid follicle namespace: uberon def: "." [http://purl.obolibrary.org/obo/uberon/tracker/6, http://purl.obolibrary.org/obo/uberon/tracker/7] comment: introducing part_of to 'cortex of lymph node' as in issue 7 introduces equivalencies; the part_of has instead been added to 'lymph node follicle' synonym: "folliculus lymphaticus" RELATED [BTO:0002684] synonym: "lymphatic follicle" RELATED [BTO:0002684] synonym: "lymphatic nodule" RELATED [BTO:0002684] synonym: "lymphoid nodule" EXACT [FMA:55222] synonym: "nodular lymphoid tissue" EXACT [FMA:55222] synonym: "nodulus lymphaticus" RELATED [BTO:0002684] synonym: "nodulus lymphoideus" RELATED [BTO:0002684] xref: BTO:0002684 xref: FMA:55222 xref: ncithesaurus:Lymphoid_Follicle xref: SCTID:64626006 xref: UMLS:C0229654 is_a: UBERON:0001744 {source="FMA"} ! lymphoid tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000454 name: cerebral subcortex namespace: uberon synonym: "Cerebral medulla" EXACT [FMA:242188] synonym: "subcortex" RELATED [BTO:0002858] xref: BTO:0002858 xref: FMA:242188 xref: ncithesaurus:Cerebral_Subcortex is_a: UBERON:0000064 ! organ part property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000458 name: endocervix namespace: uberon def: "1. The mucous membrane lining the canal of the cervix uteri. 2. The region of the opening of the uterine cervix into the uterine cavity." [BTO:0003002] xref: BTO:0003002 xref: FMA:86485 xref: ncithesaurus:Endocervix xref: SCTID:264460007 xref: UMLS:C0227837 is_a: UBERON:0000064 ! organ part property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000459 name: uterine wall namespace: uberon def: "An anatomical wall that is part of a uterus [Obol]." [OBOL:automatic] synonym: "anatomical wall of uterus" EXACT [OBOL:automatic] synonym: "uterus anatomical wall" EXACT [OBOL:automatic] synonym: "uterus wall" EXACT [OBOL:automatic] synonym: "wall of uterus" EXACT [OBOL:automatic] xref: BTO:0003083 xref: FMA:17560 xref: SCTID:245485002 is_a: UBERON:0000060 ! anatomical wall is_a: UBERON:0000064 ! organ part is_a: UBERON:0005156 ! reproductive structure relationship: part_of UBERON:0000995 ! uterus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000463 name: portion of organism substance namespace: uberon def: "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body." [CARO:MAH] subset: upper_level synonym: "body fluid or substance" EXACT [MA:0002450] synonym: "body substance" EXACT [FMA:9669] synonym: "organism substance" EXACT [] synonym: "portion of body substance" EXACT [FMA:9669] xref: AAO:0010839 xref: AEO:0000004 xref: BILA:0000004 xref: CARO:0000004 xref: EHDAA2:0003004 xref: FBbt:00007019 xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 xref: MA:0002450 xref: ncithesaurus:Body_Fluid_or_Substance xref: SPD:0000008 xref: TAO:0001487 xref: TGMA:0001824 xref: VHOG:0001726 xref: XAO:0004001 xref: ZFA:0001487 is_a: UBERON:0000465 ! material anatomical entity relationship: part_of UBERON:0000468 ! multi-cellular organism property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000464 name: anatomical space namespace: uberon def: "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures." [CARO:MAH] subset: upper_level synonym: "lumen" BROAD [] synonym: "lumen space" EXACT [] synonym: "space" BROAD [] xref: AAO:0010110 xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 xref: FBbt:00007017 xref: FMA:5897 xref: HAO:0000005 xref: ncithesaurus:Lumen_Space xref: TAO:0001668 xref: TGMA:0001825 xref: UMLS:C0524461 xref: VHOG:0001728 xref: XAO:0003190 xref: ZFA:0001643 is_a: UBERON:0000466 ! immaterial anatomical entity disjoint_from: UBERON:0006800 ! anatomical line property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000465 name: material anatomical entity namespace: uberon def: "Anatomical entity that has mass." [CARO:MAH] subset: upper_level xref: AAO:0010264 xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 xref: FBbt:00007016 xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 xref: TGMA:0001826 xref: VHOG:0001721 is_a: UBERON:0001062 ! anatomical entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000466 name: immaterial anatomical entity namespace: uberon def: "Anatomical entity that has no mass." [CARO:MAH] subset: disjointness_axiom_removed subset: upper_level synonym: "immaterial physical anatomical entity" EXACT [FMA:67112] xref: AAO:0010265 xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 xref: FBbt:00007015 xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 xref: TGMA:0001827 xref: VHOG:0001727 is_a: UBERON:0001062 ! anatomical entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000467 name: anatomical system namespace: uberon def: "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]." [CARO:0000011, CARO:MAH, Wikipedia:Organ_system] subset: uberon_slim subset: upper_level synonym: "body system" EXACT [NIF_GrossAnatomy:birnlex_14] synonym: "organ system" EXACT [] synonym: "system" BROAD [GO:0048731] xref: AAO:0000007 xref: AEO:0000011 xref: BILA:0000011 xref: CARO:0000011 xref: EHDAA2:0001330 xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 xref: FBbt:00004856 xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 xref: MA:0000003 xref: ncithesaurus:Organ_System xref: NIF_GrossAnatomy:birnlex_14 xref: OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ xref: SCTID:278195005 xref: TAO:0001439 xref: TGMA:0001831 xref: UMLS:C0460002 xref: VHOG:0001725 xref: WBbt:0005746 xref: XAO:0003002 xref: ZFA:0001439 is_a: UBERON:0000480 ! anatomical group relationship: part_of UBERON:0000468 ! multi-cellular organism property_value: external_definition "Anatomical group that has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001439", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000007", ontology="AAO", source="AAO:BJB"} property_value: external_definition "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000011", ontology="CARO", source="CARO:MAH", source="FMA:7149"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000468 name: multi-cellular organism namespace: uberon def: "Anatomical structure that is an individual member of a species and consists of more than one cell." [CARO:0000012, CARO:MAH, Wikipedia:Multi-cellular_organism] comment: TODO - split body and mc organism? body continues after death stage subset: uberon_slim subset: upper_level synonym: "adult mouse" EXACT [MA:0002405] synonym: "body" EXACT [] synonym: "Koerper" RELATED [BTO:0001489] synonym: "organism" EXACT [] synonym: "TS28" RELATED [MA:0002405] synonym: "whole body" EXACT [BTO:0001489] synonym: "whole organism" EXACT [] xref: AAO:0010026 xref: AEO:0000103 xref: AEO:0000191 xref: BILA:0000012 xref: BTO:0001489 xref: CARO:0000012 xref: EFO:0002906 xref: EHDAA2:0003103 xref: EHDAA2:0003191 xref: EHDAA:1 xref: EHDAA:9178 xref: EMAPA:25765 xref: EV:0100016 xref: FBbt:00000001 xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 xref: MA:0002405 xref: ncithesaurus:Whole_Organism xref: NIF_GrossAnatomy:birnlex_18 xref: SCTID:243928005 xref: TADS:0000001 xref: TAO:0001094 xref: TGMA:0001832 xref: VHOG:0000671 xref: WBbt:0007833 xref: XAO:0003004 xref: ZFA:0001094 is_a: UBERON:0000061 ! anatomical structure property_value: external_definition "Anatomical structure that is an individual member of a species.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001094", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "organismal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000470 name: cell part namespace: uberon def: "Anatomical structure that is a direct part of the cell." [CARO:MAH] comment: todo - move metadata to GO and obsolete this class. Note the inconsistency between the usage of the label 'cell component' in GO and CARO subset: upper_level synonym: "cell component" RELATED [CARO:0000014] xref: AAO:0010271 xref: BILA:0000014 xref: CARO:0000014 xref: FBbt:00007012 xref: FMA:86454 xref: GO:0044464 xref: HAO:0000014 xref: ncithesaurus:Cell_Part xref: NIF_Subcellular:sao-1337158144 xref: OpenCyc:Mx4rwQwkcZwpEbGdrcN5Y29ycA xref: TGMA:0001834 xref: UMLS:C1178969 is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000471 name: compound organ component namespace: uberon def: "Multi-tissue structure that is part of a compound organ." [CARO:0000019, CARO:MAH] subset: upper_level xref: AAO:0010017 xref: AEO:0000019 xref: BILA:0000019 xref: CARO:0000019 xref: EHDAA2:0003019 xref: HAO:0000019 xref: TAO:0001489 xref: TGMA:0001835 xref: XAO:0003039 xref: ZFA:0001489 is_a: UBERON:0000481 ! multi-tissue structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000473 name: testis namespace: uberon alt_id: UBERON:0002117 def: "gonad of a male animal, produces and releases sperm." [Wikipedia:Testis] subset: organ_slim subset: uberon_slim subset: vertebrate_core synonym: "genitalia of male organism gonad" EXACT [OBOL:automatic] synonym: "genitalia of male organism gonada" EXACT [OBOL:automatic] synonym: "gonad of genitalia of male organism" EXACT [OBOL:automatic] synonym: "gonad of male genitalia" EXACT [OBOL:automatic] synonym: "gonad of male genitals" EXACT [OBOL:automatic] synonym: "gonad of male organism genitalia" EXACT [OBOL:automatic] synonym: "gonad of male organism reproductive system" EXACT [OBOL:automatic] synonym: "gonad of male reproductive system" EXACT [OBOL:automatic] synonym: "gonad of reproductive system of male organism" EXACT [OBOL:automatic] synonym: "gonada of genitalia of male organism" EXACT [OBOL:automatic] synonym: "gonada of male genitalia" EXACT [OBOL:automatic] synonym: "gonada of male genitals" EXACT [OBOL:automatic] synonym: "gonada of male organism genitalia" EXACT [OBOL:automatic] synonym: "gonada of male organism reproductive system" EXACT [OBOL:automatic] synonym: "gonada of male reproductive system" EXACT [OBOL:automatic] synonym: "gonada of reproductive system of male organism" EXACT [OBOL:automatic] synonym: "male genitalia gonad" EXACT [OBOL:automatic] synonym: "male genitalia gonada" EXACT [OBOL:automatic] synonym: "male genitals gonad" EXACT [OBOL:automatic] synonym: "male gonad" EXACT [OBOL:automatic] synonym: "male organism genitalia gonad" EXACT [OBOL:automatic] synonym: "male organism genitalia gonada" EXACT [OBOL:automatic] synonym: "male organism reproductive system gonad" EXACT [OBOL:automatic] synonym: "male organism reproductive system gonada" EXACT [OBOL:automatic] synonym: "male reproductive system gonad" EXACT [OBOL:automatic] synonym: "male reproductive system gonada" EXACT [OBOL:automatic] synonym: "orchis" RELATED [BTO:0001363] synonym: "reproductive system of male organism gonad" EXACT [OBOL:automatic] synonym: "reproductive system of male organism gonada" EXACT [OBOL:automatic] synonym: "testes" RELATED PLURAL [] synonym: "testicle" EXACT [FMA:7210] synonym: "testiculus" RELATED [BTO:0001363] xref: AAO:0000606 xref: BILA:0000124 xref: BTO:0001363 xref: EFO:0000984 xref: EHDAA2:0002007 xref: EHDAA:8146 xref: EMAPA:17972 xref: EV:0100102 xref: FBbt:00004928 xref: FMA:7210 xref: GAID:396 xref: galen:Testis xref: HAO:0001007 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/c3/Gray1144.png/200px-Gray1144.png xref: MA:0000411 xref: MAT:0000132 xref: MESH:A05.360.444.849 xref: MIAA:0000132 xref: ncithesaurus:Testis xref: OpenCyc:Mx4rvVjM25wpEbGdrcN5Y29ycA xref: SCTID:181431007 xref: TAO:0000598 xref: UMLS:C0039597 xref: VHOG:0000252 xref: WBbt:0006794 xref: XAO:0000157 xref: ZFA:0000598 is_a: UBERON:0000991 ! gonad is_a: UBERON:0003135 ! male reproductive organ disjoint_from: UBERON:0000992 ! female gonad disjoint_from: UBERON:0009117 ! indifferent gonad relationship: develops_from UBERON:0009117 ! indifferent gonad relationship: part_of UBERON:0000079 ! male reproductive system property_value: external_definition "Either of paired male reproductive organs which are involved in the production of sperm and male sex hormones.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000606", ontology="AAO", source="AAO:BJB"} property_value: external_definition "Male reproductive organ.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000598", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "testicular" xsd:string property_value: homology_notes " (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000252", ontology="VHOG", source="DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000474 name: female reproductive system namespace: uberon def: "The organs of the female reproductive system." [Wikipedia:Female_genitalia] subset: uberon_slim synonym: "female genital system" RELATED [] synonym: "female genitalia" RELATED [] synonym: "female organism genitalia" EXACT [OBOL:automatic] synonym: "female organism reproductive system" EXACT [OBOL:automatic] synonym: "female reproductive tract" RELATED [MA:0000381] synonym: "genitalia of female organism" EXACT [OBOL:automatic] synonym: "gynaecological tissue" RELATED [BTO:0000083] synonym: "reproductive system of female organism" EXACT [OBOL:automatic] synonym: "systema genitale femininum" RELATED [BTO:0000083] xref: BTO:0000083 xref: EFO:0000969 xref: EHDAA2:0000506 xref: EHDAA:8116 xref: EMAPA:17959 xref: EV:0100110 xref: FBbt:00004864 xref: FMA:45663 xref: GAID:364 xref: HAO:0000324 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/68/Scheme_female_reproductive_system-en.svg/200px-Scheme_female_reproductive_system-en.svg.png xref: MA:0000381 xref: MESH:A05.360.319 xref: MIAA:0000028 xref: ncithesaurus:Female_Reproductive_System xref: OpenCyc:Mx4rvVipTZwpEbGdrcN5Y29ycA xref: SCTID:361386004 xref: TGMA:0000635 xref: UMLS:C0700038 xref: VHOG:0000726 xref: WBbt:0006748 xref: WikipediaCategory:Female_reproductive_system xref: XAO:0000156 is_a: UBERON:0000990 ! reproductive system relationship: part_of UBERON:0003100 ! female organism property_value: homology_notes "By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000726", ontology="VHOG", source="ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000475 name: organism subdivision namespace: uberon def: "Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism." [CARO:0000032, CARO:MAH, Wikipedia:Body_part] comment: Editor note: revise after CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency subset: uberon_slim subset: upper_level synonym: "anatomic region" EXACT [MA:0002433] synonym: "body part" RELATED [] synonym: "body region" RELATED [FMA:7153] synonym: "cardinal body part" RELATED [FMA:7153] xref: AAO:0010053 xref: AEO:0000032 xref: BILA:0000032 xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: FBbt:00007009 xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 xref: MA:0002433 xref: MAT:0000293 xref: MESH:A01 xref: MIAA:0000293 xref: ncithesaurus:Body_Part xref: OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA xref: TAO:0001308 xref: TGMA:0001840 xref: UMLS:C0229962 xref: VHOG:0001758 xref: XAO:0003013 xref: ZFA:0001308 is_a: UBERON:0000061 ! anatomical structure relationship: part_of UBERON:0000468 ! multi-cellular organism property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000477 name: anatomical cluster namespace: uberon def: "Anatomical group that has its parts adjacent to one another." [CARO:MAH] subset: disjointness_axiom_removed subset: upper_level xref: AAO:0010009 xref: AEO:0000041 xref: BILA:0000041 xref: CARO:0000041 xref: EHDAA2:0003041 xref: FBbt:00007277 xref: FMA:49443 xref: HAO:0000041 xref: TADS:0000605 xref: TAO:0001478 xref: TGMA:0001842 xref: VHOG:0001737 xref: XAO:0003160 xref: ZFA:0001478 is_a: UBERON:0000480 ! anatomical group property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000478 name: extraembryonic structure namespace: uberon def: "Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo." [CARO:MAH, https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279] comment: see also conceptus extraembryonic component in EHDAA2. Note that the FBbt class is *not* placed here until the tracker issue is resolved. subset: uberon_slim subset: vertebrate_core synonym: "extra-embryonic structure" EXACT [] synonym: "extraembryonic component" RELATED [] synonym: "extraembryonic tissue" RELATED [] xref: AAO:0010020 xref: AEO:0000042 xref: BILA:0000042 xref: CARO:0000042 xref: EHDAA2:0003042 xref: EHDAA:46 xref: EMAPA:16042 xref: FMA:85537 xref: HAO:0000042 xref: ncithesaurus:Extraembryonic_Structure xref: SCTID:314908006 xref: TAO:0000020 xref: TGMA:0001843 xref: UMLS:C1282438 xref: VHOG:0000292 xref: XAO:0004005 xref: ZFA:0000020 is_a: UBERON:0000061 ! anatomical structure disjoint_from: UBERON:0002050 ! embryonic structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: seeAlso FBbt:00005835 [Term] id: UBERON:0000479 name: tissue namespace: uberon def: "Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships." [CARO:0000043, CARO:MAH, FMA:9637] comment: This class was sourced from CARO, which was initially sourced from FMA. Nomenclature changes have been made. Note also AEO introduces a class AEO:0000013 'single-cell tissue' subset: upper_level synonym: "portion of tissue" EXACT [CARO:0000043] synonym: "simple tissue" EXACT [AEO:0000043] synonym: "tissue portion" EXACT [] xref: AAO:0000607 xref: AAO:0010054 xref: AEO:0000043 xref: BILA:0000043 xref: CARO:0000043 xref: EHDAA2:0003043 xref: FBbt:00007003 xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 xref: MA:0003002 xref: MESH:A10 xref: ncithesaurus:Tissue xref: NIF_GrossAnatomy:birnlex_19 xref: TAO:0001477 xref: TGMA:0001844 xref: UMLS:C0040300 xref: VHOG:0001757 xref: WBbt:0005729 xref: XAO:0003040 xref: ZFA:0001477 is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000480 name: anatomical group namespace: uberon def: "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue." [CARO:0000054, CARO:MAH] subset: upper_level xref: AAO:0010008 xref: AEO:0000054 xref: BILA:0000054 xref: CARO:0000054 xref: EHDAA2:0003054 xref: HAO:0000054 xref: TAO:0001512 xref: TGMA:0001846 xref: VHOG:0001724 xref: XAO:0003001 xref: ZFA:0001512 is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000481 name: multi-tissue structure namespace: uberon def: "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types." [CARO:0000055, CARO:MAH] subset: upper_level xref: AAO:0010048 xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 xref: FBbt:00007010 xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 xref: VHOG:0001762 xref: XAO:0003037 xref: ZFA:0001488 is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000483 name: epithelium namespace: uberon def: "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]." [CARO:MAH, Wikipedia:Epithelium] subset: uberon_slim subset: vertebrate_core synonym: "epithelial tissue" EXACT [] synonym: "portion of epithelium" EXACT [FMA:9639] xref: AAO:0000144 xref: AAO:0010055 xref: AEO:0000066 xref: BILA:0000066 xref: BTO:0000416 xref: CARO:0000066 xref: EHDAA2:0003066 xref: FBbt:00007005 xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 xref: http://upload.wikimedia.org/wikipedia/commons/c/c3/Tkanka_nablonkowa.png xref: MESH:A10.272 xref: ncithesaurus:Epithelium xref: SCTID:31610004 xref: TAO:0001486 xref: UMLS:C0014609 xref: VHOG:0000387 xref: XAO:0003045 xref: ZFA:0001486 is_a: UBERON:0000119 ! cell layer union_of: UBERON:0000486 ! multilaminar epithelium union_of: UBERON:0000490 ! unilaminar epithelium property_value: external_definition "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010055", ontology="AAO", source="AAO:BJB"} property_value: external_definition "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000066", ontology="CARO", source="CARO:MAH", source="FMA:9639"} property_value: external_definition "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001486", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "epithelial" xsd:string property_value: homology_notes "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000387", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000484 name: simple cuboidal epithelium namespace: uberon def: "Unilaminar epithelium that consists of a single layer of cuboidal cells." [CARO:MAH, Wikipedia:Simple_cuboidal_epithelium] comment: Editor notes: needs to be synchronized with CL - there is no distinct cuboidal cell in CL subset: uberon_slim subset: vertebrate_core synonym: "epithelium simplex cuboideum" EXACT [] xref: AAO:0010064 xref: AEO:0000067 xref: BILA:0000067 xref: CARO:0000067 xref: EHDAA2:0003067 xref: FMA:45566 xref: HAO:0000067 xref: http://upload.wikimedia.org/wikipedia/commons/d/d0/Gray1133.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/d/d0/Gray1133.png/200px-Gray1133.png xref: ncithesaurus:Simple_Cuboidal_Epithelium xref: TAO:0001497 xref: UMLS:C0836134 xref: XAO:0004009 xref: ZFA:0001497 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0010077 ! cuboidal epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000485 name: simple columnar epithelium namespace: uberon def: "Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]" [CARO:MAH, FMA:FMA, Wikipedia:Simple_columnar_epithelium] subset: uberon_slim subset: vertebrate_core synonym: "columnar epithelium" BROAD [EHDAA2:0003068] synonym: "columnar epithlium" BROAD [AEO:0000068] synonym: "epithelium simplex columnare" EXACT [] synonym: "simple columnar epithelium" EXACT [] xref: AAO:0010063 xref: AEO:0000068 xref: BILA:0000068 xref: CARO:0000068 xref: EHDAA2_RETIRED:0003068 xref: FBbt:00007027 xref: FMA:45567 xref: HAO:0000068 xref: http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/8/8b/Gray1059.png/200px-Gray1059.png xref: ncithesaurus:Simple_Columnar_Epithelium xref: SCTID:32210007 xref: TAO:0001496 xref: UMLS:C0836135 xref: XAO:0004008 xref: ZFA:0001496 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0012274 ! columnar epithelium property_value: external_definition "Unilaminar epithelium that consists of a single layer of columnar cells.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010063", ontology="AAO", source="AAO:BJB"} property_value: external_definition "Unilaminar epithelium that consists of a single layer of columnar cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000068", ontology="CARO", source="CARO:MAH", source="FMA:45567"} property_value: external_definition "Unilaminar epithelium that consists of a single layer of columnar cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001496", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000486 name: multilaminar epithelium namespace: uberon def: "Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]" [CARO:MAH, FMA:FMA, Wikipedia:Stratified_epithelium] subset: uberon_slim subset: vertebrate_core synonym: "laminated epithelium" RELATED [BTO:0002074] synonym: "stratified epithelium" EXACT [] xref: AAO:0010059 xref: AEO:0000069 xref: BILA:0000069 xref: BTO:0002074 xref: CARO:0000069 xref: EHDAA2:0003069 xref: FMA:45562 xref: HAO:0000069 xref: ncithesaurus:Stratified_Epithelium xref: SCTID:309044005 xref: TAO:0001494 xref: UMLS:C0682575 xref: XAO:0004006 xref: ZFA:0001494 is_a: UBERON:0000483 ! epithelium property_value: external_definition "Epithelium that consists of more than one layer of epithelial cells.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010059", ontology="AAO", source="AAO:BJB"} property_value: external_definition "Epithelium that consists of more than one layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000069", ontology="CARO", source="CARO:MAH", source="FMA:45562"} property_value: external_definition "Epithelium that consists of more than one layer of epithelial cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001494", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000487 name: simple squamous epithelium namespace: uberon def: "Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]" [CARO:MAH, FMA:45565, Wikipedia:Simple_squamous_epithelium] subset: uberon_slim subset: vertebrate_core synonym: "epithelium simplex squamosum" EXACT [] xref: AAO:0010066 xref: AEO:0000070 xref: BILA:0000070 xref: BTO:0002073 xref: CARO:0000070 xref: EHDAA2:0003070 xref: FMA:45565 xref: HAO:0000070 xref: http://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg xref: ncithesaurus:Simple_Squamous_Epithelium xref: TAO:0001498 xref: UMLS:C0836133 xref: XAO:0004010 xref: ZFA:0001498 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium property_value: external_definition "Unilaminar epithelium that consists of a single layer of squamous cells.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010066", ontology="AAO", source="AAO:BJB"} property_value: external_definition "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000070", ontology="CARO", source="CARO:MAH", source="FMA:45565"} property_value: external_definition "Unilaminar epithelium that consists of a single layer of squamous cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001498", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000488 name: atypical epithelium namespace: uberon def: "Epithelium that consists of epithelial cells not arranged in one ore more layers." [CARO:MAH] subset: vertebrate_core synonym: "heterogenous epithelium" EXACT [] xref: AAO:0010057 xref: AEO:0000071 xref: BILA:0000071 xref: CARO:0000071 xref: EHDAA2:0003071 xref: FMA:61741 xref: HAO:0000071 xref: TAO:0001493 xref: XAO:0004004 xref: ZFA:0001493 is_a: UBERON:0000483 ! epithelium property_value: external_definition "Epithelium that consists of epithelial cells not arranged in one or more layers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001493", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000489 name: cavitated compound organ namespace: uberon def: "Compound organ that contains one or more macroscopic anatomical spaces." [CARO:MAH] subset: organ_slim subset: upper_level synonym: "cavitated organ" EXACT [FMA:55671] xref: AAO:0010016 xref: AEO:0000072 xref: BILA:0000072 xref: CARO:0000072 xref: EHDAA2:0003072 xref: FMA:55671 xref: HAO:0000072 xref: TAO:0001490 xref: TGMA:0001857 xref: VHOG:0001730 xref: XAO:0003165 xref: ZFA:0001490 is_a: UBERON:0003103 ! compound organ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000490 name: unilaminar epithelium namespace: uberon def: "Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]" [CARO:MAH, FMA:45561] comment: AO/editor notes: consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable subset: vertebrate_core synonym: "simple epithelium" EXACT [FMA:45561] xref: AAO:0010062 xref: AEO:0000073 xref: BILA:0000073 xref: BTO:0002073 xref: CARO:0000073 xref: EHDAA2:0003073 xref: FMA:45561 xref: HAO:0000073 xref: ncithesaurus:Simple_Epithelium xref: SCTID:309043004 xref: TAO:0001495 xref: UMLS:C0682574 xref: XAO:0004007 xref: ZFA:0001495 is_a: UBERON:0000483 ! epithelium property_value: external_definition "Epithelium that consists of a single layer of epithelial cells.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010062", ontology="AAO", source="AAO:BJB"} property_value: external_definition "Epithelium that consists of a single layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000073", ontology="CARO", source="CARO:MAH", source="FMA:45561"} property_value: external_definition "Epithelium that consists of a single layer of epithelial cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001495", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000915 name: thoracic segment of trunk namespace: uberon def: "Organismal subdivision of body that lies between the head and the abdomen [Wikipedia]." [Wikipedia:Thorax] comment: Usage notes: note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest subset: uberon_slim synonym: "thorax" RELATED [MA:0000022] synonym: "upper body" RELATED [] xref: FMA:259209 xref: MA:0000022 xref: SCTID:302551006 is_a: UBERON:0009569 {source="FMA"} ! subdivision of trunk is_a: UBERON:0011676 ! axial subdivision of organism property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0000026 property_value: spatially_disjoint_from UBERON:0000033 property_value: spatially_disjoint_from UBERON:0002417 [Term] id: UBERON:0000916 name: abdomen namespace: uberon def: "In vertebrates such as mammals the abdomen (belly) constitutes the part of the body between the thorax (chest) and pelvis. The region enclosed by the abdomen is termed the abdominal cavity." [Wikipedia:Abdomen] comment: Taxon notes: Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class subset: uberon_slim synonym: "abdominopelvic region" EXACT [FMA:9577] synonym: "abdominopelvis" EXACT [FMA:9577] synonym: "adult abdomen" RELATED [] synonym: "belly" RELATED [] synonym: "celiac region" RELATED [] xref: BTO:0000020 xref: EFO:0000968 xref: EV:0100011 xref: FMA:9577 xref: GAID:16 xref: galen:Abdomen xref: MA:0000029 xref: MAT:0000298 xref: MESH:A01.047 xref: MIAA:0000298 xref: OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA xref: SCTID:302553009 is_a: UBERON:0009569 ! subdivision of trunk relationship: part_of UBERON:0002417 {source="MA"} ! abdominal segment of trunk property_value: has_relational_adjective "abdominal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000922 name: embryo namespace: uberon def: "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [BTO:0000379, FB:FBrf0039741, FB:FBrf0041814, GO:0009790, Wikipedia:Embryo] comment: Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo subset: uberon_slim subset: vertebrate_core synonym: "developing organism" RELATED [BILA:0000056] synonym: "developmental tissue" RELATED [] synonym: "embryonic organism" EXACT [BILA:0000056] xref: AAO:0011035 xref: AEO:0000169 xref: BILA:0000056 xref: BTO:0000379 xref: EFO:0001367 xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 xref: FBbt:00000052 xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism xref: http://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg xref: MAT:0000226 xref: MESH:A16.254 xref: MIAA:0000019 xref: ncithesaurus:Embryo xref: OGEM:000001 xref: OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA xref: SCTID:57991002 xref: UMLS:C0013935 xref: VHOG:0001766 xref: XAO:0000113 xref: ZFA:0000103 is_a: UBERON:0000468 ! multi-cellular organism property_value: has_relational_adjective "embryonic" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000923 name: germ layer namespace: uberon def: "A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm." [Wikipedia:Germ_layer] comment: Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[UBERONREF:0000002] subset: uberon_slim subset: vertebrate_core synonym: "embryonic germ layer" RELATED [] synonym: "embryonic germ layers" RELATED [] synonym: "embryonic tissue" BROAD [FMA:69069] synonym: "germinal layer" EXACT [ncithesaurus:Germinal_Layer] synonym: "primary germ layer" NARROW [GO:0001704, ZFA:0001122] xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: FBbt:00000110 xref: FMA:69069 xref: GAID:1303 xref: MESH:A16.254.425 xref: ncithesaurus:Embryonic_Tissue xref: ncithesaurus:Germinal_Layer xref: TAO:0001122 xref: UMLS:C0920502 xref: UMLS:C1708239 xref: VHOG:0001223 xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest relationship: develops_from UBERON:0002532 ! epiblast (generic) relationship: part_of UBERON:0000922 ! embryo property_value: homology_notes "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001223", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000924 name: ectoderm namespace: uberon def: "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue." [Wikipedia:Ectoderm] subset: uberon_slim subset: vertebrate_core synonym: "embryonic ectoderm" EXACT [VHOG:0000153] xref: AAO:0000137 xref: BILA:0000036 xref: BTO:0000315 xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 xref: FBbt:00000111 xref: FMA:69070 xref: GAID:1304 xref: http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png xref: MAT:0000155 xref: MAT:0000173 xref: MESH:A16.254.425.273 xref: MIAA:0000173 xref: ncithesaurus:Ectoderm xref: SCTID:362851007 xref: TAO:0000016 xref: UMLS:C0013574 xref: VHOG:0000153 xref: XAO:0000001 xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: develops_from UBERON:0006601 {source="cjm"} ! presumptive ectoderm property_value: external_definition "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000137", ontology="AAO", source="AAO:EJS"} property_value: has_relational_adjective "ectodermal" xsd:string property_value: homology_notes "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000153", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000925 name: endoderm namespace: uberon def: "Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut." [Wikipedia:Endoderm] comment: This class was created automatically from a combination of ontologies subset: uberon_slim subset: vertebrate_core synonym: "entoderm" RELATED [] xref: AAO:0000139 xref: BILA:0000038 xref: BTO:0000800 xref: EFO:0002545 xref: EHDAA2:0000436 xref: EV:0100005 xref: FBbt:00000125 xref: FMA:69071 xref: GAID:1305 xref: http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/d/df/Gray10.png/200px-Gray10.png xref: MAT:0000175 xref: MESH:A16.254.425.407 xref: MIAA:0000175 xref: ncithesaurus:Endoderm xref: SCTID:362855003 xref: TAO:0000017 xref: UMLS:C0014144 xref: VHOG:0000154 xref: XAO:0000090 xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: develops_from UBERON:0006595 {source="ZFA"} ! presumptive endoderm property_value: has_relational_adjective "endodermal" xsd:string property_value: homology_notes "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000154", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000926 name: mesoderm namespace: uberon alt_id: UBERON:0003263 def: "The middle germ layer of the embryo, between the endoderm and ectoderm." [Wikipedia:Mesoderm] comment: Taxon notes: sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates[UBERONREF:0000002] subset: uberon_slim subset: vertebrate_core synonym: "embryonic mesoderm" RELATED [VHOG:0000152] synonym: "entire mesoderm" RELATED [SCTID:362854004, UBERON:cjm] synonym: "mesodermal mantle" RELATED [] xref: AAO:0000304 xref: BILA:0000037 xref: BTO:0000839 xref: EFO:0001981 xref: EHDAA2:0001128 xref: EHDAA:124 xref: EHDAA:160 xref: EHDAA:168 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 xref: FBbt:00000126 xref: FMA:69072 xref: GAID:522 xref: http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/e/e8/Mesoderm.png/200px-Mesoderm.png xref: MAT:0000174 xref: MESH:A16.254.425.660 xref: MIAA:0000174 xref: ncithesaurus:Mesoderm xref: SCTID:362854004 xref: TAO:0000041 xref: UMLS:C0025485 xref: VHOG:0000152 xref: XAO:0000050 xref: ZFA:0000041 is_a: UBERON:0000923 {notes="sometimes not considered primary"} ! germ layer relationship: develops_from UBERON:0006603 {source="ZFA"} ! presumptive mesoderm property_value: external_definition "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000304", ontology="AAO", source="AAO:EJS"} property_value: has_relational_adjective "mesodermal" xsd:string property_value: homology_notes "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000152", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:6040 [Term] id: UBERON:0000930 name: stomodeum namespace: uberon def: "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth[ZFA]. In humans, a depression between the brain and the pericardium in an embryo, and is the precursor of the mouth and the anterior lobe of the pituitary gland. The stomodeum is lined by ectoderm, and is separated from the anterior end of the fore-gut by the buccopharyngeal membrane. This membrane is devoid of mesoderm, being formed by the apposition of the stomodeal ectoderm with the fore-gut endoderm; at the end of the third week it disappears, and thus a communication is established between the mouth and the future pharynx[WP]. The anterior part of the embryonic digestive system deriving from the stomodeal invagination of the ectoderm[FBbt]." [Wikipedia:Stomodeum] comment: Editor note: consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence. Taxon note: This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. subset: grouping_class subset: uberon_slim subset: vertebrate_core synonym: "mouth primordium" EXACT [XAO:0000269] synonym: "primitive oral cavity" EXACT [UBERON:cjm] synonym: "stomatodeum" EXACT [Wikipedia:Stomodeum] synonym: "stomodaeum" EXACT [] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 xref: FBbt:00000439 xref: http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/9/93/Gray977.png/200px-Gray977.png xref: ncithesaurus:Stomodeum xref: TAO:0001290 xref: TGMA:0000135 xref: UMLS:C1514977 xref: XAO:0000269 xref: ZFA:0001290 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0003102 {source="ZFA"} ! surface structure is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0007026 ! primitive gut property_value: external_definition "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001290", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "stomodeal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000931 name: proctodeum namespace: uberon def: "Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage[ZFA]. A proctodeum is the back ectodermal part of an alimentary canal. It is created during embryogenesis by a folding of the outer body wall[WP]." [Wikipedia:Proctodeum] comment: removed WBbt:0006795 - junction between the alimentary and genital tracts in the male. subset: uberon_slim synonym: "anal pit" RELATED [VHOG:0000139] synonym: "proctodaeum" EXACT [] xref: AAO:0011087 xref: EHDAA2:0000121 xref: FBbt:00000440 xref: ncithesaurus:Proctodeum xref: TAO:0000066 xref: UMLS:C0231054 xref: VHOG:0000139 xref: XAO:0001019 xref: ZFA:0000066 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0000924 ! ectoderm relationship: part_of UBERON:0007026 ! primitive gut property_value: external_definition "An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000066", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011087", ontology="AAO", source="ZFA:0000066"} property_value: has_relational_adjective "proctodeal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000945 name: stomach namespace: uberon def: "An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium." [ISBN10:0073040584, UBERON:cjm, Wikipedia:Stomach] comment: Taxon notes: We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa -- Stomach#In_other_animals subset: major_organ subset: organ_slim subset: uberon_slim subset: vertebrate_core synonym: "anterior intestine" RELATED [] synonym: "gaster" RELATED [BTO:0001307] synonym: "mesenteron" RELATED [] synonym: "stomach" RELATED [] synonym: "Ventricular" RELATED LATIN [Wikipedia:Stomach] synonym: "ventriculus" RELATED [] xref: AAO:0000579 xref: ANISEED:1235297 xref: BTO:0001307 xref: EFO:0000837 xref: EHDAA2:0001915 xref: EHDAA:2993 xref: EMAPA:17021 xref: EMAPA:18889 xref: EV:0100070 xref: FMA:7148 xref: GAID:293 xref: galen:Stomach xref: http://upload.wikimedia.org/wikipedia/commons/e/e0/Stomach_diagram.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/e/e0/Stomach_diagram.svg/200px-Stomach_diagram.svg.png xref: MA:0000353 xref: MAT:0000051 xref: MESH:A03.492.766 xref: MIAA:0000051 xref: ncithesaurus:Stomach xref: OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA xref: SCTID:181246003 xref: TAO:0002121 xref: UMLS:C0038351 xref: VHOG:0000408 xref: XAO:0000128 is_a: UBERON:0004921 {source="cjm"} ! subdivision of digestive tract is_a: UBERON:0010039 {source="cjm"} ! food storage organ relationship: part_of UBERON:0001041 ! foregut property_value: external_definition "Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000579", ontology="AAO", source="AAO:EJS"} property_value: homology_notes "It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000408", ontology="VHOG", source="DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:7955 {source="ZFA"} [Term] id: UBERON:0000947 name: aorta namespace: uberon def: "Artery carrying blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation" [Wikipedia:Aorta] comment: Editor notes: This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae. Taxon notes: All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches[WP]. subset: grouping_class subset: uberon_slim synonym: "aorta, arteria maxima" RELATED LATIN [Wikipedia:Aorta] synonym: "dorsal aorta" NARROW SENSU [Wikipedia:Aorta#In_other_animals, ZFA:0000014] synonym: "trunk of aortic tree" EXACT [] synonym: "trunk of systemic arterial tree" EXACT [] xref: AAO:0010213 xref: BTO:0000135 xref: EFO:0000265 xref: EMAPA:18601 xref: EV:0100027 xref: FMA:3734 xref: GAID:469 xref: galen:Aorta xref: http://upload.wikimedia.org/wikipedia/commons/9/91/Aorta_scheme.jpg xref: MA:0000062 xref: MAT:0000035 xref: MESH:A07.231.114.056 xref: MIAA:0000035 xref: ncithesaurus:Aorta xref: OpenCyc:Mx4rvVjvTpwpEbGdrcN5Y29ycA xref: SCTID:181298001 xref: UMLS:C0003483 xref: VHOG:0001523 xref: XAO:0003010 is_a: UBERON:0004573 ! systemic artery relationship: part_of UBERON:0004571 {source="Wikipedia"} ! systemic arterial system relationship: part_of UBERON:0010191 {source="EHDAA2"} ! aortic system property_value: external_definition "The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010213", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "aortic" xsd:string property_value: homology_notes "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001523", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000948 name: heart namespace: uberon def: "a myogenic muscular organ found in the cardiovascular system. It is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions. The vertebrate heart is composed of cardiac muscle, which is an involuntary striated muscle tissue found only in this organ, and connective tissue. Primitive fish have a four-chambered heart; however, the chambers are arranged sequentially so that this primitive heart is quite unlike the four-chambered hearts of mammals and birds. The first chamber is the sinus venosus, which collects de-oxygenated blood, from the body, through the hepatic and cardinal veins. From here, blood flows into the atrium and then to the powerful muscular ventricle where the main pumping action takes place. The fourth and final chamber is the conus arteriosus which contains several valves and sends blood to the ventral aorta. The ventral aorta delivers blood to the gills where it is oxygenated and flows, through the dorsal aorta, into the rest of the body. (In tetrapods, the ventral aorta has divided in two; one half forms the ascending aorta, while the other forms the pulmonary artery. In the adult fish, the four chambers are not arranged in a straight row but, instead, form an S-shape with the latter two chambers lying above the former two. This relatively simpler pattern is found in cartilaginous fish and in the more primitive ray-finned fish. In teleosts, the conus arteriosus is very small and can more accurately be described as part of the aorta rather than of the heart proper. The conus arteriosus is not present in any amniotes which presumably having been absorbed into the ventricles over the course of evolution. Similarly, while the sinus venosus is present as a vestigial structure in some reptiles and birds, it is otherwise absorbed into the right atrium and is no longer distinguishable[WP]." [Wikipedia:Heart] comment: note that we use the term 'circulatory organ' for the generic class. Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepi- thelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" doi:10.1101/gad.1485706 subset: major_organ subset: organ_slim subset: uberon_slim subset: vertebrate_core synonym: "branchial heart" NARROW SENSU [] synonym: "chambered heart" EXACT [UBERON:cjm] synonym: "Herz" RELATED [BTO:0000562] synonym: "vertebrate heart" EXACT [] xref: AAO:0010210 xref: BILA:0000020 xref: BTO:0000562 xref: EFO:0000815 xref: EHDAA2:0000738 xref: EHDAA:420 xref: EMAPA:16105 xref: EV:0100018 xref: FMA:7088 xref: GAID:174 xref: galen:Heart xref: MA:0000072 xref: MAT:0000036 xref: MESH:A07.541 xref: MIAA:0000036 xref: ncithesaurus:Heart xref: OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA xref: SCTID:302509004 xref: TAO:0000114 xref: UMLS:C0018787 xref: VHOG:0000276 xref: XAO:0000064 xref: ZFA:0000114 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0007100 ! circulatory organ is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0004141 ! heart tube relationship: part_of UBERON:0004535 ! cardiovascular system property_value: axiom_lost_from_external_ontology "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO"} property_value: external_definition "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000114", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "cardiac" xsd:string property_value: homology_notes "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000276", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000949 name: endocrine system namespace: uberon def: "Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity." [NLM:endocrine+system, Wikipedia:Endocrine_system] subset: uberon_slim subset: vertebrate_core synonym: "endocrine glandular system" EXACT [EHDAA2:0002224] synonym: "endocrine system" EXACT [] synonym: "systema endocrinum" EXACT [] xref: AAO:0010279 xref: EFO:0002969 xref: EHDAA2:0002224 xref: EV:0100128 xref: FBbt:00005068 xref: FMA:9668 xref: GAID:439 xref: MA:0000012 xref: MESH:A06 xref: ncithesaurus:Endocrine_System xref: SCTID:278876000 xref: TAO:0001158 xref: UMLS:C0014136 xref: VHOG:0000098 xref: XAO:0000158 xref: ZFA:0001158 is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0000990 ! reproductive system disjoint_from: UBERON:0001004 ! respiratory system disjoint_from: UBERON:0001007 ! digestive system disjoint_from: UBERON:0001008 ! excretory system disjoint_from: UBERON:0001009 ! circulatory system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system property_value: external_definition "Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010279", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "endocrine" xsd:string property_value: homology_notes "Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000098", ontology="VHOG", source="DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000955 name: brain namespace: uberon def: "The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals.[1] Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]." [Wikipedia:Brain] comment: include synganglion? subset: major_organ subset: uberon_slim subset: vertebrate_core synonym: "encephalon" RELATED [BTO:0000142] synonym: "synganglion" RELATED [] xref: AAO:0010478 xref: ABA:Brain xref: BILA:0000135 xref: BTO:0000142 xref: EFO:0000302 xref: EHDAA2:0000183 xref: EHDAA:2641 xref: EHDAA:6485 xref: EMAPA:16894 xref: EV:0100164 xref: FBbt:00005095 xref: FMA:50801 xref: GAID:571 xref: galen:Brain xref: MA:0000168 xref: MAT:0000098 xref: MESH:A08.186.211 xref: MIAA:0000098 xref: ncithesaurus:Brain xref: NIF_GrossAnatomy:birnlex_796 xref: OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA xref: SCTID:258335003 xref: TAO:0000008 xref: UMLS:C0006104 xref: VHOG:0000157 xref: XAO:0000010 xref: ZFA:0000008 is_a: UBERON:0000062 {source="GO"} ! organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001017 {source="FMA"} ! central nervous system property_value: external_definition "Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000008", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010478", ontology="AAO", source="AAO:BJB"} property_value: homology_notes " (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000157", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000956 name: cerebral cortex namespace: uberon def: "The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2–4 mm (0.08–0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted]." [Wikipedia:Cerebral_cortex] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "brain cortex" RELATED [BTO:0000233] synonym: "cortex cerebri" RELATED LATIN [Wikipedia:Cerebral_cortex] synonym: "cortex of cerebral hemisphere" EXACT [] synonym: "pallium of the brain" RELATED [BTO:0000233] xref: ABA:CTX xref: BM:Tel-Cx xref: BTO:0000233 xref: EFO:0000328 xref: EHDAA2:0000234 xref: EHDAA:5464 xref: EMAPA:17544 xref: EV:0100166 xref: FMA:61830 xref: GAID:629 xref: http://upload.wikimedia.org/wikipedia/commons/9/9a/Brainmaps-macaque-hippocampus.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/7/7b/Cerebral_Cortex_location.jpg/200px-Cerebral_Cortex_location.jpg xref: MA:0000185 xref: MAT:0000108 xref: MESH:A08.186.211.730.885.213 xref: MIAA:0000108 xref: ncithesaurus:Cortex xref: NIF_GrossAnatomy:birnlex_1494 xref: SCTID:362880003 xref: UMLS:C0007776 xref: VHOG:0000722 is_a: UBERON:0002791 ! regional part of telencephalon relationship: part_of UBERON:0000203 {source="ISBN10:0471888893", source="GO"} ! pallium relationship: part_of UBERON:0001869 ! cerebral hemisphere property_value: homology_notes "Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000722", ontology="VHOG", source="DOI:10.1111/j.1749-6632.1969.tb20437.x Kruger L, Experimental analyses of the reptilian nervous system. Annals of the New York Academy of Sciences (1969)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000958 name: medulla namespace: uberon def: "Middle part of an organ (as opposed to the cortex)[WP]." [Wikipedia:Bone_marrow_of_ovary] comment: This class is used in a very general sense subset: upper_level xref: BM:Me xref: FMA:61108 xref: galen:Medulla is_a: UBERON:0000471 ! compound organ component property_value: has_relational_adjective "medullary" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000964 name: cornea namespace: uberon def: "transparent front part of the eye that covers the iris, pupil, and anterior chamber. Together with the lens, the cornea refracts light, accounting for approximately two-thirds of the eye's total optical power." [Wikipedia:Cornea] comment: Taxon notes: Compared to terrestial animals, the cornea [of zebrafish] is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman’s membrane in mammals subset: uberon_slim subset: vertebrate_core synonym: "cornea of camera-type eye" EXACT [GO:0061303] synonym: "tunica cornea" RELATED [] xref: AAO:0010344 xref: BTO:0000286 xref: EFO:0000377 xref: EHDAA2:0000316 xref: EHDAA:10199 xref: EMAPA:17161 xref: EV:0100341 xref: FMA:58238 xref: GAID:892 xref: http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/1/1e/Schematic_diagram_of_the_human_eye_en.svg/200px-Schematic_diagram_of_the_human_eye_en.svg.png xref: MA:0000266 xref: MESH:A09.371.060.217 xref: ncithesaurus:Cornea xref: OpenCyc:Mx4rvViBa5wpEbGdrcN5Y29ycA xref: SCTID:181162001 xref: TAO:0000640 xref: UMLS:C0010031 xref: VHOG:0000164 xref: XAO:0000180 xref: ZFA:0000640 is_a: UBERON:0003102 ! surface structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: develops_from UBERON:0004348 {evidence="definitional"} ! optic eminence relationship: develops_from UBERON:0005427 ! corneal primordium relationship: part_of UBERON:0001801 {source="MA"} ! anterior segment of eyeball relationship: part_of UBERON:0010409 {source="MA"} ! eye surface relationship: part_of UBERON:0012430 {source="FMA"} ! tunica fibrosa of eyeball property_value: has_relational_adjective "corneal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000965 name: lens of camera-type eye namespace: uberon def: "Transparent part of camera-type eye that helps to refract light to be focused on the retina." [Wikipedia:Lens_(anatomy)] comment: Taxon notes: This class excludes compound eye corneal lenses. subset: uberon_slim subset: vertebrate_core synonym: "camera-type eye lens" EXACT [GO:0002088] synonym: "crystalline lens" RELATED [BTO:0000723] synonym: "eye lens" EXACT SENSU [] synonym: "lens" EXACT SENSU [] synonym: "lens crystallina" EXACT [Wikipedia:Lens_%28anatomy%29] synonym: "ocular lens" RELATED [BTO:0000723] xref: AAO:0010348 xref: BTO:0000723 xref: EHDAA:9057 xref: EMAPA:17838 xref: EV:0100343 xref: FMA:58241 xref: MA:0000275 xref: MAT:0000141 xref: MESH:A09.371.509 xref: MIAA:0000141 xref: ncithesaurus:Crystalline_Lens xref: OpenCyc:Mx4rvVj0fZwpEbGdrcN5Y29ycA xref: RETIRED_EHDAA2:0000975 xref: SCTID:181169005 xref: TAO:0000035 xref: UMLS:C0023317 xref: VHOG:0000169 xref: XAO:0000008 xref: ZFA:0000035 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005389 ! transparent eye structure relationship: develops_from UBERON:0003073 ! lens placode relationship: develops_from UBERON:0005426 ! lens vesicle relationship: part_of UBERON:0001801 ! anterior segment of eyeball property_value: homology_notes "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000169", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000966 name: retina namespace: uberon def: "The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [Wikipedia:Retina, ZFIN:curator] comment: Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods subset: uberon_slim subset: vertebrate_core synonym: "inner layer of eyeball" EXACT [] synonym: "Netzhaut" RELATED [BTO:0001175] synonym: "retina of camera-type eye" EXACT [GO:0060041] synonym: "tunica interna of eyeball" EXACT [] xref: AAO:0010352 xref: BTO:0001175 xref: EFO:0000832 xref: EHDAA2:0001627 xref: EHDAA:4757 xref: EMAPA:17168 xref: EV:0100348 xref: FMA:58301 xref: GAID:755 xref: http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/e/ed/Human_eye_cross-sectional_view_grayscale.png/200px-Human_eye_cross-sectional_view_grayscale.png xref: MA:0000276 xref: MAT:0000142 xref: MESH:A09.371.729 xref: MIAA:0000142 xref: ncithesaurus:Retina xref: NIF_GrossAnatomy:birnlex_1153 xref: NIF_GrossAnatomy:birnlex_1156 xref: OpenCyc:Mx4rvViTfpwpEbGdrcN5Y29ycA xref: SCTID:181171005 xref: TAO:0000152 xref: UMLS:C0035298 xref: VHOG:0000229 xref: XAO:0000009 xref: ZFA:0000152 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005388 ! photoreceptor array relationship: develops_from UBERON:0003072 {source="EHDAA2"} ! optic cup relationship: part_of UBERON:0001802 ! posterior segment of eyeball property_value: external_definition "The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000152", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "retinal" xsd:string property_value: homology_notes "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000229", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:6656 [Term] id: UBERON:0000970 name: eye namespace: uberon def: "An organ that detects light." [http://en.wikipedia.org/wiki/Eye, UBERON:cjm, Wikipedia:Eye] comment: Usage notes: This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each). Structure notes: Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva, subset: functional_classification subset: major_organ subset: organ_slim subset: uberon_slim synonym: "light-detecting organ" RELATED [] synonym: "photoreceptor" BROAD [] synonym: "visual apparatus" RELATED [EV:0100336] xref: BILA:0000017 xref: BTO:0000439 xref: EFO:0000827 xref: EV:0100336 xref: FBbt:00005162 xref: GAID:69 xref: MAT:0000140 xref: MESH:A01.456.505.420 xref: MIAA:0000140 xref: OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA is_a: UBERON:0000020 ! sense organ relationship: part_of UBERON:0002104 ! visual system property_value: has_relational_adjective "optic" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000974 name: neck namespace: uberon def: "Subdivision of body proper, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the cervical vertebral coumn, it is partially surrounded by skin of neck. Examples: There is only one neck[FMA]." [Wikipedia:Neck] comment: Usage notes: true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck. subset: uberon_slim synonym: "collum" RELATED LATIN [Wikipedia:Neck] synonym: "neck (volume)" RELATED [FMA:7155] xref: AEO:0000108 xref: BTO:0000420 xref: EFO:0000967 xref: EHDAA2:0003108 xref: FMA:7155 xref: GAID:86 xref: galen:Neck xref: http://upload.wikimedia.org/wikipedia/commons/thumb/9/99/Female_neck.jpg/200px-Female_neck.jpg xref: MA:0000024 xref: MAT:0000297 xref: MESH:A01.598 xref: MIAA:0000297 xref: ncithesaurus:Neck xref: OpenCyc:Mx4rvVjLF5wpEbGdrcN5Y29ycA xref: SCTID:302550007 xref: UMLS:C0027530 is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0000153 ! anterior region of body relationship: part_of UBERON:0007811 ! craniocervical region property_value: dubious_for_taxon NCBITaxon:32443 {source="ISBN:9780674021839"} property_value: has_relational_adjective "cervical" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000977 name: pleura namespace: uberon def: "The delicate serous membrane that lines each half of the thorax of mammals and is folded back over the surface of the lung of the same side[BTO]." [Wikipedia:Pleura] comment: In mouse, is_a cavity lining. In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See http://purl.obolibrary.org/obo/uberon/tracker/86 subset: uberon_slim synonym: "pleura" RELATED [] synonym: "pleural tissue" RELATED [BTO:0001791] synonym: "wall of pleural sac" EXACT [] xref: BTO:0001791 xref: EFO:0001980 xref: EV:0100044 xref: FMA:9583 xref: GAID:360 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/a/ab/Gray965.png/200px-Gray965.png xref: MA:0000433 xref: MESH:A04.716 xref: ncithesaurus:Pleural_Tissue xref: OpenCyc:Mx4rv3zwLZwpEbGdrcN5Y29ycA xref: SCTID:181609007 xref: UMLS:C0032225 xref: VHOG:0000394 is_a: UBERON:0000042 {source="MESH"} ! serous membrane is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure relationship: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0009778 {source="FMA"} ! pleural sac property_value: external_definition "The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000394", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: has_relational_adjective "pleural" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000982 name: skeletal joint namespace: uberon def: "Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]." [VSAO:0000101, Wikipedia:Joint] subset: organ_slim subset: uberon_slim subset: vertebrate_core synonym: "articular joint" RELATED [BTO:0001686] synonym: "articulation" BROAD [VSAO:0000101] synonym: "joint" BROAD [FMA:7490, VSAO:0000101] xref: AEO:0000182 xref: BTO:0001686 xref: EFO:0000948 xref: FMA:7490 xref: GAID:102 xref: galen:Joint xref: MA:0000319 xref: MAT:0000188 xref: MESH:A02.835.583 xref: MIAA:0000188 xref: ncithesaurus:Joint xref: OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA xref: RETIRED_EHDAA2:0003182 xref: SCTID:302536002 xref: TAO:0000367 xref: UMLS:C0022417 xref: VHOG:0001276 xref: VSAO:0000101 xref: XAO:0000171 xref: ZFA:0001596 is_a: UBERON:0004905 ! articulation union_of: UBERON:0002217 ! synovial joint union_of: UBERON:0011134 ! nonsynovial joint disjoint_from: UBERON:0001474 ! bone relationship: part_of UBERON:0004770 ! articular system property_value: external_definition "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000101", ontology="VSAO", source="PSPUB:0000170"} property_value: external_definition "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000367", ontology="TAO", source="TAO:pem"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000990 name: reproductive system namespace: uberon def: "Anatomical system that has as its parts the organs concerned with reproduction." [Wikipedia:Reproductive_system] comment: Editor notes: consider splitting genitalia from reproductive system subset: functional_classification subset: uberon_slim subset: vertebrate_core synonym: "animal reproductive system" RELATED [BTO:0000081] synonym: "genital system" RELATED [] synonym: "genitalia" RELATED PLURAL [] synonym: "Geschlechtsorgan" RELATED [BTO:0000081] synonym: "organa genitalia" RELATED [BTO:0000081] synonym: "reproductive tissue" RELATED [BTO:0000081] synonym: "systemata genitalia" RELATED LATIN [Wikipedia:Reproductive_system] xref: AAO:0010258 xref: BILA:0000103 xref: BTO:0000081 xref: EFO:0000809 xref: EHDAA2:0001603 xref: EHDAA:5923 xref: EMAPA:17381 xref: EV:0100100 xref: FBbt:00004857 xref: FMA:7160 xref: GAID:363 xref: HAO:0000374 xref: HAO:0000895 xref: http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/52/Penis.svg/200px-Penis.svg.png xref: MA:0000326 xref: MIAA:0000305 xref: ncithesaurus:Reproductive_System xref: OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA xref: SCTID:278875001 xref: TAO:0000632 xref: UMLS:C1261210 xref: VHOG:0000182 xref: WBbt:0005747 xref: XAO:0000142 xref: ZFA:0000632 is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0001004 ! respiratory system disjoint_from: UBERON:0001007 ! digestive system disjoint_from: UBERON:0001008 ! excretory system disjoint_from: UBERON:0001009 ! circulatory system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: develops_from UBERON:0000926 ! mesoderm property_value: external_definition "Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010258", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000182", ontology="VHOG", source="PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000991 name: gonad namespace: uberon def: "Reproductive organ that produces and releases eggs (ovary) or sperm (testis)." [ISBN:0140512888, Wikipedia:Gonad, ZFA:0000413, ZFIN:curator] comment: FMA xref is a 'general anatomical term' subset: major_organ subset: organ_slim subset: uberon_slim subset: vertebrate_core synonym: "gonada" EXACT [] xref: AAO:0000213 xref: BILA:0000123 xref: BTO:0000534 xref: EMAPA:16857 xref: EMAPA:17383 xref: FBbt:00004858 xref: FMA:18250 xref: GAID:368 xref: HAO:0000379 xref: MA:0002420 xref: MESH:A05.360.576 xref: ncithesaurus:Gonad xref: OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA xref: SCTID:304623008 xref: TAO:0000413 xref: UMLS:C0018067 xref: VHOG:0000397 xref: WBbt:0005175 xref: XAO:0003146 xref: ZFA:0000413 is_a: UBERON:0003133 ! reproductive organ relationship: develops_from UBERON:0005564 ! gonad primordium relationship: part_of UBERON:0000990 ! reproductive system property_value: external_definition "Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000213", ontology="AAO", source="AAO:BJB"} property_value: external_definition "The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000413", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "gonadal" xsd:string property_value: homology_notes "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000397", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000992 name: female gonad namespace: uberon def: "Ovum-producing female reproductive organ." [Wikipedia:Ovary] comment: Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo[WP]. subset: organ_slim subset: uberon_slim subset: vertebrate_core synonym: "female organism genitalia gonad" EXACT [OBOL:automatic] synonym: "female organism genitalia gonada" EXACT [OBOL:automatic] synonym: "female organism reproductive system gonad" EXACT [OBOL:automatic] synonym: "female organism reproductive system gonada" EXACT [OBOL:automatic] synonym: "female reproductive system gonad" EXACT [OBOL:automatic] synonym: "female reproductive system gonada" EXACT [OBOL:automatic] synonym: "genitalia of female organism gonad" EXACT [OBOL:automatic] synonym: "genitalia of female organism gonada" EXACT [OBOL:automatic] synonym: "gonad of female organism genitalia" EXACT [OBOL:automatic] synonym: "gonad of female organism reproductive system" EXACT [OBOL:automatic] synonym: "gonad of female reproductive system" EXACT [OBOL:automatic] synonym: "gonad of genitalia of female organism" EXACT [OBOL:automatic] synonym: "gonad of reproductive system of female organism" EXACT [OBOL:automatic] synonym: "gonada of female organism genitalia" EXACT [OBOL:automatic] synonym: "gonada of female organism reproductive system" EXACT [OBOL:automatic] synonym: "gonada of female reproductive system" EXACT [OBOL:automatic] synonym: "gonada of genitalia of female organism" EXACT [OBOL:automatic] synonym: "gonada of reproductive system of female organism" EXACT [OBOL:automatic] synonym: "ovaries" RELATED PLURAL [] synonym: "ovarium" RELATED LATIN [Wikipedia:Ovary] synonym: "ovary" EXACT [] synonym: "ovum-producing ovary" EXACT SENSU [GO:0061039] synonym: "reproductive system of female organism gonad" EXACT [OBOL:automatic] synonym: "reproductive system of female organism gonada" EXACT [OBOL:automatic] xref: AAO:0000371 xref: BILA:0000125 xref: BTO:0000975 xref: EFO:0000973 xref: EHDAA2:0001360 xref: EHDAA:8124 xref: EMAPA:17962 xref: EV:0100111 xref: FBbt:00004865 xref: FMA:7209 xref: GAID:367 xref: http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/cb/Female_anatomy.png/200px-Female_anatomy.png xref: MA:0000384 xref: MESH:A05.360.319.114.630 xref: MIAA:0000125 xref: ncithesaurus:Ovary xref: OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA xref: SCTID:181464007 xref: TAO:0000403 xref: UMLS:C0029939 xref: VHOG:0000251 xref: XAO:0000258 xref: ZFA:0000403 is_a: UBERON:0000991 ! gonad is_a: UBERON:0003134 ! female reproductive organ disjoint_from: UBERON:0009117 ! indifferent gonad relationship: develops_from UBERON:0009117 ! indifferent gonad relationship: part_of UBERON:0000474 ! female reproductive system property_value: axiom_lost_from_external_ontology "relationship type change: subclass gonad (TAO:0000413) CHANGED TO: develops_from gonad (UBERON:0000991)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000403", ontology="TAO"} property_value: external_definition "Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000371", ontology="AAO", source="AAO:BJB"} property_value: external_definition "Female reproductive organ.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000403", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "ovarian" xsd:string property_value: homology_notes " (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000251", ontology="VHOG", source="DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000995 name: uterus namespace: uberon def: "a major female hormone-responsive reproductive sex organ of most mammals including humans. One end, the cervix, opens into the vagina, while the other is connected to one or both fallopian tubes, depending on the species. It is within the uterus that the fetus develops during gestation, usually developing completely in placental mammals such as humans and partially in marsupials such as kangaroos and opossums. Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused[WP]." [Wikipedia:Uterus] comment: Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle "vagina" which functions as the birth canal. Marsupial embryos form a choriovitelline "placenta" (which can be thought of as something between a monotreme egg and a "true" placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream. subset: organ_slim subset: uberon_slim xref: BTO:0001424 xref: EFO:0000975 xref: EMAPA:29915 xref: EV:0100113 xref: FMA:17558 xref: GAID:172 xref: galen:Uterus xref: http://upload.wikimedia.org/wikipedia/commons/6/6a/Female_reproductive_system_lateral_nolabel.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/cb/Female_anatomy.png/200px-Female_anatomy.png xref: MA:0000389 xref: MAT:0000127 xref: MESH:A05.360.319.679 xref: MIAA:0000127 xref: ncithesaurus:Uterus xref: OpenCyc:Mx4rvViojJwpEbGdrcN5Y29ycA xref: SCTID:181452004 xref: UMLS:C0042149 xref: VHOG:0001137 is_a: UBERON:0003975 ! internal female genitalia relationship: develops_from UBERON:0005795 ! embryonic uterus relationship: part_of UBERON:0000474 ! female reproductive system property_value: external_definition "The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001137", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/uterus"} property_value: has_relational_adjective "uterine" xsd:string property_value: homology_notes "An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001137", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000996 name: vagina namespace: uberon def: "a fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]." [FMA:19949, Wikipedia:Vagina] comment: Taxon notes (via vHOG): "The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria." Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688 subset: uberon_slim synonym: "distal oviductal region" RELATED [] synonym: "distal portion of oviduct" RELATED [] xref: BTO:0000243 xref: EFO:0000976 xref: EMAPA:18986 xref: EV:0100117 xref: FMA:19949 xref: GAID:381 xref: galen:Vagina xref: http://upload.wikimedia.org/wikipedia/commons/1/1b/Illu_repdt_female.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/a/a4/Vaginal_opening_-_english_description.jpg/200px-Vaginal_opening_-_english_description.jpg xref: MA:0000394 xref: MAT:0000128 xref: MESH:A05.360.319.779 xref: MIAA:0000128 xref: ncithesaurus:Vagina xref: OpenCyc:Mx4rvVj1B5wpEbGdrcN5Y29ycA xref: SCTID:181441005 xref: UMLS:C0042232 xref: VHOG:0001138 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0003975 ! internal female genitalia relationship: develops_from UBERON:0000164 {source="Wikipedia"} ! primitive urogenital sinus relationship: part_of UBERON:0000474 ! female reproductive system property_value: external_definition "Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA]" xsd:string {date_retrieved="2012-11-29", external_class="FMA:19949", ontology="FMA"} property_value: external_definition "The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001138", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/vagina"} property_value: has_relational_adjective "vaginal" xsd:string property_value: homology_notes "The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001138", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001003 name: epidermis namespace: uberon def: "The outer layer of the skin[WP]. cellular, multilayered epithelium derived from the ectoderm[ZFA]." [ISBN10:0073040584, Wikipedia:Epidermis_(skin)] comment: Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes). subset: uberon_slim subset: vertebrate_core synonym: "adult epidermis" EXACT [] synonym: "skin" BROAD [] synonym: "vertebrate epidermis" EXACT [] xref: AAO:0000143 xref: BTO:0000404 xref: EFO:0000954 xref: EV:0100153 xref: FMA:70596 xref: GAID:932 xref: MA:0000153 xref: MAT:0000154 xref: MESH:A10.272.497 xref: MIAA:0000154 xref: ncithesaurus:Epidermis xref: SCTID:361694003 xref: TAO:0000105 xref: UMLS:C0014520 xref: VHOG:0000077 xref: XAO:0000028 xref: ZFA:0000105 is_a: UBERON:0007376 ! outer epithelial layer is_a: UBERON:0010371 ! ecto-epithelium relationship: develops_from UBERON:0007383 ! enveloping layer of ectoderm relationship: part_of UBERON:0002097 ! skin of body relationship: part_of UBERON:0002199 ! integument property_value: axiom_lost_from_external_ontology "relationship loss: subclass external integument structures (AAO:0000961)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000143", ontology="AAO"} property_value: external_definition "A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000105", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000143", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "epidermal" xsd:string property_value: homology_notes " (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000077", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001004 name: respiratory system namespace: uberon def: "Functional system which consists of structures involved in respiration." [Wikipedia:Respiratory_system] subset: functional_classification subset: uberon_slim subset: vertebrate_core synonym: "apparatus respiratorius" EXACT [] synonym: "apparatus respiratorius " RELATED [BTO:0000203] synonym: "Atmungssystem" RELATED [BTO:0000203] synonym: "respiratory system" EXACT [] synonym: "systema respiratorium" RELATED LATIN [Wikipedia:Respiratory_system] xref: AAO:0000541 xref: BTO:0000203 xref: EFO:0000804 xref: EHDAA2:0001604 xref: EHDAA:2203 xref: EMAPA:16727 xref: EV:0100036 xref: FMA:7158 xref: GAID:78 xref: http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/5e/Respiratory_system_complete_en.svg/200px-Respiratory_system_complete_en.svg.png xref: MA:0000327 xref: MAT:0000030 xref: MESH:A04 xref: MIAA:0000030 xref: ncithesaurus:Respiratory_System xref: OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA xref: SCTID:278197002 xref: TAO:0000272 xref: UMLS:C0035237 xref: VHOG:0000202 xref: XAO:0000117 xref: ZFA:0000272 is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0001007 ! digestive system disjoint_from: UBERON:0001008 ! excretory system disjoint_from: UBERON:0001009 ! circulatory system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system property_value: external_definition "The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000541", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000202", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} [Term] id: UBERON:0001005 name: respiratory airway namespace: uberon def: "An airway through which respiratory air passes in organisms." [Wikipedia:Trachea] comment: This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED) subset: grouping_class subset: uberon_slim xref: SCTID:361380005 is_a: UBERON:0003103 ! compound organ relationship: part_of UBERON:0001004 ! respiratory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001007 name: digestive system namespace: uberon def: "Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes." [FB:gg, NLM:alimentary+system, Wikipedia:Digestive_system\,] comment: note that many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class subset: uberon_slim subset: vertebrate_core synonym: "alimentary system" RELATED [] synonym: "alimentary tract" RELATED [] synonym: "gastrointestinal system" RELATED [] synonym: "gut" RELATED [] xref: AAO:0000129 xref: BILA:0000082 xref: BTO:0000058 xref: EFO:0000793 xref: EV:0100056 xref: FBbt:00005055 xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem xref: MA:0002431 xref: MAT:0000018 xref: MESH:A03 xref: MIAA:0000018 xref: ncithesaurus:Digestive_System xref: SCTID:278859004 xref: TADS:0000170 xref: TAO:0000339 xref: WBbt:0005748 xref: XAO:0000125 xref: ZFA:0000339 is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0001008 ! excretory system disjoint_from: UBERON:0001009 ! circulatory system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system property_value: external_definition "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000129", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "digestive" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001008 name: excretory system namespace: uberon def: "The excretory system is the system of an organism that mainly performs the function of excretion, the bodily process of discharging wastes. It is responsible for the elimination of wastes produced by the processes that maintain homeostasis." [BILA:0000015, Wikipedia:Excretory_system] comment: In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here subset: uberon_slim subset: vertebrate_core synonym: "renal or urinary system" RELATED [EHDAA:5901] synonym: "renal system" EXACT [GO:0001977] synonym: "renal/urinary system" RELATED [] synonym: "systema urinaria" EXACT [FMA:7159] synonym: "systema urinarium" EXACT [BTO:0003092] synonym: "urinary system" EXACT [] synonym: "urinary tract" EXACT [] xref: AAO:0010257 xref: BILA:0000015 xref: BTO:0001244 xref: BTO:0003092 xref: EFO:0000803 xref: EHDAA2:0001601 xref: EHDAA:5901 xref: EMAPA:17366 xref: EV:0100095 xref: FBbt:00005056 xref: FMA:7159 xref: GAID:391 xref: galen:UrinaryTract xref: MA:0000325 xref: MAT:0000027 xref: MESH:A05.810 xref: MIAA:0000027 xref: ncithesaurus:Urinary_System xref: SCTID:362204003 xref: TADS:0000162 xref: TAO:0000163 xref: UMLS:C1508753 xref: VHOG:0000723 xref: WBbt:0005736 xref: XAO:0000143 xref: ZFA:0000163 is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0001009 ! circulatory system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system property_value: external_definition "An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010257", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000723", ontology="VHOG", source="ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} property_value: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} [Term] id: UBERON:0001009 name: circulatory system namespace: uberon def: "organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]." [Wikipedia:Circulatory_system] comment: the cardiovascular system and the lymphatic system are parts of the circulatory system subset: uberon_slim synonym: "systema cardiovasculare" RELATED LATIN [Wikipedia:Circulatory_system] xref: AAO:0000959 xref: FBbt:00005057 xref: http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/29/Circulatory_System_en.svg/200px-Circulatory_System_en.svg.png xref: OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA xref: VHOG:0001248 is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0001016 ! nervous system disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system property_value: external_definition "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000959", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001248", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: never_in_taxon NCBITaxon:6073 property_value: never_in_taxon NCBITaxon:6157 [Term] id: UBERON:0001013 name: adipose tissue namespace: uberon def: "Connective tissue composed of adipocytes." [Wikipedia:Adipose_tissue] comment: Note in FMA this is dense irregular connective tissue. Taxon notes: n humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen. subset: uberon_slim subset: vertebrate_core synonym: "adipose" RELATED [BTO:0001487] synonym: "bodyfat" RELATED [BTO:0001487] synonym: "fat" EXACT [MA:0000009] synonym: "fat tissue" EXACT [] synonym: "fatty depot" RELATED [] synonym: "fatty tissue" EXACT [] xref: AAO:0000001 xref: AEO:000020 xref: BTO:0001487 xref: EFO:0000234 xref: EFO:0000790 xref: EHDAA2:0003120 xref: EV:0100381 xref: FMA:20110 xref: GAID:920 xref: galen:FattyTissue xref: MA:0000009 xref: MAT:0000015 xref: MESH:A10.165.114 xref: MIAA:0000015 xref: ncithesaurus:Adipose_Tissue xref: OpenCyc:Mx4rvVjc_ZwpEbGdrcN5Y29ycA xref: SCTID:55603005 xref: TAO:0002134 xref: UMLS:C0001527 xref: VHOG:0001284 xref: XAO:0003049 xref: ZFA:0005345 is_a: UBERON:0002384 {source="MA"} ! connective tissue disjoint_from: UBERON:0003714 ! neural tissue property_value: axiom_lost_from_external_ontology "relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000001", ontology="AAO"} property_value: external_definition "Connective tissue in which fat is stored.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002134", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000001", ontology="AAO", source="AAO:LAP"} property_value: homology_notes "Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001284", ontology="VHOG", source="DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001015 name: musculature namespace: uberon def: "A subdivision of the muscular system." [UBERON:cjm, Wikipedia:Muscular_system] comment: AO notes: In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. subset: uberon_slim subset: vertebrate_core synonym: "muscle group" EXACT [] synonym: "muscle system" RELATED [] synonym: "muscles" RELATED [] synonym: "muscles set" EXACT [] synonym: "musculature" EXACT [] synonym: "musculature system" RELATED [] synonym: "musculi" EXACT LATIN [FMA:32558, FMA:TA] synonym: "set of muscles" EXACT [FMA:32558] synonym: "set of skeletal muscles" EXACT [MA:0000165] xref: AAO:0011066 xref: BTO:0000887 xref: EFO:0001949 xref: FMA:32558 xref: http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png xref: MA:0000165 xref: ncithesaurus:Muscle xref: OpenCyc:Mx4rvVjmr5wpEbGdrcN5Y29ycA xref: TAO:0000548 xref: UMLS:C0026845 xref: VSAO:0005038 xref: WBbt:0005737 xref: ZFA:0000548 is_a: UBERON:0000480 ! anatomical group relationship: part_of UBERON:0000383 ! musculature of body property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0001474 [Term] id: UBERON:0001016 name: nervous system namespace: uberon def: "a network of specialized cells that communicate information about an organism's surroundings and itself[Wikipedia]." [ISBN:0-14-051288-8, ISBN:3110148986, NLM:nervous+system, WB:rynl, Wikipedia:Nervous_system, ZFIN:curator] comment: This class was created automatically from a combination of ontologies subset: uberon_slim subset: vertebrate_core synonym: "nerve net" NARROW [Wikipedia:Nerve_net] synonym: "Nervensystem" RELATED [BTO:0001484] synonym: "systema nervosum" RELATED LATIN [Wikipedia:Nervous_system] xref: AAO:0000324 xref: BILA:0000079 xref: BTO:0001484 xref: EFO:0000802 xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 xref: FBbt:00005093 xref: FMA:7157 xref: GAID:466 xref: http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/b/ba/Nervous_system_diagram.png/200px-Nervous_system_diagram.png xref: MA:0000016 xref: MAT:0000026 xref: MESH:A08 xref: MIAA:0000026 xref: ncithesaurus:Nervous_System xref: NIF_GrossAnatomy:birnlex_844 xref: OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA xref: SCTID:278196006 xref: TAO:0000396 xref: UMLS:C0027763 xref: VHOG:0000402 xref: WBbt:0005735 xref: XAO:0000177 xref: ZFA:0000396 is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004121 ! ectoderm-derived structure disjoint_from: UBERON:0001434 ! skeletal system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: develops_from UBERON:0000924 ! ectoderm property_value: axiom_lost_from_external_ontology "relationship type change: differentiates_from ectoderm (AAO:0000137) CHANGED TO: develops_from ectoderm (UBERON:0000924)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000324", ontology="AAO"} property_value: external_definition "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000396", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000324", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "nervous" xsd:string property_value: has_relational_adjective "neural" xsd:string property_value: homology_notes "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000402", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001017 name: central nervous system namespace: uberon def: "The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain, spinal cord and spinal nerves. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord[GO]. The part of the nervous system which in vertebrates consists of the brain and spinal cord, to which sensory impulses are transmitted and from which motor impulses pass out, and which supervises and coordinates the activity of the entire nervous system[XAO]. Neuraxis plus retina[INCF]." [FB:gg, ISBN:3110148986, NLM:central+nervous+system, Wikipedia:Central_nervous_system, ZFIN:curator] subset: uberon_slim subset: vertebrate_core synonym: "cerebrospinal axis" EXACT [FMA:55675] synonym: "CNS" EXACT [] synonym: "neuraxis" EXACT [FMA:55675] synonym: "systema nervosum centrale" EXACT LATIN [FMA:55675, FMA:TA] xref: AAO:0000090 xref: BILA:0000080 xref: BTO:0000227 xref: EFO:0000908 xref: EHDAA2:0000225 xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 xref: FBbt:00005094 xref: FMA:55675 xref: GAID:570 xref: MA:0000167 xref: MAT:0000457 xref: MESH:A08.186 xref: ncithesaurus:Central_Nervous_System xref: NIF_GrossAnatomy:birnlex_1099 xref: OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA xref: SCTID:278199004 xref: TAO:0000012 xref: UMLS:C0927232 xref: VHOG:0000293 xref: XAO:0000215 xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system property_value: external_definition "Part of the nervous system which includes the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000090", ontology="AAO", source="AAO:BJB"} property_value: external_definition "The brain and spinal cord. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000012", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes " (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000293", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} [Term] id: UBERON:0001021 name: nerve namespace: uberon def: "an enclosed, cable-like bundle of peripheral axons [wikipedia]. A portion of tissue which is a fasiculated group of axons[ZFA]. Segment of neural tree organ which has as its parts a nerve trunk and its branches; together with other nerves of the same tree it constitutes a neural tree. Examples: chorda tympani, digastric branch of facial nerve, greater petrosal nerve, posterior cutaneous branch of posterior ramus of cervical nerve, superior lateral cutaneous nerve of arm[FMA]." [FMA:65132, Wikipedia:Nervous_system, ZFA:0007009, ZFIN:curator] comment: check nerve vs peripheral nerve vs tract. Check isa hierarchy - we include under neural tissue as well as neuron projection bundle for now. FMA also has this under organ segment subset: uberon_slim subset: vertebrate_core synonym: "nerves" EXACT PLURAL [TAO:0007009] synonym: "neural subtree" RELATED [FMA:65132] xref: AAO:0011070 xref: AEO:0000137 xref: BTO:0000925 xref: EHDAA2:0003137 xref: EHDAA:2851 xref: EHDAA:3776 xref: EHDAA:4657 xref: EV:0100162 xref: FBbt:00005105 xref: FMA:65132 xref: GAID:758 xref: galen:Nerve xref: MA:0000217 xref: ncithesaurus:Nerve xref: OpenCyc:Mx4rwP3lkpwpEbGdrcN5Y29ycA xref: SCTID:256864008 xref: TAO:0007009 xref: UMLS:C0027740 xref: XAO:0003047 xref: ZFA:0007009 is_a: UBERON:0000122 {source="FBbt"} ! neuron projection bundle is_a: UBERON:0003714 {source="EHDAA2"} ! neural tissue relationship: part_of UBERON:0000010 ! peripheral nervous system property_value: external_definition "A portion of tissue which is a fasiculated group of axons.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0007009", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "nervous" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001023 name: dendrite namespace: uberon def: "The region of a neuron receiving inputs from other neurons, typically a slender neurite, often branched. In insect neurons, this is often not a clear designation and often presynaptic sites co-extend with postsynaptic ones." [http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html, Wikipedia:Dendrite] comment: TODO - use GO subset: uberon_slim xref: FBbt:00005110 xref: FMA:67314 xref: GAID:749 xref: GO:0030425 xref: MESH:A08.663.256 xref: ncithesaurus:Dendrite xref: NIF_Subcellular:sao1211023249 xref: OpenCyc:Mx4rviIdspwpEbGdrcN5Y29ycA xref: TGMA:0001373 xref: UMLS:C0011305 is_a: UBERON:0001024 ! neurite property_value: has_relational_adjective "dendritic" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001024 name: neurite namespace: uberon def: "One of the processes or extensions of a neuron, axon or dendrite or cell body fiber. // Cell appendage of the neuron which includes the axon and the dendrite." [http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html, Wikipedia:Neurite] comment: TODO - use GO subset: uberon_slim xref: FBbt:00005113 xref: FMA:61814 xref: GAID:751 xref: GO:0043005 xref: MESH:A08.663.256.500 xref: NIF_Subcellular:sao-867568886 is_a: UBERON:0000470 ! cell part property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001032 name: sensory system namespace: uberon def: "Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information." [Wikipedia:Sensory_system] comment: note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs subset: uberon_slim subset: vertebrate_core synonym: "organa sensuum" EXACT LATIN [FMA:75259, FMA:TA] synonym: "organa sensuum" RELATED LATIN [Wikipedia:Sensory_system] synonym: "sense organ subsystem" EXACT [] synonym: "sense organs" EXACT [FMA:75259] synonym: "sense organs set" EXACT [FMA:75259] synonym: "sensory organ system" RELATED [] synonym: "sensory subsystem" EXACT [] synonym: "sensory systems" EXACT PLURAL [TAO:0000282] synonym: "set of sense organs" RELATED [FMA:75259] xref: AAO:0000555 xref: BILA:0000099 xref: EFO:0000805 xref: EHDAA2:0003094 xref: FBbt:00005827 xref: FMA:75259 xref: http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/c0/Gray722.png/200px-Gray722.png xref: MA:0002442 xref: MAT:0000031 xref: MIAA:0000031 xref: NIF_GrossAnatomy:nlx_anat_090816 xref: TAO:0000282 xref: VHOG:0001674 xref: XAO:0003194 xref: ZFA:0000282 is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0004456 ! entire sense organ system property_value: homology_notes "An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001674", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001040 name: yolk sac namespace: uberon def: "Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes." [Wikipedia:Yolk_sac] comment: Taxon notes: In therians, a structure homologous to the yolk sac is is present, but contains no yolk platelets. Instead it is filled with fluid [ISBN10:0073040584 "Vertebrates, Kardong"] subset: uberon_slim synonym: "saccus vitellinus" RELATED LATIN [Wikipedia:Yolk_sac] synonym: "vesicula umbilicalis" RELATED LATIN [Wikipedia:Yolk_sac] xref: BTO:0001471 xref: EFO:0003078 xref: EHDAA2:0002212 xref: EHDAA:164 xref: EMAPA:16085 xref: FMA:87180 xref: GAID:1301 xref: http://upload.wikimedia.org/wikipedia/commons/1/17/Gray22.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/1/17/Gray22.png/200px-Gray22.png xref: MESH:A16.254.403.981 xref: ncithesaurus:Yolk_Sac xref: SCTID:362845002 xref: UMLS:C0043425 xref: VHOG:0000830 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0005631 ! extraembryonic membrane relationship: develops_from UBERON:0000925 {source="ISBN10:0073040584"} ! endoderm relationship: develops_from UBERON:0004872 {source="ISBN10:0073040584"} ! splanchnic layer of lateral plate mesoderm property_value: external_definition "One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000830", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/yolk+sac"} property_value: homology_notes "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000830", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001041 name: foregut namespace: uberon def: "Anterior subdivision of a digestive tract[CJM]. An anterior part of the alimentary canal derived from the ectoderm[WP]." [Wikipedia:Foregut] comment: Editor notes: Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class (as it appears to be in FMA) subset: developmental_classification subset: uberon_slim synonym: "praeenteron" RELATED LATIN [Wikipedia:Foregut] synonym: "proenteron" RELATED LATIN [Wikipedia:Foregut] xref: AAO:0011042 xref: BILA:0000085 xref: BTO:0000507 xref: EHDAA2:0000557 xref: EHDAA:520 xref: EMAPA:16548 xref: FBbt:00005379 xref: FMA:45616 xref: http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png xref: MA:0001526 xref: ncithesaurus:Foregut xref: SCTID:361409009 xref: TGMA:0001014 xref: UMLS:C0231051 xref: VHOG:0000285 xref: XAO:0000232 is_a: UBERON:0004921 ! subdivision of digestive tract property_value: homology_notes "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000285", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001042 name: chordate pharynx namespace: uberon def: "Funnel-shaped fibromuscular tube that conducts food to the esophagus, and air to the larynyx and lungs. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH]. Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA]." [Wikipedia:Pharynx] comment: Note that MA/FMA pharynx not part of digestive/alimentary system, we follow their lead here subset: uberon_slim subset: vertebrate_core synonym: "pharynx" BROAD SENSU [FMA:46688] xref: AAO:0000967 xref: BTO:0001049 xref: EFO:0000836 xref: EHDAA2:0001458 xref: EHDAA:2947 xref: EMAPA:16706 xref: EMAPA:18838 xref: EV:0100065 xref: FMA:46688 xref: GAID:155 xref: galen:Pharynx xref: MA:0000432 xref: MESH:A03.867 xref: ncithesaurus:Pharynx xref: OpenCyc:Mx4rvViv7ZwpEbGdrcN5Y29ycA xref: SCTID:181211006 xref: TAO:0000056 xref: UMLS:C0031354 xref: VHOG:0000462 xref: XAO:0003227 xref: ZFA:0000056 is_a: UBERON:0006562 ! pharynx relationship: develops_from UBERON:0009145 {source="EHDAA2"} ! pharyngeal region relationship: part_of UBERON:0001004 ! respiratory system property_value: axiom_lost_from_external_ontology "relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000967", ontology="AAO"} property_value: axiom_lost_from_external_ontology "relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000967", ontology="AAO"} property_value: external_definition "Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000967", ontology="AAO", source="AAO:EJS"} property_value: external_definition "Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000056", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000462", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes " (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000462", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001043 name: esophagus namespace: uberon def: "Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993)." [http://www.rivm.nl/interspeciesinfo/inter/oesophagus/, Wikipedia:Esophagus] comment: AO notes: esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995) subset: major_organ subset: organ_slim subset: uberon_slim subset: vertebrate_core synonym: "gullet" EXACT [] synonym: "oesophagus" EXACT [] synonym: "œsophagus" RELATED LATIN [Wikipedia:Esophagus] xref: AAO:0000145 xref: ANISEED:1235301 xref: BTO:0000959 xref: EFO:0000835 xref: EHDAA2:0001285 xref: EHDAA:2937 xref: EMAPA:16833 xref: EMAPA:18860 xref: EV:0100069 xref: FMA:7131 xref: GAID:291 xref: galen:Esophagus xref: http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg xref: MA:0000352 xref: MAT:0000048 xref: MESH:A03.365 xref: MIAA:0000048 xref: ncithesaurus:Esophagus xref: OpenCyc:Mx4rvVj9Q5wpEbGdrcN5Y29ycA xref: SCTID:181245004 xref: TAO:0000204 xref: UMLS:C0014876 xref: VHOG:0000450 xref: XAO:0000127 xref: ZFA:0000204 is_a: UBERON:0004921 ! subdivision of digestive tract is_a: UBERON:0005178 ! thoracic cavity organ relationship: develops_from UBERON:0009143 ! developing esophageal region property_value: external_definition "Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000145", ontology="AAO", source="AAO:EJS"} property_value: has_relational_adjective "esophageal" xsd:string property_value: homology_notes "The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000450", ontology="VHOG", source="DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001044 name: salivary gland namespace: uberon def: "saliva-secreting exocrine glands of the oral cavity[GO]. The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research[WP]." [GO:0007431, Wikipedia:Salivary_gland] comment: currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals.[3] The salivary glands of some species, however, are modified to produce enzymes; salivary amylase is found in many, but by no means all, bird and mammal species (including humans, as noted above). Furthermore, the venom glands of poisonous snakes, Gila monsters, and some shrews, are modified salivary glands subset: functional_classification subset: organ_slim subset: uberon_slim synonym: "glandulae salivariae" RELATED LATIN [Wikipedia:Salivary_gland] xref: BTO:0001203 xref: EFO:0000859 xref: EHDAA2:0001775 xref: EHDAA:7987 xref: EMAPA:17751 xref: EV:0100059 xref: FBbt:00005382 xref: FMA:9597 xref: GAID:937 xref: galen:SalivaryGland xref: http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/51/Illu_quiz_hn_02.jpg/200px-Illu_quiz_hn_02.jpg xref: MA:0000346 xref: MAT:0000079 xref: MESH:A10.336.779 xref: MIAA:0000079 xref: ncithesaurus:Salivary_Gland xref: OpenCyc:Mx4rvVjl5ZwpEbGdrcN5Y29ycA xref: SCTID:181236000 xref: UMLS:C0036098 xref: VHOG:0000376 is_a: UBERON:0003294 ! gland of foregut is_a: UBERON:0010047 ! oral gland relationship: part_of UBERON:0001041 ! foregut property_value: external_definition "A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000376", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000376", ontology="VHOG", source="ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptationm(2005) p.211", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001045 name: midgut namespace: uberon def: "Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon. That part of the alimentary canal which lies between the gizzard and the hind intestine." [GO:0007494, Wikipedia:Midgut] comment: Editor notes: Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class. AO Notes: in FMA this class has no children. subset: developmental_classification subset: uberon_slim synonym: "mesenteron" RELATED LATIN [Wikipedia:Midgut] xref: BILA:0000086 xref: BTO:0000863 xref: EFO:0001950 xref: EHDAA2:0001185 xref: EHDAA:983 xref: EMAPA:16255 xref: FBbt:00005383 xref: FMA:45617 xref: http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg xref: MA:0001564 xref: ncithesaurus:Midgut xref: SCTID:361410004 xref: TGMA:0001036 xref: UMLS:C0231052 xref: VHOG:0000290 xref: XAO:0000103 is_a: UBERON:0004921 ! subdivision of digestive tract property_value: homology_notes "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000290", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001046 name: hindgut namespace: uberon def: "Posterior subdivision of a digestive tract[CJM]." [Wikipedia:Hindgut] comment: Editor notes: Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - UBERONREF:0000002). We may explicitly make this a developmental class. AO Notes: in FMA this class has no children. subset: developmental_classification subset: uberon_slim synonym: "metenteron" RELATED LATIN [Wikipedia:Hindgut] xref: AAO:0011052 xref: BILA:0000087 xref: BTO:0000510 xref: EHDAA2:0000779 xref: EHDAA:975 xref: EMAPA:16715 xref: FBbt:00005384 xref: FMA:45618 xref: http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png xref: MA:0001527 xref: ncithesaurus:Hindgut xref: SCTID:362856002 xref: TGMA:0001020 xref: UMLS:C0231053 xref: VHOG:0000459 xref: XAO:0000104 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: develops_from UBERON:0003104 {source="Wikipedia"} ! mesenchyme property_value: homology_notes "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000459", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001048 name: primordium namespace: uberon def: "Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt]. An embryonic structure that is the rudiment or commencement of a part or organ." [BTO:0001886, FB:DJS, FB:FBrf0089570, FB:FBrf0178740, Wikipedia:Primordium] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "bud" RELATED [] synonym: "placode" RELATED [FBbt:00005495] synonym: "rudiment" RELATED [] xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 xref: FBbt:00005495 xref: FMA:86589 xref: MAT:0000482 xref: ncithesaurus:Primordium xref: UMLS:C0678727 xref: XAO:0003043 is_a: UBERON:0005423 {source="EHDAA2"} ! developing anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001049 name: neural tube namespace: uberon def: "In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]." [Wikipedia:Neural_tube] comment: The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium[GO:0021915] subset: uberon_slim subset: vertebrate_core synonym: "presumptive central nervous system" RELATED [] synonym: "tubus neuralis" RELATED LATIN [Wikipedia:Neural_tube] xref: AAO:0010617 xref: BTO:0001057 xref: EHDAA2:0001254 xref: EHDAA:2869 xref: EHDAA:908 xref: EMAPA:16164 xref: EMAPA:16530 xref: EMAPA:16757 xref: http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Gray19_with_color.png/200px-Gray19_with_color.png xref: MAT:0000069 xref: MIAA:0000069 xref: ncithesaurus:Neural_Tube xref: SCTID:362852000 xref: TAO:0001135 xref: UMLS:C0231024 xref: VHOG:0000307 xref: XAO:0003204 xref: ZFA:0001135 is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007497 ! developing epithelial placode is_a: UBERON:0010371 ! ecto-epithelium relationship: develops_from UBERON:0002346 ! neurectoderm relationship: develops_from UBERON:0005068 ! neural rod relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0001016 {source="GO"} ! nervous system property_value: external_definition "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010617", ontology="AAO", source="AAO:JOR"} property_value: external_definition "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/neural+tube"} property_value: homology_notes " (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001052 name: rectum namespace: uberon def: "The terminal portion of the intestine." [Wikipedia:Rectum] comment: Taxon notes: In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html subset: uberon_slim synonym: "intestinum rectum" RELATED [BTO:0001158] synonym: "rectal sac" RELATED [] synonym: "terminal portion of intestine" EXACT [] synonym: "terminal portion of large intestine" RELATED [] xref: AAO:0010401 xref: BTO:0001158 xref: EFO:0000848 xref: EHDAA2:0001592 xref: EHDAA:5836 xref: EMAPA:17896 xref: EMAPA:18925 xref: EV:0100081 xref: FMA:14544 xref: GAID:311 xref: galen:Rectum xref: http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif xref: http://upload.wikimedia.org/wikipedia/commons/thumb/7/75/Anorectum.gif/200px-Anorectum.gif xref: MA:0000336 xref: MAT:0000050 xref: MESH:A03.492.411.495.767 xref: MIAA:0000050 xref: ncithesaurus:Rectum xref: OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA xref: SCTID:181261002 xref: UMLS:C0034896 xref: VHOG:0000427 xref: VHOG:0001751 xref: XAO:0000238 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004921 {order="4", source="cjm"} ! subdivision of digestive tract relationship: part_of UBERON:0000059 {source="MA"} ! large intestine relationship: part_of UBERON:0006866 ! terminal part of digestive tract relationship: part_of UBERON:0012361 {source="EHDAA2"} ! internal anal region property_value: external_definition "The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001751", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: has_relational_adjective "rectal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001062 name: anatomical entity namespace: uberon def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [CARO:MAH, FMA:62955] subset: upper_level xref: AAO:0010841 xref: AEO:0000000 xref: BILA:0000000 xref: CARO:0000000 xref: EHDAA2:0002229 xref: FBbt:10000000 xref: FBbt_root:00000000 xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 xref: ncithesaurus:Anatomic_Structure_System_or_Substance xref: NIF_GrossAnatomy:birnlex_6 xref: TAO:0100000 xref: TGMA:0001822 xref: UMLS:C1515976 xref: ZFA:0100000 property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001064 name: ventral pancreatic duct namespace: uberon alt_id: UBERON:0005627 def: "a duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla." [Wikipedia:Pancreatic_duct] comment: Development notes: Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct.[WP] subset: uberon_slim synonym: "canal of Wirsung" RELATED [BTO:0002362] synonym: "chief pancreatic duct" EXACT [FMA:16003] synonym: "duct of Wirsung" EXACT [Wikipedia:Pancreatic_duct] synonym: "ductus pancreatis ventralis" RELATED [] synonym: "hepaticopancreatic duct" RELATED [BTO:0002362] synonym: "main pancreatic duct" EXACT [MA:0000126] synonym: "pancreatic duct" BROAD [MESH:A03.734.667] xref: BTO:0002362 xref: EHDAA2:0001396 xref: EHDAA:6905 xref: EMAPA:18821 xref: FMA:16003 xref: GAID:337 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/1/15/Gray1100.png/200px-Gray1100.png xref: MA:0000126 xref: MESH:A03.734.667 xref: ncithesaurus:Pancreatic_Duct xref: RETIRED_EHDAA2:0002177 xref: SCTID:245385001 xref: UMLS:C0030288 xref: VHOG:0000256 is_a: UBERON:0002394 ! bile duct is_a: UBERON:0007329 {source="FMA"} ! pancreatic duct relationship: develops_from UBERON:0003924 {source="EHDAA2"} ! ventral pancreatic bud relationship: part_of UBERON:0000017 ! exocrine pancreas property_value: homology_notes "These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000256", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001066 name: intervertebral disk namespace: uberon def: "A pad of fibrocartilage between the articular surfaces of two successive vertebral centra which has nucleus pulposus at its core." [ISBN10:0073040584, Wikipedia:Intervertebral_disk] comment: Taxon/Terminology notes: strictly speaking the term intervertebral disk [applies to intervertebral cartilage] whose gel-like core is nucleus puloposus, by this definition only in mammals subset: uberon_slim synonym: "discus intervertebralis" EXACT LATIN [FMA:10446, FMA:TA] synonym: "intervertebral disc" EXACT [] synonym: "intervertebral fibrocartilage" RELATED [BTO:0003625] synonym: "spinal disc" EXACT [Wikipedia:Spinal_disc] synonym: "spinal disk" RELATED [BTO:0003625] xref: BTO:0003625 xref: EFO:0001370 xref: FMA:10446 xref: GAID:105 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/9/92/Gray301.png/200px-Gray301.png xref: MA:0000110 xref: MESH:A02.165.410 xref: ncithesaurus:Intervertebral_Disc xref: OpenCyc:Mx4rv11AcpwpEbGdrcN5Y29ycA xref: SCTID:244570000 xref: UMLS:C0021815 is_a: UBERON:0011135 ! intervertebral cartilage property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001091 name: calcareous tooth namespace: uberon def: "Organ with a cavity which consist of dentine surrounded by enamel. Examples: incisor, molar." [FMA:12516, Wikipedia:Tooth, Wikipedia:Tooth_(animal)] comment: Editors note: we place ZFA ctb 5 tooth here for now. Consider changing name from calcaeous tooth. Note that sea cucumbers develop calcareous tooth-like structures subset: uberon_slim subset: vertebrate_core synonym: "dentine containing tooth" EXACT [] synonym: "tooth" EXACT [] synonym: "vertebrate tooth" EXACT [] xref: AEO:0000220 xref: BTO:0000397 xref: EFO:0000839 xref: EHDAA2:0004605 xref: EV:0100063 xref: FMA:12516 xref: GAID:1260 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/1/14/Teeth_by_David_Shankbone.jpg/200px-Teeth_by_David_Shankbone.jpg xref: MA:0000348 xref: MAT:0000041 xref: MESH:A14.254.860 xref: MIAA:0000041 xref: ncithesaurus:Tooth xref: OpenCyc:Mx4rvVjUEZwpEbGdrcN5Y29ycA xref: SCTID:302214001 xref: TAO:0001625 xref: UMLS:C0040426 xref: VHOG:0000127 xref: VHOG:0001733 xref: XAO:0000431 xref: ZFA:0000694 is_a: UBERON:0003913 ! tooth-like structure is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0005087 {evidence="definitional"} ! tooth placode property_value: has_relational_adjective "dental" xsd:string property_value: homology_notes "The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001733", ontology="VHOG", source="PMID:19266065 Koussoulakou DS, Margaritis LH, Koussoulakos SL, A curriculum vitae of teeth: evolution, generation, regeneration. International Journal of Biological Sciences (2009)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:8782 [Term] id: UBERON:0001096 name: wall of esophagus namespace: uberon def: "An anatomical wall that is part of a esophagus [Obol]." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "anatomical wall of esophagus" EXACT [OBOL:automatic] synonym: "anatomical wall of gullet" EXACT [OBOL:automatic] synonym: "anatomical wall of oesophagus" EXACT [OBOL:automatic] synonym: "esophageal wall" EXACT [] synonym: "esophagus anatomical wall" EXACT [OBOL:automatic] synonym: "esophagus wall" EXACT [] synonym: "gullet anatomical wall" EXACT [OBOL:automatic] synonym: "gullet wall" EXACT [OBOL:automatic] synonym: "oesophagus anatomical wall" EXACT [OBOL:automatic] synonym: "oesophagus wall" EXACT [OBOL:automatic] synonym: "wall of gullet" EXACT [OBOL:automatic] synonym: "wall of oesophagus" EXACT [OBOL:automatic] xref: FMA:12611 xref: MA:0002691 is_a: UBERON:0000060 ! anatomical wall is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0001043 ! esophagus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001130 name: vertebral column namespace: uberon def: "Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body." [https://sourceforge.net/tracker/?func=detail&aid=3530322&group_id=76834&atid=2257941, UBERON:cjm, Wikipedia:Vertebral_column] comment: Editor notes: Note that in contrast to VSAO, this is a subset of the skeletal system, and thus includes intervertebral joints, cartilage and ligaments etc. Some ontologies such as AAO seem to purely refer to the skeleton subset: uberon_slim subset: vertebrate_core synonym: "backbone" NARROW [FMA:13478] synonym: "columna vertebralis" RELATED [BTO:0000818] synonym: "spinal column" RELATED [MESH:A02.835.232.834] synonym: "spine" BROAD [FMA:13478] synonym: "vertebral column skeleton" NARROW [AAO:0000699] synonym: "vertebral region" RELATED [] xref: AAO:0000699 xref: AAO:0000734 xref: BTO:0000818 xref: EFO:0001369 xref: EHDA:10119 xref: EMAPA:16666 xref: FMA:13478 xref: GAID:106 xref: galen:SpinalColumn xref: MA:0002416 xref: MESH:A02.835.232.834 xref: ncithesaurus:Spinal_Cord_Column xref: ncithesaurus:Vertebral_Column xref: NIF_Subcellular:sao1145756102 xref: OpenCyc:Mx4rv2j-CpwpEbGdrcN5Y29ycA xref: OpenCyc:Mx4rv6GF55wpEbGdrcN5Y29ycA xref: OpenCyc:Mx4rvVkFEpwpEbGdrcN5Y29ycA xref: SCTID:44300000 xref: TAO:0001559 xref: UMLS:C0037949 xref: UMLS:C1519455 xref: VHOG:0001142 xref: VSAO:0000185 xref: XAO:0003074 xref: ZFA:0001559 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0011138 {source="cjm"} ! post-cranial axial skeletal system property_value: external_definition "Anatomical cluster that consists of all the vertebra in the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000185", ontology="VSAO", source="VSAO:curator"} property_value: external_definition "The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001142", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/vertebral+column"} property_value: homology_notes "Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001142", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.53", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001132 name: parathyroid gland namespace: uberon def: "The parathyroid gland is an organ specialised for secretion of parathyroid hormone[GO]. Parathyroid glands control the amount of calcium in the blood and within the bones[WP]." [Wikipedia:Parathyroid_gland] comment: Development notes: table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity. Additional notes: Parathyroid glands are found in all adult tetrapods, although they vary in their number, and in their exact position. Mammals typically have four parathyroids, while other groups typically have six. Fish do not possess parathyroid glands, although the ultimobranchial glands, which are found close to the oesophagus, may have a similar function and could even be homologous with the tetrapod parathyroids. Even these glands are absent in the most primitive vertebrates, the jawless fish, but as these species have no bone in their skeletons, only cartilage, it may be that they have less need to regulate calcium metabolism. The conserved homology of genes and calcium-sensing receptors in fish gills with those in the parathryroid glands of birds and mammals is recognized by evolutionary developmental biology as evolution-using genes and gene networks in novel ways to generate new structures with some similar functions and novel functions[WP]. The parathryoid gland is not formed in fish, but is only found in tetrapods. In humans and chick it emerges from pouches 3 and 4, but in mice it is exclusively generated by the third pouch[PMID:16313389] subset: organ_slim subset: uberon_slim synonym: "parathyroid" EXACT [] synonym: "parathyroid secreting cell" RELATED [] xref: AAO:0010545 xref: BTO:0000997 xref: EFO:0000862 xref: EV:0100134 xref: FMA:13890 xref: GAID:452 xref: MA:0000128 xref: MAT:0000082 xref: MESH:A06.407.560 xref: MIAA:0000082 xref: ncithesaurus:Parathyroid_Gland xref: SCTID:181121007 xref: UMLS:C0030518 xref: VHOG:0001188 xref: XAO:0000167 is_a: UBERON:0002368 ! endocrine gland relationship: part_of UBERON:0000949 ! endocrine system property_value: external_definition "Any one of several small structures, usually four, attached to the dorsal surfaces of the lateral lobes of the thyroid gland. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001188", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/parathyroid+gland"} property_value: external_definition "Either of the two pairs of small, spherical, encapsulated glands which develop from ventral growths of the third and fourth pharyngeal pouches and are closely associated with the external jugular veins. Calcitonin and parathyroid hormone are secreted by these glands.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010545", ontology="AAO", source="AAO:BJB"} property_value: homologous_to ZFA:0001200 {source="ZFA:0001200"} property_value: homology_notes "The evolution of the tetrapods, and the shift from an aquatic to a terrestrial environment, was believed to have required new controls for regulating calcium homeostasis, and thus the evolution of parathyroid glands (...) both the tetrapod parathyroid and the gills of fish contribute to the regulation of extracellular calcium levels. It is therefore reasonable to suggest that the parathyroid gland evolved as a result of the transformation of the gills into the parathyroid glands of tetrapods and the transition from an aquatic to a terrestrial environment. This interpretation would also explain the positioning of the parathyroid gland within the pharynx in the tetrapod body. Were the parathyroid gland to have emerged de novo with the evolution of the tetrapods it could, as an endocrine organ, have been placed anywhere in the body and still exert its effect.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001188", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001133 name: cardiac muscle tissue namespace: uberon alt_id: UBERON:0007096 def: "Muscle composed of cardiac muscle cells that is part of the heart[ZFA]. involuntary striated muscle found in the walls of the heart, specifically the myocardium[Wikipedia]. Tissue which consists of cardiac myocytes surrounded by cardiac endomysium. Examples: Cardiac muscle tissue proper, conducting tissue of heart[FMA]." [FMA:14068] comment: check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit subset: uberon_slim subset: vertebrate_core synonym: "cardiac muscle" EXACT [] synonym: "cardiac muscle muscle tissue" EXACT [OBOL:automatic] synonym: "cardiac muscle textus muscularis" EXACT [OBOL:automatic] synonym: "cardiac musculature" RELATED [BILA:0000134] synonym: "heart muscle muscle tissue" EXACT [OBOL:automatic] synonym: "heart muscle textus muscularis" EXACT [OBOL:automatic] synonym: "heart myocardium muscle tissue" EXACT [OBOL:automatic] synonym: "heart myocardium textus muscularis" EXACT [OBOL:automatic] synonym: "muscle of heart muscle tissue" EXACT [OBOL:automatic] synonym: "muscle of heart textus muscularis" EXACT [OBOL:automatic] synonym: "muscle tissue of cardiac muscle" EXACT [OBOL:automatic] synonym: "muscle tissue of heart muscle" EXACT [OBOL:automatic] synonym: "muscle tissue of heart myocardium" EXACT [OBOL:automatic] synonym: "muscle tissue of muscle of heart" EXACT [OBOL:automatic] synonym: "muscle tissue of myocardium" EXACT [OBOL:automatic] synonym: "myocardium muscle tissue" EXACT [OBOL:automatic] synonym: "myocardium textus muscularis" EXACT [OBOL:automatic] synonym: "textus muscularis of cardiac muscle" EXACT [OBOL:automatic] synonym: "textus muscularis of heart muscle" EXACT [OBOL:automatic] synonym: "textus muscularis of heart myocardium" EXACT [OBOL:automatic] synonym: "textus muscularis of muscle of heart" EXACT [OBOL:automatic] synonym: "textus muscularis of myocardium" EXACT [OBOL:automatic] xref: AAO:0010245 xref: AEO:0000142 xref: BILA:0000134 xref: BTO:0000199 xref: EHDAA2:0003142 xref: FMA:14068 xref: galen:CardiacMuscle xref: galen:CardiacMuscleTissue xref: ncithesaurus:Heart_Muscle xref: TAO:0005280 xref: ZFA:0005280 is_a: UBERON:0002036 ! striated muscle tissue disjoint_from: UBERON:0001134 ! skeletal muscle tissue relationship: part_of UBERON:0000948 {source="ZFA"} ! heart property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001134 name: skeletal muscle tissue namespace: uberon def: "Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]. Striated muscle tissue under control of the somatic nervous system. It is one of three major muscle types, the others being cardiac and smooth muscle. As its name suggests, most skeletal muscle is attached to bones by bundles of collagen fibers known as tendons. Skeletal muscle is made up of individual components known as muscle fibers. These fibers are formed from the fusion of developmental myoblasts. The myofibers are long, cylindrical, multinucleated cells composed of actin and myosin myofibrils repeated as a sarcomere, the basic functional unit of the cell and responsible for skeletal muscle's striated appearance and forming the basic machinery necessary for muscle contraction. The term muscle refers to multiple bundles of muscle fibers held together by connective tissue[WP]." [Wikipedia:Skeletal_striated_muscle] comment: TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle. subset: uberon_slim subset: vertebrate_core synonym: "skeletal muscle" EXACT [] synonym: "skeletal muscle organ" RELATED [] synonym: "skeletal muscle system" RELATED [BTO:0001103] synonym: "somatic muscle" RELATED [BTO:0001103] xref: AAO:0011099 xref: BTO:0001103 xref: EFO:0000888 xref: EHDAA2:0001842 xref: EHDAA:2923 xref: EHDAA:5035 xref: EHDAA:5043 xref: EHDAA:5978 xref: EHDAA:5984 xref: EHDAA:8277 xref: EHDAA:8291 xref: EHDAA:8326 xref: EHDAA:9146 xref: EV:0100377 xref: FMA:14069 xref: GAID:141 xref: http://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg xref: MA:0002439 xref: MAT:0000302 xref: MESH:A02.633.567 xref: MIAA:0000302 xref: ncithesaurus:Skeletal_Muscle_Tissue xref: OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA xref: SCTID:426215008 xref: TAO:0005277 xref: UMLS:C0242692 xref: VHOG:0000319 xref: XAO:0000174 xref: ZFA:0005277 is_a: UBERON:0002036 ! striated muscle tissue relationship: develops_from UBERON:0003082 ! myotome property_value: external_definition "Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005277", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000319", ontology="VHOG", source="PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001135 name: smooth muscle tissue namespace: uberon def: "Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. Tissue which consists of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Examples: Arrector muscle of hair, Muscularis mucosae." [Wikipedia:Smooth_muscle_tissue] comment: terminological note: GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells. subset: uberon_slim subset: vertebrate_core synonym: "involuntary muscle" EXACT [] synonym: "non-striated muscle" EXACT [] synonym: "smooth muscle" EXACT [] synonym: "textus muscularis levis; textus muscularis nonstriatus" RELATED LATIN [Wikipedia:Smooth_muscle_tissue] synonym: "textus muscularis nonstriatus" EXACT LATIN [FMA:14070, FMA:TA] synonym: "visceral muscle" NARROW SENSU [] synonym: "visceral muscle tissue" NARROW SENSU [] xref: AAO:0010244 xref: AEO:0000141 xref: BTO:0001260 xref: EFO:0000889 xref: EHDAA2:0003141 xref: EV:0100378 xref: FBbt:00003525 xref: FMA:14070 xref: GAID:167 xref: galen:SmoothMuscle xref: galen:SmoothMuscleTissue xref: http://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg xref: MA:0000166 xref: MAT:0000303 xref: MESH:A02.633.570 xref: MIAA:0000303 xref: ncithesaurus:Smooth_Muscle_Tissue xref: OpenCyc:Mx4rvvSS3pwpEbGdrcN5Y29ycA xref: TAO:0005274 xref: UMLS:C1267092 xref: VHOG:0001246 xref: WBbt:0005781 xref: XAO:0000175 xref: ZFA:0005274 is_a: UBERON:0002385 ! muscle tissue disjoint_from: UBERON:0002036 ! striated muscle tissue property_value: external_definition "A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005274", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010244", ontology="AAO", source="AAO:CAM"} property_value: homology_notes " (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an “acoel-like” smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001246", ontology="VHOG", source="DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001136 name: mesothelium namespace: uberon def: "Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri)." [FMA:14074, Wikipedia:Mesothelium] comment: This class was created automatically from a combination of ontologies subset: uberon_slim xref: AEO:0000111 xref: BTO:0002422 xref: EHDAA2_RETIRED:0003111 xref: EHDAA:2331 xref: EHDAA:2349 xref: EHDAA:295 xref: EHDAA:6073 xref: EHDAA:640 xref: EHDAA:646 xref: FMA:14074 xref: http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg xref: MA:0000565 xref: ncithesaurus:Mesothelium xref: SCTID:361918002 xref: UMLS:C0086610 is_a: UBERON:0000487 ! simple squamous epithelium is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0000926 {source="FMA-inferred"} ! mesoderm relationship: part_of UBERON:0000042 ! serous membrane property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001137 name: dorsum namespace: uberon def: "The dorsal part of an animal, which in vertebrares includes the vertebral column. [cjm]." [UBERONREF:0000006, Wikipedia:Dorsum_(anatomy)] comment: Taxon notes: In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body subset: uberon_slim synonym: "back" EXACT [FMA:14181] synonym: "back of body proper" EXACT [FMA:14181] synonym: "dorsal part of organism" EXACT [] xref: BTO:0001713 xref: EFO:0001405 xref: FMA:14181 xref: GAID:30 xref: galen:Back xref: http://upload.wikimedia.org/wikipedia/commons/thumb/e/ee/432px-Gray-back.PNG/200px-432px-Gray-back.PNG xref: MESH:A01.176 xref: ncithesaurus:Back xref: OpenCyc:Mx4rvVkEU5wpEbGdrcN5Y29ycA xref: SCTID:123961009 xref: UMLS:C0004600 is_a: UBERON:0000475 ! organism subdivision property_value: has_relational_adjective "dorsal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001140 name: renal vein namespace: uberon def: "The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted]." [Wikipedia:Renal_vein] comment: AO notes: see also MA:0002591 'kidney venous blood vessel'. in EHDAA2, the renal vein is part of the kidney subset: uberon_slim synonym: "kidney vein" EXACT [OBOL:automatic] synonym: "kidney venous blood vessel" EXACT [MA:0002591] synonym: "renal venous tree" EXACT [] synonym: "vein of kidney" EXACT [OBOL:automatic] synonym: "venae renales" RELATED LATIN [Wikipedia:Renal_vein] xref: BTO:0002681 xref: EHDAA2:0001602 xref: EHDAA:8722 xref: EMAPA:19223 xref: EMAPA:28376 xref: FMA:14334 xref: GAID:544 xref: galen:RenalVein xref: http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/7/76/Gray1122.png/200px-Gray1122.png xref: MA:0002210 xref: MESH:A07.231.908.752 xref: ncithesaurus:Renal_Vein xref: OpenCyc:Mx4rvdUXKJwpEbGdrcN5Y29ycA xref: SCTID:116358006 xref: UMLS:C0035092 is_a: UBERON:0001638 ! vein property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001153 name: caecum namespace: uberon def: "Pouch, connecting the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction." [Wikipedia:Cecum] comment: Taxon notes: A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates.[WP] Kardong: in some herbivorous lizards, a cecum is present between small and large intestines subset: uberon_slim synonym: "blind intestine" RELATED [BTO:0000166] synonym: "blindgut" RELATED [BTO:0000166] synonym: "caeca" NARROW PLURAL [NCBITaxon:8782] synonym: "ceca" NARROW PLURAL [NCBITaxon:8782] synonym: "cecum" EXACT [FMA:14541] synonym: "intestinum caecum" RELATED [BTO:0000166] synonym: "intestinum crassum caecum" EXACT [] synonym: "intestinum crassum cecum" RELATED [BTO:0000166] xref: BTO:0000166 xref: EFO:0000850 xref: EHDAA2:0000206 xref: EHDAA:3913 xref: EV:0100397 xref: FMA:14541 xref: GAID:307 xref: galen:Cecum xref: http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/8/82/Stomach_colon_rectum_diagram.svg/200px-Stomach_colon_rectum_diagram.svg.png xref: MA:0000334 xref: MESH:A03.492.411.495.209 xref: MIAA:0000288 xref: ncithesaurus:Cecum xref: OpenCyc:Mx4rve6u4JwpEbGdrcN5Y29ycA xref: SCTID:181256004 xref: UMLS:C0007531 xref: VHOG:0001559 is_a: UBERON:0009854 ! digestive tract diverticulum relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut relationship: part_of UBERON:0000059 {source="MA"} ! large intestine relationship: part_of UBERON:0001155 {source="EHDAA2"} ! colon property_value: has_relational_adjective "caecal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:32443 {source="Wikipedia"} [Term] id: UBERON:0001154 name: vermiform appendix namespace: uberon def: "a blind-ended tube connected to the cecum, from which it develops embryologically[WP]." [Wikipedia:Vermiform_appendix] subset: organ_slim subset: uberon_slim synonym: "apex of cecum" RELATED [VHOG:0001306] synonym: "appendix" EXACT [] synonym: "appendix vermiformis" EXACT LATIN [FMA:14542, FMA:TA] synonym: "appendix vermiformis" RELATED LATIN [Wikipedia:Vermiform_appendix] synonym: "caecal appendix" EXACT [] synonym: "cecal appendix" EXACT [] synonym: "vermix" BROAD [] xref: BTO:0000084 xref: EFO:0000849 xref: EHDAA2:0000588 xref: EV:0100076 xref: EV:0100080 xref: FMA:14542 xref: GAID:308 xref: galen:AppendixVermiformis xref: http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/a/ad/Gray536.png/200px-Gray536.png xref: MA:0001540 xref: MAT:0000287 xref: MESH:A03.492.411.495.209.290 xref: MIAA:0000287 xref: ncithesaurus:Vermiform_Appendix xref: OpenCyc:Mx4rvVjGgJwpEbGdrcN5Y29ycA xref: SCTID:181255000 xref: UMLS:C0003617 xref: VHOG:0001306 is_a: UBERON:0000062 ! organ is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut relationship: part_of UBERON:0001153 {source="MA"} ! caecum relationship: part_of UBERON:0004907 {source="FMA"} ! lower digestive tract property_value: external_definition "Organ with organ cavity which is continuous proximally with the cecum and distally terminates in the tip of the appendix. Examples: There is only one appendix[FMA:14542]." xsd:string {source="FMA:14542"} property_value: has_relational_adjective "appendiceal" xsd:string property_value: homology_notes "A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001306", ontology="VHOG", source="DOI:10.1111/j.1420-9101.2009.01809.x Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, Parker W, Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of Evolutionary Biology (2009)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001155 name: colon namespace: uberon def: "Last portion of the digestive system in most vertebrates; it extracts water and salt from solid wastes before they are eliminated from the body[WP] In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]. In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005." [Wikipedia:Colon_(anatomy), ZFIN:curator] comment: TODO: abstract this such that it legitimately covers all vertebrates subset: uberon_slim subset: vertebrate_core synonym: "hindgut" RELATED [] synonym: "large bowel" EXACT [] synonym: "posterior intestine" NARROW [] synonym: "posterior intestine - zebrafish" BROAD [] xref: AAO:0010400 xref: BTO:0000269 xref: EFO:0000361 xref: EMAPA:18939 xref: EV:0100079 xref: FMA:14543 xref: GAID:309 xref: galen:Colon xref: MA:0000335 xref: MAP:0000001 xref: MAT:0000526 xref: MESH:A03.492.411.495.356 xref: ncithesaurus:Colon xref: OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA xref: SCTID:302508007 xref: TAO:0000706 xref: UMLS:C0009368 xref: VHOG:0000648 xref: XAO:0000243 xref: ZFA:0000706 is_a: UBERON:0004921 {order="3", source="cjm"} ! subdivision of digestive tract relationship: part_of UBERON:0000059 {source="FMA"} ! large intestine property_value: external_definition "The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010400", ontology="AAO", source="UBERON:0001155"} property_value: external_definition "The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000706", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "colonic" xsd:string property_value: homology_notes "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000648", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001156 name: ascending colon namespace: uberon def: "Organ part which is continuous with the cecum proximally and the transverse colon distally.[FMA]" [FMA:FMA, Wikipedia:Ascending_colon] comment: Note that in MA, this is a subclass of colon subset: uberon_slim synonym: "colon ascendens" RELATED LATIN [Wikipedia:Ascending_colon] synonym: "spiral colon" RELATED SENSU [Wikipedia:Spiral_colon] xref: BTO:0000270 xref: EFO:0000843 xref: FMA:14545 xref: galen:AscendingColon xref: http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/3b/Dickdarm-Schema.svg/200px-Dickdarm-Schema.svg.png xref: MA:0001541 xref: MAT:0000311 xref: MIAA:0000311 xref: ncithesaurus:Ascending_Colon xref: OpenCyc:Mx4rv3H0FZwpEbGdrcN5Y29ycA xref: SCTID:362162009 xref: UMLS:C0227375 is_a: UBERON:0000168 {source="FMA"} ! segment of colon relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001157 name: transverse colon namespace: uberon def: "The transverse colon the longest and most movable part of the colon, passes with a downward convexity from the right hypochondrium region across the abdomen, opposite the confines of the epigastric and umbilical zones, into the left hypochondrium region, where it curves sharply on itself beneath the lower end of the spleen, forming the splenic or left colic flexure. The right colic flexure is adjacent to the liver. In its course, it describes an arch, the concavity of which is directed backward and a little upward; toward its splenic end there is often an abrupt U-shaped curve which may descend lower than the main curve. It is almost completely invested by peritoneum, and is connected to the inferior border of the pancreas by a large and wide duplicature of that membrane, the transverse mesocolon. It is in relation, by its upper surface, with the liver and gall-bladder, the greater curvature of the stomach, and the lower end of the spleen; by its under surface, with the small intestine; by its anterior surface, with the anterior layers of the greater omentum and the abdominal parietes; its posterior surface is in relation from right to left with the descending portion of the duodenum, the head of the pancreas, and some of the convolutions of the jejunum and ileum. [WP,unvetted]." [Wikipedia:Transverse_colon] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "colon transversum" RELATED LATIN [Wikipedia:Transverse_colon] xref: BTO:0000272 xref: EFO:0000844 xref: FMA:14546 xref: galen:TransverseColon xref: http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/3b/Dickdarm-Schema.svg/200px-Dickdarm-Schema.svg.png xref: MA:0001543 xref: MAT:0000312 xref: MIAA:0000312 xref: ncithesaurus:Transverse_Colon xref: OpenCyc:Mx4rvg7qyJwpEbGdrcN5Y29ycA xref: SCTID:362163004 xref: UMLS:C0227386 is_a: UBERON:0000168 {source="FMA"} ! segment of colon relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001158 name: descending colon namespace: uberon def: "The descending colon of humans passes downward through the left hypochondrium and lumbar regions, along the lateral border of the left kidney. At the lower end of the kidney it turns medialward toward the lateral border of the psoas muscle, and then descends, in the angle between psoas and quadratus lumborum, to the crest of the ilium, where it ends in the sigmoid colon. The peritoneum covers its anterior surface and sides, and therefore the descending colon is described as retroperitoneal. (The transverse colon and sigmoid colon, which are immediately proximal and distal, are intraperitoneal). Its posterior surface is connected by areolar tissue with the lower and lateral part of the left kidney, the aponeurotic origin of the transversus abdominis, and the quadratus lumborum. It is smaller in caliber and more deeply placed than the ascending colon. It has a mesentery in 33% of people, and is therefore more frequently covered with peritoneum on its posterior surface than the ascending colon (which has a mesentery in 25% of people). However, it is less likely to undergo volvulus than the ascending colon. In front of it are some coils of small intestine. [WP,unvetted]." [Wikipedia:Descending_colon] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "colon descendens" RELATED LATIN [Wikipedia:Descending_colon] xref: BTO:0000641 xref: EFO:0000845 xref: FMA:14547 xref: galen:DescendingColon xref: http://upload.wikimedia.org/wikipedia/commons/c/ca/Gray1223.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/ca/Gray1223.png/200px-Gray1223.png xref: MA:0001542 xref: MAT:0000313 xref: MIAA:0000313 xref: ncithesaurus:Descending_Colon xref: OpenCyc:Mx4rwHsNhpwpEbGdrcN5Y29ycA xref: SCTID:362165006 xref: UMLS:C0227389 is_a: UBERON:0000168 {source="FMA"} ! segment of colon relationship: develops_from UBERON:0001046 {source="Wikipedia"} ! hindgut property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001159 name: sigmoid colon namespace: uberon def: "the part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity." [Wikipedia:Sigmoid_colon] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "colon sigmoideum" RELATED LATIN [Wikipedia:Sigmoid_colon] synonym: "pelvic colon" RELATED [] synonym: "sigmoid colon" RELATED [] synonym: "sigmoid flexure" RELATED [] xref: BTO:0000645 xref: EFO:0000846 xref: FMA:14548 xref: galen:SigmoidColon xref: http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/3b/Dickdarm-Schema.svg/200px-Dickdarm-Schema.svg.png xref: MAT:0000314 xref: MESH:A03.492.411.495.356.668 xref: MIAA:0000314 xref: ncithesaurus:Sigmoid_Colon xref: ncithesaurus:Sigmoid_Flexure xref: OpenCyc:Mx4rwHX_-5wpEbGdrcN5Y29ycA xref: SCTID:362166007 xref: UMLS:C0227391 xref: UMLS:C0682612 is_a: UBERON:0000168 {source="FMA"} ! segment of colon relationship: develops_from UBERON:0001046 {source="Wikipedia"} ! hindgut property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001160 name: fundus of stomach namespace: uberon def: "The fundus is the portion of the stomach that lies above the cardiac notch, and contains the fundic glands[GO, Kardong]." [GO:0014825, ISBN10:0073040584, Wikipedia:Fundus_%28stomach%29] subset: uberon_slim synonym: "fundus gastricus" RELATED [BTO:0000502] synonym: "fundus gastricus (ventricularis)" EXACT [] synonym: "fundus gastricus ventricularis" RELATED [BTO:0000502] synonym: "fundus ventricularis" RELATED [BTO:0000502] synonym: "fundus ventriculi" RELATED [BTO:0000502] synonym: "gastric fundus" EXACT [] synonym: "stomach fundus" EXACT [] xref: BTO:0000502 xref: EFO:0002554 xref: EHDAA2:0001919 xref: EHDAA:4844 xref: FMA:14559 xref: GAID:320 xref: galen:GastricFundus xref: http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/31/Gray1046.svg/200px-Gray1046.svg.png xref: MA:0001612 xref: MESH:A03.492.766.419 xref: ncithesaurus:Fundus_of_the_Stomach xref: SCTID:362139007 xref: UMLS:C0017129 xref: VHOG:0000421 is_a: UBERON:0009870 ! zone of stomach property_value: external_definition "The greater curvature of the stomach. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000421", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000421", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001162 name: cardia of stomach namespace: uberon alt_id: UBERON:0004712 def: "The part of the stomach attached to the esophagus. The cardia begins immediately distal to the z-line of the gastroeosphageal junction, where the squamous epithelium of the esophagus gives way to the columnar epithelium of the gastrointestinal tract[WP]" [BTO:0000198, Wikipedia:Cardia] comment: Editor notes: We follow Kardong in defining stomach regions by glands. Boundary notes: There were previously conflicting statements in the academic anatomy community[10][11][12] over whether the cardia is part of the stomach, part of the esophagus or a distinct entity. Modern surgical and medical textbooks have agreed that "The gastric cardia is now clearly considered to be part of the stomach"[13][14]. Classical anatomy textbooks, and some other resources[15], describe the cardia as the first of 4 regions of the stomach. This makes sense histologically because the mucosa of the cardia is the same as that of the stomach[WP]. synonym: "antrum cardiacum" RELATED [Wikipedia:Cardia] synonym: "antrum cardiacum" RELATED LATIN [Wikipedia:Cardia] synonym: "cardiac antrum" RELATED [] synonym: "cardiac orifice" RELATED [Wikipedia:Cardia] synonym: "cardiac region" RELATED [Wikipedia:Cardia] synonym: "cardial orifice" RELATED [Wikipedia:Cardia] synonym: "cardial part of stomach" EXACT [] synonym: "gastric cardia" EXACT [] synonym: "pars cardiaca (gaster)" EXACT [] synonym: "pars cardiaca gastricae" EXACT LATIN [FMA:14561, FMA:TA] synonym: "stomach cardiac region" EXACT [MA:0001609] xref: BTO:0000198 xref: FMA:14561 xref: GAID:319 xref: http://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/33/Illu_stomach.jpg/200px-Illu_stomach.jpg xref: MA:0001609 xref: MESH:A03.492.766.163 xref: ncithesaurus:Cardia xref: SCTID:362138004 xref: UMLS:C0007144 is_a: UBERON:0009870 ! zone of stomach property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001166 name: pylorus namespace: uberon def: "The region of the stomach that connects to the duodenum. It is divided in two parts: the pyloric antrum, which connects to the body of the stomach. the pyloric canal, which connects to the duodenum. The pyloric sphincter, or valve, is a strong ring of smooth muscle at the end of the pyloric canal and lets food pass from the stomach to the duodenum. It receives sympathetic innervation from celiac ganglion. [WP,unvetted]." [Wikipedia:Pylorus] comment: Editor notes: We follow Kardong in defining stomach regions by glands subset: uberon_slim synonym: "pars pylorica" EXACT LATIN [] synonym: "pars pylorica gastricae" EXACT LATIN [FMA:14581, FMA:TA] synonym: "pyloric part of stomach" EXACT [] synonym: "pyloric region" EXACT [] synonym: "stomach pyloric region" EXACT [EHDAA2:0001580] synonym: "valvula pylori" RELATED LATIN [Wikipedia:Pylorus] xref: BTO:0001146 xref: EHDAA2:0001580 xref: EHDAA:4860 xref: EMAPA:17631 xref: EMAPA:18915 xref: FMA:14581 xref: GAID:333 xref: galen:Pylorus xref: http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/31/Gray1046.svg/200px-Gray1046.svg.png xref: MA:0002560 xref: MESH:A03.492.766.799 xref: ncithesaurus:Pylorus xref: SCTID:362143006 xref: UMLS:C0034196 xref: VHOG:0000420 is_a: UBERON:0009870 ! zone of stomach property_value: external_definition "The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000420", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: has_relational_adjective "pyloric" xsd:string property_value: homology_notes "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000420", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001167 name: wall of stomach namespace: uberon def: "An anatomical wall that is part of a stomach [Obol]." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "anatomical wall of stomach" EXACT [OBOL:automatic] synonym: "anatomical wall of ventriculus" EXACT [OBOL:automatic] synonym: "gastric wall" EXACT [] synonym: "stomach anatomical wall" EXACT [OBOL:automatic] synonym: "stomach wall" EXACT [] synonym: "ventriculus anatomical wall" EXACT [OBOL:automatic] synonym: "ventriculus wall" EXACT [OBOL:automatic] synonym: "wall of ventriculus" EXACT [OBOL:automatic] xref: FMA:14582 xref: galen:WallOfStomach xref: MA:0002692 xref: SCTID:279995000 is_a: UBERON:0000060 ! anatomical wall is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0000945 ! stomach property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001168 name: wall of small intestine namespace: uberon def: "An anatomical wall that is part of a small intestine [Obol]." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "anatomical wall of small bowel" EXACT [OBOL:automatic] synonym: "anatomical wall of small intestine" EXACT [OBOL:automatic] synonym: "small bowel anatomical wall" EXACT [OBOL:automatic] synonym: "small bowel wall" EXACT [OBOL:automatic] synonym: "small intestinal wall" EXACT [] synonym: "small intestine anatomical wall" EXACT [OBOL:automatic] synonym: "small intestine wall" EXACT [] synonym: "wall of small bowel" EXACT [OBOL:automatic] xref: FMA:14615 xref: MA:0002696 xref: ncithesaurus:Small_Intestinal_Wall_Tissue xref: UMLS:C1519375 is_a: UBERON:0001262 ! wall of intestine relationship: part_of UBERON:0002108 ! small intestine property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001169 name: wall of large intestine namespace: uberon def: "An anatomical wall that is part of a large intestine [Obol]." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "anatomical wall of large intestine" EXACT [OBOL:automatic] synonym: "large intestinal wall" EXACT [] synonym: "large intestine anatomical wall" EXACT [OBOL:automatic] synonym: "large intestine wall" EXACT [] xref: FMA:14619 xref: MA:0002695 is_a: UBERON:0001262 ! wall of intestine relationship: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0001262 ! wall of intestine property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001173 name: biliary tree namespace: uberon def: "Hollow tree organ, the organ parts of which consists of the bile ducts[FMA]." [FMA:14665, Wikipedia:Biliary_tract] subset: organ_slim subset: uberon_slim synonym: "biliary tract" EXACT [] xref: AAO:0011020 xref: FMA:14665 xref: GAID:279 xref: MA:0001273 xref: MESH:A03.159 xref: ncithesaurus:Biliary_Tract xref: SCTID:181267003 xref: UMLS:C0005423 xref: XAO:0000455 is_a: UBERON:0000062 ! organ is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0004912 ! biliary bud relationship: part_of UBERON:0002294 ! biliary system property_value: external_definition "Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011020", ontology="AAO", source="UBERON:0001173"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001178 name: visceral peritoneum namespace: uberon def: "The peritoneum that covers the external surfaces of most abdominal organs." [Wikipedia:Visceral_peritoneum, ZFIN:curator] comment: This class was created automatically from a combination of ontologies subset: uberon_slim subset: vertebrate_core xref: FMA:14703 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/5f/Gray1040.png/200px-Gray1040.png xref: SCTID:362702003 xref: TAO:0005132 xref: VHOG:0001528 xref: ZFA:0005132 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0002358 ! peritoneum property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001179 name: peritoneal cavity namespace: uberon def: "Cavity of serous sac surrounded by the peritoneum.[FMA]" [FMA:FMA, Wikipedia:Peritoneal_cavity] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "cavitas peritonealis" RELATED [BTO:0001782] synonym: "cavitas peritonealis; saccus serosus peritonei" RELATED LATIN [Wikipedia:Peritoneal_cavity] xref: BTO:0001782 xref: EHDAA2:0001446 xref: EMAPA:18452 xref: EMAPA:18454 xref: EMAPA:18461 xref: FMA:14704 xref: GAID:24 xref: MA:0000054 xref: MESH:A01.047.025.600.678 xref: ncithesaurus:Peritoneal_Cavity xref: SCTID:181616008 xref: UMLS:C1704247 xref: VHOG:0000852 is_a: UBERON:0002323 ! coelemic cavity lumen relationship: develops_from UBERON:0003887 {source="Wikipedia"} ! intraembryonic coelom relationship: part_of UBERON:0005906 ! serous sac property_value: external_definition "The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000852", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/peritoneal+cavity"} property_value: homology_notes "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000852", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001199 name: mucosa of stomach namespace: uberon def: "The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general epithelial lining of the stomach. [WP,unvetted]." [Wikipedia:Gastric_mucosa] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "gastric mucosa" EXACT [] synonym: "gastric mucous membrane" EXACT [] synonym: "Magenschleimhaut" RELATED [BTO:0001308] synonym: "mucosa of organ of stomach" EXACT [OBOL:automatic] synonym: "mucosa of organ of ventriculus" EXACT [OBOL:automatic] synonym: "mucosa of ventriculus" EXACT [OBOL:automatic] synonym: "mucous membrane of stomach" EXACT [] synonym: "mucous membrane of ventriculus" EXACT [OBOL:automatic] synonym: "organ mucosa of stomach" EXACT [OBOL:automatic] synonym: "organ mucosa of ventriculus" EXACT [OBOL:automatic] synonym: "stomach mucosa" EXACT [] synonym: "stomach mucosa of organ" EXACT [OBOL:automatic] synonym: "stomach mucous membrane" EXACT [OBOL:automatic] synonym: "stomach organ mucosa" EXACT [OBOL:automatic] synonym: "tunica mucosa (gaster)" EXACT [] synonym: "tunica mucosa gastricae" EXACT LATIN [FMA:14907, FMA:TA] synonym: "tunica mucosa gastris" RELATED [BTO:0001308] synonym: "tunica mucosa gastris" RELATED LATIN [Wikipedia:Gastric_mucosa] synonym: "ventriculus mucosa" EXACT [OBOL:automatic] synonym: "ventriculus mucosa of organ" EXACT [OBOL:automatic] synonym: "ventriculus mucous membrane" EXACT [OBOL:automatic] synonym: "ventriculus organ mucosa" EXACT [OBOL:automatic] xref: BTO:0001308 xref: FMA:14907 xref: GAID:321 xref: galen:GastricMucosa xref: http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_stomach2.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Illu_stomach2.jpg/200px-Illu_stomach2.jpg xref: MA:0002683 xref: MESH:A03.492.766.440 xref: ncithesaurus:Gastric_Mucosa xref: OpenCyc:Mx8NhB4rvcD6KJwpEbGdrcN5Y29ycB4rvmKNOpwpEbGdrcN5Y29ycB4rvVj5FpwpEbGdrcN5Y29ycB4rvVjlqpwpEbGdrcN5Y29ycA xref: SCTID:362131005 xref: UMLS:C0017136 is_a: UBERON:0004786 ! gastrointestinal system mucosa is_a: UBERON:0009034 ! stomach region relationship: part_of UBERON:0000945 ! stomach relationship: part_of UBERON:0001167 ! wall of stomach property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001204 name: mucosa of small intestine namespace: uberon def: "A mucosa that is part of a small intestine [Obol]." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "mucosa of organ of small bowel" EXACT [OBOL:automatic] synonym: "mucosa of organ of small intestine" EXACT [OBOL:automatic] synonym: "mucosa of small bowel" EXACT [OBOL:automatic] synonym: "mucous membrane of small bowel" EXACT [OBOL:automatic] synonym: "mucous membrane of small intestine" EXACT [] synonym: "organ mucosa of small bowel" EXACT [OBOL:automatic] synonym: "organ mucosa of small intestine" EXACT [OBOL:automatic] synonym: "small bowel mucosa" EXACT [OBOL:automatic] synonym: "small bowel mucosa of organ" EXACT [OBOL:automatic] synonym: "small bowel mucous membrane" EXACT [OBOL:automatic] synonym: "small bowel organ mucosa" EXACT [OBOL:automatic] synonym: "small intestinal mucosa" EXACT [] synonym: "small intestine mucosa" EXACT [] synonym: "small intestine mucosa of organ" EXACT [OBOL:automatic] synonym: "small intestine mucous membrane" EXACT [] synonym: "small intestine organ mucosa" EXACT [OBOL:automatic] synonym: "tunica mucosa (intestinum tenue)" EXACT [] synonym: "tunica mucosa intestini tenuis" EXACT LATIN [FMA:14933, FMA:TA] xref: BTO:0001259 xref: FMA:14933 xref: MA:0002686 xref: ncithesaurus:Small_Intestinal_Mucosa xref: SCTID:362144000 xref: UMLS:C0227261 is_a: UBERON:0001242 ! intestinal mucosa relationship: part_of UBERON:0001168 ! wall of small intestine relationship: part_of UBERON:0001242 ! intestinal mucosa relationship: part_of UBERON:0002108 ! small intestine property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001205 name: submucosa of small intestine namespace: uberon def: "submucosal tissue in the small intestines." [Wikipedia:Small_intestinal_submucosa] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "small bowel submucosa" EXACT [OBOL:automatic] synonym: "small intestinal submucosa" EXACT [] synonym: "small intestine submucosa" EXACT [] synonym: "submucosa of small bowel" EXACT [OBOL:automatic] synonym: "tela submucosa (intestinum tenue)" EXACT [] synonym: "tela submucosa intestini tenuis" EXACT LATIN [BTO:0002112] xref: BTO:0002112 xref: FMA:14934 xref: MA:0001562 xref: ncithesaurus:Small_Intestinal_Submucosa xref: SCTID:691000 xref: UMLS:C0227268 is_a: UBERON:0009566 ! intestinal submucosa relationship: part_of UBERON:0001168 ! wall of small intestine relationship: part_of UBERON:0002108 ! small intestine property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001207 name: mucosa of large intestine namespace: uberon def: "A mucosa that is part of a large intestine [Obol]." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "large intestinal mucosa" EXACT [] synonym: "large intestine mucosa" EXACT [] synonym: "large intestine mucosa of organ" EXACT [OBOL:automatic] synonym: "large intestine mucous membrane" EXACT [OBOL:automatic] synonym: "large intestine organ mucosa" EXACT [OBOL:automatic] synonym: "mucosa of organ of large intestine" EXACT [OBOL:automatic] synonym: "mucous membrane of large intestine" EXACT [] synonym: "organ mucosa of large intestine" EXACT [OBOL:automatic] synonym: "tunica mucosa intestini crassi" EXACT LATIN [FMA:14969, FMA:TA] xref: FMA:14969 xref: MA:0002688 xref: ncithesaurus:Large_Intestinal_Mucosa xref: UMLS:C0734203 is_a: UBERON:0001242 ! intestinal mucosa relationship: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0001169 ! wall of large intestine relationship: part_of UBERON:0001242 ! intestinal mucosa property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001211 name: Peyer's patch namespace: uberon def: "aggregations of lymphoid tissue that are usually found in the lowest portion of the small intestine ileum in humans; as such, they differentiate the ileum from the duodenum and jejunum // nodular lymphoid structures on the serosal surface of the small intestine." [Wikipedia:Peyer's_patch] comment: AO notes: FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc] - Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part. WP says duodenum and jejunum lack PPs. Taxon notes: Reptiles have accumulations of lymphocytes in their guts that may be primitive Peyer's patches (Zapata and Solas). subset: uberon_slim synonym: "aggregated lymphoid follicle of intestine" RELATED [] synonym: "aggregated lymphoid nodule" RELATED [] synonym: "noduli lymphoidei aggregati intestini tenuis" EXACT LATIN [FMA:76466, FMA:TA] xref: BTO:0001784 xref: EFO:0001381 xref: EMAPA:19028 xref: GAID:950 xref: MA:0000137 xref: MESH:A10.549.598 xref: ncithesaurus:Mouse_Peyer_s_Patches xref: ncithesaurus:Peyer_s_Patch xref: UMLS:C0031272 is_a: UBERON:0001962 ! gut-associated lymphoid tissue relationship: part_of UBERON:0000030 ! lamina propria relationship: part_of UBERON:0001242 ! intestinal mucosa property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001212 name: duodenal gland namespace: uberon def: "compound tubular submucosal glands found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP]." [Wikipedia:Brunner's_glands] comment: This class was created automatically from a combination of ontologies subset: organ_slim subset: uberon_slim synonym: "Brunner's gland" EXACT [FMA:15060] synonym: "gland of Brunner" EXACT [FMA:15060] synonym: "glandula duodenales" RELATED [BTO:0002376] synonym: "glandula duodenales Brunneri" RELATED [BTO:0002376] xref: BTO:0002376 xref: FMA:15060 xref: GAID:314 xref: MA:0001551 xref: MESH:A03.492.411.620.270.322 xref: ncithesaurus:Brunner_s_Gland xref: SCTID:41298001 xref: UMLS:C0006323 is_a: UBERON:0003408 ! gland of gut is_a: UBERON:0011148 {notes="compound tubular"} ! submucosal gland relationship: part_of UBERON:0002330 {source="MA-inferred"} ! exocrine system relationship: part_of UBERON:0003332 {source="FMA"} ! submucosa of duodenum property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001213 name: intestinal villus namespace: uberon alt_id: UBERON:0007607 def: "Tiny, finger-like projections that protrude from the epithelial lining of the intestinal wall[WP]" [Wikipedia:Intestinal_villus] comment: Editor notes: in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all speciesi for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine. AO Notes: the BTO class refers to a generic villous subset: uberon_slim subset: vertebrate_core synonym: "enteric villi" EXACT PLURAL [HP:0011473] synonym: "enteric villous" EXACT [HP:0011473] synonym: "enteric villus" EXACT [HP:0011473] synonym: "intestinal villi" EXACT PLURAL [ZFA:0005125] synonym: "intestinal villus layer" RELATED [] synonym: "small intestine villus" RELATED [MA:0001563] synonym: "villi intestinales" EXACT PLURAL [] synonym: "villi intestinales" RELATED LATIN [Wikipedia:Intestinal_villus] synonym: "villus" EXACT [BTO:0003121] synonym: "villus intestinalis (intestinum tenue)" EXACT [FMA:15072] xref: BTO:0003121 xref: FMA:15072 xref: http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/38/Small_intestine_low_mag.jpg/200px-Small_intestine_low_mag.jpg xref: MA:0001563 xref: ncithesaurus:Villus xref: SCTID:23230007 xref: TAO:0005125 xref: UMLS:C1519988 xref: ZFA:0005125 is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer relationship: part_of UBERON:0001277 {source="ZFA"} ! intestinal epithelium property_value: external_definition "The entire digestive tract is lined by well developed villi, which are longest in the intestinal bulb and decrease progressively in size towards the caudal end of the intestine. No crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips. Crosnier et al. 2005[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005125", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001224 name: renal pelvis namespace: uberon def: "funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]." [MP:0004194, Wikipedia:Renal_pelvis] comment: In this ontology, the renal pelvis is represented as the area of part-overlap between the kidney and the ureter subset: uberon_slim synonym: "kidney pelvis" EXACT [] synonym: "p. renallis" RELATED LATIN [Wikipedia:Renal_pelvis] synonym: "pelvis of ureter" EXACT [] synonym: "pyelum" RELATED [MP:0004194] xref: EMAPA:17948 xref: FMA:15575 xref: GAID:426 xref: galen:RenalPelvis xref: http://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/c0/Illu_kidney2.jpg/200px-Illu_kidney2.jpg xref: MA:0000374 xref: MESH:A05.810.453.537 xref: ncithesaurus:Renal_Pelvis xref: SCTID:362221007 xref: UMLS:C0227666 is_a: UBERON:0000063 ! organ segment is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0004111 ! anatomical conduit is_a: UBERON:0006554 ! urinary system structure disjoint_from: UBERON:0002355 ! pelvis relationship: part_of UBERON:0000056 {source="FMA"} ! ureter relationship: part_of UBERON:0002113 {source="MA"} ! kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001225 name: cortex of kidney namespace: uberon def: "Region of parenchyma of kidney representing the outer portion.[FMA]" [FMA:FMA, Wikipedia:Renal_cortex] subset: uberon_slim synonym: "cortex renalis" EXACT LATIN [FMA:15581, FMA:TA] synonym: "kidney cortex" EXACT [] synonym: "renal cortex" EXACT [] xref: BTO:0001166 xref: EMAPA:17952 xref: FMA:15581 xref: GAID:424 xref: galen:CortexOfKidney xref: http://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/69/Illu_kidney.jpg/200px-Illu_kidney.jpg xref: MA:0000372 xref: MESH:A05.810.453.324 xref: ncithesaurus:Renal_Cortex xref: SCTID:362211004 xref: UMLS:C0022655 is_a: UBERON:0001851 ! cortex is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0008987 {source="FMA"} ! renal parenchyma property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001228 name: renal papilla namespace: uberon def: "In the kidney, the renal papilla is the location where the Medullary pyramids empty urine into the renal pelvis. Histologically it is marked by medullary collecting ducts converging to channel the fluid. Transitional epithelium begins to be seen. [WP,unvetted]." [Wikipedia:Renal_papilla] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "kidney papilla" EXACT [MP:0011303] xref: BTO:0003925 xref: FMA:15622 xref: galen:RenalPapilla xref: http://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/7/7e/Kidney_PioM.png/200px-Kidney_PioM.png xref: MA:0002730 xref: MESH:A05.810.453.466 xref: ncithesaurus:Renal_Papilla xref: SCTID:362214007 xref: UMLS:C0022666 is_a: UBERON:0000064 ! organ part is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0001224 ! renal pelvis relationship: part_of UBERON:0001294 ! inner medulla of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001229 name: renal corpuscle namespace: uberon def: "In the kidney, a renal corpuscle is the initial blood-filtering component of a nephron. It consists of two structures: a glomerulus and a Bowman's capsule[WP,unvetted]." [Wikipedia:Renal_corpuscle] comment: Together, the Bowmans capsule and the glomerulus comprise the definitive renal corpuscle. http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron subset: uberon_slim subset: vertebrate_core synonym: "corpusculum renale" EXACT LATIN [] synonym: "corpusculum renis" RELATED LATIN [Wikipedia:Renal_corpuscle] synonym: "cortical renal corpuscle" RELATED [MA:0000376] synonym: "kidney corpuscle" RELATED [Wikipedia:Renal_corpuscle] synonym: "malphighian corpuscle" RELATED [MA:0000376] synonym: "malphigian corpuscle" EXACT [] synonym: "Malpighian corpuscle" EXACT [ZFA:0005281] xref: BTO:0000333 xref: EMAPA:28236 xref: EV:0100385 xref: FMA:15625 xref: http://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/22/Renal_corpuscle.svg/200px-Renal_corpuscle.svg.png xref: MA:0000376 xref: ncithesaurus:Renal_Corpuscle xref: SCTID:361329009 xref: TAO:0005281 xref: UMLS:C0227635 xref: VHOG:0001262 xref: ZFA:0005281 is_a: UBERON:0000481 {source="ZFA"} ! multi-tissue structure is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0001225 ! cortex of kidney relationship: part_of UBERON:0001285 ! nephron relationship: part_of UBERON:0007684 {source="FMA"} ! uriniferous tubule property_value: external_definition "A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO]" xsd:string {date_retrieved="2012-11-28", external_class="BTO:0000333", ontology="BTO", source="BTO:curator"} property_value: external_definition "A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO]" xsd:string {date_retrieved="2012-11-28", external_class="XAO:0000146", ontology="XAO", source="XAO:curator"} property_value: external_definition "The part of the nephron that filters blood.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005281", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001230 name: glomerular capsule namespace: uberon def: "The Bowman's capsule is a cup-like sac at the beginning of the tubular component of a nephron in the mammalian kidney. A glomerulus is enclosed in the sac. Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration. [WP,unvetted]." [Wikipedia:Bowman%27s_capsule] comment: One fold of the S-shaped body gives rise to Bowman’s capsule[GUDMAP] subset: uberon_slim subset: vertebrate_core synonym: "Bowman's capsule" EXACT [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] synonym: "bowman's capsule " RELATED [TAO:0005254] synonym: "Bowmans capsule" EXACT [KUPO:0001001] synonym: "capsula glomerularis" EXACT LATIN [] synonym: "capsula glomeruli" RELATED LATIN [] synonym: "pronephric glomerular capsule" RELATED [TAO:0005310] synonym: "renal glomerular capsule" EXACT [TAO:0005254] xref: AAO:0010526 xref: BTO:0002297 xref: EMAPA:27973 xref: EMAPA:28257 xref: FMA:15626 xref: http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/30/Gray1130.svg/200px-Gray1130.svg.png xref: KUPO:0001001 xref: MA:0001660 xref: ncithesaurus:Bowman_s_Capsule xref: SCTID:361331000 xref: TAO:0005254 xref: TAO:0005310 xref: UMLS:C0524448 xref: ZFA:0005254 xref: ZFA:0005310 is_a: UBERON:0000064 ! organ part is_a: UBERON:0006554 ! urinary system structure relationship: develops_from UBERON:0004199 ! S-shaped body relationship: part_of UBERON:0001229 ! renal corpuscle property_value: external_definition "Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010526", ontology="AAO", source="AAO:BJB"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001231 name: nephron tubule namespace: uberon alt_id: UBERON:0004210 def: "An epithelial tube that is part of the nephron, the functional part of the kidney." [GO:0072078, Wikipedia:Renal_tubule] comment: note that in ISBN10:0073040584 "Vertebrates, Kardong", the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA subset: uberon_slim subset: vertebrate_core synonym: "kidney tubule" EXACT [GAID:433] synonym: "renal tubule" BROAD [] synonym: "tubulus renalis" EXACT [] synonym: "uriniferous tubule" RELATED [MA:0000377] xref: BTO:0000343 xref: EFO:0003666 xref: EMAPA:27782 xref: EV:0100387 xref: FMA:15627 xref: GAID:433 xref: MA:0000377 xref: MESH:A05.810.453.736.560 xref: ncithesaurus:Renal_Tubule xref: SCTID:361332007 xref: TAO:0001287 xref: UMLS:C0022674 xref: ZFA:0001287 is_a: UBERON:0004211 ! nephron epithelium is_a: UBERON:0009773 {source="GO"} ! renal tubule relationship: develops_from UBERON:0003918 {notes="checkme"} ! kidney mesenchyme relationship: part_of UBERON:0001285 ! nephron property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001232 name: collecting duct of renal tubule namespace: uberon def: "The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient" [GO:0072044, Wikipedia:Collecting_tubule] comment: note that in ISBN10:0073040584 "Vertebrates, Kardong", the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron subset: uberon_slim subset: vertebrate_core synonym: "arcuate renal tubule" RELATED [Wikipedia:Connecting_tubule] synonym: "collecting duct" EXACT [GO:0072044] synonym: "collecting duct system" RELATED [BTO:0000761] synonym: "collecting tubule" RELATED [] synonym: "junctional tube" RELATED [Wikipedia:Connecting_tubule] synonym: "kidney collecting duct" EXACT [] synonym: "kidney collecting tubule" RELATED [] synonym: "renal collecting tubule" EXACT [FMA:15628] synonym: "tubulus renalis arcuatus" EXACT LATIN [Wikipedia:Connecting_tubule] synonym: "tubulus renalis colligens" EXACT [] xref: BTO:0000761 xref: EMAPA:28407 xref: EV:0100391 xref: FMA:15628 xref: GAID:434 xref: MA:0000371 xref: MESH:A05.810.453.736.560.510 xref: SCTID:28202009 xref: TAO:0005294 xref: ZFA:0005294 is_a: UBERON:0006553 ! renal duct relationship: part_of UBERON:0001285 {source="GO", notes="checkme"} ! nephron relationship: part_of UBERON:0007684 {source="FMA"} ! uriniferous tubule property_value: external_definition "Renal duct that collects the output from renal tubules.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005294", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001235 name: adrenal cortex namespace: uberon def: "Situated along the perimeter of the adrenal gland, the adrenal cortex mediates the stress response through the production of mineralocorticoids and glucocorticoids, including aldosterone and cortisol respectively. It is also a secondary site of androgen synthesis. [WP,unvetted]." [Wikipedia:Adrenal_cortex] comment: Taxon notes: Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO subset: uberon_slim synonym: "adrenal gland cortex" EXACT [] synonym: "cortex (glandula suprarenalis)" EXACT [] synonym: "cortex glandulae suprarenalis" RELATED [BTO:0000045] synonym: "cortex glandulae suprarenalis" RELATED LATIN [Wikipedia:Adrenal_cortex] synonym: "cortex of adrenal gland" EXACT [] synonym: "cortex of suprarenal gland" EXACT [] synonym: "suprarenal" RELATED [] synonym: "suprarenal cortex" EXACT [] xref: AAO:0011009 xref: BTO:0000045 xref: EFO:0000237 xref: EMAPA:18427 xref: EV:0100136 xref: FMA:15632 xref: GAID:447 xref: http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/5c/Gray1185.png/200px-Gray1185.png xref: MA:0000118 xref: MAT:0000494 xref: MESH:A06.407.071.140 xref: ncithesaurus:Adrenal_Cortex xref: SCTID:362584002 xref: UMLS:C0001613 xref: VHOG:0001481 xref: XAO:0000165 is_a: UBERON:0001851 ! cortex is_a: UBERON:0004120 ! mesoderm-derived structure relationship: develops_from UBERON:0000926 {source="Wikipedia"} ! mesoderm relationship: part_of UBERON:0002369 ! adrenal gland property_value: homology_notes "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001481", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001236 name: adrenal medulla namespace: uberon def: "The adrenal medulla is part of the adrenal gland. It is located at the center of the gland, being surrounded by the adrenal cortex. It is the innermost part of the adrenal gland, consisting of cells that secrete epinephrine, norepinephrine, and a small amount of dopamine in response to stimulation by sympathetic preganglionic neurons. Composed mainly of hormone-producing chromaffin cells, the adrenal medulla is the principal site of the conversion of the amino acid tyrosine into the catecholamines adrenaline (epinephrine), noradrenaline (norepinephrine), and dopamine[WP,unvetted]." [Wikipedia:Adrenal_medulla] subset: uberon_slim synonym: "adrenal gland medulla" EXACT [] synonym: "chromaffin cells" RELATED [] synonym: "medulla (glandula suprarenalis)" EXACT [] synonym: "medulla glandulae suprarenalis" EXACT LATIN [FMA:15633, FMA:TA] synonym: "medulla of adrenal gland" EXACT [OBOL:automatic] synonym: "medulla of glandula suprarenalis" RELATED [BTO:0000049] synonym: "medulla of suprarenal gland" EXACT [] synonym: "suprarenal medulla" EXACT [] xref: AAO:0011010 xref: BTO:0000049 xref: EFO:0000852 xref: EMAPA:18428 xref: EV:0100137 xref: FMA:15633 xref: GAID:451 xref: http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/5c/Gray1185.png/200px-Gray1185.png xref: MA:0000119 xref: MAT:0000495 xref: MESH:A06.224.161 xref: ncithesaurus:Adrenal_Medulla xref: SCTID:362585001 xref: UMLS:C0001629 xref: VHOG:0001378 xref: XAO:0000166 is_a: UBERON:0000958 ! medulla is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: develops_from UBERON:0002342 {source="Kardong", source="UBERONREF:0000002"} ! neural crest relationship: part_of UBERON:0002369 ! adrenal gland property_value: homology_notes "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001378", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001237 name: paraaortic body namespace: uberon def: "." [Wikipedia:Organ_of_Zuckerkandl] comment: This class was created automatically from a combination of ontologies subset: organ_slim subset: uberon_slim synonym: "organ of zuckerkandl" EXACT [] synonym: "para-aortic body" RELATED [] synonym: "paraganglia of zuckerkandl" RELATED [] synonym: "paraganglion of Zuckerkandl" EXACT [EMAPA:18223] xref: EMAPA:18223 xref: FMA:15647 xref: GAID:444 xref: http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/a/af/Gray531.png/200px-Gray531.png xref: MA:0001137 xref: MESH:A06.224.636 xref: ncithesaurus:Paraaortic xref: SCTID:276159005 xref: UMLS:C0442134 is_a: UBERON:0000062 {source="FMA"} ! organ relationship: part_of UBERON:0000949 ! endocrine system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001238 name: lamina propria of small intestine namespace: uberon def: "Lamina propria that is part_of the small intestine." [GOC:Obol] synonym: "lamina propria mucosa of small bowel" EXACT [OBOL:automatic] synonym: "lamina propria mucosa of small intestine" EXACT [OBOL:automatic] synonym: "lamina propria mucosae of small bowel" EXACT [OBOL:automatic] synonym: "lamina propria mucosae of small intestine" EXACT [] synonym: "lamina propria of mucosa of small intestine" EXACT [] synonym: "lamina propria of small bowel" EXACT [OBOL:automatic] synonym: "small bowel lamina propria" EXACT [OBOL:automatic] synonym: "small bowel lamina propria mucosa" EXACT [OBOL:automatic] synonym: "small bowel lamina propria mucosae" EXACT [OBOL:automatic] synonym: "small intestine lamina propria" EXACT [] synonym: "small intestine lamina propria mucosa" EXACT [OBOL:automatic] synonym: "small intestine lamina propria mucosae" EXACT [OBOL:automatic] xref: FMA:15651 xref: MA:0001554 xref: ncithesaurus:Small_Intestinal_Lamina_Propria xref: SCTID:63588008 xref: UMLS:C1711325 is_a: UBERON:0004780 ! gastrointestinal system lamina propria relationship: part_of UBERON:0001168 {source="reference_0000032"} ! wall of small intestine relationship: part_of UBERON:0001204 ! mucosa of small intestine relationship: part_of UBERON:0002108 ! small intestine property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001242 name: intestinal mucosa namespace: uberon def: "The innermost membrane of the four coats of the intestinal wall, the other three being the submucosa, muscular layers, and serosa. (Berk et al., Gastroenterology, 4th ed, v.3, p1479)" [MESH:A03.492.411.369] subset: uberon_slim synonym: "bowel mucosa" EXACT [OBOL:automatic] synonym: "bowel mucosa of organ" EXACT [OBOL:automatic] synonym: "bowel mucous membrane" EXACT [OBOL:automatic] synonym: "bowel organ mucosa" EXACT [OBOL:automatic] synonym: "intestine mucosa" EXACT [] synonym: "intestine mucosa of organ" EXACT [OBOL:automatic] synonym: "intestine mucous membrane" EXACT [OBOL:automatic] synonym: "intestine organ mucosa" EXACT [OBOL:automatic] synonym: "mucosa of bowel" EXACT [OBOL:automatic] synonym: "mucosa of intestine" EXACT [] synonym: "mucosa of organ of bowel" EXACT [OBOL:automatic] synonym: "mucosa of organ of intestine" EXACT [OBOL:automatic] synonym: "mucous membrane of bowel" EXACT [OBOL:automatic] synonym: "mucous membrane of intestine" EXACT [OBOL:automatic] synonym: "organ mucosa of bowel" EXACT [OBOL:automatic] synonym: "organ mucosa of intestine" EXACT [OBOL:automatic] synonym: "tunica mucosa intestini" EXACT [] xref: BTO:0000642 xref: FMA:15695 xref: GAID:296 xref: MA:0001537 xref: MESH:A03.492.411.369 xref: ncithesaurus:Intestinal_Mucosa xref: SCTID:362080002 xref: UMLS:C0021839 is_a: UBERON:0004786 ! gastrointestinal system mucosa relationship: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0001262 ! wall of intestine property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001249 name: spleen lymphoid follicle namespace: uberon alt_id: UBERON:0003969 def: "the area of the white pulp where the affinity maturation of B cells and the generation of memory B cells and plasma cells occur" [CL:tm, http://purl.obolibrary.org/obo/uberon/tracker/6, MP:0008470] synonym: "lymphatic follicle of spleen" EXACT [FMA:15843] synonym: "lymphoid follicle of spleen" EXACT [FMA:15843] synonym: "lymphoid nodule of spleen" EXACT [FMA:15843] synonym: "Malpighian body" EXACT [FMA:15843] synonym: "spleen B cell follicle" EXACT [CL:tm] synonym: "spleen lymphoid follicle" EXACT [MA:0002672] synonym: "spleen lymphoid nodule" RELATED [MA:0002672] synonym: "splenic B cell follicle" EXACT [CL:tm] synonym: "splenic lymphatic follicle" EXACT [FMA:15843] synonym: "splenic lymphoid follicle" EXACT [] xref: MA:0002672 xref: ncithesaurus:Splenic_Lymphoid_Follicle xref: SCTID:35845000 xref: UMLS:C1519475 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0000444 ! lymphoid follicle relationship: part_of UBERON:0001959 {source="CL:tm", source="MA"} ! white pulp of spleen relationship: part_of UBERON:0002106 ! spleen relationship: part_of UBERON:0006561 {source="FMA"} ! non-lymphatic part of lymphoid system relationship: part_of UBERON:1000024 {source="FMA"} ! parenchyma of spleen property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001250 name: red pulp of spleen namespace: uberon def: "Red pulp of the spleen is composed of connective tissue known as the cords of Billroth and many splenic sinuses that are engorged with blood, giving it a red color. Its primary function is to filter the blood of antigens, microorganisms, and defective or worn-out red blood cells. The spleen is made of red pulp and white pulp, separated by the marginal zone; 76-79% of a normal spleen is red pulp. Unlike white pulp, which mainly contains lymphocytes such as T cells, red pulp is made up of several different types of blood cells, including platelets, granulocytes, red blood cells, and plasma." [Wikipedia:Red_pulp] subset: uberon_slim synonym: "pulpa rubra" EXACT LATIN [FMA:15844, FMA:TA] synonym: "pulpa splenica" RELATED LATIN [Wikipedia:Red_pulp] synonym: "red pulp" EXACT [] synonym: "spleen red pulp" EXACT [] synonym: "splenic red pulp" EXACT [] xref: FMA:15844 xref: http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/1/15/Gray1191.png/200px-Gray1191.png xref: MA:0000756 xref: ncithesaurus:Splenic_Red_Pulp xref: SCTID:27579002 xref: UMLS:C0229687 is_a: UBERON:1000023 ! spleen pulp property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: present_in_taxon NCBITaxon:7955 {source="doi:10.1177/0192623311409597"} [Term] id: UBERON:0001251 name: marginal zone of spleen namespace: uberon def: "region at the interface between the non-lymphoid red pulp and the lymphoid white-pulp of the spleen." [Wikipedia:Marginal_zone] comment: WP says - (Some sources consider it to be the part of red pulp which borders on the white pulp, while other sources consider it to be neither red pulp nor white pulp.) - we use the adjacency relation here so it overlaps neither. FMA considers this an anatomical line. Not to be confused with: Marginal zone of spleen (e.g. AAO:0010448 marginal zone) synonym: "junctional zone of spleen" EXACT [] synonym: "marginal zone" BROAD [Wikipedia:Marginal_zone] synonym: "spleen marginal zone" EXACT [] xref: FMA:15852 xref: http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/1/15/Gray1191.png/200px-Gray1191.png xref: MA:0000755 xref: ncithesaurus:Marginal_Zone xref: UMLS:C1711368 is_a: UBERON:0000466 ! immaterial anatomical entity relationship: part_of UBERON:0002106 ! spleen property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001252 name: adventitia of ureter namespace: uberon def: "An adventitia that is part of a ureter." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "external adventitia of ureter" EXACT [] synonym: "ureter adventitia" EXACT [] synonym: "ureteral adventitia" EXACT [] xref: EMAPA:28114 xref: FMA:15892 xref: MA:0002652 xref: SCTID:392273001 xref: SCTID:47879001 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0005742 ! adventitia is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0000056 ! ureter relationship: part_of UBERON:0009916 {source="reference_0000032"} ! wall of ureter property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001254 name: urothelium of ureter namespace: uberon def: "the luminal epithelium of the tube that conducts the urine from the renal pelvis to the bladder[MP,unvetted]" [MP:0000535] comment: AO notes: MP treats ureter urothelium and ureter luminal urothelium as exact synonyms, yes MA treats these as distinct; see also: transitional epithelium vs urothelium synonym: "transitional epithelium of ureter" EXACT [] synonym: "ureter luminal urothelium" RELATED INCONSISTENT [MP:0000535] synonym: "ureter transitional epithelium" EXACT [] synonym: "ureter urothelium" EXACT [] xref: FMA:15897 xref: MA:0002655 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0000365 ! urothelium is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0000056 ! ureter property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001255 name: urinary bladder namespace: uberon def: "distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]." [MGI:anna, Wikipedia:Urinary_bladder] subset: major_organ subset: organ_slim subset: uberon_slim synonym: "bladder" EXACT [] synonym: "urocyst" RELATED [Wikipedia:Urinary_bladder] synonym: "vesica urinaria" RELATED LATIN [Wikipedia:Urinary_bladder] xref: AAO:0000623 xref: BTO:0001418 xref: EFO:0000290 xref: EHDAA2:0000174 xref: EHDAA:9328 xref: EMAPA:18321 xref: EV:0100098 xref: FMA:15900 xref: GAID:0000004 xref: galen:UrinaryBladder xref: http://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/30/Urinary_system.svg/200px-Urinary_system.svg.png xref: MA:0000380 xref: MAT:0000122 xref: MESH:A05.810.161 xref: MIAA:0000122 xref: ncithesaurus:Bladder xref: OpenCyc:Mx4rvVjMmZwpEbGdrcN5Y29ycA xref: SCTID:302512001 xref: UMLS:C0005682 xref: VHOG:0000740 xref: XAO:0000154 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0000489 ! cavitated compound organ is_a: UBERON:0002075 ! viscus is_a: UBERON:0006554 ! urinary system structure relationship: develops_from UBERON:0000164 {notes="upper part of UG sinus"} ! primitive urogenital sinus relationship: part_of UBERON:0001556 {source="FMA"} ! lower urinary tract property_value: external_definition "A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000740", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: external_definition "Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000623", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000740", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001256 name: wall of urinary bladder namespace: uberon def: "An anatomical wall that is part of a urinary bladder [Obol]." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "anatomical wall of bladder" EXACT [OBOL:automatic] synonym: "anatomical wall of urinary bladder" EXACT [OBOL:automatic] synonym: "bladder anatomical wall" EXACT [OBOL:automatic] synonym: "bladder wall" EXACT [OBOL:automatic] synonym: "urinary bladder anatomical wall" EXACT [OBOL:automatic] synonym: "urinary bladder wall" EXACT [] synonym: "wall of bladder" EXACT [OBOL:automatic] xref: BTO:0001462 xref: FMA:15902 xref: MA:0002493 xref: ncithesaurus:Bladder_Wall xref: SCTID:362225003 xref: UMLS:C0458421 is_a: UBERON:0000060 ! anatomical wall is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0001255 ! urinary bladder property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001257 name: trigone of urinary bladder namespace: uberon def: "The trigone is a smooth triangular region of the internal urinary bladder formed by the two ureteral orifices and the internal urethral orifice. The area is very sensitive to expansion and once stretched to a certain degree, the urinary bladder signals the brain of its need to empty. The signals become stronger as the bladder continues to fill. Embryologically, the trigone of the Bladder is derived from the caudal end of mesonephric ducts. In the Female the mesonephric ducts break down but, thus, the Trigone of the Bladder is less prominent but, still present. [WP,unvetted]." [Wikipedia:Trigone_of_urinary_bladder] comment: Development notes: Embryologically, the trigone of the bladder is derived from the caudal end of mesonephric ducts, which is of mesodermal origin (the rest of the bladder is endodermal). In the female the mesonephric ducts regresses, causing the trigone to be less prominent, but still present[WP] subset: uberon_slim synonym: "bladder trigone" EXACT [] synonym: "deep trigone" EXACT [] synonym: "Lieutaud's trigone" EXACT [] synonym: "musculus trigoni vesicae profundus" EXACT LATIN [FMA:15910, FMA:TA] synonym: "trigone of bladder" EXACT [] synonym: "trigonum vesicae" EXACT LATIN [FMA:15910, FMA:TA] synonym: "trigonum vesicae urinariae" RELATED LATIN [Wikipedia:Trigone_of_urinary_bladder] synonym: "urinary bladder trigone" EXACT [] synonym: "vesical trigone" EXACT [] xref: FMA:15910 xref: galen:TrigoneOfUrinaryBladder xref: http://upload.wikimedia.org/wikipedia/commons/5/57/Illu_bladder.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/57/Illu_bladder.jpg/200px-Illu_bladder.jpg xref: MA:0002492 xref: ncithesaurus:Bladder_Trigone xref: SCTID:272663002 xref: UMLS:C0447586 is_a: UBERON:0000064 ! organ part is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0006082 ! fundus of urinary bladder property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001259 name: mucosa of urinary bladder namespace: uberon def: "A mucosa that is part of a urinary bladder [Obol]." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "bladder mucosa" EXACT [] synonym: "bladder mucosa of organ" EXACT [OBOL:automatic] synonym: "bladder mucous membrane" EXACT [OBOL:automatic] synonym: "bladder organ mucosa" EXACT [OBOL:automatic] synonym: "mucosa of bladder" EXACT [OBOL:automatic] synonym: "mucosa of organ of bladder" EXACT [OBOL:automatic] synonym: "mucosa of organ of urinary bladder" EXACT [OBOL:automatic] synonym: "mucous membrane of bladder" EXACT [] synonym: "mucous membrane of urinary bladder" EXACT [] synonym: "organ mucosa of bladder" EXACT [OBOL:automatic] synonym: "organ mucosa of urinary bladder" EXACT [OBOL:automatic] synonym: "tunica mucosa (vesica urinaria)" EXACT LATIN [FMA:15928, FMA:TA] synonym: "tunica mucosa vesicae" EXACT LATIN [FMA:15928, FMA:TA] synonym: "tunica mucosa vesicae urinariae" EXACT [MP:MP] synonym: "urinary bladder mucosa" EXACT [] synonym: "urinary bladder mucosa of organ" EXACT [OBOL:automatic] synonym: "urinary bladder mucous membrane" EXACT [OBOL:automatic] synonym: "urinary bladder organ mucosa" EXACT [OBOL:automatic] xref: EFO:0000293 xref: FMA:15928 xref: galen:MucousMembraneOfUrinaryBladder xref: MA:0001692 xref: ncithesaurus:Bladder_Mucosa xref: SCTID:362224004 xref: UMLS:C0227691 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0000344 ! mucosa is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001256 ! wall of urinary bladder property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001262 name: wall of intestine namespace: uberon def: "An anatomical wall that is part of a intestine [Obol]." [OBOL:automatic] comment: Editors note: we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different synonym: "anatomical wall of bowel" EXACT [OBOL:automatic] synonym: "anatomical wall of intestine" EXACT [OBOL:automatic] synonym: "bowel anatomical wall" EXACT [OBOL:automatic] synonym: "bowel wall" EXACT [OBOL:automatic] synonym: "bowel wall" RELATED [MA:0001525] synonym: "intestinal wall" EXACT [] synonym: "intestine anatomical wall" EXACT [OBOL:automatic] synonym: "intestine wall" EXACT [] synonym: "wall of bowel" EXACT [OBOL:automatic] xref: BTO:0000647 xref: FMA:15949 xref: MA:0001525 xref: MA:0002693 xref: ncithesaurus:Intestinal_Wall_Tissue xref: UMLS:C1708548 is_a: UBERON:0000060 ! anatomical wall is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0000160 ! intestine property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001263 name: pancreatic acinus namespace: uberon def: "the secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct." [MP:0009145] comment: This class was created automatically from a combination of ontologies synonym: "acinus pancreaticus" EXACT LATIN [FMA:16011] synonym: "pancreas acinus" EXACT [] synonym: "pancreatic acinar" RELATED [TEMP:MP] synonym: "pancreatic acini" RELATED PLURAL [] xref: FMA:16011 xref: MA:0002417 xref: ncithesaurus:Pancreatic_Acinus xref: SCTID:247604006 xref: UMLS:C0227578 is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0009842 ! acinus relationship: part_of UBERON:0000017 ! exocrine pancreas relationship: part_of UBERON:0007324 {source="FMA"} ! pancreatic lobe property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001264 name: pancreas namespace: uberon def: "An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1–2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans[PMID]." [GO:0031016, PMID:16417468, Wikipedia:Pancreas] comment: taxon notes: As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52) [PMID:20959416]. The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract (Figures 16 and 17 ). The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm subset: major_organ subset: organ_slim subset: uberon_slim subset: vertebrate_core xref: AAO:0010112 xref: BTO:0000988 xref: EFO:0000855 xref: EHDAA2:0001367 xref: EHDAA:6893 xref: EMAPA:17503 xref: EMAPA:18816 xref: EV:0100092 xref: FMA:7198 xref: GAID:334 xref: galen:Pancreas xref: http://upload.wikimedia.org/wikipedia/commons/3/3f/Illu_pancrease.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/3f/Illu_pancrease.svg/200px-Illu_pancrease.svg.png xref: MA:0000120 xref: MAT:0000075 xref: MESH:A03.734 xref: MIAA:0000075 xref: ncithesaurus:Pancreas xref: OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA xref: SCTID:181277001 xref: TAO:0000140 xref: UMLS:C0030274 xref: VHOG:0000050 xref: XAO:0000136 xref: ZFA:0000140 is_a: UBERON:0002075 ! viscus relationship: part_of UBERON:0000949 ! endocrine system property_value: external_definition "Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010112", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "pancreatic" xsd:string property_value: homology_notes "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000050", ontology="VHOG", source="DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001266 name: splenic cord namespace: uberon def: "A structure found in the red pulp of the spleen between the sinusoids, consisting of fibrils and connective tissue cells with a large population of monocytes and macrophages. These cords contain half of the human body's monocytes as a reserve so that after tissue injury these monocytes can move in and aid locally sourced monocytes in wound healing. Erythrocytes pass through the cords of Billroth before entering the sinusoids. The passage into the sinusoids may be seen as a bottleneck, where erythrocytes need to be flexible in order to pass through. In disorders of erythrocyte shape and/or flexibility, such as hereditary spherocytosis, erythrocytes fail to pass through and get phagocytosed, causing extravascular hemolysis." [Wikipedia:Cords_of_Billroth] synonym: "cord of Billroth" EXACT [Wikipedia:Cords_of_Billroth] synonym: "cord of Bilroth" EXACT [FMA:16031] xref: FMA:16031 xref: MA:0002671 xref: ncithesaurus:Splenic_Cord xref: UMLS:C0735011 is_a: UBERON:0000064 ! organ part is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure relationship: part_of UBERON:0001250 {source="MA"} ! red pulp of spleen property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001276 name: epithelium of stomach namespace: uberon def: "the epithelial layer of the stomach ." [MP:0000471] comment: in FMA this is classified as simple columnar, MA divides this into squamous and glandular synonym: "epithelial tissue of stomach" EXACT [OBOL:automatic] synonym: "epithelial tissue of ventriculus" EXACT [OBOL:automatic] synonym: "epithelium of ventriculus" EXACT [OBOL:automatic] synonym: "gastric epithelium" RELATED [BTO:0000500] synonym: "stomach epithelial tissue" EXACT [OBOL:automatic] synonym: "stomach epithelium" EXACT [OBOL:automatic] synonym: "ventriculus epithelial tissue" EXACT [OBOL:automatic] synonym: "ventriculus epithelium" EXACT [OBOL:automatic] xref: BTO:0000500 xref: EHDAA2:0001918 xref: FMA:17091 xref: MA:0001610 xref: SCTID:64977002 xref: VHOG:0001433 is_a: UBERON:0000485 ! simple columnar epithelium is_a: UBERON:0003350 ! epithelium of mucosa is_a: UBERON:0003929 ! gut epithelium is_a: UBERON:0004808 ! gastrointestinal system epithelium relationship: part_of UBERON:0000945 ! stomach relationship: part_of UBERON:0001199 ! mucosa of stomach property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001277 name: intestinal epithelium namespace: uberon def: "Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005" [Wikipedia:Intestinal_epithelium, ZFIN:curator] comment: This class was created automatically from a combination of ontologies subset: uberon_slim subset: vertebrate_core synonym: "bowel epithelial tissue" EXACT [OBOL:automatic] synonym: "bowel epithelium" EXACT [OBOL:automatic] synonym: "epithelial tissue of bowel" EXACT [OBOL:automatic] synonym: "epithelial tissue of intestine" EXACT [OBOL:automatic] synonym: "epithelium of bowel" EXACT [OBOL:automatic] synonym: "epithelium of intestine" EXACT [OBOL:automatic] synonym: "intestine epithelial tissue" EXACT [OBOL:automatic] synonym: "intestine epithelium" RELATED [] synonym: "villous epithelium" EXACT [ZFA:0005124] xref: BTO:0000781 xref: FMA:17229 xref: MA:0001536 xref: ncithesaurus:Intestinal_Epithelium xref: SCTID:266135004 xref: TAO:0005124 xref: UMLS:C0226890 xref: ZFA:0005124 is_a: UBERON:0000485 ! simple columnar epithelium is_a: UBERON:0003350 ! epithelium of mucosa is_a: UBERON:0003929 ! gut epithelium is_a: UBERON:0004808 ! gastrointestinal system epithelium relationship: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0001242 ! intestinal mucosa property_value: external_definition "Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005124", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001278 name: epithelium of large intestine namespace: uberon def: "An epithelium that is part of a large intestine [Obol]." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "epithelial tissue of large intestine" EXACT [OBOL:automatic] synonym: "large intestinal epithelium" EXACT [] synonym: "large intestine epithelial tissue" EXACT [OBOL:automatic] synonym: "large intestine epithelium" EXACT [] xref: EMAPA:19257 xref: EMAPA:19262 xref: FMA:17301 xref: MA:0001545 is_a: UBERON:0001277 ! intestinal epithelium relationship: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0001207 ! mucosa of large intestine property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001280 name: liver parenchyma namespace: uberon alt_id: UBERON:0003223 def: "the functional units of the liver including the lobules." [MP:0008986] comment: This class was created automatically from a combination of ontologies synonym: "hepatic parenchyma" EXACT [FMA:17540] synonym: "hepatic parenchyme" RELATED [VHOG:0000539] synonym: "liver parenchyme" EXACT [XAO:0000454] synonym: "parenchyma of liver" EXACT [FMA:17540] xref: AAO:0010405 xref: EHDAA2:0001004 xref: EHDAA:2201 xref: EMAPA:17203 xref: FMA:17540 xref: MA:0000366 xref: SCTID:363535004 xref: VHOG:0000539 xref: XAO:0000454 is_a: UBERON:0000353 ! parenchyma is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0005171 {source="EHDAA2"} ! hepatic duct relationship: develops_from UBERON:0008835 {source="XAO"} ! hepatic diverticulum relationship: part_of UBERON:0002107 ! liver property_value: homology_notes "the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000539", ontology="VHOG", source="DOI:10.1002/ar.20524 Hardman RC, Volz DC, Kullman SW, Hinton DE, An in vivo look at vertebrate liver architecture: three-dimensional reconstruction from Medaka (Oryzias latipes). The Anatomical Record (2007)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001281 name: hepatic sinusoid namespace: uberon alt_id: UBERON:0003275 def: "Wide thin-walled blood vessels in the liver. In mammals they have neither veinous or arterial markers." [Wikipedia:Hepatic_sinusoid, ZFIN:curator] comment: This class was created automatically from a combination of ontologies subset: uberon_slim subset: vertebrate_core synonym: "hepatic sinusoids" RELATED [] synonym: "liver sinusoid" EXACT [] synonym: "liver sinusoidal blood vessel" EXACT [OBOL:automatic] synonym: "sinusoid of liver" EXACT [OBOL:automatic] synonym: "sinusoidal blood vessel of liver" EXACT [OBOL:automatic] synonym: "vas capillare sinusoideum" EXACT [] xref: EHDAA2:0000999 xref: EMAPA:17365 xref: FMA:17543 xref: MA:0000367 xref: ncithesaurus:Hepatic_Sinusoid xref: SCTID:67435004 xref: TAO:0005091 xref: UMLS:C0227523 xref: VHOG:0000708 xref: ZFA:0005091 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003497 ! abdomen blood vessel is_a: UBERON:0003909 ! sinusoid is_a: UBERON:0005911 ! endo-epithelium relationship: part_of UBERON:0002107 ! liver relationship: part_of UBERON:0004647 ! liver lobule relationship: part_of UBERON:0006877 {source="reference_0000032"} ! vasculature of liver property_value: homology_notes " (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000708", ontology="VHOG", source="DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001285 name: nephron namespace: uberon def: "The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]" [PMID:9268568, Wikipedia:Nephron] comment: Editor note: kidney terms require review for cross-vertebrate compatibility and developmental relationships. Taxon notes: In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992)[GO Kidney] subset: uberon_slim subset: vertebrate_core synonym: "mature nephron" NARROW [EMAPA:28491] synonym: "nephroneum" RELATED LATIN [Wikipedia:Nephron] synonym: "tubulus renalis" RELATED LATIN [Wikipedia:Nephron] xref: BTO:0000924 xref: EMAPA:28491 xref: EV:0100384 xref: FMA:17640 xref: GAID:428 xref: http://upload.wikimedia.org/wikipedia/commons/2/27/Gray1128.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/27/Gray1128.png/200px-Gray1128.png xref: MA:0000375 xref: MESH:A05.810.453.736 xref: ncithesaurus:Nephron xref: SCTID:361337001 xref: TAO:0002153 xref: UMLS:C0027713 xref: ZFA:0005282 is_a: UBERON:0000064 ! organ part is_a: UBERON:0006554 ! urinary system structure relationship: develops_from UBERON:0004208 {evidence="definitional"} ! nephrogenic mesenchyme relationship: part_of UBERON:0007684 {source="FMA"} ! uriniferous tubule property_value: external_definition "Functional unit of the kidney that filters waste.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002153", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001287 name: proximal convoluted tubule namespace: uberon def: "The proximal tubule is the portion of the duct system of the nephron of the kidney which leads from Bowman's capsule to the loop of Henle[WP]" [Wikipedia:Proximal_convoluted_tubule] comment: TODO - cleanly define difference between proximal tubule and proximal convoluted tubule. Make definition applicable across species. subset: uberon_slim subset: vertebrate_core synonym: "1st convoluted tubule" RELATED [] synonym: "first convoluted tubule" RELATED [] synonym: "PCT" RELATED [] synonym: "proximal convoluted renal tubule" EXACT [] synonym: "tubulus contortus proximalis" EXACT [] synonym: "tubulus contortus proximalis" RELATED LATIN [Wikipedia:Proximal_convoluted_tubule] synonym: "tubulus convolutus proximalis" RELATED LATIN [] xref: EMAPA:28287 xref: EV:0100388 xref: FMA:17693 xref: http://upload.wikimedia.org/wikipedia/commons/2/27/Gray1128.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/27/Gray1128.png/200px-Gray1128.png xref: MA:0001669 xref: ncithesaurus:Proximal_Convoluted_Tube xref: SCTID:362220008 xref: TAO:0005290 xref: UMLS:C1514580 xref: ZFA:0005290 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0004134 ! proximal tubule is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0006534 ! renal convoluted tubule is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0003220 {source="Wikipedia"} ! metanephric mesenchyme relationship: part_of UBERON:0001225 {notes="checkme"} ! cortex of kidney property_value: external_definition "Renal tubule that connects to the renal corpuscle.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005290", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001288 name: loop of Henle namespace: uberon def: "Portion of the nephron that leads from the proximal convoluted tubule to the distal convoluted tubule. The loop has a hairpin bend in the renal medulla. The main function of this structure is to create a concentration gradient in the medulla of the kidney. By means of a countercurrent multiplier system, which utilizes sodium pumps, it creates an area of high sodium concentration deep in the medulla, near the collecting duct. Water present in the filtrate in the collecting duct flows through aquaporin channels out of the collecting duct, moving passively down its concentration gradient. This process reabsorbs water and creates a concentrated urine for excretion[WP]." [Wikipedia:Loop_of_Henle] comment: Note that the definitions of some kidney parts refer to Henle's loop, even in species where this may not be present. Requires review. subset: uberon_slim synonym: "ansa nephroni" EXACT [Wikipedia:Loop_of_Henle] synonym: "Henle loop" EXACT [] synonym: "henle's loop" EXACT [] xref: BTO:0004608 xref: EMAPA:29665 xref: EMAPA:29679 xref: EV:0100390 xref: FMA:17698 xref: GAID:437 xref: http://upload.wikimedia.org/wikipedia/commons/2/27/Gray1128.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/27/Gray1128.png/200px-Gray1128.png xref: MA:0001675 xref: MESH:A05.810.453.736.560.610 xref: ncithesaurus:Loop_of_Henle xref: SCTID:361335009 xref: UMLS:C0023986 xref: VHOG:0001270 is_a: UBERON:0007685 ! region of nephron tubule property_value: external_definition "A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001270", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001289 name: descending limb of loop of Henle namespace: uberon def: "Portion of the renal tubule constituting the first part of the loop of Henle[WP]." [Wikipedia:Descending_limb_of_loop_of_henle] subset: uberon_slim synonym: "descending limb" BROAD [] synonym: "descending limb of Henle's loop" EXACT [] synonym: "loop of Henle descending limb" EXACT [] xref: FMA:17705 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/27/Gray1128.png/200px-Gray1128.png xref: MA:0001679 xref: ncithesaurus:Descending_Limb_of_the_Henle_s_Loop xref: SCTID:245350001 xref: UMLS:C0227657 is_a: UBERON:0007685 {source="FMA"} ! region of nephron tubule relationship: part_of UBERON:0001288 {source="FMA"} ! loop of Henle property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001290 name: proximal straight tubule namespace: uberon alt_id: UBERON:0005166 def: "part of the descending limb of the renal tubule, extending from the proximal convoluted tubule to the thin tubule[BTO]." [BTO:0000055, Wikipedia:Proximal_straight_tubule] comment: TODO - is S3 exactly coincident with PST? Check also relationship to DL. todo - ensure relationships work across species (loop of Henle) subset: uberon_slim subset: vertebrate_core synonym: "pars recta" RELATED [] synonym: "pars recta tubuli renalis" RELATED [BTO:0000055] synonym: "proximal tubule segment 3" RELATED [MA:0002614] synonym: "S3" EXACT [GO:0072020] synonym: "thick descending limb of proximal tubule" EXACT [] synonym: "tubulus rectus proximalis" EXACT [] xref: BTO:0000055 xref: EMAPA:29661 xref: FMA:17716 xref: MA:0002614 xref: TAO:0005291 xref: ZFA:0005291 is_a: UBERON:0006853 ! renal cortex tubule is_a: UBERON:0008404 ! proximale tubular epithelium relationship: part_of UBERON:0001289 {source="MA"} ! descending limb of loop of Henle relationship: part_of UBERON:0004134 {source="MA-isa"} ! proximal tubule relationship: part_of UBERON:0006542 {source="MA"} ! outer medulla outer stripe loop of henle property_value: external_definition "Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005291", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001291 name: thick ascending limb of loop of Henle namespace: uberon def: "a segment of the nephron in the kidney. It can be divided into two parts: that in the renal medulla, and that in the renal cortex[Wikipedia:Thick_ascending_limb_of_loop_of_Henle]." [Wikipedia:Thick_ascending_limb_of_loop_of_Henle] comment: TODO: thick/thin check. Also - does the loop of Henle overlap the distal convoluted tubule? FMA divides DCT into straight and convoluted portions subset: uberon_slim synonym: "ascending thick limb" EXACT [] synonym: "distal straight tubule" EXACT [] synonym: "loop of Henle ascending limb thick segment" EXACT [MA:0001677] synonym: "straight portion of distal convoluted renal tubule" EXACT [] synonym: "straight portion of distal convoluted tubule" EXACT [FMA:17722] synonym: "thick ascending limb" EXACT [] synonym: "thick ascending limb of distal tubule" EXACT [FMA:17722] synonym: "thick ascending limb of Henle's loop" EXACT [] synonym: "tubulus rectus distalis" EXACT [FMA:17722] synonym: "tubulus rectus distalis" RELATED LATIN [Wikipedia:Thick_ascending_limb_of_loop_of_Henle] xref: EMAPA:28396 xref: EMAPA:29671 xref: FMA:17722 xref: http://upload.wikimedia.org/wikipedia/commons/2/27/Gray1128.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/27/Gray1128.png/200px-Gray1128.png xref: MA:0001677 xref: SCTID:244953001 is_a: UBERON:0004135 ! distal tubule is_a: UBERON:0008408 ! distal tubular epithelium relationship: part_of UBERON:0005164 ! ascending limb of loop of Henle property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001292 name: distal convoluted tubule namespace: uberon def: "a portion of kidney nephron between the loop of Henle and the collecting duct system." [Wikipedia:Distal_convoluted_tubule] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "distal convoluted renal tubule" EXACT [] synonym: "second convoluted tubule" RELATED [] synonym: "tubulus contortus distalis" EXACT [] synonym: "tubulus contortus distalis" RELATED LATIN [Wikipedia:Distal_convoluted_tubule] synonym: "tubulus convolutus distalis" RELATED LATIN [] xref: EMAPA:28393 xref: EV:0100389 xref: FMA:17721 xref: http://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/21/Kidney_nephron.png/200px-Kidney_nephron.png xref: MA:0001666 xref: ncithesaurus:Distal_Convoluted_Tubule xref: SCTID:361336005 xref: UMLS:C0022676 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0004135 ! distal tubule is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0006534 ! renal convoluted tubule is_a: UBERON:0006853 ! renal cortex tubule is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0003220 ! metanephric mesenchyme relationship: part_of UBERON:0001225 ! cortex of kidney relationship: part_of UBERON:0007685 ! region of nephron tubule property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001293 name: outer medulla of kidney namespace: uberon def: "The renal outer medulla is the region of the kidney that lies between the renal cortex and the renal inner medulla[GO]." [GOC:mtg_kidney_jan10] synonym: "kidney outer medulla" RELATED [BTO:0001746] synonym: "outer renal medulla" EXACT [] synonym: "outer zone of medulla of kidney" EXACT [] synonym: "outer zone of renal medulla" EXACT [] synonym: "renal outer medulla" EXACT [BTO:0001746] synonym: "set of outer region of renal pyramids" RELATED [FMA:17733] synonym: "zona externa (medullaris renalis)" EXACT LATIN [FMA:17733, FMA:TA] xref: BTO:0001746 xref: EMAPA:28310 xref: FMA:17733 xref: MA:0001653 is_a: UBERON:0000064 ! organ part is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0000362 ! renal medulla relationship: part_of UBERON:0002113 ! kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001294 name: inner medulla of kidney namespace: uberon def: "Innermost region of the mammalian kidney." [GO:0072053] comment: Taxon notes: unique to mammals[GO:0072053] synonym: "inner renal medulla" EXACT [] synonym: "inner zone of medulla of kidney" EXACT [] synonym: "inner zone of renal medulla" EXACT [] synonym: "kidney inner medulla" RELATED [BTO:0001745] synonym: "renal inner medulla" EXACT [BTO:0001745] synonym: "set of inner region of renal pyramids" EXACT [] synonym: "zona interna (medullaris renalis)" EXACT LATIN [FMA:17734, FMA:TA] xref: BTO:0001745 xref: EMAPA:28349 xref: FMA:17734 xref: MA:0001652 is_a: UBERON:0000064 ! organ part is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0000362 ! renal medulla relationship: part_of UBERON:0002113 ! kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001296 name: myometrium namespace: uberon def: "middle layer of the uterine wall consisting of smooth muscle cells and supporting stromal and vascular tissue." [Wikipedia:Myometrium] comment: The inner layer of the uterine wall is the endometrium or uterine lining, and the outer layer the serosa or perimetrium. The myometrium stretches (the smooth muscle cells expand in both size and number[1]) during pregnancy to allow for the harboring of the pregnancy, and contracts in a coordinated fashion during the process of labor. After delivery the myometrium contracts to expel the placenta and reduce blood loss. subset: uberon_slim synonym: "tunica muscularis" RELATED LATIN [Wikipedia:Myometrium] synonym: "tunica muscularis (myometrium)" EXACT [] synonym: "uterine smooth muscle" RELATED [] xref: BTO:0000907 xref: EFO:0001970 xref: EMAPA:29923 xref: EV:0100116 xref: FMA:17743 xref: GAID:171 xref: http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/66/Illu_cervix.jpg/200px-Illu_cervix.jpg xref: MA:0000391 xref: MESH:A02.633.570.500 xref: MeSH:D009215 xref: ncithesaurus:Myometrium xref: SCTID:279879004 xref: UMLS:C0027088 xref: VHOG:0001281 is_a: UBERON:0001135 ! smooth muscle tissue is_a: UBERON:0004923 {source="FMA"} ! organ component layer is_a: UBERON:0005156 ! reproductive structure relationship: part_of UBERON:0000459 {source="FMA"} ! uterine wall property_value: external_definition "The muscular wall of the uterus. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001281", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/myometrium"} property_value: has_relational_adjective "myometrial" xsd:string property_value: homology_notes "In all mammals, the uterus develops as a specialization of the paramesonephric or Müllerian ducts, which gives rise to the infundibula, oviducts, uterus, cervix, and anterior vagina. Morphogenetic events common to development of all uteri include: 1) differentiation and growth of the myometrium, 2) differentiation and morphogenesis of the endometrial glands, and 3) organization and stratification of endometrial stroma. Uterine development is initiated in the fetus, but is only completed postnatally with differentiation and development of the endometrial glands.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001281", ontology="VHOG", source="PMID:15471813 Spencer TE, Bazer FW, Uterine and placental factors regulating conceptus growth in domestic animals. Journal of Animal Science (2004)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001305 name: ovarian follicle namespace: uberon def: "Ovarian follicles are the basic units of female reproductive biology, each of which is composed of roughly spherical aggregations of cells found in the ovary. They contain a single oocyte (aka ovum or egg). These structures are periodically initiated to grow and develop, culminating in ovulation of usually a single competent oocyte in humans. These eggs/ova are only developed once every menstrual cycle (e.g. once a month in humans)[WP]." [Wikipedia:Ovarian_follicle] comment: This class was created automatically from a combination of ontologies subset: uberon_slim subset: vertebrate_core synonym: "egg follicle" RELATED [] synonym: "follicle of ovary" EXACT [] synonym: "follicle of ovary viewed macroscopically" EXACT [FMA:18640] synonym: "folliculi ovarici primarii, folliculi ovarici vesiculosi" RELATED LATIN [Wikipedia:Ovarian_follicle] synonym: "ovary follicle" EXACT [] xref: BTO:0000475 xref: FMA:18640 xref: GAID:371 xref: http://upload.wikimedia.org/wikipedia/commons/c/ca/Human_ovarian_follicle.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/e/e6/Primary_follicle-4.JPG/200px-Primary_follicle-4.JPG xref: MA:0001707 xref: MAT:0000449 xref: MESH:A05.360.319.114.630.535 xref: ncithesaurus:Ovarian_Follicle xref: SCTID:361111009 xref: TAO:0001110 xref: UMLS:C0018120 xref: VHOG:0001536 xref: ZFA:0001110 is_a: UBERON:0000064 ! organ part is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0005156 ! reproductive structure relationship: develops_from UBERON:0005296 ! ovary sex cord relationship: part_of UBERON:0000992 ! female gonad property_value: external_definition "Oocyte development of zebrafish has been divided into five stages based on morphological criteria and on physiological and biochemical events. Stage I follicles (less than 140 microns) are primary growth stage, stage II follicles (140-340 microns) are cortical alveolus stage, stage III (340-690 microns) are vitellogenesis, stage IV (690-730 microns) are oocyte maturation, and stage V follicles are matured egg. Selman et al, 1993.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001110", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001536", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001310 name: umbilical artery namespace: uberon def: "The umbilical artery is a paired artery (with one for each half of the body) that is found in the abdominal and pelvic regions. In the fetus, it extends into the umbilical cord. [WP,unvetted]." [Wikipedia:Umbilical_artery] comment: Editor notes: todo - compare with EHDAA2. Check embryonic vs extraembryonic, developmental relationships subset: uberon_slim synonym: "a. umbilicalis" RELATED LATIN [Wikipedia:Umbilical_artery] xref: BTO:0000841 xref: EHDAA:1026 xref: EHDAA:410 xref: EMAPA:16331 xref: EMAPA:16372 xref: FMA:18820 xref: GAID:516 xref: http://upload.wikimedia.org/wikipedia/commons/e/ee/Gray502.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/e/ee/Gray502.png/200px-Gray502.png xref: MA:0002072 xref: MESH:A07.231.114.929 xref: ncithesaurus:Umbilical_Artery xref: OpenCyc:Mx4rCWdhMGWbEd2AAABQjYGu0g xref: RETIRED_EHDAA2:0002106 xref: SCTID:261404000 xref: UMLS:C0041632 is_a: UBERON:0001637 ! artery is_a: UBERON:0010260 ! umbilical blood vessel property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001343 name: seminiferous tubule of testis namespace: uberon def: "Seminiferous tubules are located in the testicles, and are the specific location of meiosis, and the subsequent creation of gametes, namely spermatozoa. The epithelium of the tubule consists of sustentacular or Sertoli cells, which are tall, columnar type cells that line the tubule. In between the Sertoli cells are spermatogenic cells, which differentiate through meiosis to sperm cells. There are two types: convoluted and straight. convuluted towards the lateral side and straight as the tubule comes medially to form ducts which will exit the testis. [WP,unvetted]." [Wikipedia:Seminiferous_tubule] subset: uberon_slim synonym: "seminiferous cord" EXACT [EMAPA:18685] synonym: "seminiferous tubule" EXACT [] synonym: "testis - seminiferous tubule" EXACT [] synonym: "tubuli seminiferi" EXACT [] synonym: "tubuli seminiferi" RELATED LATIN [Wikipedia:Seminiferous_tubule] xref: AAO:0010399 xref: BTO:0001235 xref: EFO:0001404 xref: EMAPA:18685 xref: EMAPA:31476 xref: EV:0100380 xref: FMA:19825 xref: GAID:400 xref: http://upload.wikimedia.org/wikipedia/commons/4/49/Seminiferous_tubule_and_sperm_low_mag.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/6a/Gray1145.png/200px-Gray1145.png xref: MA:0000412 xref: MAT:0000503 xref: MESH:A05.360.444.849.700 xref: ncithesaurus:Seminiferous_Cord xref: ncithesaurus:Seminiferous_Tubule xref: SCTID:279614002 xref: UMLS:C0036630 xref: UMLS:C1519236 xref: VHOG:0001363 xref: XAO:0003088 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0005904 ! duct of male reproductive system relationship: develops_from UBERON:0005297 {source="Wikipedia"} ! testis sex cord relationship: part_of UBERON:0000473 ! testis property_value: external_definition "Any of the coiled tubules located in the testes in which spermatozoa are produced.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010399", ontology="AAO", source="AAO:BJB"} property_value: external_definition "One of two or three twisted curved tubules in each lobule of the testis in which spermatogenesis occurs. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001363", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/SEMINIFEROUS+TUBULE"} property_value: homology_notes "Frogs among amphibians and the amniotes have males with testes that are composed of seminiferous tubules, which differ from ampullae in being long, highly convoluted ductules.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001363", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688 and Figure 21-28", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001347 name: white adipose tissue namespace: uberon def: "Adipose tissue, cells of which contain a single large lipid droplet.[FMA]" [FMA:FMA, Wikipedia:White_adipose_tissue] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "adipocytus unigutturalis" EXACT [] synonym: "textus adiposus albus" EXACT [] synonym: "textus adiposus albus" RELATED LATIN [Wikipedia:White_adipose_tissue] synonym: "unilocular adipose tissue" EXACT [] synonym: "white fat" EXACT [] xref: BTO:0001456 xref: EFO:0000813 xref: FMA:20117 xref: MA:0000058 xref: MAT:0000199 xref: MIAA:0000199 xref: ncithesaurus:White_Adipose_Tissue xref: UMLS:C1704223 is_a: UBERON:0001013 ! adipose tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001348 name: brown adipose tissue namespace: uberon def: "Adipose tissue, cells of which contain multiple small lipid droplets.[FMA]" [FMA:FMA, Wikipedia:Brown_adipose_tissue] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "adipocytus multigutturalis" EXACT [] synonym: "brown fat" EXACT [] synonym: "multilocular adipose tissue" EXACT [] synonym: "textus adiposus fuscus" EXACT [] synonym: "textus adiposus fuscus" RELATED LATIN [Wikipedia:Brown_adipose_tissue] xref: BTO:0000156 xref: EFO:0000812 xref: EMAPA:19209 xref: FMA:20118 xref: GAID:921 xref: http://upload.wikimedia.org/wikipedia/commons/6/69/Brownfat_PETCT.jpg xref: MA:0000057 xref: MAT:0000198 xref: MESH:A10.165.114.322 xref: MIAA:0000198 xref: ncithesaurus:Brown_Adipose_Tissue xref: SCTID:15965003 xref: UMLS:C0006298 is_a: UBERON:0001013 ! adipose tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001351 name: lacrimal sac namespace: uberon def: "The lacrimal sac is the upper dilated end of the nasolacrimal duct, and is lodged in a deep groove formed by the lacrimal bone and frontal process of the maxilla. It connects the lacrimal canaliculi, which drain tears from the eye's surface, and the nasolacrimal duct, which conveys this fluid into the nasal cavity. This is mainly for high amounts of tears, in which the lacrimal sac pumps inward and outward driven by the orbicularis muscle during blinking. It is oval in form and measures from 12 to 15 mm. in length; its upper end is closed and rounded; its lower is continued into the nasolacrimal duct. Its superficial surface is covered by a fibrous expansion derived from the medial palpebral ligament, and its deep surface is crossed by the lacrimal part of the Orbicularis oculi, which is attached to the crest on the lacrimal bone. Like the nasolacrimal duct, the sac is lined by stratified columnar epithelium with mucus-secreting goblet cells, with surrounding connective tissue. [WP,unvetted]." [Wikipedia:Lacrimal_sac] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "saccus lacrimalis" RELATED LATIN [Wikipedia:Lacrimal_sac] xref: FMA:20289 xref: http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png xref: MA:0001298 xref: ncithesaurus:Lacrimal_Sac xref: SCTID:362534009 xref: UMLS:C0229289 is_a: UBERON:0000063 ! organ segment is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001850 ! lacrimal duct property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001352 name: external acoustic meatus namespace: uberon def: "A tube running from the outer ear to the middle ear. The human ear canal extends from the pinna to the eardrum and is about 26 mm in length and 7 mm in diameter." [Wikipedia:External_acoustic_meatus] comment: AO notes: subdivision of head in FMA. Editor note: consider revisiting superclass after refinement of CARO/EAO, conduit may not be quite correct. Development notes: tympanic ring, which serves as support for the tympanic membrane, directs invagination of the first pharingeal cleft ectoderm to form the external acoustic meatus (EAM), which provides the outer layer of the membrane[PMID 11237469] subset: uberon_slim synonym: "auditory canal" EXACT [] synonym: "auditory meatus" RELATED [EHDAA2:0000460] synonym: "ear canal" EXACT [Wikipedia:Ear_canal] synonym: "external acoustic tube" EXACT [FMA:61734] synonym: "external auditory canal" EXACT [] synonym: "external auditory meatus" RELATED [] synonym: "external auditory tube" EXACT [FMA:61734] xref: EHDAA2:0000460 xref: EHDAA:8975 xref: EMAPA:17588 xref: EV:0100356 xref: FMA:61734 xref: GAID:864 xref: galen:ExternalAuditoryMeatus xref: MA:0000260 xref: MESH:A09.246.272.396 xref: ncithesaurus:External_Acoustic_Meatus xref: OpenCyc:Mx4rvli-nZwpEbGdrcN5Y29ycA xref: SCTID:181178004 xref: UMLS:C0013444 xref: VHOG:0000977 is_a: UBERON:0004111 ! anatomical conduit is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0005872 {source="PMID:11237469"} ! 1st arch pharyngeal cleft relationship: part_of UBERON:0001691 {source="FMA"} ! external ear property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001353 name: anal region namespace: uberon def: "The anus and surrounding regions. Encompasses both internal and external regions, where present" [UBERON:cjm] subset: uberon_slim xref: EFO:0000847 xref: EHDAA2:0000122 xref: EHDAA:2931 xref: EMAPA:16831 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/f/fb/Gray408.png/200px-Gray408.png xref: MA:0000329 xref: MAT:0000042 xref: MIAA:0000042 xref: ncithesaurus:Anal_Region xref: SCTID:362680001 xref: UMLS:C0230120 xref: VHOG:0000395 xref: WBbt:0006919 is_a: UBERON:0000477 {source="EHDAA2"} ! anatomical cluster is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0000931 {evidence="definitional"} ! proctodeum property_value: homology_notes "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000395", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001366 name: parietal peritoneum namespace: uberon alt_id: UBERON:0004459 def: "The peritoneum that lines the walls of the peritoneal cavity." [Wikipedia:Parietal_peritoneum, ZFIN:curator] comment: fix coordinated with ZFA subset: uberon_slim subset: vertebrate_core synonym: "peritoneal cavity lining" EXACT [MA:0000449] xref: AAO:0010816 xref: FMA:21451 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/5f/Gray1040.png/200px-Gray1040.png xref: MA:0000449 xref: SCTID:362700006 xref: TAO:0005131 xref: VHOG:0001527 xref: ZFA:0005131 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0002358 ! peritoneum property_value: external_definition "Peritoneum attached to the abdominal wall.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010816", ontology="AAO", source="AAO:JMG"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001434 name: skeletal system namespace: uberon def: "Organ system subdivision which consists of the skeleton and the articular system.[FMA]" [AAO:0000566, FMA:FMA] comment: Note that GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates subset: uberon_slim subset: vertebrate_core synonym: "set of all bones and joints" NARROW SENSU [] synonym: "skeleton system" EXACT [] synonym: "Skelettsystem" RELATED [BTO:0001486] xref: AAO:0000566 xref: BTO:0001486 xref: EFO:0000806 xref: EHDAA2:0003168 xref: FMA:23881 xref: MA:0000018 xref: ncithesaurus:Skeletal_System xref: OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA xref: TAO:0000434 xref: UMLS:C0037253 xref: VHOG:0001254 xref: VSAO:0000027 xref: XAO:0003060 xref: ZFA:0000434 is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0001474 ! bone disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002294 ! biliary system disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: part_of UBERON:0002204 ! musculoskeletal system property_value: external_definition "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000434", ontology="TAO", source="TAO:wd"} property_value: external_definition "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000027", ontology="VSAO", source="GO_REF:0000034", source="PSPUB:0000170"} property_value: external_definition "System that provides physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000566", ontology="AAO", source="AAO:LAP"} property_value: has_relational_adjective "skeletal" xsd:string property_value: homology_notes "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001254", ontology="VHOG", source="DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: seeAlso http://purl.obolibrary.org/obo/uberon/references/reference_0000025 xsd:anyURI property_value: spatially_disjoint_from UBERON:0001016 [Term] id: UBERON:0001443 name: chest namespace: uberon def: "Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper[FMA]." [FMA:9576, Wikipedia:Chest] comment: editor note - FMA:24216 present in FMA1, but gone in subsequent versions subset: uberon_slim synonym: "anterior chest" EXACT [FMA:24816] synonym: "anterior thoracic region" EXACT [] synonym: "anterolateral part of thorax" EXACT [] synonym: "front of chest" EXACT [FMA:24816] synonym: "front of thorax" EXACT [] synonym: "pectus" EXACT LATIN [FMA:24816, FMA:TA] synonym: "thoracic body wall" RELATED [MA:0000031] synonym: "thorax" RELATED [FMA:9576] synonym: "thorax" RELATED LATIN [Wikipedia:Chest] synonym: "ventral part of thoracic region" EXACT [] xref: BTO:0001368 xref: EFO:0000965 xref: EV:0100010 xref: FMA:9576 xref: GAID:91 xref: galen:Chest xref: galen:Thorax xref: http://upload.wikimedia.org/wikipedia/commons/d/db/Chest.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Chest.jpg/200px-Chest.jpg xref: MA:0000031 xref: MAT:0000295 xref: MESH:A01.911 xref: MIAA:0000295 xref: ncithesaurus:Chest xref: ncithesaurus:Thorax xref: OpenCyc:Mx4rvVikFZwpEbGdrcN5Y29ycA xref: UMLS:C0817096 xref: UMLS:C1527391 is_a: UBERON:0009569 {source="FMA-modified"} ! subdivision of trunk relationship: part_of UBERON:0000915 {source="FMA", source="MA"} ! thoracic segment of trunk property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0000916 [Term] id: UBERON:0001444 name: subdivision of head namespace: uberon comment: This class was created automatically from a combination of ontologies subset: non_informative synonym: "head region" EXACT [] synonym: "head subdivision" EXACT [] synonym: "region of head" EXACT [] xref: FMA:24218 xref: SCTID:123852005 xref: XAO:0000040 is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0000033 ! head property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001456 name: face namespace: uberon def: "Subdivision of head which consists of the facial skeleton and all layers superficial to it[FMA,modified]." [FMA:24728, Wikipedia:Face] comment: The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)[vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf] subset: uberon_slim synonym: "facia/facies" RELATED LATIN [Wikipedia:Face] synonym: "visage" RELATED [BTO:0003369] xref: BTO:0003369 xref: FMA:24728 xref: GAID:64 xref: galen:Face xref: HAO:0000316 xref: http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/55/Mona_Lisa_headcrop.jpg/200px-Mona_Lisa_headcrop.jpg xref: MA:0002473 xref: MESH:A01.456.505 xref: ncithesaurus:Face xref: OpenCyc:Mx4rvVi5GZwpEbGdrcN5Y29ycA xref: SCTID:302549007 xref: UMLS:C0015450 is_a: UBERON:0001444 ! subdivision of head property_value: has_relational_adjective "facial" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001468 name: intervertebral joint namespace: uberon def: "The joint between adjacent vertebral bodies. May be composed of the nucleus pulposus, annular ligament, and the anterior and posterior longitudinal ligaments." [http://www.medilexicon.com/medicaldictionary.php?t=87401] comment: AO notes: FMA has 'intervertebral joint' as a GAT, and has two distinct classes 'intervertebral symphysis' and 'intervertebral syndesmosis', but note that the latter do not connect the centra synonym: "inter-centrum joint" EXACT [] synonym: "inter-vertebral joint" EXACT [] synonym: "intervertebral symphysis" EXACT [FMA:25511] synonym: "joint of vertebral body" EXACT [FMA:25511] synonym: "vertebral joint" BROAD [] xref: FMA:25511 xref: MA:0001514 xref: ncithesaurus:Vertebral_Joint xref: SCTID:244512000 xref: UMLS:C1182940 is_a: UBERON:0002216 {source="FMA"} ! symphysis is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0001130 {source="FMA"} ! vertebral column property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001473 name: lymphatic vessel namespace: uberon def: "A vessel that contains or conveys lymph, that originates as an interfibrillar or intercellular cleft or space in a tissue or organ, and that if small has no distinct walls or walls composed only of endothelial cells and if large resembles a vein in structure[BTO]." [BTO:0000752, Wikipedia:Lymphatic_vessel] subset: uberon_slim subset: vertebrate_core synonym: "lymph vessel" EXACT [] synonym: "vas lymphaticum" RELATED LATIN [Wikipedia:Lymphatic_vessel] xref: AAO:0011005 xref: BTO:0000752 xref: EFO:0000873 xref: FMA:30315 xref: http://upload.wikimedia.org/wikipedia/commons/4/44/Illu_lymph_capillary.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/4/44/Illu_lymph_capillary.jpg/200px-Illu_lymph_capillary.jpg xref: MA:0000138 xref: MAT:0000443 xref: ncithesaurus:Lymphatic_Vessel xref: OpenCyc:Mx4rwA1fYZwpEbGdrcN5Y29ycA xref: SCTID:279089004 xref: TAO:0005105 xref: UMLS:C0229889 xref: VHOG:0001249 xref: XAO:0000375 is_a: UBERON:0000055 ! vessel disjoint_from: UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004536 ! lymph vasculature relationship: part_of UBERON:0006558 ! lymphatic part of lymphoid system property_value: external_definition "A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005105", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "A vessel that contains or conveys lymph.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011005", ontology="AAO", source="AAO:EJS"} property_value: homology_notes "Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001249", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001474 name: bone namespace: uberon def: "Skeletal element that is composed of bone tissue[VSAO]." [VSAO:0000057, Wikipedia:Bone] comment: Alternate definition: Organ with cavitated organ parts, which primarily consists of compact (cortical) and cancellous bone, which surround bone marrow cavities; together with other bones, cartilages and joints, it constitutes the skeletal system. Examples: femur, sternum, maxilla, vertebra, talus[FMA] subset: major_organ subset: organ_slim subset: uberon_slim subset: vertebrate_core synonym: "bone element" EXACT [VSAO:0000057] synonym: "bone organ" EXACT [] xref: AAO:0000047 xref: AEO:0000082 xref: BTO:0000140 xref: EFO:0000298 xref: EHDAA2:0003082 xref: ENVO:00002039 xref: EV:0100140 xref: FMA:30317 xref: FMA:5018 xref: GAID:92 xref: galen:Bone xref: MA:0001459 xref: MAT:0000299 xref: MIAA:0000299 xref: ncithesaurus:Bone xref: OpenCyc:Mx4rvViDlpwpEbGdrcN5Y29ycA xref: OpenCyc:Mx4rvVkCG5wpEbGdrcN5Y29ycA xref: SCTID:90780006 xref: TAO:0001514 xref: UMLS:C0262950 xref: VHOG:0001190 xref: VSAO:0000057 xref: XAO:0000169 xref: ZFA:0001514 is_a: UBERON:0004765 ! skeletal element disjoint_from: UBERON:0001630 ! muscle organ disjoint_from: UBERON:0005090 ! muscle structure relationship: part_of UBERON:0001434 ! skeletal system property_value: axiom_lost_from_external_ontology "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000047", ontology="AAO"} property_value: external_definition "Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000047", ontology="AAO", source="AAO:LAP"} property_value: external_definition "Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001514", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Skeletal element that is composed of bone tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000057", ontology="VSAO", source="PSPUB:0000170"} property_value: homology_notes "The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001190", ontology="VHOG", source="DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0001015 property_value: spatially_disjoint_from UBERON:0001630 property_value: spatially_disjoint_from UBERON:0002385 [Term] id: UBERON:0001515 name: thoracic aorta namespace: uberon def: "The thoracic aorta is contained in the posterior mediastinal cavity. It begins at the lower border of the fourth thoracic vertebra where it is continuous with the aortic arch, and ends in front of the lower border of the twelfth thoracic vertebra, at the aortic hiatus in the diaphragm where it becomes the abdominal aorta. At its commencement, it is situated on the left of the vertebral column; it approaches the median line as it descends; and, at its termination, lies directly in front of the column. The vessel describes a curve which is concave forward; as the branches given off from it are small, its diminution in size is insignificant. It has a radius of approximately 1.16 cm. [WP,unvetted]." [Wikipedia:Thoracic_aorta] subset: uberon_slim synonym: "aorta thoracalis" RELATED LATIN [Wikipedia:Thoracic_aorta] synonym: "pars thoracica aortae" RELATED LATIN [Wikipedia:Thoracic_aorta] synonym: "thoracic part of aorta" EXACT [] xref: BTO:0000157 xref: EFO:0002525 xref: EMAPA:18603 xref: FMA:3786 xref: GAID:471 xref: galen:ThoracicAorta xref: http://upload.wikimedia.org/wikipedia/commons/7/75/Gray530.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/7/75/Gray530.png/200px-Gray530.png xref: MA:0002569 xref: MESH:A07.231.114.056.372 xref: ncithesaurus:Thoracic_Aorta xref: OpenCyc:Mx4rveb9TpwpEbGdrcN5Y29ycA xref: SCTID:302510009 xref: UMLS:C1522460 is_a: UBERON:0005800 {source="FMA"} ! segment of aorta relationship: part_of UBERON:0000915 ! thoracic segment of trunk property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001529 name: brachiocephalic artery namespace: uberon def: "The brachiocephalic artery (or brachiocephalic trunk or innominate artery) is an artery of the mediastinum that supplies blood to the right arm and the head and neck. It is the first branch of the aortic arch, and soon after it emerges, the brachiocephalic artery divides into the right common carotid artery and the right subclavian artery. There is no brachiocephalic artery for the left side of the body. The left common carotid, and the left subclavian artery, come directly off the aortic arch. However, there are two brachiocephalic veins. [WP,unvetted]." [Wikipedia:Brachiocephalic_artery] subset: uberon_slim synonym: "brachiocephalic trunk" EXACT [MA:0001922] synonym: "innominate artery" EXACT [] synonym: "truncus brachiocephalicus" EXACT LATIN [FMA:3932, FMA:TA] synonym: "truncus brachiocephalicus" RELATED LATIN [Wikipedia:Brachiocephalic_artery] xref: EFO:0002550 xref: EHDAA2:0000835 xref: EMAPA:17615 xref: FMA:3932 xref: GAID:476 xref: galen:BrachioCephalicArtery xref: http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/e/e6/Gray506.svg/200px-Gray506.svg.png xref: MA:0001922 xref: MESH:A07.231.114.145 xref: ncithesaurus:Innominate_Artery xref: OpenCyc:Mx4rv9mMTpwpEbGdrcN5Y29ycA xref: SCTID:244244002 xref: UMLS:C0006094 is_a: UBERON:0004573 ! systemic artery relationship: part_of UBERON:0007204 ! brachiocephalic vasculature property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001533 name: subclavian artery namespace: uberon def: "One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta" [ISBN10:0073040584, UBERON:cjm, Wikipedia:Subclavian_artery] comment: Editors notes: Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO) subset: uberon_slim subset: unverified_taxonomic_grouping subset: vertebrate_core synonym: "arteria subclavia" EXACT [XAO:0000365] synonym: "arteria subclavia" RELATED LATIN [Wikipedia:Subclavian_artery] synonym: "arterial tree of upper limb" EXACT [] synonym: "PA" RELATED [] synonym: "pectoral artery" EXACT [] synonym: "subclavian arterial tree" EXACT [] xref: AAO:0010232 xref: EHDAA2:0001933 xref: EHDAA:4357 xref: EMAPA:17617 xref: FMA:3951 xref: GAID:511 xref: http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/e/e6/Gray506.svg/200px-Gray506.svg.png xref: MA:0002045 xref: MESH:A07.231.114.839 xref: ncithesaurus:Subclavian_Artery xref: OpenCyc:Mx4rvp8u1JwpEbGdrcN5Y29ycA xref: SCTID:265790007 xref: TAO:0005086 xref: UMLS:C0038530 xref: XAO:0000365 xref: ZFA:0005086 is_a: UBERON:0004573 ! systemic artery property_value: external_definition "Artery which supplies blood via branches to the various muscles of the shoulder region and to the forelimb.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010232", ontology="AAO", source="AAO:BJB"} property_value: external_definition "In human anatomy, the subclavian artery is a major artery of the upper thorax that mainly supplies blood to the head and arms. It is located below the clavicle, hence the name. There is a left subclavian and a right subclavian. On the left side of the body, the subclavian comes directly off the arch of aorta. On the right side of the body, the subclavian arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery. The usual branches of the subclavian on both sides of the body are the vertebral artery, the internal thoracic artery, the thyrocervical trunk, the costocervical trunk and the dorsal scapular artery. The subclavian becomes the axillary artery at the lateral border of the first rib[WP]" xsd:string {source="Wikipedia:Subclavian_artery"} property_value: external_definition "The pectoral (subclavian) arteries originate from the dorsal aorta and takes the blood outward into the fin from the paired portion of the dorsal aorta posterior to the last aortic arch. Kimmel et al. 1993[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005086", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001552 name: arcuate artery namespace: uberon def: "One of the curved arteries at the corticomedullary border of the kidney that arise from the interlobar arteries and give rise to the interlobular arteries." [MP:0011315, Wikipedia:Arcuate_artery_of_the_foot] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "kidney arcuate artery" EXACT [MP:0011315] xref: EMAPA:28215 xref: FMA:44594 xref: http://upload.wikimedia.org/wikipedia/commons/e/ee/Gray553.png xref: MA:0002583 xref: SCTID:244331005 is_a: UBERON:0001637 ! artery is_a: UBERON:0003644 ! kidney arterial blood vessel relationship: part_of UBERON:0001225 ! cortex of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001555 name: digestive tract namespace: uberon def: "Tube extending from the mouth to the anus." [http://en.wikipedia.org/wiki/Talk\:Human_gastrointestinal_tract, http://sourceforge.net/tracker/?func=detail&atid=440764&aid=2991587&group_id=36855] comment: Terminology notes: we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this. AO notes: GO says gut is region of DT, from intestines to anus. ZFA treats as synonym for alimentary canal, and treats it as the sum of DT + organs (ZF has no term from stomach). GO says intestines to anus (excludes stomach and esophagus). MA appears to agree with GO (stomach and esophagus are not parts). FMA includes stomach and esophagus as parts of gut -- the FMA divides gut into lower and upper GI tract; it's not clear if this is exhaustive (small intestine is in neither), but lower GI tract may correspond better to the GO definition. NOTE: GO now changed, see sf id in def xref. Note that FMA also has a term 'gastrointestinal tract', but this includes the liver. subset: uberon_slim subset: vertebrate_core synonym: "alimentary canal" NARROW [] synonym: "digestive tube" EXACT [] synonym: "enteric tract" EXACT [ZFA:0000112] synonym: "gut" BROAD [] synonym: "gut tube" RELATED [] xref: AAO:0010023 xref: BILA:0000083 xref: BTO:0000511 xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 xref: FBbt:00003125 xref: FMA:45615 xref: galen:AlimentaryTract xref: ncithesaurus:Gastrointestinal_Tract xref: OpenCyc:Mx4rvVi0GpwpEbGdrcN5Y29ycA xref: TAO:0000112 xref: TGMA:0001819 xref: UMLS:C0017189 xref: VHOG:0000309 xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0007026 {source="NBK10107"} ! primitive gut relationship: part_of UBERON:0001007 ! digestive system property_value: external_definition "The alimentary or digestive tract, and associated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000112", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000309", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: never_in_taxon NCBITaxon:41324 {source="doi:10.1371/journal.pone.0016309"} [Term] id: UBERON:0001556 name: lower urinary tract namespace: uberon def: "Subdivision of urinary system which consists of the urinary bladder and the urethra." [FMA:45659] subset: uberon_slim xref: FMA:45659 xref: galen:LowerUrinaryTract xref: MA:0002636 xref: SCTID:181420004 is_a: UBERON:0000477 ! anatomical cluster is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0001008 ! excretory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001557 name: upper respiratory tract namespace: uberon def: "Subdivision of respiratory system which consists of the nose, nasopharynx, oropharynx and larynx[FMA]" [FMA:FMA, Wikipedia:Upper_respiratory_tract] comment: Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage.[WP] subset: uberon_slim xref: EHDAA2:0002136 xref: EMAPA:17669 xref: FMA:45661 xref: http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/c3/Illu_conducting_passages.jpg/200px-Illu_conducting_passages.jpg xref: MA:0000442 xref: OpenCyc:Mx4rtT2HwgJMEdyAAADggVbxzQ xref: SCTID:361381009 xref: VHOG:0000406 is_a: UBERON:0000072 ! segment of respiratory tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0001558 [Term] id: UBERON:0001558 name: lower respiratory tract namespace: uberon def: "The segment of respiratory tract from the trachea to the lungs[WP,modified]" [Wikipedia:Lower_respiratory_tract] subset: uberon_slim xref: EHDAA2:0001036 xref: EMAPA:16738 xref: FMA:45662 xref: http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/c3/Illu_conducting_passages.jpg/200px-Illu_conducting_passages.jpg xref: MA:0000435 xref: OpenCyc:Mx4rQRqjUgAKEdyHxgDggVfs8g xref: SCTID:281488008 xref: VHOG:0000382 is_a: UBERON:0000072 ! segment of respiratory tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001560 name: neck of organ namespace: uberon synonym: "organ neck" EXACT [] xref: FMA:45733 is_a: UBERON:0000064 ! organ part property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001606 name: muscle of iris namespace: uberon def: "." [Wikipedia:Iris_muscle] subset: uberon_slim synonym: "iris muscle" EXACT [] synonym: "iris muscle organ" EXACT [OBOL:automatic] synonym: "muscle organ of iris" EXACT [OBOL:automatic] xref: FMA:49154 xref: MA:0001287 xref: SCTID:280888007 is_a: UBERON:0011222 {source="FMA"} ! intra-ocular muscle relationship: part_of UBERON:0001769 ! iris property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001607 name: sphincter pupillae namespace: uberon def: "The iris sphincter muscle (pupillary sphincter, circular muscle of iris, circular fibers) is a muscle in the part of the eye called the iris. It encircles the eye, appropriate to its function as a constrictor. It is found in vertebrates and some cephalopods. In humans, it functions to constrict the pupil in bright light or during accommodation. Its dimensions are about 0.75 mm wide by 0.15 mm thick. It is controlled by parasympathetic fibers that originate from the Edinger-Westphal nucleus, travel along the oculomotor nerve (CN III), synapse in the ciliary ganglion, and then enter the eye via the short ciliary nerves. Initially, all the myocytes are of the smooth muscle type, but much later in life, so that ultimately most cells are of the striated muscle type. [WP,unvetted]." [Wikipedia:Iris_sphincter_muscle] comment: Taxon notes: WP says: It is found in vertebrates and some cephalopods; this class refers to the vertebrate structure. Function notes: constricts iris subset: uberon_slim synonym: "circular fibers" RELATED [Wikipedia:Iris_sphincter_muscle] synonym: "constrictor pupillae" RELATED [Wikipedia:Iris_sphincter_muscle] synonym: "iris constrictor" RELATED [] synonym: "iris constrictor muscle" RELATED [Wikipedia:Iris_sphincter_muscle] synonym: "iris sphincter" RELATED [Wikipedia:Iris_sphincter_muscle] synonym: "iris sphincter muscle" EXACT [BTO:0000656] synonym: "M. sphincter pupillae" EXACT [] synonym: "m. sphincter pupillae" RELATED LATIN [Wikipedia:Iris_sphincter_muscle] synonym: "musculus sphincter pupillae" EXACT [BTO:0000656] synonym: "pupillary constrictor muscle" RELATED [Wikipedia:Iris_sphincter_muscle] synonym: "pupillary sphincter" RELATED [Wikipedia:Iris_sphincter_muscle] synonym: "pupillary sphincter muscle" RELATED [Wikipedia:Iris_sphincter_muscle] synonym: "sphincter muscle of pupil" EXACT [BTO:0000656] synonym: "sphincter pupillae" RELATED [Wikipedia:Iris_sphincter_muscle] synonym: "sphincter pupillae muscle" RELATED [Wikipedia:Iris_sphincter_muscle] synonym: "spincter pupillae" RELATED [Wikipedia:Iris_sphincter_muscle] xref: BTO:0000656 xref: FMA:49157 xref: http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/2f/Gray878.png/200px-Gray878.png xref: MA:0001289 xref: ncithesaurus:Sphincter_Pupillae_Muscle xref: SCTID:280889004 xref: UMLS:C0229189 is_a: UBERON:0004234 {source="BTO"} ! iris smooth muscle is_a: UBERON:0007521 ! smooth muscle sphincter relationship: part_of UBERON:0001769 ! iris property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001608 name: dilatator pupillae namespace: uberon def: "The iris dilator muscle (pupil dilator muscle, pupillary dilator, radial muscle of iris, radiating fibers), is a smooth muscle of the eye, running radially in the iris and therefore fit as a dilator. It is innervated by the sympathetic system, which acts by releasing noradrenaline, which acts on α1-receptors. Thus, when presented with a threatening stimuli that activates the fight-or-flight response, this innervation dilates the iris, thus temporarily letting more light reach the retina. [WP,unvetted]." [Wikipedia:Iris_dilator_muscle] subset: uberon_slim synonym: "dilator muscle of pupil" EXACT [] synonym: "dilator of pupil" EXACT [] synonym: "dilator pupillae" EXACT [] synonym: "dilator pupillae muscle" EXACT [Wikipedia:Iris_dilator_muscle] synonym: "dilator pupillae muscle" RELATED [BTO:0001371] synonym: "iris dilator" RELATED [Wikipedia:Iris_dilator_muscle] synonym: "iris dilator muscle" EXACT [BTO:0001371] synonym: "musculus dilatator pupillae" EXACT LATIN [FMA:49158, FMA:TA] synonym: "musculus dilatator pupillae" RELATED LATIN [Wikipedia:Iris_dilator_muscle] synonym: "musculus dilator pupillae" RELATED [BTO:0001371] synonym: "pupil dilator" RELATED [Wikipedia:Iris_dilator_muscle] synonym: "pupil dilator muscle" RELATED [Wikipedia:Iris_dilator_muscle] synonym: "pupillary dilator" RELATED [Wikipedia:Iris_dilator_muscle] synonym: "pupillary dilator muscle" EXACT [Wikipedia:Iris_dilator_muscle] synonym: "pupillary muscle" RELATED [Wikipedia:Iris_dilator_muscle] synonym: "radial muscle" RELATED [Wikipedia:Iris_dilator_muscle] synonym: "radial muscle of iris" EXACT [Wikipedia:Iris_dilator_muscle] synonym: "radiating fibers" RELATED [Wikipedia:Iris_dilator_muscle] xref: BTO:0001371 xref: FMA:49158 xref: http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/2f/Gray878.png/200px-Gray878.png xref: MA:0001288 xref: ncithesaurus:Dilator_Pupillae_Muscle xref: SCTID:280890008 xref: UMLS:C0229190 is_a: UBERON:0004234 {source="BTO"} ! iris smooth muscle property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001621 name: coronary artery namespace: uberon def: "An artery that supplies the myocardium." [Wikipedia:Coronary_circulation#Coronary_anatomy] subset: uberon_slim synonym: "coronary arterial tree" EXACT [] xref: BTO:0000290 xref: EFO:0002551 xref: EMAPA:19160 xref: EMAPA:25968 xref: EV:0100383 xref: FMA:49893 xref: galen:CoronaryArtery xref: http://upload.wikimedia.org/wikipedia/commons/thumb/4/46/Gray492.png/200px-Gray492.png xref: MA:0002453 xref: ncithesaurus:Coronary_Artery xref: OpenCyc:Mx4rvoL56ZwpEbGdrcN5Y29ycA xref: SCTID:181294004 xref: UMLS:C0205042 xref: VHOG:0001557 is_a: UBERON:0003498 ! heart blood vessel is_a: UBERON:0004573 ! systemic artery relationship: part_of UBERON:0000948 ! heart property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001630 name: muscle organ namespace: uberon def: "Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. Nonparenchymatous organ that primarily consists of skeletal muscle tissue aggregated into macroscopic fasciculi by connective tissue; together with other muscles, it constitutes the muscular system. Examples: biceps, diaphragm, masseter, right third external intercostal muscle, external oblique, levator ani, serratus anterior[FMA]." [GO:0007517] subset: organ_slim subset: uberon_slim subset: vertebrate_core synonym: "muscle" BROAD [ZFA:0005145] xref: AAO:0011066 xref: EV:0100146 xref: FMA:5022 xref: GAID:131 xref: galen:Muscle xref: MA:0000015 xref: OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA xref: SCTID:71616004 xref: TAO:0005145 xref: VHOG:0001245 xref: XAO:0000172 xref: ZFA:0005145 is_a: UBERON:0000062 ! organ is_a: UBERON:0005090 ! muscle structure relationship: part_of UBERON:0001015 ! musculature property_value: external_definition "Portion of tissue composed of contractile fibers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005145", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "muscular" xsd:string property_value: homology_notes "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001245", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001637 name: artery namespace: uberon def: "An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]." [AEO:JB] comment: Editor notes: Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme. subset: uberon_slim subset: vertebrate_core synonym: "arterial subtree" EXACT [] synonym: "arterial system" RELATED [] synonym: "arterial tree organ part" EXACT [] synonym: "arterial vessel" RELATED [] synonym: "arteries" EXACT PLURAL [TAO:0000005] xref: AAO:0010211 xref: AEO:0000208 xref: BTO:0000573 xref: EFO:0000814 xref: EHDAA2:0000143 xref: EHDAA2:0003253 xref: EV:0100026 xref: FMA:50720 xref: GAID:468 xref: galen:Artery xref: MA:0000064 xref: MAT:0000034 xref: MESH:A07.231.114 xref: MIAA:0000034 xref: ncithesaurus:Artery xref: OpenCyc:Mx4rvVjknZwpEbGdrcN5Y29ycA xref: SCTID:362877004 xref: TAO:0000005 xref: UMLS:C0003842 xref: VHOG:0001251 xref: XAO:0000114 xref: ZFA:0000005 is_a: UBERON:0003509 ! arterial blood vessel relationship: part_of UBERON:0004572 ! arterial system property_value: external_definition "Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010211", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "arterial" xsd:string property_value: homology_notes "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001251", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001638 name: vein namespace: uberon def: "Any of the tubular branching vessels that carry blood from the capillaries toward the heart." [Wikipedia:Vein] comment: TODO - check with MA - vein vs venous blood vessel subset: uberon_slim subset: vertebrate_core synonym: "vena" RELATED LATIN [Wikipedia:Vein] synonym: "venae" RELATED PLURAL [VHOG:0001743] synonym: "venous subtree" BROAD [] synonym: "venous tree organ part" EXACT [] synonym: "venous vessel" BROAD [] xref: AAO:0010212 xref: AEO:0000209 xref: BTO:0000234 xref: EFO:0000816 xref: EHDAA2:0003254 xref: EV:0100031 xref: FMA:50723 xref: GAID:492 xref: galen:Vein xref: http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/c2/Venous_system_en.svg/200px-Venous_system_en.svg.png xref: MA:0000067 xref: MAT:0000037 xref: MESH:A07.231.908 xref: MIAA:0000037 xref: ncithesaurus:Vein xref: OpenCyc:Mx4rvVjkWpwpEbGdrcN5Y29ycA xref: SCTID:181367001 xref: TAO:0000082 xref: UMLS:C0042449 xref: VHOG:0001252 xref: VHOG:0001743 xref: XAO:0000115 xref: ZFA:0000082 is_a: UBERON:0003920 ! venous blood vessel property_value: external_definition "Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010212", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001743", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001678 name: temporal bone namespace: uberon def: "The temporal bones are situated at the sides and base of the skull, and lateral to the temporal lobes of the cerebrum." [Wikipedia:Temporal_bone] comment: The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. AO notes: Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA. Taxon notes: fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic)[chond.] + styloid process[splanc.] // In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone subset: uberon_slim synonym: "os temporale" RELATED LATIN [Wikipedia:Temporal_bone] xref: EHDAA:6035 xref: EMAPA:17682 xref: EMAPA:18020 xref: FMA:52737 xref: GAID:232 xref: http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/66/Illu_cranial_bones2.jpg/200px-Illu_cranial_bones2.jpg xref: MA:0001476 xref: MESH:A02.835.232.781.885 xref: ncithesaurus:Temporal_Bone xref: OpenCyc:Mx4rvbkAk5wpEbGdrcN5Y29ycA xref: SCTID:181795004 xref: UMLS:C0039484 xref: VHOG:0000800 is_a: UBERON:0003462 ! facial bone is_a: UBERON:0008193 {source="FMA"} ! pneumatized bone property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001690 name: ear namespace: uberon def: "Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals." [GO:0042471, Wikipedia:Ear] comment: This class was created automatically from a combination of ontologies subset: organ_slim subset: uberon_slim synonym: "auditory apparatus" RELATED [] synonym: "auris" RELATED [BTO:0000368] xref: AAO:0011014 xref: BTO:0000368 xref: EFO:0000826 xref: EHDAA2:0000423 xref: EHDAA:502 xref: EMAPA:16193 xref: EV:0100353 xref: FMA:52780 xref: GAID:62 xref: galen:Ear xref: http://upload.wikimedia.org/wikipedia/commons/b/b8/Ear.jpg xref: MA:0000236 xref: MAT:0000138 xref: MESH:A01.456.313 xref: MIAA:0000138 xref: ncithesaurus:Ear xref: NIF_GrossAnatomy:birnlex_1062 xref: OpenCyc:Mx4rvViXS5wpEbGdrcN5Y29ycA xref: OpenCyc:Mx4rvVjL05wpEbGdrcN5Y29ycA xref: SCTID:1910005 xref: UMLS:C0013443 xref: VHOG:0000330 xref: XAO:0000189 is_a: UBERON:0000020 ! sense organ is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0002105 ! vestibulo-auditory system property_value: external_definition "The organ of hearing and of equilibrium. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000330", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/ear"} property_value: has_relational_adjective "auricular" xsd:string property_value: homology_notes "Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000330", ontology="VHOG", source="DOI:10.1002/dvdy.20207 Boekhoff-Falk G, Hearing in Drosophila: Development of Johnston's organ and emerging parallels to vertebrate ear development. Developmental Dynamics (2005)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001691 name: external ear namespace: uberon def: "Part of the ear external to the tympanum (eardrum). It consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull[GO]." [GO:0042473, Wikipedia:External_ear] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "auricular region" BROAD [] synonym: "auricular region of head" EXACT [] synonym: "auris externa" RELATED [BTO:0002100] synonym: "outer ear" EXACT [] xref: AAO:0011037 xref: BTO:0002100 xref: EFO:0004221 xref: EHDAA2:0000462 xref: EHDAA:3786 xref: EMAPA:16991 xref: EV:0100354 xref: FMA:52781 xref: GAID:104 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/29/Gray907.png/200px-Gray907.png xref: MA:0000258 xref: MAT:0000147 xref: MESH:A09.246.272 xref: MIAA:0000147 xref: ncithesaurus:External_Ear xref: NIF_GrossAnatomy:birnlex_1705 xref: OpenCyc:Mx4rwOHtXJwpEbGdrcN5Y29ycA xref: SCTID:181176000 xref: UMLS:C0013453 xref: VHOG:0000311 xref: XAO:0000190 is_a: UBERON:0001444 ! subdivision of head relationship: part_of UBERON:0001690 ! ear property_value: external_definition "The external part of the organ, which consists of an outer portion (external auditory meatus) which leads to the tympanum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000311", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "Some species, like Amolops tormotus (Feng et al. 2006), have a cavity in front of the tympanic membrane which is considered to be an ear canal and thus an outer ear. (...) The ancestral lineage of amphibians separated from the mammalian lineage, approximately 350 million years ago, in the paleozoic era. Many of the important developments in the auditory systems emerged after the ancestral paths separated (Manley and Clack 2003). This implies that shared features, like the tympanic middle ear, developed independently in different vertebrate lineages.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000311", ontology="VHOG", source="DOI:10.1007/s00359-008-0327-1 Schoffelen RLM, Segenhout JM, Van Dijk P, Mechanics of the exceptional anuran ear. Journal of Comparative Physiology A (2008)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:9709 {source="Wikipedia"} [Term] id: UBERON:0001694 name: petrous part of temporal bone namespace: uberon def: "The petrous portion of the temporal bone or pyramid is pyramidal and is wedged in at the base of the skull between the sphenoid and occipital bones. Directed medially, forward, and a little upward, it presents for examination a base, an apex, three surfaces, and three angles, and contains, in its interior, the essential parts of the organ of hearing. The petrous portion is among the most basal elements of the skull and forms part of the endocranium.[WP,unvetted]." [Wikipedia:Petrous_part_of_the_temporal_bone] comment: derivative of prootic and opisthotic subset: uberon_slim synonym: "pars petrosa (os temporale)" EXACT [FMA:52871] synonym: "pars petrosa ossis temporalis" EXACT [] synonym: "petromastoid part of temporal bone" EXACT [FMA:52871] synonym: "petrosal" BROAD [VHOG:0001553] synonym: "petrosal bone" EXACT [FMA:52871] synonym: "petrous bone" EXACT [FMA:52871] synonym: "temporal bone petrous part" EXACT [] xref: EHDAA2:0001452 xref: EMAPA:17683 xref: FMA:52871 xref: GAID:234 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/9/96/Gray137.png/200px-Gray137.png xref: MA:0001477 xref: MESH:A02.835.232.781.885.681 xref: ncithesaurus:Ciliary_Process xref: SCTID:361733004 xref: UMLS:C1261761 xref: VHOG:0001553 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005913 ! zone of bone organ is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0001678 ! temporal bone relationship: part_of UBERON:0002517 {source="FMA"} ! basicranium property_value: external_definition "The petrosal bone arises from the two otic bones on the lateral wall of the chondrocranium and encases the inner ear of mammals. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.258, see_Liem_KF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001553", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001703 name: neurocranium namespace: uberon def: "Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof." [PMID:11523816, TAO:MAH, Wikipedia:Neuroranium, ZFA:0001580] comment: Development notes: The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]. Composition notes: It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton[WP] AO notes: It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ... subset: uberon_slim subset: vertebrate_core synonym: "brain box" EXACT [] synonym: "brain case" RELATED [ZFA:0001580] synonym: "brain pan" RELATED [http://www.thefreedictionary.com/braincase] synonym: "braincase" RELATED [ZFA:0001580] xref: AAO:0010153 xref: EHDAA2:0000243 xref: FMA:53672 xref: MA:0000317 xref: SCTID:361731002 xref: TAO:0001580 xref: XAO:0003170 xref: ZFA:0001580 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0011158 {source="FMA"} ! primary subdivision of skull relationship: develops_from UBERON:0004761 ! cartilaginous neurocranium relationship: part_of UBERON:0003128 ! cranium property_value: external_definition "Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001580", ontology="TAO", source="TAO:MAH"} property_value: has_relational_adjective "neurocranial" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001708 name: jaw skeleton namespace: uberon def: "Subdivision of skeleton which includes upper and lower jaw skeletons." [UBERON:cjm, Wikipedia:Jaw] comment: TODO: move ZFA:0001227 (it is the entire jaw skeleton). Editor notes: in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates. Development notes: There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983). subset: uberon_slim subset: vertebrate_core synonym: "anterior splanchnocranium" RELATED [] synonym: "jaw" EXACT [MA:0001905] synonym: "jaw cartilage" EXACT [ZFA:0001227] synonym: "jaws" RELATED [] synonym: "mandibular arch" RELATED [TAO:0001227] synonym: "mandibular arch skeleton" EXACT [ZFA:0001227] synonym: "oral jaw skeleton" RELATED [] synonym: "pharyngeal arch 1 skeleton" RELATED [] synonym: "visceral arch 1" RELATED [] xref: AAO:0000988 xref: BTO:0001749 xref: FMA:54396 xref: GAID:214 xref: galen:Jaw xref: MA:0001905 xref: MESH:A02.835.232.781.324.502 xref: ncithesaurus:Jaw xref: OpenCyc:Mx4rvVjjEZwpEbGdrcN5Y29ycA xref: SCTID:181811001 xref: TAO:0001227 xref: UMLS:C0022359 xref: ZFA:0001227 is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0011595 ! jaw region property_value: external_definition "Skeletal and cartilaginous elements of the first pharyngeal arch.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001227", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001711 name: eyelid namespace: uberon def: "An eyelid is a thin fold of skin that covers and protects an eyeball. With the exception of the prepuce and the labia minora, it has the thinnest skin of the whole body. The levator palpebrae superioris muscle retracts the eyelid to 'open' the eye. This can be either voluntarily or involuntarily. The human eyelid features a row of eyelashes which serve to heighten the protection of the eye from dust and foreign debris, as well as from perspiration. 'Palpebral' (and 'blepharo') means relating to the eyelids. Its key function is to regularly spread the tears and other secretion on the eye surface to keep it moist, since the cornea must be continuously moist. They keep the eyes from drying out when asleep. Moreover, the blink reflex protects the eye from foreign bodies. [WP,unvetted]." [Wikipedia:Eyelid] comment: Each eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva. AO notes: FMA divides this into skin, fascia, conjunctiva. Consider adding 'eye surface', like MA subset: uberon_slim synonym: "blephara" RELATED PLURAL [] synonym: "blepharon" EXACT [] synonym: "palpebra" EXACT [] synonym: "palpebrae" RELATED PLURAL [] xref: BTO:0002241 xref: EHDAA2:0000487 xref: EHDAA:9037 xref: EMAPA:17829 xref: EV:0100338 xref: FMA:54437 xref: GAID:72 xref: http://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/8/84/Eye_makeup.jpg/200px-Eye_makeup.jpg xref: MA:0000268 xref: MESH:A01.456.505.420.504 xref: ncithesaurus:Eyelid xref: OpenCyc:Mx4rvVi4m5wpEbGdrcN5Y29ycA xref: SCTID:265782007 xref: UMLS:C0015426 xref: VHOG:0000016 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000019 {source="multiple"} ! camera-type eye property_value: has_relational_adjective "palpebral" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001735 name: tonsillar ring namespace: uberon def: "lymphoid tissue ring located in the pharynx and to the back of the oral cavity. The ring consists of (from superior to inferior): Pharyngeal tonsil (also known as 'adenoids' when infected) Tubal tonsil (where Eustachian tube opens in the nasopharynx) Palatine tonsils (commonly called 'the tonsils' in the vernacular, less commonly termed 'faucial tonsils') Lingual tonsils Some animals, but not humans, have one or two additional tonsils: Soft palate tonsil Paraepiglottic tonsil[WP]." [Wikipedia:Waldeyer's_ring] comment: see also FMA:79771 naso-pharyngeal lymphoid tissue subset: uberon_slim synonym: "anulus lymphoideus pharyngis" EXACT LATIN [FMA:55070, FMA:TA] synonym: "oropharyngeal lymphoid tissue" EXACT [] synonym: "pharyngeal lymphatic ring" EXACT [] synonym: "pharyngeal lymphoid ring" EXACT [] synonym: "Waldeyer's ring" EXACT [] synonym: "Waldeyer's tonsillar ring" EXACT [] xref: FMA:55070 xref: MA:0000752 xref: ncithesaurus:Waldeyers_Tonsillar_Ring xref: SCTID:56411004 xref: UMLS:C0459892 is_a: UBERON:0001962 ! gut-associated lymphoid tissue relationship: part_of UBERON:0001042 ! chordate pharynx property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001744 name: lymphoid tissue namespace: uberon def: "Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP]." [Wikipedia:Lymphoid_tissue] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "lymphatic tissue" EXACT [] synonym: "lymphocytic tissue" EXACT [] xref: BTO:0000753 xref: FMA:55220 xref: GAID:342 xref: galen:LymphoidTissue xref: MA:0002436 xref: MESH:A10.549 xref: ncithesaurus:Lymphoid_Tissue xref: SCTID:181768009 xref: UMLS:C0024296 is_a: UBERON:0000479 ! tissue relationship: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002465 ! lymphoid system property_value: dubious_for_taxon NCBITaxon:7776 {notes="lampreys lack organized lymphoid tissue", source="NBK27108"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001745 name: secondary nodular lymphoid tissue namespace: uberon def: "A lymphoid follicle that contains a germinal center." [CL:tm] subset: uberon_slim synonym: "peripheral lymphoid tissue" EXACT [] synonym: "secondary lymphoid nodule" EXACT [] synonym: "secondary lymphoid tissue" EXACT [] xref: FMA:55224 xref: GAID:946 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/2f/Keimzentrum.jpg/200px-Keimzentrum.jpg is_a: UBERON:0000444 ! lymphoid follicle relationship: develops_from UBERON:0010422 ! primary nodular lymphoid tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001747 name: parenchyma of thyroid gland namespace: uberon def: "A parenchyma that is part of a thyroid follicle [Obol]." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "parenchyma of thyroid" EXACT [OBOL:accepted] synonym: "parenchyma of thyroid follicle" EXACT [OBOL:automatic] synonym: "parenchyma of thyroid gland follicle" EXACT [OBOL:automatic] synonym: "thyroid follicle parenchyma" EXACT [OBOL:automatic] synonym: "thyroid gland follicle parenchyma" EXACT [OBOL:automatic] synonym: "thyroid gland parenchyma" EXACT [] synonym: "thyroid parenchyma" EXACT [OBOL:accepted] xref: BTO:0004579 xref: FMA:55515 xref: MA:0000730 xref: SCTID:371402001 is_a: UBERON:0000353 ! parenchyma is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0002046 ! thyroid gland property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001750 name: lacrimal apparatus namespace: uberon def: "The lacrimal apparatus is the physiologic system containing the orbital structures for tear production and drainage. It consists of: (a) the lacrimal gland, which secretes the tears, and its excretory ducts, which convey the fluid to the surface of the eye; (b) the lacrimal canaliculi, the lacrimal sac, and the nasolacrimal duct, by which the fluid is conveyed into the cavity of the nose. [WP,unvetted]." [Wikipedia:Lacrimal_apparatus] comment: todo - resolve canaliculus vs tear duct vs lacrimal vs nasolacrimal. AO notes: this is an eye appendage in ncit, along with eyelid and eyebrow. in MA, part of eye surface part_of eye subset: uberon_slim synonym: "apparatus lacrimalis" RELATED LATIN [Wikipedia:Lacrimal_apparatus] synonym: "nasolacrimal drainage system" RELATED [UBERON:cjm] xref: FMA:55605 xref: GAID:901 xref: http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png xref: MA:0000274 xref: MESH:A09.371.463 xref: ncithesaurus:Lacrimal_Apparatus xref: UMLS:C0022903 is_a: UBERON:0000477 ! anatomical cluster is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000019 {source="FMA", source="MA"} ! camera-type eye relationship: part_of UBERON:0010409 {source="MA"} ! eye surface property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001751 name: dentine namespace: uberon def: "Collagen-rich odontogenic tissue characteristic of teeth and tooth-like skeletal elements (e.g., odontodes); mature dentine is mineralized and develops from predentine tissue; often (but not always) tubular and acellular[VSAO]." [VSAO:0000069, Wikipedia:Dentin] comment: Dentine is found in the fossil record as early as the late Cambrian, in fish, where it may have had a role in electrochemical sensing of the environment as well as assisting in defense[WP]. Editors note: note the asserted dual is_a parentage, as dentine is both skeletal tissue and a substance subset: uberon_slim subset: vertebrate_core synonym: "dentin" EXACT [MA:0002542] synonym: "dentine of tooth" EXACT [] synonym: "predentin" NARROW [GO:0070468] xref: BTO:0003453 xref: FMA:55628 xref: GAID:1272 xref: MA:0002542 xref: MESH:A14.254.900.280 xref: ncithesaurus:Dentin xref: SCTID:362112004 xref: TAO:0005143 xref: UMLS:C0011429 xref: VHOG:0001589 xref: VSAO:0000069 xref: XAO:0004051 xref: ZFA:0005143 is_a: UBERON:0001973 ! substance of tooth is_a: UBERON:0010365 {source="VSAO"} ! odontoid tissue relationship: develops_from UBERON:0011587 {source="VSAO"} ! pre-dentine property_value: external_definition "Mineralized collagen containing substance that forms the tooth structure.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005143", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "dentinal" xsd:string property_value: homology_notes "Dentine is a bona fide vertebrate novelty, and dentine-secreting odontoblasts represent a cell type that is exclusively derived from the neural crest.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001589", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001752 name: enamel namespace: uberon def: "A dentine-like hypermineralized substance that covers the tooth tip. Enamel's primary mineral is hydroxylapatite, which is a crystalline calcium phosphate. Unlike dentin and bone, enamel does not contain collagen. Instead, it has two unique classes of proteins called amelogenins and enamelins[WP]." [Wikipedia:Enamel_organ, ZFIN:curator] comment: AO notes: part_of tooth enamel organ in MA. Editor notes: current classification under substance of tooth may be turned into taxon GCI (e.g. sharks have enamel in dermal denticles) subset: uberon_slim subset: vertebrate_core synonym: "enamel of tooth" EXACT [] synonym: "enamel tissue" EXACT [VSAO:curator] synonym: "enameloid" RELATED [] synonym: "tooth enamel" EXACT [] xref: BTO:0001844 xref: FMA:55629 xref: http://upload.wikimedia.org/wikipedia/commons/6/66/Enamelorgan11-17-05.jpg xref: MA:0002543 xref: MESH:A14.254.900.255 xref: ncithesaurus:Enamel xref: SCTID:362113009 xref: UMLS:C0011350 xref: VSAO:0000065 xref: XAO:0004198 is_a: UBERON:0001973 {source="FMA"} ! substance of tooth is_a: UBERON:0010365 {source="VSAO"} ! odontoid tissue relationship: develops_from UBERON:0011588 {source="VSAO"} ! pre-enamel property_value: external_definition "Skeletal tissue that consists of an avascular, noncollagenous, hypermineralized matrix that is deposited by ameloblasts that are excluded from the matrix. Enamel develops from organic pre-enamel tissue that is replaced by a largely inorganic matrix.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000065", ontology="VSAO", source="PSPUB:0000170"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:9359 {source="PMID:19730686"} property_value: never_in_taxon NCBITaxon:9816 {source="PMID:19730686"} [Term] id: UBERON:0001753 name: cementum namespace: uberon def: "A bone-like mineralized tissue secreted by cementoblasts on the surface of root dentine or, in some animals, crown enamel[Diekwisch 2001]. Substance of tooth produced by cementoblasts; surrounds the dentine of the root of the tooth[FMA]. a specialized calcified substance covering the root of a tooth. Cementum is excreted by cells called cementoblasts within the root of the tooth and is thickest at the root apex. Its coloration is yellowish and it is softer than enamel and dentin due to being less mineralized[WP]." [Wikipedia:Cementum] comment: Cementum, the supporting tissue that anchors mammalian and crocodylian teeth into their sockets, differs among species and can have features of dentine, of bone, and of calcified cartilage, as well as unique features. Cementum is deposited by cementoblasts onto existing dentine. As in bone and dentine, cementoblasts produce an organic matrix, the main constituent of which is collagen type I (Bosshardt, 2005), but cementum, dentine, and bone also share a number of important noncollagenous matrix components such as osteopontin, osteocalcin, bone sialoprotein, a2-HS- glycoprotein, dentine matrix protein, dentine sialoprotein, and den- tine phosphoprotein (McKee et al., 1996; Bosshardt, 2005). it has been argued that in all rodents and ruminants, cementum is a form of calcified cartilage[H&W] synonym: "bone of attachment" RELATED [VSAO:0000062] synonym: "cement" EXACT [] synonym: "cement of tooth" EXACT [] synonym: "cementum" EXACT [] synonym: "cementum of tooth" EXACT [] xref: BTO:0002525 xref: FMA:55630 xref: http://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg xref: MA:0002541 xref: MESH:A14.254.646.267 xref: ncithesaurus:Cementum xref: SCTID:362114003 xref: UMLS:C0011343 xref: VSAO:0000062 xref: XAO:0004196 is_a: UBERON:0001973 ! substance of tooth is_a: UBERON:0010365 {source="VSAO"} ! odontoid tissue property_value: external_definition "Odontoid tissue that is deposited by cementoblasts onto dentine tissue and functions to attach teeth, odontodes and other odontogenic derivatives to bone tissue and the integument.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000062", ontology="VSAO", source="PSPUB:0000170"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001754 name: dental pulp namespace: uberon def: "the part in the center of a tooth made up of living soft tissue and cells called odontoblasts[WP]." [Wikipedia:Dental_pulp] subset: uberon_slim subset: vertebrate_core synonym: "dental pulp cell" RELATED [BTO:0000339] synonym: "pulp of tooth" EXACT [] synonym: "tooth pulp" EXACT [ZFA:0005141] xref: BTO:0000339 xref: FMA:55631 xref: GAID:1270 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/2e/Tooth_Section.svg/200px-Tooth_Section.svg.png xref: MA:0001599 xref: MESH:A14.254.900.260 xref: ncithesaurus:Dental_Pulp xref: SCTID:362110007 xref: TAO:0005141 xref: UMLS:C0011399 xref: VHOG:0001469 xref: ZFA:0005141 is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0011825 {source="FMA"} ! loose connective tissue relationship: develops_from UBERON:0001763 {source="ZFA"} ! odontogenic papilla relationship: part_of UBERON:0001091 ! calcareous tooth property_value: external_definition "Material in the center of the dentine of the mature tooth. In secondary teeth the pulp contains blood vessels and odontoblast.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005141", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "The oral cavity of vertebrates is generally thought to arise as an ectodermal invagination. Consistent with this, oral teeth are proposed to arise exclusively from ectoderm, contributing to tooth enamel epithelium, and from neural crest derived mesenchyme, contributing to dentin and pulp (reference 1); Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin (reference 2).[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001469", ontology="VHOG", source="DOI:10.1038/nature07304 Soukup V, Epperlein HH, Horacek I, Cerny R, Dual epithelial origin of vertebrate oral teeth. Nature (2008), DOI:10.1186/1471-2148-11-307 The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula. BMC Evolutionary Biology (2011)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001756 name: middle ear namespace: uberon def: "The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window)[GO]." [GO:0042474, Wikipedia:Middle_ear] subset: uberon_slim synonym: "auris media" RELATED LATIN [Wikipedia:Middle_ear] synonym: "auris media" RELATED [BTO:0002099] xref: AAO:0011065 xref: BTO:0002099 xref: EHDAA2:0001181 xref: EHDAA:5693 xref: EMAPA:17000 xref: EV:0100357 xref: FMA:56513 xref: GAID:165 xref: MA:0000253 xref: MAT:0000146 xref: MESH:A09.246.397 xref: MIAA:0000146 xref: ncithesaurus:Middle_Ear xref: NIF_GrossAnatomy:birnlex_1695 xref: OpenCyc:Mx4rvbw1j5wpEbGdrcN5Y29ycA xref: SCTID:181185000 xref: UMLS:C0013455 xref: VHOG:0000312 xref: XAO:0000191 is_a: UBERON:0000477 ! anatomical cluster relationship: part_of UBERON:0001690 ! ear property_value: external_definition "The intermediate portion of the ear which consists of a small air-filled and membrane-lined chamber. It is lodged in the temporal bone and continues with the nasopharynx through the Eustachian tube. It is separated from the external ear by the tympanic membrane and from the inner ear by the fenestrae. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000312", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000312", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001758 name: periodontium namespace: uberon def: "The tissues that invest or help to invest and support the teeth, including the periodontal ligament, gingivae, cementum, and alveolar and supporting bone[BTO]." [BTO:0001021, Wikipedia:Periodontium] comment: note FMA treats periodontium and periodontal ligament as the same synonym: "paradentium" RELATED [MESH:A14.254.646] synonym: "periodontal ligament" RELATED INCONSISTENT [FMA:56665] synonym: "periodontal membrane" RELATED [MA:0002467] synonym: "tooth supporting structure" RELATED [MESH:A14.254.646] xref: BTO:0001021 xref: FMA:56665 xref: GAID:216 xref: http://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg xref: MESH:A14.254.646 xref: ncithesaurus:Periodontium xref: UMLS:C0031093 is_a: UBERON:0000479 {source="cjm"} ! tissue is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0003672 {source="cjm"} ! dentition property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001763 name: odontogenic papilla namespace: uberon def: "Tissue of the developing tooth. It is composed of pre-odontoblast and undiffentiated mesnchyme cells and connects to the basal lamina[ZFA]. The dental papilla is a condensation of ectomesenchymal cells called odontoblasts, seen in histologic sections of a developing tooth. It lies below a cellular aggregation known as the enamel organ. The dental papilla appears after 8-10 weeks intra uteral life. The dental papilla gives rise to the dentin and pulp of a tooth. The enamel organ, dental papilla, and dental follicle together forms one unit, called the tooth germ. This is of importance because all the tissues of a tooth and its supporting structures form from these distinct cellular aggregations." [Wikipedia:Dental_papilla, ZFA:0005140] subset: uberon_slim subset: vertebrate_core synonym: "dental papilla" RELATED [MA:0001598] synonym: "dentinal papilla" RELATED [BTO:0001839] synonym: "dermal papilla" RELATED INCONSISTENT [ISBN10:0073040584] synonym: "odontogenic condensation" EXACT [VSAO:0000025] synonym: "papilla dentis" RELATED LATIN [Wikipedia:Dental_papilla] synonym: "pharyngeal tooth mesenchyme" NARROW SENSU [ZFA:0005140] synonym: "tooth mesenchyme" RELATED [ZFA:0005140] xref: BTO:0001839 xref: FMA:57662 xref: GAID:1277 xref: http://upload.wikimedia.org/wikipedia/commons/2/22/Gray1011.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/22/Gray1011.png/200px-Gray1011.png xref: MA:0001598 xref: MESH:A14.254.900.720.250 xref: TAO:0005140 xref: VHOG:0001465 xref: VSAO:0000025 xref: XAO:0004045 xref: ZFA:0005140 is_a: UBERON:0003856 ! odontogenic mesenchyme is_a: UBERON:0005856 {source="JB"} ! developing mesenchymal condensation relationship: develops_from UBERON:0003856 {source="ZFA"} ! odontogenic mesenchyme relationship: part_of UBERON:0005176 {source="BTO", notes="suspect"} ! tooth enamel organ property_value: external_definition "Cell condensation that is a well-defined population of densely organized mesenchymal cells that aggregates adjacent to an epithelium.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000025", ontology="VSAO", source="PSPUB:0000170"} property_value: external_definition "Tissue of the developing tooth. It is composed of pre-odontoblast and undiffentiated mesnchyme cells and connects to the basal lamina.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005140", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001465", ontology="VHOG", source="DOI:10.1186/1471-2148-11-307 The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula. BMC Evolutionary Biology (2011)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001765 name: mammary duct namespace: uberon def: "Epithelial tube that transports milk[GO]." [GO:0060603, Wikipedia:Lactiferous_duct] comment: This structure regresses in most males subset: uberon_slim synonym: "ductus lactiferi" RELATED LATIN [Wikipedia:Lactiferous_duct] synonym: "ductus lactiferi" RELATED [BTO:0002845] synonym: "galactophorous tubule" RELATED [BTO:0002845] synonym: "lactiferous duct" EXACT [FMA:58006] synonym: "lactiferous gland duct" EXACT [Obol:automatic] synonym: "lactiferous tubule" RELATED [BTO:0002845] synonym: "mammary gland duct" EXACT [] xref: BTO:0002845 xref: FMA:58006 xref: http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg xref: MA:0000791 xref: ncithesaurus:Lactiferous_Duct xref: SCTID:361719004 xref: UMLS:C0222613 is_a: UBERON:0000058 ! duct is_a: UBERON:0003244 ! epithelium of mammary gland is_a: UBERON:0003914 ! epithelial tube relationship: part_of UBERON:0001911 ! mammary gland property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001766 name: anterior chamber of eyeball namespace: uberon def: "the fluid-filled space inside the eye between the iris and the cornea's innermost surface, the endothelium.[1] Aqueous humor is the fluid that fills the anterior chamber. Hyphema and glaucoma are two main pathologies in this area. In hyphema, blood fills the anterior chamber. In glaucoma, blockage of the canal of Schlemm prevents the normal outflow of aqueous humor, resulting in accumulation of fluid, increased intraocular pressure, and eventually blindness." [Wikipedia:Anterior_chamber_of_eyeball] comment: AO notes: space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball synonym: "anterior chamber" EXACT [HP:0000593, MP:0010709] synonym: "anterior chamber of eye" EXACT [] synonym: "camera anterior" EXACT [] synonym: "camera anterior bulbi oculi" RELATED LATIN [Wikipedia:Anterior_chamber_of_eyeball] synonym: "eye anterior chamber" EXACT [] xref: BTO:0002084 xref: EHDAA2:0000129 xref: EHDAA:9033 xref: EMAPA:18231 xref: FMA:58078 xref: GAID:889 xref: http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/1/1e/Schematic_diagram_of_the_human_eye_en.svg/200px-Schematic_diagram_of_the_human_eye_en.svg.png xref: MA:0000262 xref: MESH:A09.371.060.067 xref: ncithesaurus:Anterior_Chamber_of_the_Eye xref: SCTID:181160009 xref: UMLS:C0003151 xref: VHOG:0001431 is_a: UBERON:0006311 {source="FMA"} ! chamber of eyeball relationship: part_of UBERON:0001801 ! anterior segment of eyeball property_value: external_definition "The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001431", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/anterior+chamber"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001768 name: uvea namespace: uberon def: "pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]." [Wikipedia:Uvea] comment: TODO - check child terms, isa vs partof. See also MA:0001284 subset: uberon_slim synonym: "pars iridica retinae" RELATED [Wikipedia:Uvea] synonym: "tunica vasculatis oculi" RELATED [Wikipedia:Uvea] synonym: "tunica vasculosa bulbi" RELATED LATIN [Wikipedia:Uvea] synonym: "tunica vasculosa of eyeball" EXACT [FMA:58103] synonym: "uvea" EXACT [FMA:58103] synonym: "uveal tract" EXACT [FMA:58103] synonym: "vascular layer of eyeball" RELATED [FMA:58103] xref: FMA:58103 xref: GAID:912 xref: http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/e/eb/Gray869.png/200px-Gray869.png xref: MA:0002480 xref: MESH:A09.371.894 xref: ncithesaurus:Uvea xref: SCTID:280648000 xref: UMLS:C0042160 is_a: UBERON:0002203 ! vasculature of eye relationship: part_of UBERON:0001801 ! anterior segment of eyeball property_value: has_relational_adjective "uveal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: present_in_taxon NCBITaxon:7955 {source="doi:10.1177/0192623311409597"} [Term] id: UBERON:0001769 name: iris namespace: uberon def: "a membrane in the eye, responsible for controlling the amount of light reaching the retina. The iris consists of pigmented fibrovascular tissue known as a stroma. It is the most forward portion of the eye and the only one seen on superficial inspection. The stroma connects a sphincter muscle (sphincter pupillae), which contracts the pupil, and a set of dilator muscles (dilator pupillae) which open it. The back surface is covered by a heavily pigmented epithelial layer two cells thick (the iris pigment epithelium), but the front surface has no epithelium. The high pigment content blocks light from passing through the iris and restricts it to the pupil. The outer edge of the iris, known as the root, is attached to the sclera and the anterior ciliary body. The iris and ciliary body together are known as the anterior uvea. Just in front of the root of the iris is the region through which the aqueous humour constantly drains out of the eye, with the result that diseases of the iris often have important effects on intraocular pressure, and indirectly on vision. Depending on the amount of light, the iris makes the pupil larger or smaller." [Wikipedia:Iris_(anatomy)] comment: Taxon notes: The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development - dx.doi.org/10.1006/dbio.1998.9019 subset: uberon_slim subset: vertebrate_core synonym: "anterior uvea" RELATED [] synonym: "irises" RELATED PLURAL [VHOG:0000101] xref: AAO:0010347 xref: BTO:0000653 xref: EFO:0004245 xref: EMAPA:19154 xref: EV:0100345 xref: FMA:58235 xref: GAID:917 xref: MA:0000273 xref: MESH:A09.371.894.513 xref: ncithesaurus:Iris xref: OpenCyc:Mx4rvVjbppwpEbGdrcN5Y29ycA xref: SCTID:181164000 xref: TAO:0001238 xref: UMLS:C0022077 xref: VHOG:0000101 xref: XAO:0000185 xref: ZFA:0001238 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0004128 {source="XAO"} ! optic vesicle relationship: part_of UBERON:0011892 ! anterior uvea property_value: external_definition "The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000101", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000101", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001770 name: lacrimal canaliculus namespace: uberon def: "The lacrimal canaliculi, also known as the lacrimal canals or lacrimal ducts, are the small channels in each eyelid that commence at minute orifices, termed puncta lacrimalia, on the summits of the papillae lacrimales, seen on the margins of the lids at the lateral extremity of the lacus lacrimalis. The superior duct, the smaller and shorter of the two, at first ascends, and then bends at an acute angle, and passes medialward and downward to the lacrimal sac. The inferior duct at first descends, and then runs almost horizontally to the lacrimal sac. At the angles they are dilated into ampullæ. Microscopically, they are lined by nonkeratinizing stratified squamous epithelium surrounded by fibrous tissue. Outside the latter is a layer of striped muscle, continuous with the lacrimal part of the Orbicularis oculi; at the base of each lacrimal papilla the muscular fibers are circularly arranged and form a kind of sphincter. [WP,unvetted]." [Wikipedia:Lacrimal_canaliculi] comment: todo - resolve canaliculus vs tear duct vs lacrimal vs nasolacrimal subset: uberon_slim synonym: "canaliculus lacrimalis" RELATED LATIN [Wikipedia:Lacrimal_canaliculi] xref: FMA:58245 xref: MA:0001294 xref: ncithesaurus:Lacrimal_Canaliculus xref: SCTID:263348000 xref: UMLS:C0459631 is_a: UBERON:0000063 ! organ segment is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001850 ! lacrimal duct property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001773 name: sclera namespace: uberon def: "The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted]." [Wikipedia:Sclera] comment: Development notes: Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]. Taxon notes: Multi-tissue structure that composes the opaque fibrous outer layer of the eye[ZFA] Seko et al demonstrate chondrogenic potential doi:10.1371/journal.pone.0003709 and identify this as connective tissue. Disease notes: implicated in rheumatoid arthritis. Structure notes: continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe. Taxon notes: in fish, reptiles and monotremes the connective tissue of the sclera is skeletal subset: uberon_slim subset: vertebrate_core synonym: "scleral capsule" RELATED [] xref: AAO:0010354 xref: BTO:0001606 xref: EMAPA:19027 xref: EV:0100342 xref: FMA:58269 xref: GAID:911 xref: http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/1/1e/Schematic_diagram_of_the_human_eye_en.svg/200px-Schematic_diagram_of_the_human_eye_en.svg.png xref: MA:0000280 xref: MESH:A09.371.784 xref: ncithesaurus:Sclera xref: OpenCyc:Mx4rv7yR55wpEbGdrcN5Y29ycA xref: SCTID:181163006 xref: UMLS:C0036410 xref: VHOG:0001274 xref: XAO:0000183 xref: ZFA:0005563 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0012430 {source="FMA"} ! tunica fibrosa of eyeball property_value: external_definition "The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001274", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/sclera"} property_value: has_relational_adjective "scleral" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001775 name: ciliary body namespace: uberon def: "circumferential tissue inside the eye composed of the ciliary muscle and ciliary processes." [Wikipedia:Ciliary_body] subset: uberon_slim subset: vertebrate_core synonym: "anterior uvea" RELATED [] synonym: "ciliary bodies" RELATED PLURAL [VHOG:0000102] synonym: "corpus ciliare" RELATED LATIN [Wikipedia:Ciliary_body] synonym: "corpus ciliare" RELATED [Wikipedia:Ciliary_body] synonym: "ocular ciliary body" EXACT [] xref: AAO:0010341 xref: BTO:0000260 xref: EMAPA:19065 xref: EV:0100346 xref: FMA:58295 xref: GAID:916 xref: http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/1/1e/Schematic_diagram_of_the_human_eye_en.svg/200px-Schematic_diagram_of_the_human_eye_en.svg.png xref: MA:0000264 xref: MESH:A09.371.894.280 xref: ncithesaurus:Ciliary_Body xref: SCTID:263340007 xref: UMLS:C0008779 xref: VHOG:0000102 xref: XAO:0000186 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0011892 ! anterior uvea property_value: homology_notes "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000102", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001776 name: optic choroid namespace: uberon def: "vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]." [Wikipedia:Choroid] comment: check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA subset: uberon_slim subset: vertebrate_core synonym: "chorioid" RELATED [BTO:0001829] synonym: "choroid" EXACT [MA:0000263] synonym: "choroid coat" EXACT [Wikipedia:Choroid] synonym: "choroidea" EXACT [Wikipedia:Choroid] synonym: "choroidea" RELATED LATIN [Wikipedia:Choroid] synonym: "eye choroid" EXACT [VHOG:0001568] synonym: "optic choroid" RELATED [ZFA:0005229] synonym: "posterior uvea" EXACT [Wikipedia:Uvea#Regions] xref: BTO:0001829 xref: EMAPA:19077 xref: EMAPA:25087 xref: EV:0100347 xref: FMA:58298 xref: GAID:913 xref: http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/1/1e/Schematic_diagram_of_the_human_eye_en.svg/200px-Schematic_diagram_of_the_human_eye_en.svg.png xref: MA:0000263 xref: MESH:A09.371.894.223 xref: ncithesaurus:Choroid xref: SCTID:181172003 xref: TAO:0005229 xref: UMLS:C0008520 xref: VHOG:0001568 xref: ZFA:0005229 is_a: UBERON:0002203 ! vasculature of eye relationship: part_of UBERON:0001768 {source="MA"} ! uvea property_value: has_relational_adjective "choroidal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001777 name: substantia propria of cornea namespace: uberon def: "The substantia propria (or stroma of cornea) is fibrous, tough, unyielding, and perfectly transparent. It is composed of about 200 flattened lamellæ (plates of collagen fibrils), superimposed one on another. They are each about 1.5-2.5 micrometres in thickness. These fibrils run at different angles between the limbi. Fibres of the layers frequently interweave, the anterior lamellæ interweaving more than posterior lamellæ. The fibres of each lamella are parallel with one another, but at right angles to those of adjacent lamellæ. The lamellæ are produced by keratocytes (corneal corpuscles), which occupy about 10% of the substantia propria. These lamellæ are made up of bundles of modified connective tissue, the fibres of which are directly continuous with those of the sclera. More collagen fibres run in a temporal-nasal direction than run in the superior-inferior direction. This is often ignored by corneal transplant surgeons, leading to poor corneal mechanical strength in corneal transplant patients. [WP,unvetted]." [Wikipedia:Corneal_stroma] comment: This class was created automatically from a combination of ontologies subset: uberon_slim subset: vertebrate_core synonym: "cornea stroma" EXACT [] synonym: "corneal stroma" EXACT [] synonym: "stroma of cornea" EXACT [] synonym: "substantia propria" RELATED [] xref: EFO:0002514 xref: EMAPA:17602 xref: FMA:58306 xref: GAID:893 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/66/Gray871.png/200px-Gray871.png xref: MA:0001245 xref: MESH:A09.371.060.217.228 xref: ncithesaurus:Corneal_Stroma xref: SCTID:362511000 xref: TAO:0002189 xref: UMLS:C0010040 xref: ZFA:0001685 is_a: UBERON:0003566 ! head connective tissue is_a: UBERON:0003891 ! stroma is_a: UBERON:0010313 ! neural crest-derived structure relationship: develops_from UBERON:0002342 {source="UBERONREF:0000002"} ! neural crest relationship: part_of UBERON:0000964 ! cornea property_value: axiom_lost_from_external_ontology "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002189", ontology="TAO"} property_value: axiom_lost_from_external_ontology "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002189", ontology="TAO"} property_value: external_definition "Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002189", ontology="TAO", source="ZFIN:ZDB-PUB-061010-3"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001778 name: ciliary epithelium namespace: uberon def: "A double layer covering the ciliary body that produces aqueous humor." [Wikipedia:Ciliary_body#Ciliary_epithelium] synonym: "ciliary body epithelium" EXACT [FMA:58464] synonym: "epithelium of ciliary body" EXACT [FMA:58464] synonym: "ocular ciliary epithelium" EXACT [] xref: BTO:0001770 xref: FMA:58464 xref: MA:0001238 xref: ncithesaurus:Ciliary_Epithelium xref: SCTID:280870004 xref: UMLS:C0459736 is_a: UBERON:0000488 {source="FMA"} ! atypical epithelium is_a: UBERON:0007625 ! pigment epithelium of eye is_a: UBERON:0010371 ! ecto-epithelium relationship: part_of UBERON:0001775 {source="MA"} ! ciliary body property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001780 name: spinal nerve namespace: uberon def: "Neural tree (organ) which is directly continuous with the spinal cord. Examples: Fifth cervical spinal nerve, third lumbar spinal nerve." [Wikipedia:Spinal_nerve] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "backbone nerve" EXACT [OBOL:automatic] synonym: "nerve of backbone" EXACT [OBOL:automatic] synonym: "nerve of spinal column" EXACT [OBOL:automatic] synonym: "nerve of spine" EXACT [OBOL:automatic] synonym: "nerve of vertebral column" EXACT [OBOL:automatic] synonym: "nervi spinales" RELATED LATIN [Wikipedia:Spinal_nerve] synonym: "spinal column nerve" EXACT [OBOL:automatic] synonym: "spinal nerve tree" EXACT [] synonym: "spine nerve" EXACT [OBOL:automatic] synonym: "vertebral column nerve" EXACT [OBOL:automatic] xref: AAO:0011101 xref: BTO:0000870 xref: EHDAA2:0001898 xref: EMAPA:16989 xref: FMA:5858 xref: GAID:841 xref: http://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg xref: MA:0000233 xref: MESH:A08.800.800.720 xref: ncithesaurus:Spinal_Nerve xref: OpenCyc:Mx4rwK_iFJwpEbGdrcN5Y29ycA xref: SCTID:361099009 xref: UMLS:C0037941 xref: VHOG:0000824 xref: XAO:0003101 is_a: UBERON:0001021 ! nerve relationship: part_of UBERON:0000010 ! peripheral nervous system property_value: external_definition "Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000824", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/spinal+nerve"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001781 name: layer of retina namespace: uberon def: "any of the layers that make up the retina[MP]." [MP:0003727] comment: Note that MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers subset: vertebrate_core synonym: "retina layer" EXACT [] synonym: "retina neuronal layer" EXACT [MP:0006069] synonym: "retinal layer" EXACT [] synonym: "retinal neuronal layer" EXACT [MP:0006069] xref: AAO:0010353 xref: FMA:58617 xref: MA:0001319 xref: ncithesaurus:Retina_Layer xref: SCTID:280657006 xref: UMLS:C0459649 xref: XAO:0000266 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 ! organ component layer relationship: part_of UBERON:0000966 ! retina property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001782 name: pigmented layer of retina namespace: uberon def: "A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup[ZFA]. the pigmented cell layer just outside the neurosensory retina that nourishes retinal visual cells, and is firmly attached to the underlying choroid and overlying retinal visual cells[WP]." [Wikipedia:Retinal_pigment_epithelium, ZFIN:curator] comment: editor note - we follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers subset: uberon_slim subset: vertebrate_core synonym: "epithelium, retinal pigment" RELATED [BTO:0001177] synonym: "outer pigmented layer of retina" EXACT [] synonym: "pigment epithelium of retina" EXACT [] synonym: "pigmented epithelium" RELATED [] synonym: "pigmented retina" RELATED [] synonym: "pigmented retina epithelium" EXACT [] synonym: "pigmented retinal epithelium" EXACT [] synonym: "PRE" RELATED [] synonym: "retinal pigment epithelium" EXACT [MP:0005201, Wikipedia:Retinal_pigment_epithelium] synonym: "retinal pigment layer" RELATED [VHOG:0000536] synonym: "retinal pigmented epithelium" EXACT [ZFA:0000144] synonym: "RPE" RELATED [] synonym: "stratum pigmentosa retinae, p. pigmentosa retinae" RELATED LATIN [Wikipedia:Retinal_pigment_epithelium] synonym: "stratum pigmentosum (retina)" EXACT [] xref: AAO:0011096 xref: BTO:0001177 xref: EHDAA2:0001465 xref: EHDAA:4765 xref: EMAPA:17172 xref: FMA:58627 xref: http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/55/Gray881.png/200px-Gray881.png xref: MA:0000279 xref: ncithesaurus:Retinal_Pigment_Epithelium xref: SCTID:280662007 xref: TAO:0000144 xref: UMLS:C0035322 xref: VHOG:0000536 xref: XAO:0003217 xref: ZFA:0000144 is_a: UBERON:0001781 ! layer of retina is_a: UBERON:0007625 ! pigment epithelium of eye is_a: UBERON:0010371 ! ecto-epithelium relationship: develops_from UBERON:0005424 ! presumptive retinal pigmented epithelium property_value: external_definition "A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000144", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "The monolayer of pigmented epithelium covering the neural retina.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011096", ontology="AAO", source="ZFA:0000144"} property_value: homology_notes " (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000536", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001800 name: sensory ganglion namespace: uberon def: "the clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells." [MP:0000960] comment: This class was created automatically from a combination of ontologies synonym: "ganglion sensorium" EXACT [] xref: AEO:0001000 xref: FMA:5885 xref: MA:0002566 xref: MESH:A08.340.390 xref: ncithesaurus:Sensory_Ganglion xref: UMLS:C0206429 is_a: UBERON:0000045 ! ganglion property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001801 name: anterior segment of eyeball namespace: uberon def: "The anterior segment is the front third of the eye that includes the structures in front of the vitreous humour: the cornea, iris, ciliary body, and lens. Within the anterior segment are two fluid-filled spaces: the anterior chamber between the posterior surface of the cornea (i.e. the corneal endothelium) and the iris; the posterior chamber between the iris and the front face of the vitreous. Aqueous humor fills these spaces within the anterior segment and provides nutrients to the surrounding structures." [Wikipedia:Anterior_segment_of_eyeball] subset: vertebrate_core synonym: "anterior segment of eye" EXACT [] synonym: "anterior segment of the eye" EXACT [] synonym: "eye anterior segment" EXACT [] synonym: "segmentum anterius (bulbus oculi)" EXACT [] synonym: "segmentum anterius bulbi oculi" RELATED LATIN [Wikipedia:Anterior_segment_of_eyeball] xref: FMA:58865 xref: http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png xref: MA:0002484 xref: MESH:A09.371.060 xref: ncithesaurus:Anterior_Eye_Segment xref: SCTID:280658001 xref: UMLS:C0003153 xref: ZFA:0005566 is_a: UBERON:0000063 ! organ segment is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0001802 [Term] id: UBERON:0001802 name: posterior segment of eyeball namespace: uberon def: "The posterior segment is the back two-thirds of the eye that includes the anterior hyaloid membrane and all structures behind it: the vitreous humor, retina, choroid, and optic nerve. On the anterior side of the lens is the aqueous humour which is bounded on all sides by the lens, ciliary body, suspensory ligaments, and by the cornea. It lets light through without refraction, helps maintain the shape of the eye and suspends the delicate lens. In some animals, the retina contains a reflective layer (the tapetum lucidum) which increases the amount of light each photosensitive cell perceives, allowing the animal to see better under low light conditions." [Wikipedia:Posterior_segment_of_eyeball] subset: vertebrate_core synonym: "eye posterior segment" EXACT [] synonym: "posterior segment of eye" EXACT [] synonym: "posterior segment of the eye" EXACT [] synonym: "segmentum posterius (bulbus oculi)" EXACT [] synonym: "segmentum posterius bulbi oculi" RELATED LATIN [Wikipedia:Posterior_segment_of_eyeball] xref: FMA:58868 xref: http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/1/1e/Schematic_diagram_of_the_human_eye_en.svg/200px-Schematic_diagram_of_the_human_eye_en.svg.png xref: MA:0002485 xref: ncithesaurus:Posterior_Eye_Segment xref: SCTID:280659009 xref: UMLS:C0278450 xref: ZFA:0005567 is_a: UBERON:0000063 ! organ segment is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001803 name: epithelium of lens namespace: uberon def: "The cells of the lens epithelium regulate most of the homeostatic functions of the lens.[6] As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions." [Wikipedia:Lens_(anatomy)#Lens_Epithelium] comment: Usage notes: this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former subset: vertebrate_core synonym: "epithelial tissue of eye lens" EXACT [OBOL:automatic] synonym: "epithelial tissue of lens" EXACT [OBOL:automatic] synonym: "epithelium lentis" EXACT LATIN [FMA:58871, FMA:TA] synonym: "epithelium of eye lens" EXACT [OBOL:automatic] synonym: "eye lens epithelial tissue" EXACT [OBOL:automatic] synonym: "eye lens epithelium" EXACT [OBOL:automatic] synonym: "lens epithelial tissue" EXACT [OBOL:automatic] synonym: "lens epithelium" EXACT [] xref: BTO:0001873 xref: FMA:58871 xref: MA:0001301 xref: SCTID:362523006 xref: TAO:0001326 xref: XAO:0004094 xref: ZFA:0001326 is_a: UBERON:0000484 ! simple cuboidal epithelium is_a: UBERON:0007625 ! pigment epithelium of eye is_a: UBERON:0010371 ! ecto-epithelium relationship: part_of UBERON:0000965 ! lens of camera-type eye property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001811 name: conjunctiva namespace: uberon def: "The conjunctiva is a clear mucous membrane consisting of cells and underlying basement membrane that covers the sclera (white part of the eye) and lines the inside of the eyelids. It is made of epithelial tissue. [WP,unvetted]." [Wikipedia:Conjunctiva] subset: uberon_slim synonym: "wall of conjunctival sac" EXACT [] xref: AAO:0010343 xref: BTO:0003415 xref: EFO:0000374 xref: EV:0100340 xref: FMA:59011 xref: GAID:898 xref: http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/55/Gray883.png/200px-Gray883.png xref: MA:0000265 xref: MESH:A09.371.192 xref: ncithesaurus:Conjunctiva xref: SCTID:181161008 xref: UMLS:C0009758 xref: XAO:0000182 is_a: UBERON:0000060 {source="FMA"} ! anatomical wall is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0005908 {source="cjm"} ! conjunctival sac relationship: part_of UBERON:0010409 {source="MA"} ! eye surface property_value: has_relational_adjective "conjunctival" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001820 name: sweat gland namespace: uberon def: "Sweat glands are exocrine glands, found in the skin of all mammal species, that are used for body temperature regulation. In humans a system of apocrine - and merocrine sweat glands is the main method of cooling. Many other mammals rely on panting or other means as a primary source of cooling, but still use sweat glands to aid in body temperature regulation. Sweat also serves a purpose of increasing friction on the palms of hands or the pads of paws. Both apocrine and merocrine sweat glands contain myoepithelial cells (from Greek myo-, 'muscle'), specialized epithelial cells located between the gland cells and the underlying basal lamina. Myoepithelial cell contractions squeeze the gland and discharge the accumulated secretions. The secretory activities of the gland cells and the contractions of myoepithelial cells are controlled by both the autonomic nervous system and by the circulating hormones. Additionally, ceruminous glands, which produce ear wax, and mammary glands, which produce milk, are frequently considered to be modified sweat glands. [WP,unvetted]." [Wikipedia:Sweat_gland] comment: todo - check if all sweat glands are epidermal - see EMAPA:29743 subset: organ_slim subset: uberon_slim synonym: "glandula sudorifera" RELATED [BTO:0001331] synonym: "sudoriferous gland" RELATED [BTO:0001331] synonym: "sudoriparous gland" RELATED [BTO:0001331] xref: BTO:0001331 xref: EV:0100160 xref: FMA:59152 xref: GAID:943 xref: http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Skin.svg/200px-Skin.svg.png xref: MA:0000150 xref: MESH:A10.336.899 xref: ncithesaurus:Sweat_Gland xref: OpenCyc:Mx4rvVjx15wpEbGdrcN5Y29ycA xref: SCTID:361700009 xref: UMLS:C0038989 xref: VHOG:0001467 is_a: UBERON:0002365 {source="MA"} ! exocrine gland is_a: UBERON:0007771 ! epidermis gland relationship: develops_from UBERON:0005089 {evidence="definitional"} ! sweat gland placode relationship: part_of UBERON:0001003 {source="FMA"} ! epidermis property_value: external_definition "A gland that secretes sweat, found in the dermis or subcutaneous tissue, opening by a duct on the body surface. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001467", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/sweat+gland"} property_value: homology_notes "Sweat glands (also called sudoriferous glands) are unique to mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001467", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.101", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001821 name: sebaceous gland namespace: uberon def: "A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP]." [MP:0000647, Wikipedia:Sebaceous_gland] comment: Usage notes: sebaceous glands are also found in glabrous areas of eyelids, nose, penis, labia minora and nipples, and do not always secrete into hair follices. This causes some confusion in classification. In addition some structures, such as preputial glands are sometimes called 'modified' sebaceous glands, implying a non-subclass relationship. we follow MP and MA in keeping this class generic and creating a distinct subclass for sebaceuous glands of the skin. The FMA class may be better placed under this subclass. subset: organ_slim subset: uberon_slim synonym: "glandula sebacea" RELATED LATIN [Wikipedia:Sebaceous_gland] synonym: "glandula sebaceae" RELATED [BTO:0001980] synonym: "sebaceous follicle" RELATED [BTO:0001980] xref: BTO:0001980 xref: EV:0100161 xref: FMA:59160 xref: GAID:900 xref: http://upload.wikimedia.org/wikipedia/commons/4/49/HairFollicle.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/4/49/HairFollicle.png/200px-HairFollicle.png xref: MA:0002565 xref: MESH:A10.336.827 xref: ncithesaurus:Sebaceous_Gland xref: SCTID:361697005 xref: UMLS:C0036505 xref: VHOG:0001468 is_a: UBERON:0002365 ! exocrine gland is_a: UBERON:0007771 ! epidermis gland is_a: UBERON:0012344 {source="Wikipedia"} ! holocrine gland relationship: develops_from UBERON:0005088 {evidence="definitional"} ! sebaceous gland placode relationship: part_of UBERON:0001003 {source="FMA", inconsistent_with="BTO"} ! epidermis relationship: part_of UBERON:0002330 ! exocrine system relationship: part_of UBERON:0006003 ! skin adnexa property_value: external_definition "Any of the numerous holocrine glands in the dermis that empty into a hair follicle and produce and secrete sebum. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001468", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/sebaceous+gland"} property_value: homology_notes "Sebaceous glands are also limited to mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001468", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.102", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001826 name: nasal cavity mucosa namespace: uberon def: "the mucous membrane that lines the nasal cavity[MP]." [MP:0002238] comment: TODO - check lining vs part of. split olfactory and nasal mucosa? synonym: "mucosa of nose" EXACT [FMA:59684] synonym: "mucous membrane of nose" EXACT [FMA:59684] synonym: "nasal mucosa" RELATED [] synonym: "tunica mucosa nasalis" EXACT [] synonym: "tunica mucosa nasi" EXACT LATIN [FMA:59684, FMA:TA] xref: BTO:0000912 xref: FMA:59684 xref: GAID:302 xref: SCTID:310211009 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004785 ! respiratory system mucosa relationship: part_of UBERON:0000004 ! olfactory apparatus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001828 name: gingiva namespace: uberon def: "The fibrous investing tissue, covered by keratinized epithelium, that immediately surrounds a tooth and is contiguous with its periodontal ligament and with the mucosal tissues of the mouth[Glossary of Periodontal Terms 2001]." [ISBN10:0013002015, Wikipedia:Gingiva] comment: Editor notes: FMA has a 3-level breakdown of jaws into: region, jaw (skeleton+gums), skeleton. subset: uberon_slim synonym: "gingival mucosa" RELATED [] synonym: "gum" EXACT [FMA:59762] synonym: "gum tissue" EXACT [UBERON:cjm] synonym: "gums" EXACT [] xref: BTO:0000519 xref: EFO:0001925 xref: EV:0100064 xref: FMA:59762 xref: GAID:1257 xref: galen:Gingiva xref: http://upload.wikimedia.org/wikipedia/commons/2/2e/Tooth_Section.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/2e/Tooth_Section.svg/200px-Tooth_Section.svg.png xref: MA:0000342 xref: MESH:A14.254.646.480 xref: ncithesaurus:Gingiva xref: OpenCyc:Mx4rvViWnZwpEbGdrcN5Y29ycA xref: SCTID:181224006 xref: UMLS:C0017562 xref: VHOG:0001269 is_a: UBERON:0003729 ! mouth mucosa relationship: part_of UBERON:0003729 {source="Carranza"} ! mouth mucosa relationship: part_of UBERON:0011595 ! jaw region property_value: has_relational_adjective "gingival" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001839 name: bony labyrinth namespace: uberon def: "A system of fluid passages in the inner ear, including both the cochlea, which is part of the auditory system, and the vestibular system, which provides the sense of balance. The bony labyrinth, or osseous labyrinth, is the network of passages with bony walls lined with periosteum. The bony labyrinth is lined with the membranous labyrinth. There is a layer of perilymph between them. The three parts of the bony labyrinth are the vestibule of the ear, the semicircular canals, and the cochlea. The vestibular system is the region of the inner ear where the semicircular canals converge, close to the cochlea (the hearing organ). The vestibular system works with the visual system to keep objects in focus when the head is moving. Joint and muscle receptors also are important in maintaining balance. The brain receives, interprets, and processes the information from these systems that control our balance. [WP,unvetted]." [Wikipedia:Bony_labyrinth] comment: Ideally we would place a spatially disjoint from relationship to membranous labyrinth, but there are many parts in common. this should be resolved. subset: uberon_slim synonym: "labyrinthus osseus" RELATED LATIN [Wikipedia:Bony_labyrinth] synonym: "osseous labyrinth" EXACT [] synonym: "osseus labyrinth" RELATED [] xref: AAO:0011078 xref: BTO:0004685 xref: EV:0100362 xref: FMA:60179 xref: http://upload.wikimedia.org/wikipedia/commons/2/22/Gray920.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/22/Gray920.png/200px-Gray920.png xref: MA:0000238 xref: ncithesaurus:Osseous_Labyrinth xref: SCTID:279727008 xref: UMLS:C0458699 xref: VHOG:0001219 xref: XAO:0000193 is_a: UBERON:0000477 ! anatomical cluster is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0001694 ! petrous part of temporal bone relationship: part_of UBERON:0001846 ! internal ear relationship: part_of UBERON:0004681 ! vestibular system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001840 name: semicircular canal namespace: uberon def: "One of three half-circular, interconnected tubes located inside each ear[WP]. Fluid-filled toroidal spaces, arranged orthogonally to each other in the ear, that detect angular accelerations. (See Anatomical Atlas entry for semicircular canals by T. Whitfield.)" [Wikipedia:Semicircular_canal, ZFIN:curator] comment: Note that MA divides this into osseous and duct. In FMA, this is systemically part of the bony labyrinth. Note this is an anatomical space in ZFA. The MA treatment has advantages for representing the neuroepithelium, which should not be part of bone. Also check duct vs canal subset: uberon_slim subset: vertebrate_core synonym: "canalis semicircularis" RELATED LATIN [Wikipedia:Semicircular_canal] synonym: "ductus semicirculares" RELATED PLURAL [BTO:0003383, FMA:71880, FMA:TA] synonym: "scc" RELATED [TAO:0000431] synonym: "semicircular canals" EXACT PLURAL [TAO:0000431] xref: AAO:0011098 xref: BTO:0003383 xref: EV:0100365 xref: FMA:60186 xref: GAID:776 xref: http://upload.wikimedia.org/wikipedia/commons/3/33/Balance_Disorder_Illustration_A.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/33/Balance_Disorder_Illustration_A.png/200px-Balance_Disorder_Illustration_A.png xref: MA:0000249 xref: MESH:A09.246.631.663 xref: ncithesaurus:Semicircular_Canal xref: SCTID:279757004 xref: TAO:0000431 xref: UMLS:C0036622 xref: VHOG:0001144 xref: XAO:0000198 xref: ZFA:0000431 is_a: UBERON:0000025 {source="GO"} ! tube is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: develops_from UBERON:0003051 ! ear vesicle relationship: part_of UBERON:0001846 {source="MA"} ! internal ear relationship: part_of UBERON:0001849 {source="OG"} ! membranous labyrinth property_value: external_definition "Fluid-filled toroidal spaces, arranged orthogonally to each other in the ear, that detect angular accelerations. (See Anatomical Atlas entry for semicircular canals by T. Whitfield.)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000431", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. These ducts are sometimes called canals, but technically the term semicircular canal applies to the spaces in the osseus labyrinth in which the semicircular ducts lie.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001144", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.414", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001844 name: cochlea namespace: uberon def: "The cochlea is the auditory portion of the inner ear. Its core component is the Organ of Corti, the sensory organ of hearing, which is distributed along the partition separating fluid chambers in the coiled tapered tube of the cochlea. The name is from the Latin for snail, which is from the Greek kokhlias 'snail, screw,' from kokhlos 'spiral shell,' in reference to its coiled shape; the cochlea is coiled in most mammals, monotremes being the exceptions. [WP,unvetted]." [Wikipedia:Cochlea] comment: AO notes: sources vary in connection to bony labyrinth. Taxon notes: The association with 'lagena' in frog and fish comes from HOG, although HOG is inconsistent here, associating lagena with XAO cochlea and ZFA cochlear duct. NBK53175 says: "In contrast, the ventrally located auditory chambers have undergone more extensive evolutionary modifications. The saccule and lagena are prominent auditory organs in fish but the saccule has a vestibular role in mammals and birds, and the lagena is absent in mammals. The primary au- ditory organ in mammals and birds is the cochlea, which has no known counterpart in amphibians and fish (Riley and Phillips, 2003)" subset: uberon_slim subset: vertebrate_core synonym: "cochlear organ" RELATED [BTO:0000267] synonym: "cochlear part of bony labyrinth" EXACT [] synonym: "lagena" EXACT SENSU [XAO:0000197] xref: AAO:0000253 xref: BTO:0000267 xref: EFO:0000357 xref: EMAPA:17597 xref: EV:0100363 xref: FMA:60201 xref: GAID:724 xref: http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/c7/Cochlea-crosssection.png/200px-Cochlea-crosssection.png xref: MA:0000240 xref: MAT:0000144 xref: MESH:A09.246.631.246 xref: MIAA:0000144 xref: ncithesaurus:Cochlea xref: NIF_GrossAnatomy:birnlex_1190 xref: NIF_GrossAnatomy:birnlex_883 xref: OpenCyc:Mx4rvqfJmJwpEbGdrcN5Y29ycA xref: SCTID:181187008 xref: TAO:0000374 xref: UMLS:C0009195 xref: VHOG:0000691 xref: XAO:0000197 xref: ZFA:0000374 is_a: UBERON:0000477 ! anatomical cluster is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0001839 ! bony labyrinth property_value: external_definition "A spiral-shaped cavity in the petrous portion of the temporal bone of the inner ear, containing the nerve endings essential for hearing and forming one of the divisions of the labyrinth. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000691", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/cochlea"} property_value: has_relational_adjective "cochlear" xsd:string property_value: homology_notes "Because achieving high sensitivity is generally advantageous for auditory organs, it is not surprising that evidence for cochlear amplification is also seen in nonmammals. Spontaneous otoacoustic emissions (SOAEs) are narrow-band sound signals emitted from the inner ear, and it is generally assumed that their energy derives from the hair-cell molecular motors underlying cochlear amplification. However, all terrestrial vertebrates studied so far (including amphibians) show very similar SOAEs. The most parsimonious explanation for the universality of this phenomena is that some kind of amplifying mechanism is at least as old as land vertebrates themselves.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000691", ontology="VHOG", source="DOI:10.1016/S0959-4388(98)80033-0 Manley GA, Koeppl C, Phylogenetic development of the cochlea and its innervation. Current Opinion in Neurobiology (1998)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001846 name: internal ear namespace: uberon def: "Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation." [PMID:16217737, Wikipedia:Internal_ear, ZFIN:curator] comment: This class was created automatically from a combination of ontologies subset: uberon_slim subset: vertebrate_core synonym: "auris interna" RELATED [BTO:0000630] synonym: "inner ear" EXACT [] synonym: "labyrinth" RELATED [] synonym: "otocyst" RELATED [] xref: AAO:0000238 xref: BTO:0000630 xref: EFO:0001363 xref: EHDAA2:0000831 xref: EHDAA:504 xref: EMAPA:16194 xref: EV:0100361 xref: FMA:60909 xref: GAID:871 xref: galen:InnerEar xref: http://upload.wikimedia.org/wikipedia/commons/thumb/1/19/Gray923.png/200px-Gray923.png xref: MA:0000237 xref: MAT:0000145 xref: MESH:A09.246.631 xref: MIAA:0000145 xref: ncithesaurus:Internal_Ear xref: NIF_GrossAnatomy:birnlex_1196 xref: OpenCyc:Mx4rwJ8SsJwpEbGdrcN5Y29ycA xref: SCTID:181189006 xref: TAO:0000217 xref: UMLS:C0022889 xref: VHOG:0000284 xref: XAO:0000192 xref: ZFA:0000217 is_a: UBERON:0000477 ! anatomical cluster is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0003051 {evidence="definitional"} ! ear vesicle relationship: part_of UBERON:0001690 ! ear property_value: external_definition "The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000217", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000284", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001849 name: membranous labyrinth namespace: uberon def: "Organ with organ cavity which consists of the vestibular labyrinth and the cochlear labyrinth. Examples: There are only two membranous labyrinths, the right and the left.[FMA]" [FMA:FMA, Wikipedia:Membranous_labyrinth] comment: inner ear has parts membranous and osseuous/bony labyrinth. it's not clear where the edinburgh terms 'labyrinth' belong, we place them here for now subset: organ_slim subset: uberon_slim synonym: "labyrinthus membranaceus" RELATED LATIN [Wikipedia:Membranous_labyrinth] xref: AAO:0011060 xref: EHDAA:4698 xref: EMAPA:17815 xref: EV:0100367 xref: FMA:61022 xref: http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray924.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/8/8c/Gray924.png/200px-Gray924.png xref: MA:0000242 xref: ncithesaurus:Membranous_Labyrinth xref: SCTID:263790009 xref: UMLS:C0458700 xref: VHOG:0000729 xref: XAO:0000194 is_a: UBERON:0000062 ! organ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0001846 ! internal ear property_value: external_definition "A system of communicating epithelial sacs and ducts within the bony labyrinth, containing the endolymph. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000729", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/membranous+labyrinth"} property_value: homology_notes "The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000729", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001850 name: lacrimal duct namespace: uberon def: "Organ with organ cavity which connects the vestibule of the conjunctival sac to the nasal cavity. Examples: There are only two lacrimal ducts, the right and the left lacrimal ducts.[FMA]" [FMA:61063, Wikipedia:Lacrimal_canaliculi] comment: todo - resolve canaliculus vs tear duct vs lacrimal vs nasolacrimal subset: uberon_slim synonym: "lacrimal caniculus" RELATED [Wikipedia:Lacrimal_duct] synonym: "tear duct" RELATED [MA:0001295] xref: EMAPA:19245 xref: FMA:61063 xref: MA:0001295 is_a: UBERON:0000058 ! duct is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001750 {source="FMA"} ! lacrimal apparatus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001851 name: cortex namespace: uberon def: "Outermost layer of an organ[WP]." [Wikipedia:Cortex_(anatomy)] comment: Note that this class is used more generically than in FMA, and includes e.g. cortex of hair subset: uberon_slim subset: upper_level synonym: "cortex" EXACT [FMA:61109] synonym: "cortex of organ" EXACT [] xref: EFO:0000383 xref: EHDAA:9344 xref: FMA:61109 xref: galen:Cortex is_a: UBERON:0000064 ! organ part property_value: has_relational_adjective "cortical" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001853 name: utricle of membranous labyrinth namespace: uberon def: "one of the two otolith organs located in the vertebrate inner ear. These use small stones and a viscous fluid to stimulate hair cells to detect motion and orientation. The utricle is larger than the saccule and is of an oblong form, compressed transversely, and occupies the upper and back part of the vestibule, lying in contact with the recessus ellipticus and the part below it. The utricle contains mechanoreceptors called hair cells that distinguish between degrees of tilting of the head, thanks to their apical cilia set-up. These are covered by otolith which, due to gravity, pull on the cilia and tilt them. Depending on whether the tilt is in the direction of the kinocilium or not, the resulting hair cell polarisation is excitatory (depolarising) or inhibitory (hyperpolarisation), respectively. This signal to the vestibular nerve (which takes it to the brainstem) does not adapt with time. The effect of this is that, for example, an individual lying down to sleep will continue to detect that they are lying down hours later when they awaken[WP]." [Wikipedia:Utricle_(ear)] comment: XAO/AAO to be checked - see https://github.com/seger/aao/issues/5; AAO has both utricle and utriculus; these are generally considered synonyms - e.g. http://www.fishbase.org/glossary/Glossary.php?q=utriculus subset: organ_slim subset: uberon_slim subset: vertebrate_core synonym: "membranous labyrinth utricle" EXACT [] synonym: "utricle" EXACT [] synonym: "utriculus" EXACT [ZFA:0000700] synonym: "utriculus (labyrinthus vestibularis)" EXACT [] xref: AAO:0000625 xref: AAO:0011109 xref: BTO:0001807 xref: EHDAA2:0002153 xref: EHDAA:4726 xref: EMAPA:17293 xref: EV:0100368 xref: FMA:61113 xref: MA:0000247 xref: ncithesaurus:Utricle xref: SCTID:279817006 xref: TAO:0000700 xref: UMLS:C0042158 xref: VHOG:0000289 xref: XAO:0000195 xref: ZFA:0000700 is_a: UBERON:0002518 {source="ZFA", source="Wikipedia"} ! otolith organ property_value: external_definition "The portion of the membranous labyrinth of the ear into which the semicircular ducts find their outlet. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000289", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000289", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001854 name: saccule of membranous labyrinth namespace: uberon def: "A bed of sensory cells situated in the inner ear. The saccule translates head movements into neural impulses which the brain can interpret. The saccule is sensitive to linear translations of the head, specifically movements up and down (think about moving on an elevator). When the head moves vertically, the sensory cells of the saccule are disturbed and the neurons connected to them begin transmitting impulses to the brain. These impulses travel along the vestibular portion of the eighth cranial nerve to the vestibular nuclei in the brainstem. is the smaller of the two vestibular sacs. It is globular in form and lies in the recessus sphæricus near the opening of the scala vestibuli of the cochlea. Its cavity does not directly communicate with that of the utricle. The anterior part of the saccule exhibits an oval thickening, the macula acustica sacculi, or macula, to which are distributed the saccular filaments of the vestibular branch of the vestibulocochlear nerve, also known as the acoustic nerve or cranial nerve VIII[WP]." [Wikipedia:Saccule] comment: XAO/AAO to be checked - see https://github.com/seger/aao/issues/5 subset: organ_slim subset: uberon_slim subset: vertebrate_core synonym: "membranous labyrinth saccule" EXACT [] synonym: "saccule" EXACT [] synonym: "sacculus" EXACT [ZFA:0000428] synonym: "sacculus" RELATED LATIN [Wikipedia:Saccule] synonym: "sacculus (labyrinthus vestibularis)" EXACT [] xref: AAO:0000550 xref: BTO:0001805 xref: EHDAA2:0001769 xref: EHDAA:4712 xref: EMAPA:17290 xref: EV:0100369 xref: FMA:61116 xref: http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/cb/Bigotolith.jpg/200px-Bigotolith.jpg xref: MA:0000246 xref: ncithesaurus:Saccule xref: SCTID:279827000 xref: TAO:0000428 xref: UMLS:C0036029 xref: VHOG:0000374 xref: XAO:0000196 xref: ZFA:0000428 is_a: UBERON:0002518 {source="ZFA", source="Wikipedia"} ! otolith organ property_value: external_definition "The most ventral chamber of the membranous labyrinth. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000374", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. (...) In all gnathostomes, the utriculus connects ventrally with a larger sac, called the sacculus (...) .[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000374", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001855 name: cochlear duct of membranous labyrinth namespace: uberon def: "An endolymph filled cavity inside the cochlea, located in between the scala tympani and the scala vestibuli, separated by the basilar membrane and Reissner's membrane (the vestibular membrane) respectively. Houses the organ of Corti[WP]." [Wikipedia:Cochlear_duct] comment: TODO: check cochlear duct vs cochlear aqueduct vs scala media subset: uberon_slim synonym: "cochlea duct" EXACT [NIF_GrossAnatomy:birnlex_2562] synonym: "cochlear aqueduct" RELATED [] synonym: "cochlear duct" EXACT [] synonym: "ductus cochlearis" RELATED [BTO:0001692] synonym: "ductus cochlearis" RELATED LATIN [Wikipedia:Cochlear_duct] synonym: "membranous cochlea" RELATED [BTO:0001692] synonym: "Reissner's canal" EXACT [] synonym: "reissners canal" EXACT [NIF_GrossAnatomy:birnlex_2562] synonym: "scala media" RELATED [Wikipedia:Cochlear_duct] synonym: "scala medias" EXACT [NIF_GrossAnatomy:birnlex_2562] synonym: "scala of Loewenberg" RELATED [BTO:0001692] xref: BTO:0001692 xref: EHDAA2:0000262 xref: EHDAA:4718 xref: EMAPA:17598 xref: FMA:61119 xref: GAID:874 xref: http://upload.wikimedia.org/wikipedia/commons/b/bc/Gray928.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/b/bc/Gray928.png/200px-Gray928.png xref: MA:0000243 xref: MESH:A09.246.631.246.292 xref: ncithesaurus:Cochlear_Duct xref: NIF_GrossAnatomy:birnlex_2562 xref: SCTID:279849006 xref: UMLS:C1323110 xref: VHOG:0000507 is_a: UBERON:0000058 ! duct is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005744 ! cranial conduit is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0001844 ! cochlea relationship: part_of UBERON:0001849 ! membranous labyrinth relationship: part_of UBERON:0002499 ! cochlear labyrinth property_value: external_definition "The coiled portion of the membranous labyrinth located inside the cochlea. It contains endolymph. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000507", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/cochlear+duct"} property_value: homology_notes "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. (...) In all gnathostomes, the utriculus connects ventrally with a larger sac, called the sacculus (...) In most groups of gnathostomes, the caudoventral evagination of the sacculus forms a small lagena, and in some diapsids and mammals the lagena develops into a longer duct. The lagena becomes greatly elongated in therians and coils to form the cochlear duct.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000507", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001856 name: semicircular duct namespace: uberon def: "any of the three loop-shaped membranous inner tubular parts of the semicircular canals that are about one-fourth the diameter of the corresponding outer bony canals, that communicate at each end with the utricle, and that have near one end an expanded ampulla containing an area of sensory epithelium" [http://dictionary.reference.com/browse/semicircular+duct] comment: TODO - check canal vs duct. see http://en.wikipedia.org/wiki/File:Gray927.png synonym: "ductus semicirculares" RELATED PLURAL [FMA:71880, FMA:TA] synonym: "membranous semicircular canal" RELATED [MA:0000251] xref: FMA:61122 xref: MA:0000251 xref: ncithesaurus:Semicircular_Duct xref: SCTID:279833009 xref: UMLS:C1323109 xref: VHOG:0000238 is_a: UBERON:0000058 ! duct is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0001840 {source="MA"} ! semicircular canal relationship: part_of UBERON:0001862 {source="FMA", source="MA"} ! vestibular labyrinth property_value: homology_notes "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus (...); Gnathostome ears have a horizontal semicircular duct. This brings their complement to three semicircular ducts, a pattern retained throughout gnathostome evolution.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000238", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414 and p.58", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001862 name: vestibular labyrinth namespace: uberon def: "The part of the membranous labyrinth that includes the utricle and saccule lodged within the vestibule and the semicircular ducts lodged eccentrically in the corresponding canals." [BTO:0001856] synonym: "labyrinthus vestibularis" RELATED [BTO:0001856] synonym: "vestibular apparatus" RELATED [] xref: BTO:0001856 xref: EHDAA2:0000832 xref: EMAPA:17286 xref: FMA:61255 xref: MA:0000245 xref: ncithesaurus:Vestibular_Labyrinth xref: SCTID:181188003 xref: UMLS:C0042606 xref: XAO:0004145 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0001849 ! membranous labyrinth property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001869 name: cerebral hemisphere namespace: uberon def: "One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA]" [FMA:FMA, Wikipedia:Cerebral_hemisphere] subset: uberon_slim synonym: "hemisphere" RELATED [VHOG:0001639] synonym: "hemispherium cerebri" RELATED LATIN [Wikipedia:Cerebral_hemisphere] synonym: "telencephalic vesicle" RELATED [] xref: AAO:0010480 xref: BTO:0000231 xref: EFO:0002521 xref: FMA:61817 xref: galen:CerebralHemisphere xref: http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png xref: MA:0000133 xref: ncithesaurus:Cerebral_Hemisphere xref: NIF_GrossAnatomy:birnlex_1042 xref: OpenCyc:Mx4rvigx5ZwpEbGdrcN5Y29ycA xref: SCTID:278251007 xref: UMLS:C0228174 xref: VHOG:0001639 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001893 ! telencephalon property_value: external_definition "Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010480", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001639", ontology="VHOG", source="DOI:10.1146/annurev.ne.04.030181.001505 Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001886 name: choroid plexus namespace: uberon def: "A network formed by blood vessels and the tela choroidea which secretes CSF into the ventricular spaces." [ISBN10:0471888893, Wikipedia:Choroid_plexus] comment: TODO - check relationship to ventricle. Check subclass - ZFA says vasculature. Note that FMA:61934 (choroid plexus of cerebral hemisphere) has exact synonym 'choroid plexus' but it is not clear that this belongs here, as the fourth ventricle is not in the cerebral hemisphere subset: uberon_slim subset: vertebrate_core synonym: "chorioid plexus" EXACT [FMA:61934] synonym: "choroid plexus of cerebral hemisphere" RELATED [FMA:61934] synonym: "plexus choroideus" EXACT LATIN [FMA:61934, FMA:TA] synonym: "plexus choroideus" RELATED LATIN [Wikipedia:Choroid_plexus] synonym: "ventricular choroid plexus" RELATED [] xref: BTO:0000258 xref: EFO:0001915 xref: FMA:61934 xref: GAID:607 xref: http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray708.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/b/b9/Gray708.svg/200px-Gray708.svg.png xref: MA:0000823 xref: MESH:A08.186.211.276.298 xref: ncithesaurus:Choroid_Plexus xref: SCTID:264450003 xref: TAO:0001443 xref: UMLS:C0008524 xref: VHOG:0001377 xref: ZFA:0001443 is_a: UBERON:0005284 ! brain vasculature is_a: UBERON:0005629 ! vascular plexus relationship: part_of UBERON:0004086 ! brain ventricle relationship: part_of UBERON:0005283 ! tela choroidea property_value: external_definition "A tuft of capillaries that project into the ventricles of the brain and secretes cerebral spinal fluid. The choroid plexus is covered by a cuboidal epithelium which maintains the integrity of the blood-brain barrier.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001443", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Fringe of the tela choroidea of the brain ventricles[MP]" xsd:string {source="MP:0000820"} property_value: has_relational_adjective "choroidal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001890 name: forebrain namespace: uberon def: "The most anterior region the brain including both the telencephalon and diencephalon." [Wikipedia:Forebrain, ZFIN:ZDB-PUB-961014-576] subset: uberon_slim subset: vertebrate_core synonym: "prosencephalon" RELATED [] xref: AAO:0010147 xref: BTO:0000478 xref: EFO:0000909 xref: EHDAA2:0000556 xref: EHDAA:3470 xref: EMAPA:16895 xref: FMA:61992 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/54/EmbryonicBrain.svg/200px-EmbryonicBrain.svg.png xref: MA:0000170 xref: MAT:0000105 xref: MESH:A08.186.211.730 xref: MIAA:0000105 xref: ncithesaurus:Fore-Brain xref: ncithesaurus:Prosencephalon xref: NIF_GrossAnatomy:birnlex_1509 xref: SCTID:362291003 xref: TAO:0000109 xref: UMLS:C0085140 xref: VHOG:0000383 xref: XAO:0000011 xref: ZFA:0000109 is_a: UBERON:0002616 ! regional part of brain relationship: develops_from UBERON:0003080 ! anterior neural tube relationship: part_of UBERON:0000955 ! brain property_value: axiom_lost_from_external_ontology "relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000109", ontology="TAO"} property_value: external_definition "Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010147", ontology="AAO", source="AAO:BJB"} property_value: external_definition "The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000109", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "prosencephalic" xsd:string property_value: homology_notes "In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000383", ontology="VHOG", source="PMID:8787764 Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001891 name: midbrain namespace: uberon def: "Organ component of neuraxis that has as its parts the tectum, cerebral peduncle, midbrain tegmentum and cerebral aqueduct[FMA]. The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally[ZFA]. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]." [FMA:61993, GO:0030901, Wikipedia:Midbrain, ZFIN:curator] comment: Editors note: developmental relationships need revised. AO notes: part of brainstem in ABA - we reject this in favor of ISBN10:0471888893 which has an implicit overlaps relationships subset: uberon_slim subset: vertebrate_core synonym: "mesencephalon" RELATED LATIN [Wikipedia:Midbrain] xref: AAO:0010149 xref: ABA:MB xref: BM:MB xref: BTO:0000138 xref: EFO:0000919 xref: EHDAA2:0001162 xref: EHDAA:3694 xref: EMAPA:16974 xref: EV:0100242 xref: FMA:61993 xref: http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG xref: http://upload.wikimedia.org/wikipedia/commons/thumb/f/f9/Human_brain_inferior_view_description.JPG/200px-Human_brain_inferior_view_description.JPG xref: MA:0000207 xref: MAT:0000106 xref: MESH:A08.186.211.132.659 xref: MIAA:0000106 xref: ncithesaurus:Mesencephalon xref: NIF_GrossAnatomy:birnlex_1667 xref: OpenCyc:Mx4rvsBUqpwpEbGdrcN5Y29ycA xref: RETIRED_EHDAA2:0001104 xref: SCTID:279099009 xref: TAO:0000128 xref: UMLS:C0025462 xref: VHOG:0000069 xref: XAO:0000014 xref: ZFA:0000128 is_a: UBERON:0002616 ! regional part of brain is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0009616 {evidence="definitional"} ! presumptive midbrain relationship: part_of UBERON:0000955 ! brain property_value: external_definition "Middle part of the brain composed of the optic tectum and penducular region.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010149", ontology="AAO", source="AAO:BJB"} property_value: external_definition "The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000128", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "mesencephalic" xsd:string property_value: homology_notes "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000069", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0001894 {source="ABA"} property_value: spatially_disjoint_from UBERON:0002028 {source="ABA"} [Term] id: UBERON:0001893 name: telencephalon namespace: uberon def: "Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA]." [FMA:62000, Wikipedia:Telencephalon] comment: The telencephalon is the name for a large region within the brain that is attributed many functions. Many people refer to it as the cerebrum; however, it is technically referred to as the telencephalon. As a more technical definition, the telencephalon refers to the cerebral hemispheres and other, smaller structures within the brain, although the telencephalon is one of the larger divisions (in terms of number). It is the anterior-most embryological division of the brain that develops from the prosencephalon. The telencephalon is composed of the following sub-regions; Limbic system; Cerebral cortex or cortices of the cerebral hemispheres, Basal ganglia, Olfactory bulb. The telencephalon comprises what most people think of as the 'brain' It lies on top of the brainstem and is the largest and most well-developed of the five major divisions of the brain. The telencephalon is the newest structure in the phylogenetic sense, with mammals having the largest and most well-developed among all species. It emerges from the prosencephalon, the first of three vesicles that form from the embryonic neural tube (Christine Fennema-Notestine, NIF_GrossAnatomy:birnlex_1115). subset: uberon_slim subset: vertebrate_core synonym: "cerebrum" EXACT [http://en.wikipedia.org/wiki/Talk\:Cerebrum] synonym: "endbrain" EXACT [Swanson:2004] xref: AAO:0010479 xref: ABA:CH xref: BM:Tel xref: BTO:0000239 xref: EFO:0000912 xref: EHDAA2:0001982 xref: EMAPA:16652 xref: EMAPA:16910 xref: EV:0100165 xref: FMA:62000 xref: GAID:621 xref: MA:0000183 xref: MAT:0000421 xref: MESH:A08.186.211.730.885 xref: MIAA:0000421 xref: NIF_GrossAnatomy:birnlex_1115 xref: SCTID:263353005 xref: TAO:0000079 xref: VHOG:0000283 xref: XAO:0000012 xref: ZFA:0000079 is_a: UBERON:0002780 ! regional part of forebrain is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001890 ! forebrain property_value: axiom_lost_from_external_ontology "relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000079", ontology="TAO"} property_value: external_definition "Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010479", ontology="AAO", source="AAO:BJB"} property_value: external_definition "The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000079", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "cerebral" xsd:string property_value: has_relational_adjective "telenencephalic" xsd:string property_value: homology_notes "From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000283", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0002037 {source="ABA"} property_value: taxon_notes "dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight." xsd:string {source="http://en.wikipedia.org/wiki/Telencephalon#Variation_among_species"} property_value: taxon_notes "In mammals the cortex covers almost the whole of the cerebral hemispheres." xsd:string {source="http://en.wikipedia.org/wiki/Telencephalon#Variation_among_species"} property_value: taxon_notes "In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles." xsd:string {source="http://en.wikipedia.org/wiki/Telencephalon#Variation_among_species"} property_value: taxon_notes "In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum." xsd:string {source="http://en.wikipedia.org/wiki/Telencephalon#Variation_among_species"} property_value: taxon_notes "In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb." xsd:string {source="http://en.wikipedia.org/wiki/Telencephalon#Variation_among_species"} property_value: taxon_notes "The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure." xsd:string {source="http://en.wikipedia.org/wiki/Telencephalon#Variation_among_species"} [Term] id: UBERON:0001894 name: diencephalon namespace: uberon def: "Organ component of neuraxis that has as its parts the epithalamus, thalamus, hypothalamus, subthalamus[FMA]. The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995." [FMA:62001, Wikipedia:Diencephalon, ZFIN:curator] comment: Note that in ABA, this is part of the brain stem subset: uberon_slim subset: vertebrate_core synonym: "between brain" EXACT [] synonym: "betweenbrain" RELATED [BTO:0000342] synonym: "diencephalon" RELATED LATIN [Wikipedia:Diencephalon] synonym: "interbrain" EXACT [Swanson:2004] synonym: "mature diencephalon" EXACT [FMA:62001] xref: AAO:0010481 xref: ABA:IB xref: BM:Die xref: BTO:0000342 xref: EFO:0000911 xref: EHDAA2:0000385 xref: EHDAA:1969 xref: EHDAA:2645 xref: EHDAA:3472 xref: EMAPA:16641 xref: EMAPA:16896 xref: EV:0100194 xref: FMA:62001 xref: GAID:618 xref: http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/54/EmbryonicBrain.svg/200px-EmbryonicBrain.svg.png xref: MA:0000171 xref: MAT:0000420 xref: MESH:A08.186.211.730.385 xref: MIAA:0000420 xref: ncithesaurus:Diencephalon xref: NIF_GrossAnatomy:birnlex_1503 xref: OpenCyc:Mx4rwC-V0JwpEbGdrcN5Y29ycA xref: SCTID:279328001 xref: TAO:0000101 xref: UMLS:C0012144 xref: VHOG:0000318 xref: XAO:0000013 xref: ZFA:0000101 is_a: UBERON:0002780 ! regional part of forebrain is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001890 ! forebrain property_value: external_definition "The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000101", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010481", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "diencephalic" xsd:string property_value: homology_notes "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000318", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0001891 {source="ABA"} property_value: spatially_disjoint_from UBERON:0002028 {source="ABA"} [Term] id: UBERON:0001895 name: metencephalon namespace: uberon def: "Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum." [Wikipedia:Metencephalon] comment: the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA]. subset: uberon_slim synonym: "epencephalon" EXACT [ncithesaurus:Epencephalon] synonym: "epencephalon-2" RELATED [FMA:62003] xref: BTO:0000673 xref: EHDAA2:0001149 xref: EHDAA:5498 xref: EMAPA:17071 xref: FMA:62003 xref: GAID:594 xref: http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/5/54/EmbryonicBrain.svg/200px-EmbryonicBrain.svg.png xref: MA:0000197 xref: MESH:A08.186.211.132.810.428 xref: ncithesaurus:Epencephalon xref: NIF_GrossAnatomy:birnlex_965 xref: UMLS:C1516904 xref: VHOG:0000741 is_a: UBERON:0004733 ! segmental subdivision of hindbrain is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0002028 ! hindbrain property_value: dubious_for_taxon NCBITaxon:7955 property_value: external_definition "The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000741", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/metencephalon"} property_value: homology_notes "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000741", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001898 name: hypothalamus namespace: uberon def: "A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia]." [Wikipedia:Hypothalamus, ZFIN:curator] comment: Taxon notes: all vertebrates contain a hypothalamus[WP]. subset: uberon_slim subset: vertebrate_core synonym: "hypothalamus" RELATED LATIN [Wikipedia:Hypothalamus] synonym: "preoptico-hypothalamic area" EXACT [] synonym: "preoptico-hypothalamic region" EXACT [] xref: AAO:0010484 xref: ABA:HY xref: BM:Die-Hy xref: BTO:0000614 xref: EFO:0000107 xref: EHDAA2:0000802 xref: EHDAA:5446 xref: EMAPA:17536 xref: EV:0100225 xref: FMA:62008 xref: GAID:460 xref: galen:Hypothalamus xref: http://upload.wikimedia.org/wikipedia/commons/9/9f/LocationOfHypothalamus.jpg xref: MA:0000173 xref: MAT:0000112 xref: MESH:A08.186.211.577.482 xref: MIAA:0000112 xref: ncithesaurus:Hypothalamus xref: NIF_GrossAnatomy:birnlex_734 xref: OpenCyc:Mx4rwEgr9JwpEbGdrcN5Y29ycA xref: SCTID:264483005 xref: TAO:0000032 xref: UMLS:C0020663 xref: VHOG:0000179 xref: XAO:0004070 xref: ZFA:0000032 is_a: UBERON:0002784 ! regional part of diencephalon relationship: part_of UBERON:0000349 ! limbic system relationship: part_of UBERON:0001894 ! diencephalon property_value: external_definition "A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000032", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Part of the diencephalon ventral to the thalamus consisting of connecting fibers and is a center for control of the autonomous nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010484", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "hypothalamic" xsd:string property_value: homology_notes "For instance, the vertebrate ventral diencephalon generates the hypothalamus which functions as a major endocrine center in cooperation with the hypophysis, the anterior part of the pituitary gland, located just ventral to the hypothalamus. In the amphioxus brain, the presence of a hypothalamus-like structure has been reported associated with the ventrally located Hatschek's pit, the hypothetical hypophysial homologue. It is thus conceivable that a hypothalamus-like structure originally involved in endocrine functions may have already been present before the establishment of vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000179", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0001897 {source="ABA"} [Term] id: UBERON:0001901 name: epithelium of trachea namespace: uberon alt_id: UBERON:0003227 def: "An epithelium that is part of a trachea." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "epithelial tissue of trachea" EXACT [OBOL:automatic] synonym: "epithelial tissue of windpipe" EXACT [OBOL:automatic] synonym: "epithelium of windpipe" EXACT [OBOL:automatic] synonym: "trachea epithelial tissue" EXACT [OBOL:automatic] synonym: "trachea epithelium" EXACT [] synonym: "tracheal epithelium" EXACT [] synonym: "windpipe epithelial tissue" EXACT [OBOL:automatic] synonym: "windpipe epithelium" EXACT [OBOL:automatic] xref: BTO:0001389 xref: EHDAA2:0002069 xref: EHDAA:5007 xref: EMAPA:16855 xref: EMAPA:18409 xref: FMA:62015 xref: MA:0001862 xref: ncithesaurus:Tracheal_Epithelium xref: UMLS:C1179002 xref: VHOG:0001045 is_a: UBERON:0000485 ! simple columnar epithelium is_a: UBERON:0004815 ! lower respiratory tract epithelium relationship: develops_from UBERON:0003258 ! endoderm of foregut relationship: part_of UBERON:0003126 ! trachea property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001902 name: epithelium of small intestine namespace: uberon def: "An epithelium that is part of a small intestine [Obol]." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies subset: vertebrate_core synonym: "epithelial tissue of small bowel" EXACT [OBOL:automatic] synonym: "epithelial tissue of small intestine" EXACT [OBOL:automatic] synonym: "epithelium of small bowel" EXACT [OBOL:automatic] synonym: "mid intestine epithelium" EXACT [ZFA:0005127] synonym: "small bowel epithelial tissue" EXACT [OBOL:automatic] synonym: "small bowel epithelium" EXACT [OBOL:automatic] synonym: "small intestinal epithelium" EXACT [] synonym: "small intestine epithelial tissue" EXACT [OBOL:automatic] synonym: "small intestine epithelium" EXACT [] xref: BTO:0001258 xref: FMA:62017 xref: MA:0001553 xref: SCTID:45480009 xref: TAO:0005127 xref: ZFA:0005127 is_a: UBERON:0001277 ! intestinal epithelium relationship: part_of UBERON:0001204 ! mucosa of small intestine relationship: part_of UBERON:0002108 ! small intestine property_value: external_definition "Intestinal epithelium which lines the lumen of the mid intestine.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005127", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001911 name: mammary gland namespace: uberon def: "The specialized accessory gland of the skin of female mammals that secretes milk. In the human female, it is a compound tubuloalveolar gland composed of 15 to 25 lobes arranged radially about the nipple and separated by connective and adipose tissue, each lobe having its own excretory (lactiferous) duct opening on the nipple. The lobes are subdivided into lobules, with the alveolar ducts and alveoli being the secretory portion of the gland[BTO]. The mouse forms five to six pairs of mammary glands that extend from the neck to the groin." [BTO:0000817, Wikipedia:Mammary_gland] comment: Note that this class corresponds to the generic mammary gland. The human mammary gland is in the thoracic/breast region and is therefore covered by the subclass "thoracic mammary gland" // Males typically only have rudimentary mammary glands, The male Dayak fruit bat has lactating mammary glands. Male lactation occurs infrequently in some species. We make a part_of association to female organism for now as this is the canonical case // AO notes: in MP, this is implicitly part of female reproductive system, but not female genitalia // A mouse mammary gland contains a single duct or sinus, forming 5-10 secondary ducts subset: organ_slim subset: uberon_slim synonym: "Brustdruese" RELATED [BTO:0000817] synonym: "dug" RELATED [Wikipedia:Mammary_gland] synonym: "glandula mammaria" EXACT PLURAL [FMA:57983, FMA:TA] synonym: "glandula mammaria" RELATED LATIN [Wikipedia:Mammary_gland] synonym: "lactiferous gland" EXACT [FMA:62088] synonym: "lobe of breast" EXACT [] synonym: "lobe of mammary gland" EXACT [] synonym: "mamma" RELATED [BTO:0000817] xref: BTO:0000817 xref: EFO:0000854 xref: EMAPA:17759 xref: EV:0100125 xref: http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Illu_breast_anatomy.jpg/200px-Illu_breast_anatomy.jpg xref: MA:0000145 xref: MAT:0000073 xref: MESH:A10.336.482 xref: MIAA:0000073 xref: ncithesaurus:Mammary_Gland xref: OpenCyc:Mx4rvVjVq5wpEbGdrcN5Y29ycA xref: SCTID:361720005 xref: UMLS:C0929301 xref: VHOG:0000398 is_a: UBERON:0002365 {source="MA"} ! exocrine gland is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005398 ! female reproductive gland relationship: develops_from UBERON:0005333 ! mammary bud relationship: part_of UBERON:0000474 {notes="see comments", source="VHOG"} ! female reproductive system relationship: part_of UBERON:0003100 {notes="see comments"} ! female organism property_value: external_definition "Any of the milk-producing apocrine glands typically occurring in pairs in female mammals and consisting of lobes containing clusters of alveoli with a system of ducts to convey the milk to an external nipple or teat. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000398", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/mammary+gland"} property_value: has_relational_adjective "mammary" xsd:string property_value: homology_notes "The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000398", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001912 name: lobule of lactiferous gland namespace: uberon def: "Organ component of the mammary gland which consists of an aggregate of mammary alveoli that communicate with a lobular lactiferous duct.[FMA]" [FMA:62090] comment: TODO - ensure correct terminology for lobes/lobules. FMA uses lobule for core term, but also has 'set of mammary gland lobes'. ISBN10:0123813611 states no separate lobes in mouse subset: uberon_slim synonym: "acinus of mammary gland" EXACT [] synonym: "breast lobe" RELATED [BTO:0004718] synonym: "lactiferous acinus" EXACT [] synonym: "lactiferous gland lobule" EXACT [] synonym: "lactiferous lobule" EXACT [] synonym: "lobe of breast" RELATED [BTO:0004718] synonym: "lobe of mammary gland" RELATED [BTO:0004718] synonym: "lobi glandulae mammariae" RELATED [BTO:0004718] synonym: "lobule of mammary gland" EXACT [] synonym: "lobus glandulae mammariae" RELATED [BTO:0004718] synonym: "mammary acinus" EXACT [] synonym: "mammary gland lobule" EXACT [] xref: BTO:0004718 xref: FMA:62090 xref: MA:0000793 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005156 ! reproductive structure relationship: part_of UBERON:0001911 ! mammary gland property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001915 name: endothelium of capillary namespace: uberon def: "An endothelium that is part of a capillary [Obol]." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "blood capillary endothelium" EXACT [OBOL:automatic] synonym: "capillary endothelium" EXACT [] synonym: "capillary vessel endothelium" EXACT [OBOL:automatic] synonym: "endothelium of blood capillary" EXACT [OBOL:automatic] synonym: "endothelium of capillary vessel" EXACT [OBOL:automatic] xref: BTO:0004954 xref: FMA:62114 xref: MA:0000711 xref: ncithesaurus:Capillary_Endothelium xref: UMLS:C0006904 is_a: UBERON:0004638 ! blood vessel endothelium relationship: part_of UBERON:0001982 ! capillary property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001917 name: endothelium of artery namespace: uberon def: "An endothelium that is part of an artery [Obol]." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "arterial endothelium" EXACT [] synonym: "artery endothelium" EXACT [] xref: AAO:0011013 xref: BTO:0004757 xref: FMA:62116 xref: MA:0000707 xref: ncithesaurus:Artery_Endothelium xref: UMLS:C1179025 xref: VHOG:0001215 xref: XAO:0000357 is_a: UBERON:0003915 ! endothelial tube is_a: UBERON:0004638 ! blood vessel endothelium is_a: UBERON:0004700 ! arterial system endothelium relationship: part_of UBERON:0001637 ! artery property_value: external_definition "The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011013", ontology="AAO", source="XAO:curator"} property_value: homology_notes "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001215", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001930 name: paraventricular nucleus of hypothalamus namespace: uberon def: "The paraventricular nucleus (PVN) is a neuronal nucleus in the hypothalamus. It contains multiple subpopulations of neurons that are activated by a variety of stressful and/or physiological changes. Many PVH neurons project directly to the posterior pituitary where they release oxytocin or vasopressin into the general circulation. Other PVN neurons control various anterior pituitary functions, while still others directly regulate appetite and autonomic functions in the brainstem and spinal cord. [WP,unvetted]." [Wikipedia:Paraventricular_nucleus_of_hypothalamus] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "filiform nucleus" EXACT [] synonym: "nuclei paraventricularis hypothalami" RELATED LATIN [Wikipedia:Paraventricular_nucleus_of_hypothalamus] synonym: "nucleus paraventricularis hypothalami" RELATED [BTO:0002476] synonym: "paraventricular hypothalamic nucleus" EXACT [] synonym: "paraventricular nucleus" EXACT [] xref: ABA:PVH xref: BM:Die-Hy-PAH xref: BTO:0002476 xref: EFO:0002469 xref: EV:0100229 xref: FMA:62320 xref: GAID:643 xref: http://upload.wikimedia.org/wikipedia/commons/e/ef/PVNss.jpg xref: http://upload.wikimedia.org/wikipedia/en/thumb/e/ef/PVNss.jpg/200px-PVNss.jpg xref: MA:0000848 xref: MESH:A08.186.211.730.385.357.342.400 xref: NIF_GrossAnatomy:birnlex_1407 xref: SCTID:369131006 is_a: UBERON:0006568 ! hypothalamic nucleus relationship: part_of UBERON:0002271 ! periventricular zone of hypothalamus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0001929 {source="ABA"} property_value: spatially_disjoint_from UBERON:0001932 {source="ABA"} [Term] id: UBERON:0001948 name: regional part of spinal cord namespace: uberon def: "A multi-tissue structure that is part of a spinal cord." [OBOL:automatic] subset: non_informative synonym: "spinal cord part" RELATED [] xref: ncithesaurus:Spinal_Cord_Part xref: NIF_GrossAnatomy:birnlex_1496 xref: SCTID:244437008 xref: UMLS:C1268166 is_a: UBERON:0000073 ! regional part of nervous system relationship: part_of UBERON:0002240 ! spinal cord property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001949 name: gingival epithelium namespace: uberon def: "A stratified squamous epithelium consisting of a basal layer; it is keratinized or parakeratinized[BTO]." [BTO:0004998] comment: In humans: 15% orthokeratinized, 75% parakeratinized, 10% non-keratinized; diurnal; decreased keratinization with age. Note that in FMA this is classified as keratinized squamous - this perhaps refers to the epithelium of the attached or free gingiva synonym: "epithelial tissue of gingiva" EXACT [OBOL:automatic] synonym: "epithelium of gingiva" EXACT [] synonym: "gingiva epithelial tissue" EXACT [OBOL:automatic] synonym: "gingiva epithelium" EXACT [OBOL:automatic] xref: BTO:0004998 xref: FMA:62423 xref: MA:0001576 xref: ncithesaurus:Gingival_Epithelium xref: UMLS:C1179154 is_a: UBERON:0002424 ! oral epithelium is_a: UBERON:0006915 ! stratified squamous epithelium relationship: part_of UBERON:0001828 ! gingiva property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001954 name: Ammon's horn namespace: uberon alt_id: UBERON:0003940 alt_id: UBERON:0004165 def: "A paired structure, with mirror-image halves in the left and right sides of the brain. The hippocampus is closely associated with the cerebral cortex, and in primates is located in the medial temporal lobe, underneath the cortical surface. It is shaped like a curved tube[WP]." [Wikipedia:Hippocampus] comment: WP: Non-mammalian species do not have a brain structure that looks like the mammalian hippocampus, but they have one that is considered homologous to it. The hippocampus, as pointed out above, is essentially the medial edge of the cortex. Only mammals have a fully developed cortex, but the structure it evolved from, called the pallium, is present in all vertebrates, even the most primitive ones such as the lamprey or hagfish.[82] The pallium is usually divided into three zones: medial, lateral, and dorsal. The medial pallium forms the precursor of the hippocampus. It does not resemble the hippocampus visually, because the layers are not warped into an S shape or enwrapped by the dentate gyrus, but the homology is indicated by strong chemical and functional affinities. There is now evidence that these hippocampal-like structures are involved in spatial cognition in birds, reptiles, and fish. In birds, the correspondence is sufficiently well established that most anatomists refer to the medial pallial zone as the "avian hippocampus". The story for fish is more complex. In teleost fish (which make up the great majority of existing species), the forebrain is distorted in comparison to other types of vertebrates: most neuroanatomists believe that the teleost forebrain is essentially everted, like a sock turned inside-out, so that structures that lie in the interior, next to the ventricles, for most vertebrates, are found on the outside in teleost fish, and vice versa.[86] One of the consequences of this is that the medial pallium ("hippocampal" zone) of a typical vertebrate is thought to correspond to the lateral pallium of a typical fish. Several types of fish (particularly goldfish) have been shown experimentally to have strong spatial memory abilities, even forming "cognitive maps" of the areas they inhabit.[80] There is evidence that damage to the lateral pallium impairs spatial memory. subset: uberon_slim synonym: "ammon gyrus" EXACT [GO:0021541] synonym: "ammon horn" EXACT [NIF_GrossAnatomy:birnlex_721] synonym: "Ammon's horn" EXACT [GO:0021541] synonym: "cornu ammonis" RELATED [GO:0021541] synonym: "hippocampus" RELATED [MA:0000191] synonym: "hippocampus major" EXACT [] synonym: "hippocampus proper" EXACT [] synonym: "hippocampus proprius" EXACT LATIN [FMA:62493, FMA:TA] xref: ABA:CA xref: BM:Tel-CAM xref: BTO:0003705 xref: EFO:0000530 xref: EHDAA2:0004443 xref: EMAPA:19039 xref: EMAPA:19148 xref: EV:0100180 xref: FMA:62493 xref: GAID:623 xref: http://scalablebrainatlas.incf.org/services/thumbnail.php?template=ABA07&size=L&dim=2d3d&format=png®ion=CA xref: http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray739-emphasizing-hippocampus.png xref: MA:0000191 xref: MAT:0000114 xref: MESH:A08.186.211.577.405 xref: MIAA:0000114 xref: ncithesaurus:Cornu_Ammonis xref: ncithesaurus:Hippocampus xref: NIF_GrossAnatomy:birnlex_721 xref: OpenCyc:Mx4rv3piFJwpEbGdrcN5Y29ycA xref: SCTID:361561007 xref: UMLS:C0019564 xref: VHOG:0001177 is_a: UBERON:0002619 ! regional part of cerebral cortex relationship: part_of UBERON:0000349 {source="FMA"} ! limbic system relationship: part_of UBERON:0002421 {source="ABA"} ! hippocampal formation relationship: part_of UBERON:0002600 {source="FMA"} ! limbic lobe property_value: has_relational_adjective "hippocampal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0001885 {source="ABA"} property_value: spatially_disjoint_from UBERON:0002601 {source="ABA"} [Term] id: UBERON:0001955 name: epithelium of respiratory bronchiole namespace: uberon def: "An epithelium that is part of a respiratory bronchiole [Obol]." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "bronchiolus respiratorius epithelial tissue" EXACT [OBOL:automatic] synonym: "bronchiolus respiratorius epithelium" EXACT [OBOL:automatic] synonym: "epithelial tissue of bronchiolus respiratorius" EXACT [OBOL:automatic] synonym: "epithelial tissue of respiratory bronchiole" EXACT [OBOL:automatic] synonym: "epithelium of bronchiolus respiratorius" EXACT [OBOL:automatic] synonym: "respiratory bronchiole epithelial tissue" EXACT [OBOL:automatic] synonym: "respiratory bronchiole epithelium" EXACT [] xref: FMA:62498 xref: MA:0001773 xref: ncithesaurus:Respiratory_Bronchiole_Epithelium xref: UMLS:C1179179 is_a: UBERON:0002051 ! epithelium of bronchiole relationship: part_of UBERON:0002188 ! respiratory bronchiole property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001958 name: epithelium of terminal bronchiole namespace: uberon def: "An epithelium that is part of a terminal bronchiole [Obol]." [OBOL:automatic] comment: This class was created automatically from a combination of ontologies synonym: "bronchiolus terminalis epithelial tissue" EXACT [OBOL:automatic] synonym: "bronchiolus terminalis epithelium" EXACT [OBOL:automatic] synonym: "epithelial tissue of bronchiolus terminalis" EXACT [OBOL:automatic] synonym: "epithelial tissue of terminal bronchiole" EXACT [OBOL:automatic] synonym: "epithelium of bronchiolus terminalis" EXACT [OBOL:automatic] synonym: "terminal bronchiole epithelial tissue" EXACT [OBOL:automatic] synonym: "terminal bronchiole epithelium" EXACT [] xref: FMA:62794 xref: MA:0001774 xref: ncithesaurus:Terminal_Bronchiole_Epithelium xref: UMLS:C1179400 is_a: UBERON:0002051 ! epithelium of bronchiole relationship: part_of UBERON:0002187 ! terminal bronchiole property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001959 name: white pulp of spleen namespace: uberon def: "The white pulp contains T cells, B cells and accessory cells. The function of the white pulp is to mount an immunological response to antigens within the blood. The white pulp is present in the form of a periarteriolar lymphoid sheath. This sheath contains B cell follicles and T cells. At the edge of the T zone is a region known as the marginal zone where larger lymphocytes and antigen presenting dendritic cells are located." [Wikipedia:White_pulp] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "noduli lymphoidei splenici" RELATED LATIN [Wikipedia:White_pulp] synonym: "pulpa alba" EXACT LATIN [FMA:62805, FMA:TA] synonym: "spleen white pulp" EXACT [] synonym: "splenic white pulp" EXACT [] synonym: "white pulp" EXACT [] xref: FMA:62805 xref: http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/1/15/Gray1191.png/200px-Gray1191.png xref: MA:0000762 xref: ncithesaurus:Splenic_White_Pulp xref: UMLS:C0229686 is_a: UBERON:1000023 ! spleen pulp property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001961 name: mucosa-associated lymphoid tissue namespace: uberon def: "diffuse system of small concentrations of lymphoid tissue found in various sites of the body such as the gastrointestinal tract, thyroid, breast, lung, salivary glands, eye, and skin[WP]. Mucosal-associated lymphoid tissue is typically found as nodules associated with mucosal epithelia with distinct internal structures including B- and T-zones for the activation of lymphocytes[GO]." [Wikipedia:Mucosa-associated_lymphoid_tissue] comment: Editor notes: todo - add part relationships to specific layers subset: uberon_slim synonym: "epithelio-lymphoid tissue" EXACT [FMA:62819] synonym: "MALT" EXACT [] synonym: "mucosa associated lymphatic tissue" EXACT [] synonym: "mucosa associated lymphoid tissue" EXACT [] synonym: "mucosa-associated lymphoid tissue" EXACT [GO:0048537] synonym: "mucosal-associated lymphatic tissue" EXACT [GO:0048537] synonym: "mucosal-associated lymphoid tissue" EXACT [GO:0048537] xref: FMA:62819 xref: MA:0000140 xref: ncithesaurus:Mucosa-Associated_Lymphoid_Tissue xref: UMLS:C0599921 is_a: UBERON:0012069 {source="FMA"} ! epithelium-associated lymphoid tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001962 name: gut-associated lymphoid tissue namespace: uberon def: "Mucosa-associated lymphoid tissue in digestive tract. includes Peyer's patches, appendix, and solitary lymph nodules[GO]." [Wikipedia:Gut-associated_lymphoid_tissue] comment: Editor notes: phylogenetic relationships to be added. Taxon notes: guts of jawless fish contains cells with lymphocyte-like morphology (Mayer 2002). subset: uberon_slim synonym: "GALT" RELATED [] synonym: "gut associated lymphoid tissue" EXACT [] xref: FMA:62820 xref: MA:0000136 xref: ncithesaurus:Gut_Associated_Lymphoid_Tissue xref: UMLS:C0596638 is_a: UBERON:0001961 ! mucosa-associated lymphoid tissue is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0001555 ! digestive tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001963 name: bronchial-associated lymphoid tissue namespace: uberon def: "A diffuse collection of lymphpoid cells that participate in airway immune responses" [ISBN10:0123813611] comment: Lymphoid tissue associated with airways in mice has functional similarities to human BALT[ISBN10:0123813611] Notes: FMA classifies this as organized, not diffuse synonym: "BALT" RELATED [] synonym: "bronchus associated lymphoid tissue" EXACT [] xref: FMA:62821 xref: MA:0000135 xref: ncithesaurus:Bronchus-Associated_Lymphoid_Tissue xref: UMLS:C1179418 is_a: UBERON:0001961 ! mucosa-associated lymphoid tissue is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0002185 ! bronchus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001973 name: substance of tooth namespace: uberon def: "Body substance in solid state produced by odontoblasts, amyloblasts or cementoblasts.[FMA]" [FMA:63001] comment: note the asserted dual parentage. This is deliberate, pending better definitions of the distinction between substance and tissue subset: uberon_slim synonym: "portion of substance of tooth" EXACT [FMA:63001] synonym: "tooth substance" EXACT [] xref: FMA:63001 xref: MA:0002540 is_a: UBERON:0000463 ! portion of organism substance relationship: part_of UBERON:0001091 ! calcareous tooth property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001976 name: epithelium of esophagus namespace: uberon def: "An epithelium that is part of a esophagus." [OBOL:automatic] comment: todo check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar subset: uberon_slim subset: vertebrate_core synonym: "epithelial tissue of esophagus" EXACT [OBOL:automatic] synonym: "epithelial tissue of gullet" EXACT [OBOL:automatic] synonym: "epithelial tissue of oesophagus" EXACT [OBOL:automatic] synonym: "epithelium of gullet" EXACT [OBOL:automatic] synonym: "epithelium of oesophagus" EXACT [OBOL:automatic] synonym: "esophageal epithelium" EXACT [] synonym: "esophagus epithelial tissue" EXACT [OBOL:automatic] synonym: "esophagus epithelium" EXACT [] synonym: "gullet epithelial tissue" EXACT [OBOL:automatic] synonym: "gullet epithelium" EXACT [OBOL:automatic] synonym: "oesophagus epithelial tissue" EXACT [OBOL:automatic] synonym: "oesophagus epithelium" RELATED [] xref: BTO:0001578 xref: EFO:0003041 xref: EHDAA2:0001287 xref: EMAPA:16835 xref: FMA:63063 xref: MA:0001565 xref: ncithesaurus:Esophageal_Epithelium xref: TAO:0001499 xref: UMLS:C1179544 xref: ZFA:0001499 is_a: UBERON:0003350 ! epithelium of mucosa is_a: UBERON:0003929 ! gut epithelium relationship: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0002469 {source="FMA"} ! esophagus mucosa property_value: external_definition "Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001499", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001979 name: venule namespace: uberon def: "Subdivision of venous tree (organ) which is directly continuous with the capillary vessel." [Wikipedia:Venule] comment: This class was created automatically from a combination of ontologies subset: uberon_slim subset: vertebrate_core synonym: "venula" RELATED LATIN [Wikipedia:Venule] xref: BTO:0002626 xref: FMA:63130 xref: http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/d/da/Illu_capillary.jpg/200px-Illu_capillary.jpg xref: MA:0000071 xref: MESH:A07.231.432.952 xref: ncithesaurus:Venule xref: SCTID:341687009 xref: TAO:0005315 xref: UMLS:C0042520 xref: VHOG:0001765 xref: ZFA:0005315 is_a: UBERON:0003920 ! venous blood vessel relationship: part_of UBERON:0001009 ! circulatory system property_value: external_definition "Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005315", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001980 name: arteriole namespace: uberon def: "the smallest division of the artery located between the muscular arteries and the capillaries[GO]. Subdivision of arterial tree (organ) which is directly continuous with capillary vessel[FMA]." [FMA:63182, GO:0014830, Wikipedia:Arteriole] comment: This class was created automatically from a combination of ontologies subset: uberon_slim subset: vertebrate_core synonym: "arteriola" RELATED LATIN [Wikipedia:Arteriole] xref: AAO:0010253 xref: BTO:0001997 xref: FMA:63182 xref: http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/d/da/Illu_capillary.jpg/200px-Illu_capillary.jpg xref: MA:0000063 xref: MESH:A07.231.114.060 xref: ncithesaurus:Arteriole xref: SCTID:337724002 xref: TAO:0002138 xref: UMLS:C0003847 xref: VHOG:0001763 xref: ZFA:0005255 is_a: UBERON:0003509 ! arterial blood vessel relationship: part_of UBERON:0001637 ! artery property_value: external_definition "Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002138", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Small, terminal branch of an artery which generally connects to capillaries.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010253", ontology="AAO", source="AAO:BJB"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001981 name: blood vessel namespace: uberon def: "A vessel through which blood circulates in the body." [BTO:0001102, Wikipedia:Blood_vessel] comment: note that FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX. Taxon notes: annelids have blood vessels, but this class is not applicable to annelids. subset: uberon_slim subset: vertebrate_core synonym: "region of vascular tree organ" EXACT [FMA:50722] synonym: "vas sanguineum" RELATED LATIN [Wikipedia:Blood_vessel] synonym: "vascular tree organ region" EXACT [FMA:50722] xref: AAO:0011004 xref: AEO:0000207 xref: BTO:0001102 xref: EFO:0000817 xref: EHDAA2:0003252 xref: EHDAA:240 xref: FMA:50722 xref: FMA:63183 xref: GAID:169 xref: http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/29/Circulatory_System_en.svg/200px-Circulatory_System_en.svg.png xref: MA:0000060 xref: MAT:0000393 xref: MESH:A07.231 xref: ncithesaurus:Blood_Vessel xref: NIF_GrossAnatomy:nlx_anat_090901 xref: OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA xref: SCTID:361097006 xref: TAO:0002137 xref: UMLS:C0005847 xref: VHOG:0001250 xref: XAO:0001011 xref: ZFA:0005314 is_a: UBERON:0000055 ! vessel is_a: UBERON:0007500 {source="EHDAA2"} ! epithelial tube open at both ends is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm relationship: develops_from UBERON:0006965 {source="GO:0072360"} ! vascular cord relationship: part_of UBERON:0004537 ! blood vasculature property_value: external_definition "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: external_definition "Any of the vessels through which blood circulates in the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011004", ontology="AAO", source="AAO:EJS"} property_value: homology_notes "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001982 name: capillary namespace: uberon def: "Any of the smallest blood vessels connecting arterioles with venules." [ISBN10:0073040584, Wikipedia:Capillary] comment: Structure notes: capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs subset: uberon_slim subset: vertebrate_core synonym: "blood capillary" EXACT [] synonym: "capillary vessel" EXACT [] xref: AAO:0010252 xref: BTO:0002045 xref: EFO:0001906 xref: EMAPA:28039 xref: EMAPA:28075 xref: EV:0100035 xref: FMA:63194 xref: http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary\,_pancreatic_tissue_-_TEM.jpg xref: MA:0000065 xref: MESH:A07.231.432.410 xref: ncithesaurus:Capillary xref: NIF_GrossAnatomy:nlx_anat_090902 xref: OpenCyc:Mx4rvWEU-5wpEbGdrcN5Y29ycA xref: TAO:0005250 xref: UMLS:C0935624 xref: VHOG:0001253 xref: XAO:0000116 xref: ZFA:0005250 is_a: UBERON:0001981 ! blood vessel is_a: UBERON:0010523 {source="ZFA"} ! microcirculatory vessel property_value: external_definition "Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010252", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001253", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001983 name: crypt of Lieberkuhn namespace: uberon def: "A gland found in the epithelial lining of the intestine and colon." [Wikipedia:Intestinal_crypt] subset: organ_slim synonym: "crypt of lieberkuhn" EXACT [] synonym: "crypt of Lieberkühn" EXACT [] synonym: "crypts of Lieberkühn" EXACT PLURAL [] synonym: "intestinal crypt" EXACT [] synonym: "intestinal crypts" EXACT PLURAL [] synonym: "intestinal gland" BROAD [Wikipedia:Crypts_of_Lieberkuhn] synonym: "Lieberkuhn crypt" EXACT [] synonym: "lieberkuhn crypt" EXACT [] xref: FMA:63621 xref: http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/38/Small_intestine_low_mag.jpg/200px-Small_intestine_low_mag.jpg xref: MA:0001535 xref: ncithesaurus:Crypts_of_the_Lieberkuhn xref: SCTID:118652008 xref: UMLS:C1621887 is_a: UBERON:0000333 ! intestinal gland relationship: part_of UBERON:0001242 ! intestinal mucosa property_value: external_definition "In histology, an intestinal crypt, also crypt of LieberkCKimmel et al, 1995." [ZFIN:curator] synonym: "presumptive somite mesoderm" RELATED [] synonym: "PSM" RELATED [] synonym: "segmental plate" EXACT [] synonym: "somitogenic mesoderm" RELATED [] synonym: "unsegmented mesenchyme" RELATED [VHOG:0000559] synonym: "unsegmented paraxial mesoderm" EXACT [UBERON:cjm] xref: AAO:0011086 xref: EFO:0001982 xref: TAO:0000279 xref: VHOG:0000559 xref: XAO:0000057 xref: ZFA:0000279 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0007282 {evidence="definitional"} ! presumptive segmental plate relationship: part_of UBERON:0003077 ! paraxial mesoderm property_value: external_definition "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000279", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000559", ontology="VHOG", source="DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003060 name: pronephric duct namespace: uberon def: "In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]." [Wikipedia:Pronephric_duct] subset: uberon_slim synonym: "archinephric duct" RELATED [VHOG:0000082] synonym: "ductus pronephricus" RELATED LATIN [Wikipedia:Pronephric_duct] xref: AAO:0011088 xref: ncithesaurus:Pronephric_Duct xref: SCTID:361406002 xref: TAO:0000150 xref: UMLS:C1283945 xref: VHOG:0000082 xref: XAO:0000063 xref: ZFA:0000150 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0009201 {source="GO"} ! nephric duct is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0003064 {source="Wikipedia"} ! intermediate mesoderm relationship: develops_from UBERON:0005721 {source="XAO"} ! pronephric mesoderm relationship: part_of UBERON:0002120 ! pronephros property_value: external_definition "Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000150", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes " (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003061 name: blood island namespace: uberon def: "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]." [Wikipedia:Blood_island_of_umbilical_vesicle] comment: AO notes: EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac subset: uberon_slim subset: vertebrate_core synonym: "blood islands" EXACT PLURAL [] synonym: "caudal hematopoietic tissue" RELATED [] synonym: "posterior blood island" RELATED [] synonym: "posterior ICM" RELATED [] synonym: "VBI" RELATED [] synonym: "ventral blood island" RELATED [] synonym: "ventral lateral plate mesoderm" BROAD [] xref: AAO:0011006 xref: EFO:0003489 xref: EHDAA:207 xref: ncithesaurus:Blood_Island xref: TAO:0000094 xref: TE:E5.11.2.0.0.0.4 xref: UMLS:C1511224 xref: VHOG:0000085 xref: XAO:0000067 xref: ZFA:0000094 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0003081 ! lateral plate mesoderm relationship: part_of UBERON:0000922 ! embryo property_value: axiom_lost_from_external_ontology "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO"} property_value: external_definition "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011006", ontology="AAO", source="AAO:EJS"} property_value: homology_notes "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000085", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003063 name: prechordal plate namespace: uberon alt_id: UBERON:0004881 def: "a thickening of the endoderm at the cranial end of the primitive streak formed by the involution of Spemann's organizer cells. The prechordal plate and the notochord induce the formation of the neural plate from the overlying ectodermal cells[GO]. Axial hypoblast located anterior to the chordamesoderm; the polster is its most anterior region[ZFA]. Uniquely thickened portion of the endoderm that is in contact with ectoderm immediately rostral to the cephalic tip of the notochord[WP]." [Wikipedia:Prechordal_plate, ZFIN:curator] comment: todo - check; developmental relationship to anterior hypoblast in ZFA? subset: uberon_slim subset: vertebrate_core synonym: "head mesenchyme" BROAD [XAO:0000079] synonym: "head mesoderm" BROAD [XAO:0000079] xref: AAO:0011085 xref: EHDAA2:0001493 xref: EHDAA:181 xref: TAO:0000060 xref: VHOG:0000086 xref: XAO:0000079 xref: ZFA:0000060 is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0003068 {source="ZFA"} ! axial mesoderm property_value: external_definition "Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000060", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000086", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000086", ontology="VHOG", source="DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003064 name: intermediate mesoderm namespace: uberon def: "The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads." [GOC:curators, Wikipedia:Intermediate_mesoderm] comment: note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). subset: uberon_slim subset: vertebrate_core synonym: "IM" RELATED [] synonym: "intermediate mesenchyme" RELATED [UBERONREF:0000002] synonym: "intermediate plate mesoderm" RELATED [UBERON:cjm] synonym: "mesenchyma intermedium" RELATED LATIN [Wikipedia:Intermediate_mesoderm] xref: AAO:0010575 xref: EMAPA:16178 xref: http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Gray19_with_color.png/200px-Gray19_with_color.png xref: ncithesaurus:Intermediate_Mesoderm xref: SCTID:361476001 xref: TAO:0001206 xref: UMLS:C1284010 xref: VHOG:0000087 xref: XAO:0000085 xref: ZFA:0001206 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0000926 {source="XAO"} ! mesoderm relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000926 {source="AAO"} ! mesoderm relationship: part_of UBERON:0005256 {source="EMAPA"} ! trunk mesenchyme property_value: external_definition "Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010575", ontology="AAO", source="AAO:EJS"} property_value: homology_notes "(...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000087", ontology="VHOG", source="http://bgee.unil.ch/", source="http://en.wikipedia.org/wiki/Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003067 name: dorsolateral placode namespace: uberon def: "Lateral neurogenic placodes positioned dorsal of the epibranchial placodes." [ZFIN:curator] comment: The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode synonym: "dorsolateral placodes" EXACT PLURAL [ZFA:0001310] xref: TAO:0001310 xref: VHOG:0000103 xref: XAO:0000187 xref: ZFA:0001310 is_a: UBERON:0009955 {source="NBK53175"} ! neurogenic placode property_value: homology_notes "In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000103", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003068 name: axial mesoderm namespace: uberon def: "The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord." [GO:0048318, Wikipedia:Chordamesoderm] subset: uberon_slim synonym: "chordamesoderm" RELATED [Wikipedia:Chordamesoderm] xref: AAO:0011017 xref: EFO:0003647 xref: http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Gray19_with_color.png/200px-Gray19_with_color.png xref: TAO:0001204 xref: VHOG:0000107 xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0000926 ! mesoderm relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000926 ! mesoderm property_value: external_definition "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000107", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003069 name: otic placode namespace: uberon def: "A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK]" [NBK:NBK53175, Wikipedia:Otic_placode] comment: With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991).[NBK53175] subset: uberon_slim subset: vertebrate_core synonym: "auditory placode" RELATED [] synonym: "ear placode" RELATED [] synonym: "ear/otic placode" RELATED [] synonym: "octaval placode" RELATED [ISBN10:0471888893] synonym: "octaval VIII placode" RELATED [ISBN10:0471888893] synonym: "placoda otica" EXACT LATIN [] xref: AAO:0011079 xref: EFO:0003429 xref: EHDAA2:0001339 xref: EHDAA:506 xref: EMAPA:16195 xref: ncithesaurus:Otic_Placodes xref: TAO:0000138 xref: UMLS:C1518677 xref: VHOG:0000235 xref: XAO:0000223 xref: ZFA:0000138 is_a: UBERON:0003067 {source="NBK:NBK53175", notes="invaginates"} ! dorsolateral placode relationship: part_of UBERON:0001690 ! ear property_value: external_definition "Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000138", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000235", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003071 name: eye primordium namespace: uberon alt_id: UBERON:0005060 def: "Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles." [GO:0046619, ZFA:0000570] comment: AO notes: TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium synonym: "eye anlage" RELATED [XAO:0000227] synonym: "eye field" RELATED [] synonym: "eye placode" EXACT [OBOL:automatic] synonym: "occular primordium" EXACT [] synonym: "ocular primordium" EXACT [] synonym: "optic field" RELATED [] synonym: "optic placode" EXACT [GO:0046619] synonym: "optic placode of camera-type eye" EXACT [GO:0046619, UBERON:cjm] synonym: "optic primordium" EXACT [] xref: AAO:0011038 xref: EFO:0003541 xref: EHDAA2:0004431 xref: TAO:0000570 xref: XAO:0000227 xref: XAO:0004090 xref: ZFA:0000570 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007497 ! developing epithelial placode is_a: UBERON:0010371 ! ecto-epithelium relationship: develops_from UBERON:0003056 ! pre-chordal neural plate relationship: part_of UBERON:0003056 {source="PMID:16496288", source="XAO"} ! pre-chordal neural plate property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003072 name: optic cup namespace: uberon def: "Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]." [MP:0004269, Optic_cup_(embryology), ZFA:0001202] subset: vertebrate_core synonym: "eye cup" RELATED [] synonym: "ocular cup" RELATED [VHOG:0000167] xref: EHDAA2:0001303 xref: EHDAA:2912 xref: EMAPA:16674 xref: ncithesaurus:Optic_Cup xref: SCTID:308789007 xref: TAO:0001202 xref: UMLS:C0231109 xref: VHOG:0000167 xref: ZFA:0001202 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0004128 {source="ZFA"} ! optic vesicle relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye property_value: homology_notes " (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000167", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003073 name: lens placode namespace: uberon def: "A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]." [Wikipedia:Lens_placode, ZFIN:curator] comment: Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)[NBK53175] subset: uberon_slim subset: vertebrate_core synonym: "placoda lentis" RELATED LATIN [Wikipedia:Lens_placode] xref: AAO:0011055 xref: EFO:0003494 xref: EHDAA2:0000982 xref: EHDAA:2908 xref: EMAPA:16672 xref: http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png xref: ncithesaurus:Lens_Placodes xref: TAO:0000122 xref: UMLS:C1517770 xref: VHOG:0000166 xref: XAO:0000240 xref: ZFA:0000122 is_a: UBERON:0002546 ! cranial placode is_a: UBERON:0010312 ! immature eye is_a: UBERON:0011814 {source="NBK53175"} ! non-neurogenic ectodermal placode relationship: part_of UBERON:0000076 ! external ectoderm relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye property_value: external_definition "Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000122", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes " (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000166", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003074 name: mesonephric duct namespace: uberon def: "Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]." [Wikipedia:Mesonephric_duct, ZFIN:curator] comment: TODO - mesonephric portion of the nephric duct. Development notes: In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts. subset: uberon_slim subset: vertebrate_core synonym: "archinephric duct" RELATED [VHOG:0000082, Wikipedia:Wolffian_duct] synonym: "ductus mesonephricus; ductus Wolffi" RELATED LATIN [Wikipedia:Mesonephric_duct] synonym: "Leydig's duct" RELATED [Wikipedia:Wolffian_duct] synonym: "renal duct" RELATED [] synonym: "Wolffian duct" EXACT [GOC:yaf, Wikipedia:Wolffian_duct, ZFA:0000546] xref: AAO:0000637 xref: EHDAA2:0001243 xref: EHDAA:1590 xref: EMAPA:16577 xref: GAID:1315 xref: http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Gray1109.png/200px-Gray1109.png xref: MESH:A16.254.940 xref: ncithesaurus:Mesonephric_Duct xref: SCTID:308800003 xref: TAO:0000546 xref: UMLS:C0043204 xref: VHOG:0000082 xref: XAO:0000242 xref: ZFA:0000546 is_a: UBERON:0000083 ! mesonephric tubule is_a: UBERON:0009201 {source="GO"} ! nephric duct relationship: develops_from UBERON:0003060 ! pronephric duct relationship: part_of UBERON:0000080 ! mesonephros property_value: external_definition "Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000637", ontology="AAO", source="AAO:BJB"} property_value: external_definition "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes " (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003075 name: neural plate namespace: uberon def: "A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]" [ISBN:0815318960, OMD:neural+plate, Wikipedia:Neural_plate, ZFIN:curator] subset: uberon_slim subset: vertebrate_core synonym: "lamina neuralis" RELATED LATIN [Wikipedia:Neural_plate] synonym: "presumptive central nervous system" RELATED [] xref: AAO:0011072 xref: BTO:0001765 xref: EHDAA:346 xref: EHDAA:902 xref: EMAPA:16095 xref: EMAPA:16527 xref: EMAPA:16756 xref: http://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png xref: ncithesaurus:Neural_Plate xref: RETIRED_EHDAA2:0001252 xref: TAO:0000132 xref: UMLS:C0920623 xref: VHOG:0000068 xref: XAO:0000249 xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium relationship: develops_from UBERON:0002346 ! neurectoderm relationship: develops_from UBERON:0007284 {source="ZFA"} ! presumptive neural plate relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0002346 {source="XAO"} ! neurectoderm property_value: external_definition "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000132", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes " (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000068", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003076 name: posterior neural tube namespace: uberon comment: This class was created automatically from a combination of ontologies xref: AAO:0011082 xref: TAO:0007037 xref: VHOG:0001383 xref: XAO:0000250 xref: ZFA:0007037 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0003057 ! chordal neural plate relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0001049 ! neural tube property_value: homology_notes " (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001383", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003077 name: paraxial mesoderm namespace: uberon def: "The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]" [GO:0048339, Wikipedia:Paraxial_mesoderm] comment: AO notes: note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) subset: uberon_slim subset: vertebrate_core synonym: "mesoderma paraxiale" RELATED LATIN [Wikipedia:Paraxial_mesoderm] synonym: "paraxial mesenchyme" EXACT [UBERONREF:0000002, ZFA:0000255] synonym: "somitic mesoderm" EXACT [ISBN:9780878932504] xref: AAO:0010568 xref: EFO:0003515 xref: EMAPA:16183 xref: EMAPA:16751 xref: http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Gray19_with_color.png/200px-Gray19_with_color.png xref: ncithesaurus:Paraxial_Mesoderm xref: SCTID:361475002 xref: TAO:0000255 xref: UMLS:C1284009 xref: VHOG:0000114 xref: XAO:0000259 xref: ZFA:0000255 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: develops_from UBERON:0007285 {source="ZFA"} ! presumptive paraxial mesoderm relationship: part_of UBERON:0000926 {source="XAO"} ! mesoderm property_value: external_definition "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010568", ontology="AAO", source="AAO:EJS"} property_value: homology_notes "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000114", ontology="VHOG", source="DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003080 name: anterior neural tube namespace: uberon comment: editor note: TODO - add grouping class for the anterior end of the neural tube at all stages xref: AAO:0011012 xref: TAO:0007038 xref: VHOG:0001384 xref: XAO:0000307 xref: ZFA:0007038 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0003056 ! pre-chordal neural plate relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0001049 ! neural tube property_value: homology_notes " (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001384", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003081 name: lateral plate mesoderm namespace: uberon alt_id: UBERON:0006258 def: "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." [MP:0010117, Wikipedia:Lateral_plate_mesoderm] comment: AO notes: subclass of mesoderm in ZFA. subset: uberon_slim synonym: "lateral mesoderm" EXACT [GO:0048368] synonym: "lateral plate" RELATED [] synonym: "lateral plate mesenchyme" RELATED [EHDAA2:0000919] synonym: "mesoderma laminae lateralis" RELATED LATIN [Wikipedia:Lateral_plate_mesoderm] xref: AAO:0010574 xref: EHDAA2:0000919 xref: EHDAA:379 xref: EMAPA:16179 xref: http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Gray19_with_color.png/200px-Gray19_with_color.png xref: ncithesaurus:Lateral_Mesoderm xref: SCTID:361477005 xref: TAO:0000121 xref: UMLS:C1517749 xref: VHOG:0000118 xref: XAO:0000311 xref: ZFA:0000121 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: develops_from UBERON:0000926 {source="EHDAA2", source="XAO"} ! mesoderm relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm property_value: external_definition "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010574", ontology="AAO", source="AAO:EJS"} property_value: external_definition "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003082 name: myotome namespace: uberon def: "A group of tissues formed from somites that develop into the body wall muscle[WP]. Somitic compartment that is a precursor of muscle. mesoderm that is derived from the somite that is fated to become the musculature[MP]. Portion of the somites giving rise to body wall muscle masses[ZFA]" [MP:0003939, PMID:17313522, Wikipedia:Myotome, ZFIN:curator] comment: Editors note: The term "myotome" is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class. subset: uberon_slim subset: vertebrate_core synonym: "muscle plate" RELATED [] synonym: "myomere" RELATED [] synonym: "myomeres" EXACT PLURAL [TAO:0001056] synonym: "myotome region" RELATED [] synonym: "myotomes" RELATED [] synonym: "myotomus" RELATED LATIN [Wikipedia:Myotome] xref: AAO:0011067 xref: AEO:0001018 xref: BTO:0000742 xref: EHDAA2:0003431 xref: EHDAA:1721 xref: EHDAA:1727 xref: EHDAA:1733 xref: EHDAA:1739 xref: http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/9/96/Gray65.png/200px-Gray65.png xref: ncithesaurus:Myotome_Region xref: SCTID:344535001 xref: TAO:0001056 xref: UMLS:C1513802 xref: VHOG:0001244 xref: XAO:0000315 xref: ZFA:0001056 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0004290 {source="EHDAA2"} ! dermomyotome relationship: part_of UBERON:0000926 ! mesoderm property_value: external_definition "Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001056", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001244", ontology="VHOG", source="DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003083 name: trunk neural crest namespace: uberon def: "Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia]." [ISBN:0815318960, Wikipedia:Trunk_neural_crest] comment: This class was created automatically from a combination of ontologies subset: uberon_slim synonym: "trunk crest" RELATED [] xref: AAO:0010582 xref: EFO:0003605 xref: EHDAA2:0001901 xref: TAO:0001024 xref: VHOG:0000062 xref: XAO:0000319 xref: ZFA:0001024 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0002342 ! neural crest property_value: external_definition "Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010582", ontology="AAO", source="AAO:EJS"} property_value: homology_notes "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000062", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003084 name: heart primordium namespace: uberon def: "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone." [ZFIN:curator] comment: editor note: should probably be fused with heart rudiment. subset: uberon_slim synonym: "fused heart primordium" RELATED [] xref: AAO:0011044 xref: BTO:0001887 xref: ncithesaurus:Primordium_of_the_Heart xref: TAO:0000028 xref: UMLS:C1514450 xref: XAO:0000336 xref: ZFA:0000028 is_a: UBERON:0001048 {source="Obol"} ! primordium relationship: develops_from UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm relationship: develops_from UBERON:0004140 ! heart field relationship: develops_from UBERON:0007005 {source="XAO"} ! cardiac mesoderm relationship: part_of UBERON:0004535 {source="ZFA"} ! cardiovascular system property_value: axiom_lost_from_external_ontology "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO"} property_value: external_definition "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011044", ontology="AAO", source="XAO:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003089 name: sclerotome namespace: uberon def: "Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]." [Wikipedia:Sclerotome, XB:curator] comment: AO notes: part_of somite in XAO subset: uberon_slim subset: vertebrate_core synonym: "sclerotomes" EXACT PLURAL [TAO:0001080] synonym: "sclerotomus" RELATED LATIN [Wikipedia:Sclerotome] xref: AAO:0010571 xref: AEO:0000212 xref: EHDAA2:0003439 xref: http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/9/96/Gray65.png/200px-Gray65.png xref: ncithesaurus:Sclerotome xref: TAO:0001080 xref: UMLS:C0183176 xref: VHOG:0000680 xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population relationship: develops_from UBERON:0002329 {source="ZFA"} ! somite property_value: external_definition "Skeletogenic portion of somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010571", ontology="AAO", source="AAO:EJS"} property_value: homology_notes "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000680", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003091 name: thyroid primordium namespace: uberon def: "The initial thyroid precursor, the thyroid primordium, starts as a simple midline thickening and develops to form the thyroid diverticulum. This structure is initially hollow, although it later solidifies and becomes bilobed. The 2 lobes are located on either side of the midline and are connected via an isthmus." [http://emedicine.medscape.com/article/845125-overview] comment: In all vertebrates the thyroid arises from the ventral aspect of the second pouch[PMID:16313389]. Note that we follow EHDAA2 in dividing this into endoderm and mesenchyme. In this ontology we place the broad developmental relationship at this level, and include specific relationships to the pharyngeal endoderm at the level of the endoderm subset: vertebrate_core xref: AAO:0011106 xref: BTO:0004709 xref: EHDAA2:0002033 xref: EHDAA:952 xref: EMAPA:16361 xref: EMAPA:16558 xref: ncithesaurus:Thyroid_Primordium xref: TAO:0001081 xref: UMLS:C1519512 xref: XAO:0000444 xref: ZFA:0001081 is_a: UBERON:0000479 {source="ZFA"} ! tissue is_a: UBERON:0001048 ! primordium is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0007123 {source="ISBN10:0073040584", source="PMID:16313389"} ! pharyngeal pouch 2 relationship: part_of UBERON:0000949 {source="ZFA"} ! endocrine system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003099 name: cranial neural crest namespace: uberon def: "The cranial neural crest arises in the anterior and populates the face and the pharyngeal arches giving rise to bones, cartilage, nerves and connective tissue [Wikipedia]." [Wikipedia:Cranial_neural_crest, ZFA:0001194, ZFIN:curator] comment: This class was created automatically from a combination of ontologies subset: uberon_slim subset: vertebrate_core synonym: "cephalic neural crest" RELATED [EMAPA:16091] synonym: "crista neuralis cranialis" RELATED LATIN [Wikipedia:Cranial_neural_crest] synonym: "head crest" RELATED [] synonym: "head neural crest" RELATED [] xref: AAO:0010580 xref: EFO:0003645 xref: EHDAA2:0004420 xref: EMAPA:16091 xref: TAO:0001194 xref: VHOG:0000063 xref: XAO:0001001 xref: ZFA:0001194 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0002342 ! neural crest property_value: external_definition "Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010580", ontology="AAO", source="AAO:EJS"} property_value: external_definition "Neural crest that is part of the head.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001194", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000063", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003100 name: female organism namespace: uberon def: "Gonochoristic organism that can produce female gametes." [CARO:0000028] subset: vertebrate_core synonym: "female" RELATED [TAO:0000303] synonym: "female human body" NARROW SENSU [FMA:67812] xref: AAO:0010030 xref: BILA:0000028 xref: CARO:0000028 xref: FBbt:00007011 xref: FMA:67812 xref: HAO:0000028 xref: SCTID:362608006 xref: TAO:0000303 xref: TGMA:0001839 xref: XAO:0003005 xref: ZFA:0000303 is_a: UBERON:0000468 ! multi-cellular organism disjoint_from: UBERON:0003101 ! male organism property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0003101 [Term] id: UBERON:0003101 name: male organism namespace: uberon def: "Gonochoristic organism that can produce male gametes." [CARO:0000027] subset: vertebrate_core synonym: "male" RELATED [TAO:0000242] synonym: "male human body" NARROW SENSU [FMA:67811] xref: AAO:0010033 xref: BILA:0000027 xref: CARO:0000027 xref: FBbt:00007004 xref: FMA:67811 xref: HAO:0000027 xref: SCTID:362609003 xref: TAO:0000242 xref: TGMA:0001838 xref: WBbt:0007850 xref: XAO:0003006 xref: ZFA:0000242 is_a: UBERON:0000468 ! multi-cellular organism property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003102 name: surface structure namespace: uberon def: "Organism subdivision that is the collection of anatomical structures on the body surface[ZFA]." [http://purl.obolibrary.org/obo/uberon/tracker/24, VSAO:0000001, Wikipedia:Surface_structure, ZFA:0000292] subset: upper_level synonym: "anatomical surface feature" EXACT [EHDAA2:0003010] xref: AAO:0010337 xref: AEO:0000010 xref: EHDAA2:0003010 xref: galen:SurfaceRegion xref: TAO:0000292 xref: VSAO:0000001 xref: XAO:0003028 xref: ZFA:0000292 is_a: UBERON:0000061 ! anatomical structure property_value: external_definition "Organism subdivision that is the collection of anatomical structures on the body surface.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010337", ontology="AAO", source="AAO:BJB"} property_value: external_definition "Organism subdivision which is the collection of anatomical structures on the body surface.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000292", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Organism subdivision which is the collection of anatomical structures on the body surface.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000001", ontology="VSAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003103 name: compound organ namespace: uberon def: "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types." [CARO:0000024] subset: organ_slim subset: upper_level synonym: "organ" RELATED [] xref: AAO:0010015 xref: AEO:0000024 xref: BILA:0000024 xref: CARO:0000024 xref: EHDAA2:0003024 xref: HAO:0000024 xref: TADS:0000598 xref: TAO:0000496 xref: TGMA:0001837 xref: VHOG:0001723 xref: XAO:0003041 xref: ZFA:0000496 is_a: UBERON:0000062 ! organ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003104 name: mesenchyme namespace: uberon def: "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]." [BTO:0001393, Wikipedia:Mesenchyme, ZFIN:curator] comment: Editors notes: the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense subset: uberon_slim subset: vertebrate_core synonym: "mesenchyma" RELATED LATIN [Wikipedia:Mesenchyme] synonym: "mesenchymal tissue" EXACT [] synonym: "mesenchyme tissue" EXACT [] synonym: "portion of mesenchymal tissue" EXACT [] synonym: "portion of mesenchyme tissue" EXACT [] xref: AAO:0010427 xref: AEO:0000145 xref: BTO:0001393 xref: EHDAA2:0003145 xref: EV:0100007 xref: http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/f/f4/Mesenchymal_Stem_Cell.jpg/200px-Mesenchymal_Stem_Cell.jpg xref: ncithesaurus:Mesenchyme xref: TAO:0000393 xref: UMLS:C0162415 xref: VHOG:0000170 xref: XAO:0003046 xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue relationship: part_of UBERON:0009142 ! entire mesenchyme property_value: external_definition "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000393", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010427", ontology="AAO", source="AAO:EJS"} property_value: has_relational_adjective "mesenchymal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003124 name: chorion namespace: uberon def: "The chorion is one of the membranes that exists during pregnancy between the developing fetus and mother. It is formed by extraembryonic mesoderm and the two layers of trophoblast and surrounds the embryo and other membranes. The chorionic villi emerge from the chorion, invade the endometrium, and allow transfer of nutrients from maternal blood to fetal blood." [Wikipedia:Chorion] comment: Development notes: Extra-embryonic ectoderm[PMID:19829370]. Taxon notes: The chorion of placentals is bilaminar as in reptiles and birds, but forms from the trophoblast and includes the ajdacent mesodermal layer [ISBN10:0073040584 "Vertebrates, Kardong"]. subset: uberon_slim synonym: "chorion (vertebrates)" EXACT [] synonym: "chorion frondosum" RELATED [Wikipedia:Chorion] synonym: "chorionic sac" RELATED [Wikipedia:Chorion] synonym: "embryonic chorion" EXACT [] synonym: "fetal chorion" EXACT [] xref: BTO:0000252 xref: EFO:0002780 xref: EHDAA2:0000245 xref: EHDAA:150 xref: EMAPA:16112 xref: EV:0100121 xref: FMA:80224 xref: GAID:1299 xref: http://upload.wikimedia.org/wikipedia/commons/5/51/Gray24.png xref: MESH:A16.254.403.473 xref: ncithesaurus:Chorion xref: ncithesaurus:Chorionic_Sac xref: UMLS:C0008503 xref: UMLS:C1516505 xref: VHOG:0000200 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005631 ! extraembryonic membrane relationship: develops_from UBERON:0005971 {source="ISBN10:0073040584"} ! amniotic fold property_value: external_definition "The outer membrane enclosing the embryo in reptiles, birds, and mammals. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000200", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/chorion"} property_value: external_definition "The outer membrane of the two membranes enclosing the embryo in reptiles, birds, and mammals. In placental mammals it contributes to the development of the placenta[BTO:0000252]." xsd:string {source="BTO:0000252"} property_value: has_relational_adjective "chorionic" xsd:string property_value: homology_notes "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000200", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003126 name: trachea namespace: uberon def: "The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]." [GO:0060438, Wikipedia:Vertebrate_trachea] comment: Taxon notes: in mouse 15-18 C-rings, 15-20 in human. [ISBN10:0123813611]. In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx. subset: major_organ subset: uberon_slim synonym: "cartilaginous trachea" EXACT [] synonym: "tracheal tubule" RELATED [BTO:0001388] synonym: "vertebrate trachea" EXACT SENSU [] synonym: "windpipe" EXACT [] xref: AAO:0010140 xref: BTO:0001388 xref: EFO:0000935 xref: EHDAA2:0002066 xref: EHDAA:3078 xref: EMAPA:16853 xref: EV:0100040 xref: FMA:7394 xref: GAID:361 xref: http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/c/c3/Illu_conducting_passages.jpg/200px-Illu_conducting_passages.jpg xref: MA:0000441 xref: MAT:0000137 xref: MESH:A04.889 xref: MIAA:0000137 xref: ncithesaurus:Trachea xref: OpenCyc:Mx4rvViOX5wpEbGdrcN5Y29ycA xref: SCTID:181213009 xref: UMLS:C0040578 xref: VHOG:0000371 xref: XAO:0000118 is_a: UBERON:0000117 ! respiratory tube relationship: develops_from UBERON:0008947 {source="EHDAA2"} ! respiratory primordium relationship: part_of UBERON:0007196 ! tracheobronchial tree property_value: external_definition "An elongated tube which carries air to and from the lungs.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010140", ontology="AAO", source="AAO:BJB"} property_value: external_definition "The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000371", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: has_relational_adjective "tracheal" xsd:string property_value: homology_notes "In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000371", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.409", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003128 name: cranium namespace: uberon def: "Upper portion of the skull that excludes the mandible (when present in the organism)." [Wikipedia:Cranium_(anatomy)] comment: The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton[WP]. AO notes: the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium subset: uberon_slim subset: vertebrate_core synonym: "bones of cranium" EXACT [FMA:71325] synonym: "calvarium" RELATED [BTO:0001328] synonym: "epicranial plate" RELATED [] synonym: "ossa cranii" EXACT LATIN [FMA:71325, FMA:TA] synonym: "set of bones of cranium" EXACT [FMA:71325] synonym: "skeletal system of head" RELATED [] synonym: "skull minus mandible" EXACT [] synonym: "upper part of skull" EXACT [] xref: BTO:0001328 xref: EFO:0000831 xref: EHDAA:6029 xref: FMA:71325 xref: MA:0000316 xref: MAT:0000340 xref: MIAA:0000340 xref: OpenCyc:Mx4rvVlEyJwpEbGdrcN5Y29ycA xref: SCTID:181889008 xref: VHOG:0000334 is_a: UBERON:0000075 {source="FMA-inferred"} ! subdivision of skeletal system relationship: part_of UBERON:0003129 ! skull property_value: has_relational_adjective "cranial" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0003278 [Term] id: UBERON:0003129 name: skull namespace: uberon def: "Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]." [http://sourceforge.net/tracker/?func=detail&aid=2962656&group_id=76834&atid=1205376, PMID:11523816, Wikipedia:Skull] comment: In FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible. // A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates[WP]. Editor/AO notes: in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton subset: uberon_slim synonym: "cranial skeleton" RELATED [] synonym: "skeletal system of head" RELATED [] xref: BTO:0001295 xref: EHDAA2:0000325 xref: EMAPA:17680 xref: FMA:46565 xref: GAID:82 xref: galen:Skull xref: MESH:A02.835.232.781 xref: ncithesaurus:Skull xref: OpenCyc:Mx4rvVjOsZwpEbGdrcN5Y29ycA xref: SCTID:110530005 xref: UMLS:C0037303 xref: WikipediaCategory:Skull is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0010323 ! cranial skeletal system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003133 name: reproductive organ namespace: uberon def: "An organ involved in reproduction" [UBERON:xp] comment: GO uses genitalia for the singular organ subset: functional_classification subset: organ_slim synonym: "genital organ" EXACT [] synonym: "genitalia" RELATED PLURAL [] synonym: "reproductive system organ" EXACT [] synonym: "sex organ" EXACT [] xref: EMAPA:17381 xref: MA:0001752 xref: MESH:A05.360 xref: ncithesaurus:Genitalia xref: OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA xref: SCTID:128181006 xref: TGMA:0000591 xref: UMLS:C0017420 xref: WBbt:0008422 is_a: UBERON:0000062 ! organ is_a: UBERON:0005156 ! reproductive structure relationship: part_of UBERON:0000990 ! reproductive system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003134 name: female reproductive organ namespace: uberon def: "A female organ involved in reproduction" [UBERON:xp] subset: organ_slim synonym: "female organism reproductive organ" EXACT [OBOL:automatic] synonym: "female organism reproductive structure" EXACT [OBOL:automatic] synonym: "female organism reproductive system organ" EXACT [OBOL:automatic] synonym: "female organism sex organ" EXACT [OBOL:automatic] synonym: "female reproductive gland/organ" EXACT [MA:0000544] synonym: "female reproductive system organ" EXACT [] synonym: "female sex organ" EXACT [] synonym: "reproductive organ of female organism" EXACT [OBOL:automatic] synonym: "reproductive structure of female organism" EXACT [OBOL:automatic] synonym: "reproductive system organ of female organism" EXACT [OBOL:automatic] synonym: "sex organ of female organism" EXACT [OBOL:automatic] xref: EMAPA:17959 xref: MA:0000544 is_a: UBERON:0003133 ! reproductive organ relationship: part_of UBERON:0000474 ! female reproductive system relationship: part_of UBERON:0003100 ! female organism property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003135 name: male reproductive organ namespace: uberon def: "A male organ involved in reproduction" [UBERON:xp] subset: organ_slim synonym: "male organism reproductive organ" EXACT [OBOL:automatic] synonym: "male organism reproductive structure" EXACT [OBOL:automatic] synonym: "male organism reproductive system organ" EXACT [OBOL:automatic] synonym: "male organism sex organ" EXACT [OBOL:automatic] synonym: "male reproductive gland/organ" EXACT [MA:0000545] synonym: "male reproductive system organ" EXACT [] synonym: "male sex organ" EXACT [] synonym: "reproductive organ of male organism" EXACT [OBOL:automatic] synonym: "reproductive structure of male organism" EXACT [OBOL:automatic] synonym: "reproductive system organ of male organism" EXACT [OBOL:automatic] synonym: "sex organ of male organism" EXACT [OBOL:automatic] xref: MA:0000545 is_a: UBERON:0003133 ! reproductive organ relationship: part_of UBERON:0000079 ! male reproductive system relationship: part_of UBERON:0003101 ! male organism property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003210 name: blood-cerebrospinal fluid barrier namespace: uberon def: "barrier in the choroid plexus located in the lateral, third, and fourth brain ventricles that controls the entrance of substances into the cerebrospinal fluid from the blood[MP]." [MP:0006088] is_a: UBERON:0000119 ! cell layer property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003214 name: mammary gland alveolus namespace: uberon def: "a sac-like structure that is found in the mature gland[GO]." [GO:0060749] synonym: "alveolus of lactiferous gland" EXACT [OBOL:automatic] synonym: "alveolus of lobe of breast" EXACT [OBOL:automatic] synonym: "alveolus of lobe of mammary gland" EXACT [OBOL:automatic] synonym: "alveolus of mammary gland" EXACT [OBOL:automatic] synonym: "lactiferous alveolus" EXACT [] synonym: "lactiferous gland alveolus" EXACT [] synonym: "lobe of breast alveolus" EXACT [OBOL:automatic] synonym: "lobe of mammary gland alveolus" EXACT [OBOL:automatic] synonym: "mammary alveolus" EXACT [] xref: FMA:73285 xref: MA:0002760 is_a: UBERON:0003215 ! alveolus is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005156 ! reproductive structure relationship: part_of UBERON:0001911 ! mammary gland relationship: part_of UBERON:0001912 ! lobule of lactiferous gland property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003215 name: alveolus namespace: uberon def: "organ part that has the form of a hollow cavity[WP]." [Wikipedia:Alveolus] xref: EFO:0002513 xref: EV:0100043 xref: FMA:82493 xref: ncithesaurus:Alveolus xref: OpenCyc:Mx4rwN8NFZwpEbGdrcN5Y29ycA xref: UMLS:C0034051 is_a: UBERON:0000064 ! organ part property_value: has_relational_adjective "alveolar" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003220 name: metanephric mesenchyme namespace: uberon def: "one of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO]" [GO:0072075, Wikipedia:Metanephric_blastema] comment: Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] synonym: "metanephric blastema" EXACT [Wikipedia:Metanephric_blastema] synonym: "metanephric mesoderm" EXACT [Wikipedia:Metanephric_blastema] synonym: "metanephrogenic mesenchyme" EXACT [EHDAA:5021] synonym: "metanephros associated mesenchyme" EXACT [RETIRED_EHDAA2:0001139] xref: EHDAA2:0004062 xref: EHDAA:4041 xref: EHDAA:5021 xref: EHDAA:5915 xref: EMAPA:17208 xref: EMAPA:17375 xref: EMAPA:29990 xref: SCTID:361529008 xref: VHOG:0000540 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0003918 ! kidney mesenchyme is_a: UBERON:0005291 ! embryonic tissue relationship: develops_from UBERON:0003074 ! mesonephric duct relationship: part_of UBERON:0000922 ! embryo property_value: external_definition "A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000540", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/metanephric+mesenchyme"} property_value: homology_notes "When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000540", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003241 name: epithelium of utricle namespace: uberon def: "An epithelium that is part of a utricle of membranous labyrinth [Obol]." [OBOL:automatic] comment: todo - check relationships w.r.t macula synonym: "epithelial tissue of membranous labyrinth utricle" EXACT [OBOL:automatic] synonym: "epithelial tissue of utricle" EXACT [OBOL:automatic] synonym: "epithelial tissue of utricle of membranous labyrinth" EXACT [OBOL:automatic] synonym: "epithelial tissue of utriculus (labyrinthus vestibularis)" EXACT [OBOL:automatic] synonym: "epithelium of macula of utricle of membranous labyrinth" NARROW [FMA:75604] synonym: "epithelium of membranous labyrinth utricle" EXACT [OBOL:automatic] synonym: "epithelium of utricle of membranous labyrinth" EXACT [OBOL:automatic] synonym: "epithelium of utriculus (labyrinthus vestibularis)" EXACT [OBOL:automatic] synonym: "membranous labyrinth utricle epithelial tissue" EXACT [OBOL:automatic] synonym: "membranous labyrinth utricle epithelium" EXACT [OBOL:automatic] synonym: "utricle epithelial tissue" EXACT [OBOL:automatic] synonym: "utricle epithelium" EXACT [OBOL:automatic] synonym: "utricle of membranous labyrinth epithelial tissue" EXACT [OBOL:automatic] synonym: "utricle of membranous labyrinth epithelium" EXACT [OBOL:automatic] synonym: "utriculus (labyrinthus vestibularis) epithelial tissue" EXACT [OBOL:automatic] synonym: "utriculus (labyrinthus vestibularis) epithelium" EXACT [OBOL:automatic] xref: EHDAA:4730 xref: EMAPA:17295 xref: EMAPA:17298 xref: EMAPA:17301 xref: EMAPA:17820 xref: EMAPA:17823 xref: FMA:75604 xref: MA:0001204 xref: RETIRED_EHDAA2:0002155 xref: VHOG:0000634 is_a: UBERON:0006932 {source="FMA"} ! vestibular epithelium relationship: part_of UBERON:0001853 ! utricle of membranous labyrinth relationship: part_of UBERON:0002214 {source="FMA"} ! macula of utricle of membranous labyrinth property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003242 name: epithelium of saccule namespace: uberon def: "An epithelium that is part of a saccule of membranous labyrinth [Obol]." [OBOL:automatic] comment: todo - check relationships w.r.t macula synonym: "epithelial tissue of membranous labyrinth saccule" EXACT [OBOL:automatic] synonym: "epithelial tissue of saccule" EXACT [OBOL:automatic] synonym: "epithelial tissue of saccule of membranous labyrinth" EXACT [OBOL:automatic] synonym: "epithelial tissue of sacculus (labyrinthus vestibularis)" EXACT [OBOL:automatic] synonym: "epithelium of macula of saccule of membranous labyrinth" RELATED [FMA:75605] synonym: "epithelium of membranous labyrinth saccule" EXACT [OBOL:automatic] synonym: "epithelium of saccule of membranous labyrinth" EXACT [OBOL:automatic] synonym: "epithelium of sacculus (labyrinthus vestibularis)" EXACT [OBOL:automatic] synonym: "membranous labyrinth saccule epithelial tissue" EXACT [OBOL:automatic] synonym: "membranous labyrinth saccule epithelium" EXACT [OBOL:automatic] synonym: "saccule epithelial tissue" EXACT [OBOL:automatic] synonym: "saccule epithelium" EXACT [OBOL:automatic] synonym: "saccule of membranous labyrinth epithelial tissue" EXACT [OBOL:automatic] synonym: "saccule of membranous labyrinth epithelium" EXACT [OBOL:automatic] synonym: "sacculus (labyrinthus vestibularis) epithelial tissue" EXACT [OBOL:automatic] synonym: "sacculus (labyrinthus vestibularis) epithelium" EXACT [OBOL:automatic] xref: EHDAA:4724 xref: EMAPA:17292 xref: FMA:75605 xref: MA:0001202 xref: RETIRED_EHDAA2:0001771 xref: VHOG:0000633 is_a: UBERON:0006932 ! vestibular epithelium relationship: part_of UBERON:0001854 ! saccule of membranous labyrinth property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003244 name: epithelium of mammary gland namespace: uberon def: "An epithelium that is part of a lactiferous gland [Obol]." [OBOL:automatic] synonym: "epithelial tissue of lactiferous gland" EXACT [OBOL:automatic] synonym: "epithelial tissue of lobe of breast" EXACT [OBOL:automatic] synonym: "epithelial tissue of lobe of mammary gland" EXACT [OBOL:automatic] synonym: "epithelial tissue of mammary gland" EXACT [OBOL:automatic] synonym: "epithelium of lactiferous gland" EXACT [FMA:74445] synonym: "epithelium of lobe of breast" EXACT [OBOL:automatic] synonym: "epithelium of lobe of mammary gland" EXACT [OBOL:automatic] synonym: "lactiferous gland epithelial tissue" EXACT [OBOL:automatic] synonym: "lactiferous gland epithelium" EXACT [OBOL:automatic] synonym: "lobe of breast epithelial tissue" EXACT [OBOL:automatic] synonym: "lobe of breast epithelium" EXACT [OBOL:automatic] synonym: "lobe of mammary gland epithelial tissue" EXACT [OBOL:automatic] synonym: "lobe of mammary gland epithelium" EXACT [OBOL:automatic] synonym: "mammary epithelium" EXACT [BTO:0001430] synonym: "mammary gland epithelial tissue" EXACT [OBOL:automatic] synonym: "mammary gland epithelium" EXACT [OBOL:automatic] xref: BTO:0001430 xref: EHDAA2:0001057 xref: EHDAA:6526 xref: EMAPA:17760 xref: FMA:74445 xref: MA:0000792 xref: ncithesaurus:Mammary_Epithelium xref: UMLS:C0596882 xref: VHOG:0001088 is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0011272 {source="EHDAA2", source="Wikipathways:WP2062"} ! embryonic skin basal layer relationship: part_of UBERON:0001911 ! mammary gland property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003258 name: endoderm of foregut namespace: uberon def: "An endoderm that is part of a foregut [Obol]." [OBOL:automatic] comment: TODO - check synonym: "foregut endoderm" EXACT [OBOL:automatic] xref: EHDAA2:0000566 xref: EHDAA:524 is_a: UBERON:0000925 ! endoderm is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0001041 ! foregut property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003281 name: mesentery of stomach namespace: uberon def: "The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum." [http://medical-dictionary.thefreedictionary.com/mesogastrium] comment: todo - check primitive vs developed synonym: "mesentery of ventriculus" EXACT [OBOL:automatic] synonym: "mesogaster" EXACT [http://medical-dictionary.thefreedictionary.com/mesogastrium] synonym: "mesogastium" EXACT [MA:0001617] synonym: "mesogastrium" EXACT [http://www.vivo.colostate.edu/hbooks/pathphys/misc_topics/peritoneum.html] synonym: "stomach mesentery" EXACT [Obol:obol] synonym: "ventriculus mesentery" EXACT [OBOL:automatic] xref: EHDAA2:0001922 xref: EHDAA:2999 xref: EMAPA:17024 xref: EMAPA:18902 xref: MA:0001617 xref: SCTID:261623000 xref: VHOG:0000358 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0004854 {source="MA"} ! gastrointestinal system mesentery is_a: UBERON:0009034 ! stomach region relationship: part_of UBERON:0000945 {source="MA"} ! stomach property_value: external_definition "The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000358", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/mesogastrium"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003294 name: gland of foregut namespace: uberon def: "A gland that is part of a foregut [Obol]." [OBOL:automatic] synonym: "foregut gland" EXACT [OBOL:automatic] xref: EHDAA2:0000567 xref: EHDAA:950 xref: EMAPA:16557 xref: VHOG:0000650 is_a: UBERON:0003408 ! gland of gut relationship: part_of UBERON:0001041 ! foregut property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003295 name: pharyngeal gland namespace: uberon def: "Racemose mucous glands beneath the mucous membrane of the pharynx." [Biology-Online_Dictionary:http\://www.biology-online.org/dictionary/] subset: organ_slim synonym: "glandulae pharyngeae" RELATED [BTO:0004849] synonym: "pharynx gland" EXACT [EHDAA2:0001461] xref: BTO:0004849 xref: EHDAA2:0001461 xref: EHDAA:2967 xref: FMA:55075 is_a: UBERON:0003408 ! gland of gut relationship: part_of UBERON:0001042 {source="BTO"} ! chordate pharynx property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003296 name: gland of diencephalon namespace: uberon def: "A gland that is part of a diencephalon [Obol]." [OBOL:automatic] synonym: "between brain gland" EXACT [OBOL:automatic] synonym: "diencephalon gland" EXACT [OBOL:automatic] synonym: "gland of between brain" EXACT [OBOL:automatic] synonym: "gland of interbrain" EXACT [OBOL:automatic] synonym: "gland of mature diencephalon" EXACT [OBOL:automatic] synonym: "interbrain gland" EXACT [OBOL:automatic] synonym: "mature diencephalon gland" EXACT [OBOL:automatic] xref: EHDAA2:0000395 xref: EHDAA:4475 xref: EMAPA:16646 xref: EMAPA:16897 xref: VHOG:0000653 is_a: UBERON:0002530 ! gland is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001894 ! diencephalon property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003297 name: gland of integumental system namespace: uberon def: "A gland that is part of a integumental system [Obol]." [OBOL:automatic] synonym: "integumental system gland" EXACT [OBOL:automatic] xref: EHDAA2:0000837 xref: EHDAA:6522 xref: EMAPA:17758 xref: MA:0000144 xref: VHOG:0000654 is_a: UBERON:0002530 ! gland relationship: part_of UBERON:0002416 ! integumental system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003332 name: submucosa of duodenum namespace: uberon def: "A submucosa that is part of a duodenum [Obol]." [OBOL:automatic] synonym: "doudenal submucosa" EXACT [FMA:14943] synonym: "duodenal submucosa" EXACT [FMA:14943] synonym: "duodenum submucosa" EXACT [OBOL:automatic] xref: EMAPA:27027 xref: EMAPA:27097 xref: EMAPA:27239 xref: FMA:14943 xref: SCTID:76519004 is_a: UBERON:0001205 ! submucosa of small intestine relationship: part_of UBERON:0002114 ! duodenum property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003338 name: ganglion of peripheral nervous system namespace: uberon def: "A ganglion that is part of a peripheral nervous system [Obol]." [OBOL:automatic] comment: We follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS synonym: "peripheral nervous system ganglion" EXACT [OBOL:automatic] xref: BTO:0001123 xref: EMAPA:18371 xref: MA:0001161 is_a: UBERON:0000045 ! ganglion relationship: part_of UBERON:0000010 ! peripheral nervous system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003350 name: epithelium of mucosa namespace: uberon def: "A layer of epithelial cells on the surface of the mucosa." [BTO:0003752] synonym: "lamina epithelialis mucosa" RELATED [BTO:0003752] synonym: "lamina epithelialis mucosae" RELATED [BTO:0003752] xref: BTO:0003752 xref: EMAPA:18668 xref: EMAPA:18835 xref: EMAPA:18857 xref: EMAPA:18862 xref: EMAPA:18868 xref: EMAPA:18893 xref: EMAPA:18899 xref: EMAPA:18912 xref: EMAPA:18917 xref: EMAPA:18927 xref: EMAPA:18934 xref: EMAPA:18941 xref: EMAPA:19078 xref: EMAPA:26961 xref: EMAPA:26985 xref: EMAPA:27019 xref: EMAPA:27033 xref: EMAPA:27047 xref: EMAPA:27061 xref: EMAPA:27075 xref: EMAPA:27089 xref: EMAPA:27103 xref: EMAPA:27131 xref: EMAPA:27145 xref: EMAPA:27159 xref: EMAPA:27175 xref: EMAPA:27191 xref: EMAPA:27207 xref: EMAPA:27219 xref: EMAPA:27229 xref: EMAPA:27307 is_a: UBERON:0000483 ! epithelium relationship: part_of UBERON:0000344 ! mucosa property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003351 name: pharyngeal epithelium namespace: uberon def: "An epithelium that is part of a pharynx [Obol]." [OBOL:automatic] subset: vertebrate_core synonym: "epithelial tissue of pharynx" EXACT [OBOL:automatic] synonym: "epithelium of pharynx" EXACT [OBOL:automatic] synonym: "pharynx epithelial tissue" EXACT [OBOL:automatic] synonym: "pharynx epithelium" EXACT [OBOL:automatic] xref: EMAPA:16551 xref: EMAPA:16708 xref: MA:0002725 xref: RETIRED_EHDAA2:0001460 xref: TAO:0001174 xref: XAO:0003202 xref: ZFA:0001174 is_a: UBERON:0003929 ! gut epithelium is_a: UBERON:0004807 ! respiratory system epithelium relationship: develops_from UBERON:0007690 {source="ZFA"} ! early pharyngeal endoderm relationship: part_of UBERON:0001042 {source="ZFA"} ! chordate pharynx property_value: external_definition "Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001174", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003353 name: epithelium of hindgut namespace: uberon def: "An epithelium that is part of a hindgut [Obol]." [OBOL:automatic] synonym: "epithelial tissue of hindgut" EXACT [OBOL:automatic] synonym: "hindgut epithelial tissue" EXACT [OBOL:automatic] synonym: "hindgut epithelium" EXACT [OBOL:automatic] xref: EHDAA2:0000782 xref: EMAPA:16717 is_a: UBERON:0003929 ! gut epithelium relationship: part_of UBERON:0001046 ! hindgut property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003386 name: smooth muscle of eye namespace: uberon def: "A portion of smooth muscle tissue that is part of a eye [Obol]." [OBOL:automatic] synonym: "ocular smooth muscle" EXACT [MA:0001268] xref: EMAPA:18807 xref: MA:0001268 is_a: UBERON:0001135 ! smooth muscle tissue is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000019 ! camera-type eye property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003408 name: gland of gut namespace: uberon def: "A gland that is part of a digestive tract [Obol]." [OBOL:automatic] synonym: "digestive tract gland" EXACT [OBOL:automatic] synonym: "gland of digestive tract" EXACT [OBOL:automatic] synonym: "gland of lower gastrointestinal tract" EXACT [OBOL:automatic] synonym: "gut gland" EXACT [OBOL:automatic] synonym: "lower gastrointestinal tract gland" EXACT [OBOL:automatic] xref: EMAPA:18815 is_a: UBERON:0002530 ! gland is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0001555 ! digestive tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003422 name: mesenchyme of umbilical cord namespace: uberon def: "a gelatinous substance within the umbilical cord, largely made up of mucopolysaccharides (hyaluronic acid and chondroitin sulfate). It also contains some fibroblasts and macrophages. It is derived from Extra Embryonic Mesoderm[WP]" [Wikipedia:Wharton's_jelly] comment: todo - check synonym: "umbilical cord mesenchyme" EXACT [OBOL:automatic] synonym: "Wharton's jelly" EXACT [EMAPA:26127] xref: EMAPA:26127 xref: SCTID:368069009 is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0002331 ! umbilical cord property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003454 name: small intestine Peyer's patch namespace: uberon def: "nodular lymphoid structures on the serosal surface of the small intestine." [] comment: Editor's note: add subtypes for jejunum, ileum synonym: "aggregated lymphoid follicle of small intestine" EXACT [FMA:15054] synonym: "Peyer's patch" BROAD [FMA:15054] synonym: "Peyer's patch of small bowel" EXACT [OBOL:automatic] synonym: "Peyer's patch of small intestine" EXACT [OBOL:automatic] synonym: "small bowel Peyer's patch" EXACT [OBOL:automatic] synonym: "small intestine Peyer's patch" EXACT [OBOL:automatic] xref: FMA:15054 xref: MA:0001557 xref: SCTID:38986009 is_a: UBERON:0001211 ! Peyer's patch relationship: part_of UBERON:0001204 {source="ncithesaurus"} ! mucosa of small intestine relationship: part_of UBERON:0002108 ! small intestine property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003455 name: inner renal medulla loop of henle namespace: uberon def: "A loop of Henle that is part of a inner medulla of kidney [Obol]." [OBOL:automatic] synonym: "Henle loop of inner medulla of kidney" EXACT [OBOL:automatic] synonym: "Henle loop of inner renal medulla" EXACT [OBOL:automatic] synonym: "Henle loop of inner zone of medulla of kidney" EXACT [OBOL:automatic] synonym: "Henle loop of inner zone of renal medulla" EXACT [OBOL:automatic] synonym: "henle's loop of inner medulla of kidney" EXACT [OBOL:automatic] synonym: "henle's loop of inner renal medulla" EXACT [OBOL:automatic] synonym: "henle's loop of inner zone of medulla of kidney" EXACT [OBOL:automatic] synonym: "henle's loop of inner zone of renal medulla" EXACT [OBOL:automatic] synonym: "inner medulla of kidney Henle loop" EXACT [OBOL:automatic] synonym: "inner medulla of kidney henle's loop" EXACT [OBOL:automatic] synonym: "inner medulla of kidney loop of Henle" EXACT [OBOL:automatic] synonym: "inner renal medulla Henle loop" EXACT [OBOL:automatic] synonym: "inner renal medulla henle's loop" EXACT [OBOL:automatic] synonym: "inner renal medulla loop of Henle" EXACT [OBOL:automatic] synonym: "inner zone of medulla of kidney Henle loop" EXACT [OBOL:automatic] synonym: "inner zone of medulla of kidney henle's loop" EXACT [OBOL:automatic] synonym: "inner zone of medulla of kidney loop of Henle" EXACT [OBOL:automatic] synonym: "inner zone of renal medulla Henle loop" EXACT [OBOL:automatic] synonym: "inner zone of renal medulla henle's loop" EXACT [OBOL:automatic] synonym: "inner zone of renal medulla loop of Henle" EXACT [OBOL:automatic] synonym: "kidney inner medulla loop of henle" EXACT [MA:0002623] synonym: "loop of Henle of inner medulla of kidney" EXACT [OBOL:automatic] synonym: "loop of Henle of inner renal medulla" EXACT [OBOL:automatic] synonym: "loop of Henle of inner zone of medulla of kidney" EXACT [OBOL:automatic] synonym: "loop of Henle of inner zone of renal medulla" EXACT [OBOL:automatic] xref: MA:0002623 is_a: UBERON:0001288 ! loop of Henle relationship: part_of UBERON:0001294 ! inner medulla of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003457 name: head bone namespace: uberon def: "A bone that is part of a head [Obol]." [OBOL:automatic] synonym: "adult head bone" EXACT [OBOL:automatic] synonym: "adult head bone organ" EXACT [OBOL:automatic] synonym: "bone of adult head" EXACT [OBOL:automatic] synonym: "bone of head" EXACT [OBOL:automatic] synonym: "bone organ of adult head" EXACT [OBOL:automatic] synonym: "bone organ of head" EXACT [OBOL:automatic] synonym: "head bone organ" EXACT [OBOL:automatic] xref: MA:0000576 xref: SCTID:118646007 is_a: UBERON:0007914 ! head or neck bone relationship: part_of UBERON:0000033 ! head property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003462 name: facial bone namespace: uberon def: "A bone that is part of a facial skeleton [Obol]." [OBOL:automatic] comment: Editors note: test whether 'facial bone' is an exact synonym synonym: "bone of facial skeleton" EXACT [OBOL:automatic] synonym: "bone of viscerocranium" EXACT [OBOL:automatic] synonym: "facial bone" EXACT [EMAPA:19019] synonym: "facial skeleton bone" EXACT [OBOL:automatic] synonym: "viscerocranium bone" EXACT [OBOL:automatic] xref: EMAPA:19019 xref: MA:0001482 xref: ncithesaurus:Facial_Bone xref: SCTID:181799005 xref: UMLS:C0015455 is_a: UBERON:0003457 ! head bone is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0011156 {source="MA"} ! facial skeleton property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003469 name: respiratory system artery namespace: uberon def: "An artery that is part of a respiratory system [Obol]." [OBOL:automatic] xref: MA:0001804 is_a: UBERON:0001637 ! artery is_a: UBERON:0003643 ! respiratory system arterial blood vessel relationship: part_of UBERON:0001004 ! respiratory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003487 name: skin sebaceous gland namespace: uberon def: "A holocrine gland of the dermis that secretes sebum into hair follicles." [MP:0009535] synonym: "cutaneous sebaceous gland" EXACT [] synonym: "sebaceous gland of skin" EXACT [OBOL:automatic] xref: MA:0000149 xref: SCTID:115977007 is_a: UBERON:0001821 ! sebaceous gland relationship: part_of UBERON:0002097 ! skin of body relationship: part_of UBERON:0011932 {source="FMA"} ! pilosebaceous unit property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003496 name: head blood vessel namespace: uberon def: "A blood vessel that is part of a head [Obol]." [OBOL:automatic] synonym: "adult head blood vessel" EXACT [OBOL:automatic] synonym: "blood vessel of adult head" EXACT [OBOL:automatic] synonym: "blood vessel of head" EXACT [OBOL:automatic] xref: MA:0000575 xref: SCTID:127865000 is_a: UBERON:0001981 ! blood vessel relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0011362 {source="reference_0000032", is_inferred="true"} ! cranial blood vasculature property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003497 name: abdomen blood vessel namespace: uberon def: "A blood vessel that is part of an abdomen [Obol]." [OBOL:automatic] synonym: "blood vessel of abdomen" EXACT [OBOL:automatic] xref: MA:0000518 is_a: UBERON:0003835 ! abdominal segment blood vessel relationship: part_of UBERON:0000916 ! abdomen property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: seeAlso UBERON:0012254 xsd:string {notes="abdominal aorta artery"} [Term] id: UBERON:0003498 name: heart blood vessel namespace: uberon def: "A blood vessel that is part of a heart [Obol]." [OBOL:automatic] synonym: "blood vessel of heart" EXACT [OBOL:automatic] xref: MA:0002483 is_a: UBERON:0001981 ! blood vessel is_a: UBERON:0005985 ! coronary vessel relationship: part_of UBERON:0000948 ! heart property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003504 name: respiratory system blood vessel namespace: uberon def: "A blood vessel that is part of a respiratory system [Obol]." [OBOL:automatic] synonym: "apparatus respiratorius blood vessel" EXACT [OBOL:automatic] synonym: "blood vessel of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "blood vessel of respiratory system" EXACT [OBOL:automatic] xref: MA:0001799 is_a: UBERON:0001981 ! blood vessel is_a: UBERON:0004807 ! respiratory system epithelium relationship: part_of UBERON:0001004 ! respiratory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003509 name: arterial blood vessel namespace: uberon def: "A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta." [UBERON:cjm] comment: only in MA - supertype of artery, arteriole, aorta. xref: MA:0000061 is_a: UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004572 ! arterial system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003513 name: trunk blood vessel namespace: uberon def: "A blood vessel that is part of a trunk [Obol]." [OBOL:automatic] synonym: "blood vessel of torso" EXACT [OBOL:automatic] synonym: "blood vessel of trunk" EXACT [OBOL:automatic] synonym: "torso blood vessel" EXACT [OBOL:automatic] xref: MA:0000511 is_a: UBERON:0001981 ! blood vessel relationship: part_of UBERON:0002100 ! trunk property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003517 name: kidney blood vessel namespace: uberon def: "A blood vessel that is part of a kidney [Obol]." [OBOL:automatic] subset: vertebrate_core synonym: "blood vessel of kidney" EXACT [OBOL:automatic] synonym: "renal blood vessel" EXACT [OBOL:automatic] xref: MA:0001682 xref: TAO:0005306 xref: ZFA:0005306 is_a: UBERON:0003497 ! abdomen blood vessel is_a: UBERON:0004819 ! kidney epithelium is_a: UBERON:0006555 ! excretory tube relationship: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0006544 ! kidney vasculature property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003527 name: kidney capillary namespace: uberon def: "A capillary that is part of a kidney [Obol]." [OBOL:automatic] synonym: "blood capillary of kidney" EXACT [OBOL:automatic] synonym: "capillary of kidney" EXACT [OBOL:automatic] synonym: "capillary vessel of kidney" EXACT [OBOL:automatic] synonym: "kidney blood capillary" EXACT [OBOL:automatic] synonym: "kidney capillary vessel" EXACT [OBOL:automatic] synonym: "renal capillary" EXACT [OBOL:automatic] xref: EMAPA:31443 xref: MA:0002586 xref: SCTID:275409003 is_a: UBERON:0001982 ! capillary is_a: UBERON:0003517 ! kidney blood vessel relationship: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0006544 {source="reference_0000032"} ! kidney vasculature property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003528 name: brain grey matter namespace: uberon def: "A gray matter of neuraxis that is part of a brain [Obol]." [OBOL:automatic] synonym: "brain gray matter" EXACT [OBOL:automatic] synonym: "brain gray matter of neuraxis" EXACT [OBOL:automatic] synonym: "brain grey substance" EXACT [OBOL:automatic] synonym: "gray matter of brain" EXACT [OBOL:automatic] synonym: "gray matter of neuraxis of brain" EXACT [OBOL:automatic] synonym: "grey matter of brain" EXACT [OBOL:automatic] synonym: "grey substance of brain" EXACT [OBOL:automatic] xref: MA:0000810 xref: ncithesaurus:Cerebral_Gray_Matter xref: UMLS:C1707348 is_a: UBERON:0002020 ! gray matter of neuraxis relationship: part_of UBERON:0000955 ! brain property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003566 name: head connective tissue namespace: uberon def: "A portion of connective tissue that is part of a head [Obol]." [OBOL:automatic] synonym: "adult head connective tissue" EXACT [OBOL:automatic] synonym: "adult head portion of connective tissue" EXACT [OBOL:automatic] synonym: "adult head textus connectivus" EXACT [OBOL:automatic] synonym: "connective tissue of adult head" EXACT [OBOL:automatic] synonym: "connective tissue of head" EXACT [OBOL:automatic] synonym: "head portion of connective tissue" EXACT [OBOL:automatic] synonym: "head textus connectivus" EXACT [OBOL:automatic] synonym: "portion of connective tissue of adult head" EXACT [OBOL:automatic] synonym: "portion of connective tissue of head" EXACT [OBOL:automatic] synonym: "textus connectivus of adult head" EXACT [OBOL:automatic] synonym: "textus connectivus of head" EXACT [OBOL:automatic] xref: MA:0000577 is_a: UBERON:0002384 ! connective tissue relationship: part_of UBERON:0000033 ! head property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003567 name: abdomen connective tissue namespace: uberon def: "A portion of connective tissue that is part of an abdomen [Obol]." [OBOL:automatic] synonym: "abdomen portion of connective tissue" EXACT [OBOL:automatic] synonym: "abdomen textus connectivus" EXACT [OBOL:automatic] synonym: "connective tissue of abdomen" EXACT [OBOL:automatic] synonym: "portion of connective tissue of abdomen" EXACT [OBOL:automatic] synonym: "textus connectivus of abdomen" EXACT [OBOL:automatic] xref: MA:0000519 is_a: UBERON:0003838 ! abdominal segment connective tissue relationship: part_of UBERON:0000916 ! abdomen property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003586 name: trunk connective tissue namespace: uberon def: "A portion of connective tissue that is part of a trunk [Obol]." [OBOL:automatic] synonym: "connective tissue of torso" EXACT [OBOL:automatic] synonym: "connective tissue of trunk" EXACT [OBOL:automatic] synonym: "portion of connective tissue of torso" EXACT [OBOL:automatic] synonym: "portion of connective tissue of trunk" EXACT [OBOL:automatic] synonym: "textus connectivus of torso" EXACT [OBOL:automatic] synonym: "textus connectivus of trunk" EXACT [OBOL:automatic] synonym: "torso connective tissue" EXACT [OBOL:automatic] synonym: "torso portion of connective tissue" EXACT [OBOL:automatic] synonym: "torso textus connectivus" EXACT [OBOL:automatic] synonym: "trunk portion of connective tissue" EXACT [OBOL:automatic] synonym: "trunk textus connectivus" EXACT [OBOL:automatic] xref: MA:0000513 is_a: UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002100 ! trunk property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003643 name: respiratory system arterial blood vessel namespace: uberon def: "An arterial blood vessel that is part of a respiratory system [Obol]." [OBOL:automatic] xref: MA:0001800 is_a: UBERON:0003504 ! respiratory system blood vessel is_a: UBERON:0003509 ! arterial blood vessel relationship: part_of UBERON:0001004 ! respiratory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003644 name: kidney arterial blood vessel namespace: uberon def: "An arterial blood vessel that is part of a kidney [Obol]." [OBOL:automatic] xref: MA:0002578 is_a: UBERON:0003509 ! arterial blood vessel is_a: UBERON:0003517 ! kidney blood vessel relationship: part_of UBERON:0002113 ! kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003672 name: dentition namespace: uberon comment: In FMA this is an anatomical set synonym: "dentes" EXACT LATIN [FMA:75150, FMA:TA] synonym: "set of teeth" EXACT [FMA:75150] synonym: "teeth" EXACT [FMA:75150] synonym: "teeth" RELATED [] synonym: "teeth set" EXACT [FMA:75150] xref: AAO:0000126 xref: FMA:75150 xref: GAID:1249 xref: MESH:A14.254 xref: ncithesaurus:Dentition xref: OpenCyc:Mx4rvVi65JwpEbGdrcN5Y29ycA xref: SCTID:245543004 xref: UMLS:C0011443 is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0000165 {source="FMA"} ! mouth relationship: part_of UBERON:0010323 ! cranial skeletal system property_value: external_definition "Dentition refers to set of teeth, especially with regard to their number, kind, and arrangement, in the mouth.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000126", ontology="AAO", source="AAO:LAP"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003688 name: omentum namespace: uberon xref: EV:0100084 xref: FMA:14650 xref: GAID:23 xref: galen:Omentum xref: MESH:A01.047.025.600.573 xref: ncithesaurus:Omentum xref: SCTID:362710002 xref: UMLS:C0028977 is_a: UBERON:0000063 ! organ segment is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0001178 ! visceral peritoneum property_value: has_relational_adjective "omental" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003697 name: abdominal wall namespace: uberon def: "The abdominal wall represents the boundaries of the abdominal cavity. The abdominal wall is split into the posterior (back), lateral (sides) and anterior (front) walls. There is a common set of layers covering and forming all the walls: the deepest being the extraperitoneal fat, the parietal peritoneum, and a layer of fascia which has different names over where it covers (eg transversalis, psoas fascia). Superficial to these, but not present in the posterior wall are the three layers of muscle, the transversus abdominis (transverse abdominal muscle), the internal (obliquus internus) and the external oblique (obliquus externus)." [Wikipedia:Abdominal_wall] synonym: "layers of the abdominal wall" RELATED [Wikipedia:Abdominal_wall] synonym: "paries abdominalis" EXACT [Wikipedia:Abdominal_wall] synonym: "paries abdominalis" RELATED LATIN [Wikipedia:Abdominal_wall] synonym: "wall of abdomen" EXACT [FMA:259054] synonym: "wall of abdomen proper" EXACT [FMA:10429] xref: FMA:10429 xref: FMA:259054 xref: GAID:26 xref: http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg xref: MESH:A01.047.050 xref: ncithesaurus:Abdominal_Wall xref: SCTID:181613000 xref: UMLS:C0836916 is_a: UBERON:0000060 ! anatomical wall relationship: part_of UBERON:0000916 ! abdomen property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003704 name: intrahepatic bile duct namespace: uberon def: "Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct." [MESH:A03.159.183.158] subset: vertebrate_core synonym: "bile duct intrahepatic part" EXACT [MA:0001630] synonym: "intrahepatic biliary system" RELATED [] xref: FMA:15766 xref: GAID:287 xref: MA:0001630 xref: MESH:A03.159.183.158 xref: ncithesaurus:Intrahepatic_Bile_Duct xref: SCTID:362193005 xref: TAO:0005169 xref: UMLS:C0005401 xref: ZFA:0005169 is_a: UBERON:0002394 {source="FMA"} ! bile duct relationship: part_of UBERON:0002107 {source="MA"} ! liver property_value: external_definition "Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005169", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003714 name: neural tissue namespace: uberon def: "Portion of tissue which consists of neurons, neuroglia and vasculature. Examples: Neural tissue of brain, neural tissue of peripheral ganglion, neural tissue of nerve[FMA]." [FMA:9642] comment: FMA definition includes vasculature synonym: "nerve tissue" EXACT [FMA:9642] synonym: "nervous tissue" EXACT [FMA:9642] synonym: "portion of neural tissue" EXACT [FMA:9642] xref: AAO:0000325 xref: AEO:0000123 xref: EHDAA2:0003123 xref: FMA:9642 xref: GAID:609 xref: MESH:A08.561 xref: ncithesaurus:Nervous_Tissue xref: OpenCyc:Mx4rVmfYCsQ_QdeM_bFAeS8NRQ xref: SCTID:91728009 xref: UMLS:C0027757 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure disjoint_from: UBERON:0004755 ! skeletal tissue relationship: part_of UBERON:0001016 ! nervous system property_value: external_definition "One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000325", ontology="AAO", source="AAO:LAP"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003729 name: mouth mucosa namespace: uberon def: "the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized." [Wikipedia:Oral_mucosa] comment: Usage notes: this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa) synonym: "buccal mucosa" RELATED [GAID:951] synonym: "mouth mucosa" EXACT [FMA:59660] synonym: "mouth mucous membrane" EXACT [OBOL:accepted] synonym: "mouth organ mucosa" EXACT [OBOL:accepted] synonym: "mucosa of mouth" EXACT [OBOL:accepted] synonym: "mucosal lining of mouth" RELATED [MA:0002794] synonym: "mucous membrane of mouth" EXACT [FMA:59660] synonym: "oral mucosa" RELATED [GAID:951] synonym: "oral mucous membrane" EXACT [] synonym: "oral part of viscerocranial mucosa" EXACT [FMA:59660] synonym: "tunica mucosa oris" EXACT LATIN [FMA:59660, FMA:TA] synonym: "tunica mucosa oris" RELATED LATIN [Wikipedia:Oral_mucosa] xref: BTO:0002860 xref: FMA:59660 xref: GAID:951 xref: MA:0002794 xref: MESH:A10.615.550.599 xref: ncithesaurus:Oral_Mucosa xref: UMLS:C0026639 is_a: UBERON:0000344 ! mucosa is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000165 ! mouth property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003820 name: prostate bud namespace: uberon def: "A region of the fetal urogenital sinus epithelium destined to become the prostate[GO]." [GO:0060513] comment: AR activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth. There are three phases of prostatic budding: (1) the specification phase, when instructive developmental cues define where buds will form in the UGS, (2) the initiation phase, when prostatic buds begin to form, and (3) the elongation phase, when proliferation, cell adhesion, and cell migration coordinate outgrowth of prostatic buds into UGM. Timing of prostatic bud formation and the quantity and pattern of buds that are formed in the UGS are strictly regulated [3, 4]. The position of prostatic buds as they emerge from the UGS in utero determines the arrangement of prostate ducts in adulthood.[PMID:18977204] synonym: "prostate ductal progenitor" EXACT [PMID:18977204] synonym: "prostatic bud" EXACT [] is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0005153 {source="GO:0060572"} ! epithelial bud is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0009847 {source="PMID:18977204"} ! prostate field relationship: part_of UBERON:0000922 ! embryo property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003835 name: abdominal segment blood vessel namespace: uberon def: "A blood vessel that is part of an abdominal segment of trunk [Obol]." [OBOL:automatic] synonym: "abdominal segment of trunk blood vessel" EXACT [OBOL:automatic] synonym: "blood vessel of abdominal segment of trunk" EXACT [OBOL:automatic] xref: MA:0000524 is_a: UBERON:0003513 ! trunk blood vessel relationship: part_of UBERON:0002417 ! abdominal segment of trunk property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003838 name: abdominal segment connective tissue namespace: uberon def: "A portion of connective tissue that is part of an abdominal segment of trunk [Obol]." [OBOL:automatic] synonym: "abdominal segment of trunk connective tissue" EXACT [OBOL:automatic] synonym: "abdominal segment of trunk portion of connective tissue" EXACT [OBOL:automatic] synonym: "abdominal segment of trunk textus connectivus" EXACT [OBOL:automatic] synonym: "connective tissue of abdominal segment of trunk" EXACT [OBOL:automatic] synonym: "portion of connective tissue of abdominal segment of trunk" EXACT [OBOL:automatic] synonym: "textus connectivus of abdominal segment of trunk" EXACT [OBOL:automatic] xref: MA:0000526 is_a: UBERON:0003586 ! trunk connective tissue relationship: part_of UBERON:0002417 ! abdominal segment of trunk property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003856 name: odontogenic mesenchyme namespace: uberon def: "Mesenchyme that gives rise to an odontogenic papilla." [UBERON:cjm] comment: Editor notes: we follow ZFA in introducing an additional distinction between the dental papilla and the (uncondensed) mesenchyme. Note that in some species such as zebrafish teeth are not part of the mouth, and sharks have dermal denticles which share similar developmental origins with teeth. For now we assume a NC origin for all and add a taxon restriction to 1st arch mesenchyme subset: vertebrate_core synonym: "dental mesenchyme" EXACT [ZFA:0005139] synonym: "dental organ mesenchyme" EXACT [OBOL:automatic] synonym: "enamel organ mesenchyme" EXACT [OBOL:automatic] synonym: "tooth enamel organ mesenchyme" EXACT [OBOL:automatic] synonym: "tooth mesenchyme" EXACT [OBOL:automatic] xref: TAO:0005139 xref: VHOG_RETIRED:0001444 xref: ZFA:0005139 is_a: UBERON:0007213 ! mesenchyme derived from head neural crest relationship: develops_from UBERON:0007213 {notes="see comments"} ! mesenchyme derived from head neural crest relationship: part_of UBERON:0005176 {source="ZFA"} ! tooth enamel organ property_value: external_definition "Mesenchyme enclosed by dental organ.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005139", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003869 name: presumptive ganglion namespace: uberon def: "A presumptive structure that develops_into a ganglion." [OBOL:automatic] is_a: UBERON:0006598 ! presumptive structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003886 name: body cavity precursor namespace: uberon def: "An anatomical cavity that develops_into a coelemic cavity lumen." [OBOL:automatic] subset: grouping_class subset: non_informative is_a: UBERON:0000464 ! anatomical space property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003887 name: intraembryonic coelom namespace: uberon def: "In the development of the human embryo the intraembryonic coelom (or somatic coelom) is a portion of the conceptus forming in the mesoderm. During the second week of development, the lateral mesoderm splits into a dorsal somatic mesoderm (somatopleure) and a ventral splanchnic mesoderm (splanchnopleure). The resulting cavity between the somatopleure and splanchnopleure is called the intraembryonic coelom. This space will give rise to the thoracic and abdominal cavities. It briefly has a connection with the extraembryonic coelom[WP]." [Wikipedia:Intraembryonic_coelom] comment: Editor notes: consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. Todo: check ZFA, which appears to be a structure present in adults synonym: "somatic coelom" EXACT [Wikipedia:Intraembryonic_coelom] xref: EHDAA:251 xref: EMAPA:16088 xref: ncithesaurus:Intraembryonic_Coelom xref: UMLS:C1512940 xref: VHOG:0000316 is_a: UBERON:0003886 ! body cavity precursor relationship: develops_from UBERON:0003081 {source="Wikipedia"} ! lateral plate mesoderm property_value: homology_notes " (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000316", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003891 name: stroma namespace: uberon def: "Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma." [Wikipedia:Stroma_of_ovary_%28animal_tissue%29] subset: grouping_class xref: FMA:81494 xref: ncithesaurus:Stroma_Connective_Tissue xref: UMLS:C0927195 is_a: UBERON:0002384 ! connective tissue property_value: has_relational_adjective "stromal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003893 name: capsule namespace: uberon def: "a cover or envelope partly or wholly surrounding a structure. Examples: egg shell, articular capsules, renal capsules[WP]." [Wikipedia:Capsule_(anatomy)] comment: see also: protective structure surrounding some species of bacteria and fungi. Note that FMA has classes such as Articular capsule that are not subtypes of Capsule (which is undefined in FMA). GO has 'capsule' which is a fungal structure, and 'external encapsulating structure' which is restricted to cells subset: grouping_class xref: EHDAA:4739 xref: EHDAA:9061 xref: FMA:85272 xref: galen:Capsule is_a: UBERON:0000158 ! membranous layer property_value: has_relational_adjective "capsular" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003894 name: liver primordium namespace: uberon def: "A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum." [ISBN:3211492755] comment: Editor's note: consider adding further subdivisions of the endoderm, e.g. ventral foregut. Note we place two EFO classes here, it's not clear how they differ subset: vertebrate_core synonym: "embryological hepatic plate" EXACT [UBERON:cjm] synonym: "hepatic plate" RELATED [EHDAA2:0000744] synonym: "liver bud" RELATED INCONSISTENT [XAO:0003266, ZFA:0000124] synonym: "liver endoderm" RELATED [EFO:0002577] synonym: "primordium of the liver" EXACT [ncithesaurus:Primordium_of_the_Liver] xref: AAO:0011058 xref: BTO:0003391 xref: EFO:0002577 xref: EFO:0003428 xref: EHDAA2:0000744 xref: EHDAA:973 xref: EMAPA:16847 xref: ncithesaurus:Hepatic_Cord xref: ncithesaurus:Primordium_of_the_Liver xref: TAO:0000124 xref: UMLS:C0734013 xref: UMLS:C1514451 xref: XAO:0003266 xref: ZFA:0000124 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007497 ! developing epithelial placode is_a: UBERON:0009497 ! epithelium of foregut-midgut junction relationship: develops_from UBERON:0001041 {notes="ventral foregut endoderm", source="Zaret 1996"} ! foregut relationship: part_of UBERON:0009550 {source="EHDAA2"} ! endoderm of foregut-midgut junction property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003909 name: sinusoid namespace: uberon def: "small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP]." [Wikipedia:Sinusoid_(blood_vessel)] comment: AO notes - some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined). subset: vertebrate_core synonym: "endothelium of irregular blood filled space" RELATED [] synonym: "sinusoidal blood vessel" EXACT [] synonym: "sinusoidal blood vessel endothelium" EXACT [ZFA:0005261] synonym: "sinusoidal capillary" RELATED [http://www.medilexicon.com/medicaldictionary.php?t=13986] synonym: "sinusoidal endothelium" RELATED [] xref: FMA:63131 xref: SCTID:340163004 xref: TAO:0005261 xref: ZFA:0005261 is_a: UBERON:2005260 {source="ZFA", source="Wikipedia"} ! fenestrated capillary property_value: external_definition "Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005261", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "sinusoidal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003913 name: tooth-like structure namespace: uberon def: "hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food." [GOC:cjm] comment: see dermal denticle subset: grouping_class synonym: "tooth-like organ" EXACT [GOC:cjm] xref: HAO:0001019 is_a: UBERON:0004765 ! skeletal element property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003914 name: epithelial tube namespace: uberon def: "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system." [GO:0060562, PMID:12526790] xref: AEO:0000114 xref: EHDAA2:0003114 xref: FBbt:00007474 is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003915 name: endothelial tube namespace: uberon def: "Any endothelium that has the quality of being cylindrical [Obol]." [OBOL:automatic] is_a: UBERON:0001986 ! endothelium is_a: UBERON:0003914 ! epithelial tube property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003918 name: kidney mesenchyme namespace: uberon def: "Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]." [GO:0072074] comment: check this synonym: "mesenchyme of kidney" EXACT [] is_a: UBERON:0003104 ! mesenchyme property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003920 name: venous blood vessel namespace: uberon def: "a blood vessel that carries blood from the capillaries toward the heart" [http://www.thefreedictionary.com/venous+blood+vessel] comment: Compare to: vein synonym: "segment of venous tree organ" EXACT [FMA:86188] synonym: "venous tree organ segment" EXACT [FMA:86188] xref: FMA:86188 xref: MA:0000066 is_a: UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004582 ! venous system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003921 name: pancreas primordium namespace: uberon def: "embryonic structure that develops into pancreatic bud." [http://en.wikipedia.org/wiki/Pancreas#Embryological_development] comment: AO notes: in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds. Terminology notes: revisit after standardizing terms 'primordium', 'anlagen', 'bud' subset: vertebrate_core synonym: "pancreatic anlage" RELATED [] synonym: "pancreatic endoderm" RELATED [EFO:0002579] synonym: "pancreatic primordium" EXACT [] synonym: "primordial pancreas" RELATED [FMA:79792] xref: EFO:0002579 xref: EFO:0003434 xref: EHDAA2:0001382 xref: EHDAA:2163 xref: EMAPA:17066 xref: FMA:79792 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Gray982.png/200px-Gray982.png xref: TAO:0000254 xref: XAO:0001101 xref: ZFA:0000254 is_a: UBERON:0001048 {source="EHDAA2"} ! primordium relationship: develops_from UBERON:0000925 {source="Wikipedia"} ! endoderm relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0007026 ! primitive gut property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003922 name: pancreatic bud namespace: uberon def: "The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. In humans, an embryonic structure that is an outgrowth of the duodenum during embryogenesis - joins together to form the adult pancreas[WP]." [PMID:16417468, Wikipedia:Pancreatic_bud] synonym: "pancreatic anlage" RELATED [] synonym: "pancreatic buds" EXACT PLURAL [TAO:0001390] xref: EFO:0003470 xref: http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/4/49/Suckale08FBS_fig1_pancreas_development.jpeg/300px-Suckale08FBS_fig1_pancreas_development.jpeg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Gray982.png/200px-Gray982.png xref: ncithesaurus:Pancreatic_Bud xref: SCTID:360398004 xref: TAO:0001390 xref: UMLS:C1283285 xref: ZFA:0001390 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac relationship: develops_from UBERON:0001041 {source="Wikipedia:Pancreas#Embryological_development"} ! foregut relationship: develops_from UBERON:0001555 ! digestive tract relationship: develops_from UBERON:0002114 {exception="zebrafish", source="Wikipedia:Pancreatic_bud"} ! duodenum relationship: develops_from UBERON:0009497 {source="EHDAA2-inferred"} ! epithelium of foregut-midgut junction relationship: part_of UBERON:0003921 {source="EHDAA2"} ! pancreas primordium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003923 name: dorsal pancreatic bud namespace: uberon def: "pancreatic bud that gives rise to the accessory pancreatic duct." [Wikipedia:Pancreatic_bud] subset: vertebrate_core synonym: "dorsal pancreas anlage" RELATED [] synonym: "dorsal pancreatic anlage" RELATED [] synonym: "pancreas dorsal primordium duct bud" EXACT [EHDAA2:0001385] synonym: "pancreas primordium dorsal bud" EXACT [] synonym: "posterior pancreatic anlage" RELATED [] synonym: "posterior pancreatic bud" RELATED [] xref: AAO:0011031 xref: EFO:0003465 xref: EHDAA2:0001385 xref: EMAPA:17067 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Gray982.png/200px-Gray982.png xref: SCTID:361435005 xref: TAO:0001370 xref: VHOG:0001428 xref: XAO:0000467 xref: ZFA:0001370 is_a: UBERON:0003922 ! pancreatic bud relationship: develops_from UBERON:0001045 {source="XAO"} ! midgut relationship: part_of UBERON:0010375 {source="EHDAA2"} ! pancreas dorsal primordium property_value: external_definition "The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011031", ontology="AAO", source="XAO:curator"} property_value: homology_notes "In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001428", ontology="VHOG", source="DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003924 name: ventral pancreatic bud namespace: uberon def: "pancreatic bud that gives rise to the major pancreatic duct." [Wikipedia:Pancreatic_bud] comment: Development notes: the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship. // The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP] subset: vertebrate_core synonym: "anterior pancreatic anlage" RELATED [] synonym: "anterior pancreatic bud" RELATED [] synonym: "pancreas primordium ventral bud" EXACT [] synonym: "pancreas ventral primordium duct bud" EXACT [EHDAA2:0001389] synonym: "ventral pancreas anlage" RELATED [] synonym: "ventral pancreatic anlage" RELATED [] xref: AAO:0011111 xref: EFO:0003464 xref: EHDAA2:0001389 xref: EMAPA:17256 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Gray982.png/200px-Gray982.png xref: SCTID:361437002 xref: TAO:0001369 xref: VHOG:0001429 xref: XAO:0001103 xref: ZFA:0001369 is_a: UBERON:0003922 ! pancreatic bud relationship: develops_from UBERON:0008835 {source="PMID:16417468", source="WP"} ! hepatic diverticulum relationship: part_of UBERON:0010376 {source="EHDAA2"} ! pancreas ventral primordium property_value: homology_notes "In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001429", ontology="VHOG", source="DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003928 name: digestive system duct namespace: uberon def: "A duct that is part of a digestive system [Obol]." [OBOL:automatic] synonym: "duct of digestive system" EXACT [OBOL:automatic] synonym: "duct of gastrointestinal system" EXACT [OBOL:automatic] synonym: "gastrointestinal system duct" EXACT [OBOL:automatic] xref: TAO:0005162 xref: ZFA:0005162 is_a: UBERON:0000058 ! duct relationship: part_of UBERON:0001007 ! digestive system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003929 name: gut epithelium namespace: uberon def: "An epithelium that is part of a digestive tract [Obol]." [OBOL:automatic] synonym: "digestive tract epithelial tissue" EXACT [OBOL:automatic] synonym: "digestive tract epithelium" EXACT [OBOL:automatic] synonym: "epithelial tissue of digestive tract" EXACT [OBOL:automatic] synonym: "epithelial tissue of gut" EXACT [OBOL:automatic] synonym: "epithelial tissue of lower gastrointestinal tract" EXACT [OBOL:automatic] synonym: "epithelium of digestive tract" EXACT [OBOL:automatic] synonym: "epithelium of gut" EXACT [OBOL:automatic] synonym: "epithelium of lower gastrointestinal tract" EXACT [OBOL:automatic] synonym: "gut epithelial tissue" EXACT [OBOL:automatic] synonym: "lower gastrointestinal tract epithelial tissue" EXACT [OBOL:automatic] synonym: "lower gastrointestinal tract epithelium" EXACT [OBOL:automatic] xref: BTO:0000956 xref: EHDAA2:0004567 xref: ncithesaurus:Gut_Epithelium xref: TAO:0005123 xref: UMLS:C0836205 xref: XAO:0003200 xref: ZFA:0005123 is_a: UBERON:0005911 ! endo-epithelium relationship: part_of UBERON:0001555 ! digestive tract property_value: external_definition "Epithelium lining the lumen of the gut.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005123", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003937 name: sex gland namespace: uberon def: "any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction" [MP:0000653] subset: organ_slim synonym: "genitalia gland" EXACT [OBOL:automatic] synonym: "gland of genitalia" EXACT [OBOL:automatic] synonym: "gland of reproductive system" EXACT [OBOL:automatic] synonym: "reproductive gland" EXACT [MA:0001751] synonym: "reproductive system gland" EXACT [OBOL:automatic] xref: MA:0001751 is_a: UBERON:0002530 ! gland is_a: UBERON:0005156 ! reproductive structure relationship: part_of UBERON:0000990 ! reproductive system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003947 name: brain ventricle/choroid plexus namespace: uberon def: "the brain ventricles or their associated choroid plexuses" [MP:0002200] comment: TODO - check relationship between CP and BV. If this is part of then this class should be obsoleted is_a: UBERON:0004121 ! ectoderm-derived structure union_of: UBERON:0001886 ! choroid plexus union_of: UBERON:0004086 ! brain ventricle relationship: part_of UBERON:0000955 ! brain property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003956 name: aqueous drainage system namespace: uberon def: "the structures associated with drainage of the aqueous humor from the eye, that include the trabecular meshwork, Schlemm's canal, the uveoscleral network, and the aqueous veins" [MP:0005198] is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001768 ! uvea property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0003975 name: internal female genitalia namespace: uberon def: "the internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina." [MP:0009209] subset: organ_slim synonym: "female internal genitalia" EXACT [FMA:45654] synonym: "internal female genital organ" EXACT [BTO:0003099] synonym: "internal genitalia of female reproductive system" EXACT [OBOL:automatic] synonym: "organa genitalia feminina interna" RELATED [BTO:0003099] xref: BTO:0003099 xref: FMA:45654 xref: SCTID:303518005 is_a: UBERON:0003134 ! female reproductive organ is_a: UBERON:0004175 ! internal reproductive organ relationship: part_of UBERON:0000474 ! female reproductive system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004001 name: olfactory bulb layer namespace: uberon def: "." [MP:0009946] comment: TODO - check isa parentage synonym: "cytoarchitectural part of olfactory bulb" EXACT [NIF_GrossAnatomy:nlx_anat_20090402] xref: NIF_GrossAnatomy:nlx_anat_20090402 is_a: UBERON:0000119 ! cell layer is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0002264 ! olfactory bulb property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004043 name: semicircular canal ampulla namespace: uberon def: "the spherical enlargement at the base of each semicircular canal where they connect with the utricle, containing the crista ampullaris which detects movement of the fluid within the canals" [MP:0008488, Wikipedia:Osseous_ampullae] comment: TODO check duct vs canal. Also check FMA - has many subtypes of semicircular canal such as 'ampulla of anterior semicircular canal' synonym: "ampullae osseae" RELATED LATIN [Wikipedia:Osseous_ampullae] synonym: "membraneous ampulla of the semicircular duct" RELATED [MP:0008488] synonym: "semicircular duct ampulla" RELATED [MA:0002770] xref: http://upload.wikimedia.org/wikipedia/commons/6/65/Vestibular_system%27s_semicircular_canal-_a_cross-section.jpg xref: http://upload.wikimedia.org/wikipedia/commons/thumb/6/65/Vestibular_system%27s_semicircular_canal-_a_cross-section.jpg/200px-Vestibular_system%27s_semicircular_canal-_a_cross-section.jpg xref: MA:0002770 xref: SCTID:279759001 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0001840 ! semicircular canal relationship: part_of UBERON:0001856 {source="MA"} ! semicircular duct property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004086 name: brain ventricle namespace: uberon def: "one of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid" [] comment: Note that FMA draws the distinction between e.g. 'fourth ventricle' and 'cavity of fourth ventricle'. The latter is a cavity, and part of the former, which is a region. The superclass of 'fourth ventricle' is_a 'region of ventricular system of the brain'. We place this class here, although it is not equivalent to ventricles, as it includes ventricle bodies. synonym: "cerebral ventricle" EXACT [HP:0002118] synonym: "region of ventricular system of brain" EXACT [FMA:78447] xref: BTO:0001442 xref: EFO:0001914 xref: FMA:78447 xref: MA:0000818 xref: MESH:A08.186.211.276 xref: ncithesaurus:Ventricle_Brain xref: NIF_GrossAnatomy:birnlex_1356 xref: OpenCyc:Mx4rvmTY65wpEbGdrcN5Y29ycA xref: SCTID:180929003 xref: UMLS:C0007799 is_a: UBERON:0005358 ! ventricle of nervous system relationship: part_of UBERON:0005282 ! ventricular system of brain property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004088 name: ocular region namespace: uberon def: "." [HP:0000284] comment: TODO: consider the following: eyeball (eye proper) part_of eye (= eyeball+eyelid etc) part_of ocular region (= eye + adnexa such as eyebrow); note the FMA class is more narrow though, and is more like eye + muscles + vasculature // in HP covers eyelid, eyebrow. synonym: "content of orbital part of eye" EXACT [FMA:260119] synonym: "eye region" EXACT [OBOL:accepted] synonym: "orbital content" RELATED [FMA:260119] xref: FMA:260119 is_a: UBERON:0000477 ! anatomical cluster relationship: part_of UBERON:0001456 ! face property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004089 name: midface namespace: uberon def: "the middle of the face including the nose and its associated bony structures[MW]." [HP:0000309, http://www.merriam-webster.com/medical/midface] comment: editors note: this class is currently a union of the snout (e.g. in mouse), the midface and the lower face. Note that in MA, snout includes the whole jaw and should thus be more alike the lower face than the midface, so its placement here is not strictly accurate. In future we might introduce specific classes for each of these, and include the full parthood relationships. if this is done, then care should be taken to preserve inferences such as an abnormality of the lower face being an abnormality of the midface. synonym: "lower face" RELATED [] synonym: "midface/lower face" RELATED [] synonym: "snout" RELATED SENSU [MA:0001910] xref: MA:0001910 is_a: UBERON:0000061 ! anatomical structure relationship: part_of UBERON:0001456 ! face property_value: has_relational_adjective "midfacial" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004111 name: anatomical conduit namespace: uberon def: "any opening in the body." [Wikipedia:Foramen] comment: note that FMA has both conduit and conduit space. In EHDAA2 this is a surface feature synonym: "foramen" NARROW [EHDAA2:0003080] synonym: "foramina" NARROW PLURAL [UBERON:cjm] xref: AEO:0000080 xref: EHDAA2:0003080 xref: FMA:242873 is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004117 name: pharyngeal pouch namespace: uberon def: "embryonic structure that forms on the endodermal side between the pharyngeal arches, and pharyngeal grooves (or clefts) form the lateral ectodermal surface of the neck region to separate the arches. The pouches line up with the clefts, and these thin segments become gills in fish[WP]. Outpocketings of pharyngeal endoderm that interdigitate with the neural crest derived pharyngeal arches. The pouches later fuse with the surface ectoderm to form the gill slits[ZFA]." [Wikipedia:Pharyngeal_pouch_(embryology)] comment: AO notes: VHOG and EMAPAA distinguish between pouch endoderm and pouch but we merge those here. Editor notes: consider adding location (precursor) - i.e. internal (endodermal) // The pouches are polarized structures. For example, whereas the rostral half of each pouch expresses Bmp-7, the caudal half expresses FGF-8 and the dorsal aspect of each pouch is marked via its expression of Pax-1. each pouch has an individual sense of identity. Shh expression is a prominent early feature of the caudal endoderm of the second arch, and individual pouches mark the anterior limits of expression of Hox genes within the pharyngeal endoderm; Hox-a2 has a rostral boundary at the second pouch, Hox-a3 at the third pouch and Hox-a4 at the most caudal pouch[PMID:16313389] subset: vertebrate_core synonym: "branchial pouch" EXACT [Wikipedia:Branchial_pouch] synonym: "pharyngeal pouches" RELATED [VHOG:0001203] synonym: "visceral pouch" EXACT SENSU [] synonym: "visceral pouches" RELATED [VHOG:0001203] xref: AAO:0011113 xref: EFO:0003627 xref: EHDAA:1086 xref: EHDAA:1669 xref: EHDAA:579 xref: EHDAA:617 xref: ncithesaurus:Pharyngeal_Pouch xref: SCTID:34674002 xref: TAO:0001106 xref: UMLS:C0231067 xref: VHOG:0001203 xref: XAO:0000282 xref: ZFA:0001106 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0005911 ! endo-epithelium relationship: develops_from UBERON:0007690 {source="EHDAA2", source="ZFA"} ! early pharyngeal endoderm relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0008814 ! pharyngeal system property_value: external_definition "Outpocketings of pharyngeal endoderm that interdigitate with the neural crest derived pharyngeal arches. The pouches later fuse with the surface ectoderm to form the gill slits. Crump et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001106", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001203", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004119 name: endoderm-derived structure namespace: uberon def: "An anatomical structure that develops (entirely or partially) from the endoderm." [UBERON:cjm] comment: Grouping term for query purposes subset: grouping_class is_a: UBERON:0000061 ! anatomical structure relationship: develops_from UBERON:0000925 ! endoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004120 name: mesoderm-derived structure namespace: uberon def: "An anatomical structure that develops (entirely or partially) from the mesoderm." [UBERON:cjm] comment: Grouping term for query purposes subset: grouping_class is_a: UBERON:0000061 ! anatomical structure relationship: develops_from UBERON:0000926 ! mesoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004121 name: ectoderm-derived structure namespace: uberon def: "An anatomical structure that develops (entirely or partially) from the ectoderm." [UBERON:cjm] comment: Grouping term for query purposes subset: grouping_class is_a: UBERON:0000061 ! anatomical structure relationship: develops_from UBERON:0000924 ! ectoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004122 name: genitourinary system namespace: uberon def: "An anatomical system that has_part a reproductive system and has_part a excretory system." [OBOL:automatic] synonym: "genitourinary tract" RELATED [] synonym: "GU tract" RELATED [] synonym: "urogenital system" EXACT [] synonym: "urogenital tract" RELATED [BTO:0003091] synonym: "Urogenitalsystem" RELATED [BTO:0003091] xref: AAO:0000624 xref: BILA:0000122 xref: BTO:0003091 xref: EFO:0003864 xref: EHDAA:1013 xref: EMAPA:16367 xref: EV:0100094 xref: GAID:362 xref: galen:GenitoUrinarySystem xref: MESH:A05 xref: ncithesaurus:Genitourinary_System xref: OpenCyc:Mx4rQRpVMgAKEdyHxgDggVfs8g xref: SCTID:278861008 xref: UMLS:C0042066 xref: VHOG:0000286 xref: XAO:0000140 is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure relationship: develops_from UBERON:0003064 {source="AAO"} ! intermediate mesoderm property_value: axiom_lost_from_external_ontology "relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000624", ontology="AAO"} property_value: external_definition "Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000624", ontology="AAO", source="AAO:EJS"} property_value: has_relational_adjective "genitourinary" xsd:string property_value: has_relational_adjective "urogenital" xsd:string property_value: homology_notes "Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000286", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004128 name: optic vesicle namespace: uberon def: "The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]." [GO:0003404, Wikipedia:Optic_vesicles] comment: Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 "Developmental Biology"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode PMID:16496288 subset: vertebrate_core synonym: "evagination" RELATED [] synonym: "ocular vesicle" RELATED [VHOG:0000165] xref: AAO:0011039 xref: EHDAA2:0001320 xref: EMAPA:16540 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/e/e0/Gray863.png/200px-Gray863.png xref: ncithesaurus:Optic_Vesicle xref: SCTID:362864008 xref: TAO:0000050 xref: UMLS:C0231106 xref: VHOG:0000165 xref: XAO:0000228 xref: ZFA:0000050 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0003071 {source="ZFA"} ! eye primordium relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye property_value: homology_notes " (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000165", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004134 name: proximal tubule namespace: uberon def: "In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]." [GO:0072014] comment: todo - ensure definition works across species. synonym: "kidney proximal tubule" EXACT [MA:0002611] synonym: "proximal kidney tubule" EXACT [MESH:A05.810.453.736.560.570] synonym: "renal proximal tubule" EXACT [] xref: BTO:0001498 xref: EMAPA:28281 xref: MA:0002611 xref: MESH:A05.810.453.736.560.570 is_a: UBERON:0006853 ! renal cortex tubule relationship: part_of UBERON:0001225 {notes="checkme"} ! cortex of kidney relationship: part_of UBERON:0001231 {source="multiple"} ! nephron tubule property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004135 name: distal tubule namespace: uberon def: "The distal tubule is a nephron tubule that consists of the convoluted and straight distal tubule segments" [GO:0072017] synonym: "kidney distal tubule" EXACT [MA:0002633] synonym: "renal distal tubule" EXACT [] xref: BTO:0000482 xref: EMAPA:28387 xref: MA:0002633 xref: MESH:A05.810.453.736.560.540 is_a: UBERON:0007685 ! region of nephron tubule property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004136 name: intermediate tubule namespace: uberon def: "The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules" [GO:0072018] comment: todo - check for applicability across species synonym: "renal intermediate tubule" EXACT [] synonym: "tubulus attenuatus" EXACT [FMA:17718] xref: FMA:17718 is_a: UBERON:0007685 ! region of nephron tubule relationship: part_of UBERON:0001288 {source="FMA"} ! loop of Henle property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004139 name: cardiogenic plate namespace: uberon def: "The first recognizable structure derived from the heart field" [GO:0003142] comment: TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO synonym: "cardiogenic crescent" RELATED [GO:0003142] synonym: "heart rudiment" RELATED [] synonym: "myocardial plate" EXACT [EHDAA2:0000215] xref: EHDAA2:0000215 xref: EMAPA:16106 xref: VHOG:0000975 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0003084 ! heart primordium relationship: part_of UBERON:0000922 ! embryo property_value: homology_notes " (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000975", ontology="VHOG", source="PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004140 name: heart field namespace: uberon def: "a specific region of the lateral mesoderm in which the heart will develop." [GO:0003128] comment: note that this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] synonym: "primary heart field" EXACT [PMID:17276708, XAO:0004185] xref: XAO:0004185 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0003081 {source="GO:0003128"} ! lateral plate mesoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004141 name: heart tube namespace: uberon def: "Cavitated compound organ that will become the adult heart following looping morphogenesis and valve formation[ZFA]." [GO:0003143, ZFA:0000360] subset: vertebrate_core synonym: "early primitive heart tube" EXACT [EMAPA:16208] synonym: "embryonic heart tube" RELATED [] xref: AAO:0010411 xref: EFO:0003526 xref: EHDAA:424 xref: EMAPA:16208 xref: TAO:0000360 xref: XAO:0000337 xref: ZFA:0000360 is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0005498 {source="ZFA"} ! primitive heart tube property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004145 name: outflow tract namespace: uberon def: "The outflow tract is the portion of the heart through which blood flows into the arteries" [GO:0003151] synonym: "cardiac outflow tract" EXACT [] xref: EHDAA2:0001351 xref: EHDAA:464 xref: EHDAA:798 xref: EMAPA:16229 xref: EMAPA:16346 xref: MA:0000100 xref: VHOG:0000670 xref: XAO:0004139 is_a: UBERON:0004111 ! anatomical conduit is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0000948 ! heart property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004146 name: His-Purkinje system namespace: uberon def: "The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles" [GO:0003164] synonym: "distal conduction system" EXACT [ZFA:0005071] synonym: "His-Purkinji network" EXACT [ZFA:0005071] synonym: "HPS" EXACT [ZFA:0005071] xref: TAO:0005071 xref: ZFA:0005071 is_a: UBERON:0002350 ! conducting system of heart property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004151 name: cardiac chamber namespace: uberon def: "A cardiac chamber surrounds an enclosed cavity within the heart" [GO:0003205] comment: generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus synonym: "chamber of heart" EXACT [] synonym: "heart chamber" EXACT [] xref: FMA:7095 xref: OpenCyc:Mx4rmexpjPdAEduAAAAOpmP6tw xref: SCTID:276456008 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0000948 ! heart property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004160 name: proepicardium namespace: uberon def: "An outpouching of the septum transversum[GO]. An embryonic group of progenitor cells that forms near the venous pole of the heart and gives rise to the epicardium[Wiktionary]" [GO:0003342, http://en.wiktionary.org/wiki/proepicardium] is_a: UBERON:0005256 ! trunk mesenchyme relationship: part_of UBERON:0004161 ! septum transversum property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004161 name: septum transversum namespace: uberon def: "A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG]." [VHOG:0000019, Wikipedia:Septum_transversum] comment: Note that in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum synonym: "transverse septum" EXACT [UBERON:cjm] xref: EHDAA2:0001829 xref: EHDAA:736 xref: EMAPA:16318 xref: ncithesaurus:Septum_Transversum xref: SCTID:308819008 xref: UMLS:C0231004 xref: VHOG:0000019 is_a: UBERON:0005256 ! trunk mesenchyme relationship: part_of UBERON:0002100 ! trunk property_value: external_definition "A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000019", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/transverse+septum"} property_value: homology_notes "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000019", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004175 name: internal reproductive organ namespace: uberon def: "The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals" [GO:0035260] subset: organ_slim synonym: "internal genitalia" EXACT [] synonym: "internal reproductive organ" EXACT [] synonym: "internal sex organ" EXACT [] xref: FMA:45652 is_a: UBERON:0003133 ! reproductive organ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004176 name: external reproductive organ namespace: uberon def: "The external genitalia are the outer sex organs, such as the penis or vulva in mammals" [GO:0035261] subset: organ_slim synonym: "external genitalia" EXACT [] synonym: "external reproductive organ" EXACT [] synonym: "external sex organ" EXACT [] xref: FMA:45643 xref: SCTID:362207005 is_a: UBERON:0003133 ! reproductive organ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004177 name: hemopoietic organ namespace: uberon def: "Organ that is part of the hematopoietic system." [GOC:Obol] comment: note that the FMA class 'lymphoid organ' is a general anatomical term subset: organ_slim synonym: "haematological system organ" EXACT [OBOL:automatic] synonym: "haemopoietic system organ" EXACT [OBOL:automatic] synonym: "hematopoeitic or lymphoid organ" NARROW [] synonym: "hematopoietic system organ" EXACT [OBOL:automatic] synonym: "lymphoid organ" NARROW [BTO:0004605, FMA:7143] synonym: "organ of haematological system" EXACT [OBOL:automatic] synonym: "organ of haemopoietic system" EXACT [OBOL:automatic] synonym: "organ of hematopoietic system" EXACT [OBOL:automatic] synonym: "organ of organa haemopoietica" EXACT [OBOL:automatic] synonym: "organa haemopoietica organ" EXACT [OBOL:automatic] xref: BTO:0004605 xref: FMA:7143 xref: SCTID:361338006 is_a: UBERON:0000062 ! organ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0002390 ! hematopoietic system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004178 name: aorta smooth muscle tissue namespace: uberon def: "A portion of smooth muscle tissue that is part of an aorta [Obol]." [OBOL:automatic] synonym: "adult aorta involuntary muscle" EXACT [OBOL:automatic] synonym: "adult aorta non-striated muscle" EXACT [OBOL:automatic] synonym: "adult aorta smooth muscle" EXACT [OBOL:automatic] synonym: "adult aorta smooth muscle tissue" EXACT [OBOL:automatic] synonym: "aorta involuntary muscle" EXACT [OBOL:automatic] synonym: "aorta non-striated muscle" EXACT [OBOL:automatic] synonym: "aorta smooth muscle" EXACT [OBOL:automatic] synonym: "aortic smooth muscle" EXACT [BTO:0001685] synonym: "dorsal aorta involuntary muscle" EXACT [OBOL:automatic] synonym: "dorsal aorta non-striated muscle" EXACT [OBOL:automatic] synonym: "dorsal aorta smooth muscle" EXACT [OBOL:automatic] synonym: "dorsal aorta smooth muscle tissue" EXACT [OBOL:automatic] synonym: "involuntary muscle of adult aorta" EXACT [OBOL:automatic] synonym: "involuntary muscle of aorta" EXACT [OBOL:automatic] synonym: "involuntary muscle of dorsal aorta" EXACT [OBOL:automatic] synonym: "involuntary muscle of trunk of aortic tree" EXACT [OBOL:automatic] synonym: "non-striated muscle of adult aorta" EXACT [OBOL:automatic] synonym: "non-striated muscle of aorta" EXACT [OBOL:automatic] synonym: "non-striated muscle of dorsal aorta" EXACT [OBOL:automatic] synonym: "non-striated muscle of trunk of aortic tree" EXACT [OBOL:automatic] synonym: "smooth muscle of adult aorta" EXACT [OBOL:automatic] synonym: "smooth muscle of aorta" EXACT [OBOL:automatic] synonym: "smooth muscle of dorsal aorta" EXACT [OBOL:automatic] synonym: "smooth muscle of trunk of aortic tree" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of adult aorta" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of aorta" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of dorsal aorta" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of trunk of aortic tree" EXACT [OBOL:automatic] synonym: "trunk of aortic tree involuntary muscle" EXACT [OBOL:automatic] synonym: "trunk of aortic tree non-striated muscle" EXACT [OBOL:automatic] synonym: "trunk of aortic tree smooth muscle" EXACT [OBOL:automatic] synonym: "trunk of aortic tree smooth muscle tissue" EXACT [OBOL:automatic] xref: BTO:0001685 xref: EFO:0002775 xref: MA:0000702 xref: ncithesaurus:Aorta_Smooth_Muscle_Tissue xref: UMLS:C1706825 is_a: UBERON:0002111 ! artery smooth muscle tissue relationship: part_of UBERON:0000947 ! aorta property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004179 name: prostate glandular acinus namespace: uberon def: "A saclike structure of the prostate gland, comprised of at least three cell layers: an innermost layer of secretory columnar luminal epithelium, a middle layer of squamous basal epithelium that also contains neuroendocrine cells, transit amplifying cells, and stem cells, and an outer layer of smooth muscle intermixed with other stromal cells" [GO:0060525, PMID:18977204] comment: Concurrent with branching morphogenesis, the solid cords of epithelium formed by budding arborize and differentiate postnatally into glandular acin. The basic prostate architecture is established by puberty and acquires secretory function thereafter[PMID:18977204] synonym: "prostatic acinus" EXACT [FMA:66808] synonym: "prostatic follicle" EXACT [FMA:66808] xref: FMA:66808 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0009842 {source="FMA"} ! acinus relationship: develops_from UBERON:0009843 {source="PMID:18977204"} ! prostate epithelial cord relationship: part_of UBERON:0000428 {source="GO"} ! prostate epithelium relationship: part_of UBERON:0002367 ! prostate gland property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004185 name: endodermal gut namespace: uberon def: "A portions of the gut that is derived from endoderm." [GO:0061031] is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0000925 ! endoderm relationship: part_of UBERON:0001555 ! digestive tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004186 name: olfactory bulb mitral cell layer namespace: uberon def: "The mitral cell layer is composed of pyramidal neurons whose cell bodies are located between the granule cell layer and the plexiform layer" [GO:0061034] comment: note that NIF divides this into main and accessory synonym: "mitral cell body layer" EXACT [NIF_GrossAnatomy:nlx_anat_100201] synonym: "mitral cell layer" EXACT [BTO:0001108] synonym: "olfactory bulb main mitral cell body layer" RELATED [NIF_GrossAnatomy:nlx_anat_100201] xref: BTO:0001108 xref: MA:0000973 xref: NIF_GrossAnatomy:nlx_anat_100201 is_a: UBERON:0004001 ! olfactory bulb layer property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004188 name: glomerular epithelium namespace: uberon def: "The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros." [GO:0072010] comment: TODO - check - GO says outer, BTO says inner. Make this a superclass synonym: "epithelium of glomerulus" EXACT [] synonym: "epithelium of kidney glomerulus" EXACT [] synonym: "epithelium of renal glomerulus" EXACT [] synonym: "glomerular epithelial cell" RELATED [BTO:0001515] synonym: "kidney glomerular epithelium" EXACT [MA:0002847] xref: BTO:0001515 xref: MA:0002847 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0004211 ! nephron epithelium is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0000074 ! renal glomerulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004189 name: glomerular endothelium namespace: uberon def: "The glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus" [GO:0072011] synonym: "endothelium of renal glomerulus" EXACT [OBOL:automatic] synonym: "renal glomerulus endothelium" EXACT [OBOL:automatic] xref: BTO:0004631 is_a: UBERON:0004188 ! glomerular epithelium is_a: UBERON:0004852 ! cardiovascular system endothelium relationship: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0004190 ! glomerulus vasculature property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004190 name: glomerulus vasculature namespace: uberon def: "The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus" [GO:0072012] synonym: "renal glomerulus vascular network" EXACT [OBOL:automatic] synonym: "renal glomerulus vasculature" EXACT [OBOL:automatic] synonym: "vascular network of renal glomerulus" EXACT [OBOL:automatic] synonym: "vasculature of renal glomerulus" EXACT [OBOL:automatic] is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0006544 ! kidney vasculature relationship: part_of UBERON:0000074 ! renal glomerulus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004193 name: loop of Henle ascending limb thin segment namespace: uberon def: "A sub-portion of the loop of Henle in the nephron of the kidney that is permeable to ions but not to water" [GO:0072021, Wikipedia:Thin_ascending_limb_of_loop_of_Henle] comment: check relationship to distal tubule synonym: "ascending limb thin segment of loop of Henle" EXACT [] synonym: "ascending thin limb" EXACT [FMA:17720] synonym: "pars ascendens (tubulus attenuatus)" EXACT [FMA:17720] synonym: "thin ascending limb" EXACT [EMAPA:28328] synonym: "thin ascending limb of loop of Henle" EXACT [] xref: EMAPA:28328 xref: EMAPA:28361 xref: FMA:17720 xref: http://upload.wikimedia.org/wikipedia/commons/2/27/Gray1128.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/27/Gray1128.png/200px-Gray1128.png xref: MA:0001678 is_a: UBERON:0007685 ! region of nephron tubule is_a: UBERON:0008408 ! distal tubular epithelium relationship: part_of UBERON:0003455 ! inner renal medulla loop of henle relationship: part_of UBERON:0005164 ! ascending limb of loop of Henle property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004198 name: comma-shaped body namespace: uberon def: "The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron" [GO:0072049] xref: EMAPA:27681 xref: EMAPA:27835 xref: ZFA:0005588 is_a: UBERON:0001231 ! nephron tubule is_a: UBERON:0010532 {source="cjm"} ! primitive nephron relationship: develops_from UBERON:0004209 {source="ZFA"} ! renal vesicle relationship: part_of UBERON:0001285 ! nephron property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004199 name: S-shaped body namespace: uberon def: "The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron" [GO:0072050] comment: TODO synonym: "stage II nephron" EXACT [http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html] xref: EMAPA:27756 xref: EMAPA:27853 xref: ZFA:0005589 is_a: UBERON:0010532 {source="cjm"} ! primitive nephron relationship: develops_from UBERON:0004198 {source="GO"} ! comma-shaped body property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004201 name: kidney outer medulla inner stripe namespace: uberon def: "The inner stripe is a deep, centrally located portion of the renal outer medulla and is traversed by thick and thin portions of nephron tubules" [GO:0072057] synonym: "inner stripe" EXACT [GO:0072057] synonym: "inner stripe of medulla of kidney" EXACT [FMA:76663] synonym: "inner stripe of outer medulla" EXACT [EMAPA:29675] synonym: "inner stripe of renal medulla" EXACT [FMA:76663] synonym: "outer medulla inner stripe" EXACT [MA:0002626] synonym: "stria interna medullae renalis" EXACT LATIN [FMA:76663, FMA:TA] xref: EMAPA:29675 xref: FMA:76663 xref: MA:0002626 is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0001293 ! outer medulla of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004202 name: kidney outer medulla outer stripe namespace: uberon def: "The outer stripe is the region of the kidney that lies distal to the line of termination of the straight renal tubules" [GO:0072058] synonym: "outer medulla outer stripe" EXACT [MA:0002629] synonym: "outer stripe" EXACT [GO:0072058] synonym: "outer stripe of medulla of kidney" EXACT [FMA:76662] synonym: "outer stripe of outer medulla" EXACT [EMAPA:29663] synonym: "outer stripe of renal medulla" EXACT [FMA:76662] synonym: "stria externa medullae renalis" EXACT LATIN [FMA:76662, FMA:TA] xref: EMAPA:29663 xref: FMA:76662 xref: MA:0002629 is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0001293 ! outer medulla of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004208 name: nephrogenic mesenchyme namespace: uberon def: "Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron" [GO:0072076] comment: The detailed events associated with the differentiation of the nephrogenic mesenchyme are somewhat complex. It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman’s capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman’s capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman’s capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] synonym: "mesenchyme of nephron" EXACT [OBOL:automatic] synonym: "nephron mesenchyme" EXACT [OBOL:automatic] is_a: UBERON:0003104 ! mesenchyme property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004209 name: renal vesicle namespace: uberon def: "The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells. " [GO:0072077] comment: Editor notes: note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 synonym: "stage I nephron" EXACT [http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html, ZFA:0005586] is_a: UBERON:0004211 ! nephron epithelium is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle relationship: develops_from UBERON:0004208 ! nephrogenic mesenchyme relationship: part_of UBERON:0001285 ! nephron property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004211 name: nephron epithelium namespace: uberon def: "The nephron epithelium is a tissue that covers the surface of a nephron" [GO:0072088] synonym: "epithelial tissue of nephron" EXACT [OBOL:automatic] synonym: "epithelium of nephron" EXACT [OBOL:automatic] synonym: "nephron epithelial tissue" EXACT [OBOL:automatic] is_a: UBERON:0004819 ! kidney epithelium relationship: part_of UBERON:0001285 ! nephron property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004212 name: glomerular capillary namespace: uberon def: "A capillary that is part of a renal glomerulus [Obol]." [OBOL:automatic] subset: vertebrate_core synonym: "blood capillary of renal glomerulus" EXACT [OBOL:automatic] synonym: "capillary of renal glomerulus" EXACT [OBOL:automatic] synonym: "capillary vessel of renal glomerulus" EXACT [OBOL:automatic] synonym: "glomerular capillaries" RELATED PLURAL [] synonym: "glomerular capillary system" RELATED [MA:0002587] synonym: "renal glomerulus blood capillary" EXACT [OBOL:automatic] synonym: "renal glomerulus capillary" EXACT [OBOL:automatic] synonym: "renal glomerulus capillary vessel" EXACT [OBOL:automatic] xref: EMAPA:28245 xref: MA:0002587 xref: ncithesaurus:Glomerular_Capillary xref: SCTID:362049007 xref: TAO:0005284 xref: UMLS:C0226356 xref: ZFA:0005284 is_a: UBERON:0001231 ! nephron tubule is_a: UBERON:0003527 ! kidney capillary is_a: UBERON:0004188 ! glomerular epithelium relationship: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0004190 {source="reference_0000032"} ! glomerulus vasculature property_value: external_definition "Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005284", ontology="TAO", source="ZFIN:ZDB-PUB-000824-1", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004227 name: kidney pelvis smooth muscle namespace: uberon def: "A portion of smooth muscle tissue that is part of a renal pelvis [Obol]." [OBOL:automatic] synonym: "involuntary muscle of kidney pelvis" EXACT [OBOL:automatic] synonym: "involuntary muscle of pelvis of ureter" EXACT [OBOL:automatic] synonym: "involuntary muscle of renal pelvis" EXACT [OBOL:automatic] synonym: "kidney pelvis involuntary muscle" EXACT [OBOL:automatic] synonym: "kidney pelvis non-striated muscle" EXACT [OBOL:automatic] synonym: "kidney pelvis smooth muscle tissue" EXACT [OBOL:automatic] synonym: "non-striated muscle of kidney pelvis" EXACT [OBOL:automatic] synonym: "non-striated muscle of pelvis of ureter" EXACT [OBOL:automatic] synonym: "non-striated muscle of renal pelvis" EXACT [OBOL:automatic] synonym: "pelvis of ureter involuntary muscle" EXACT [OBOL:automatic] synonym: "pelvis of ureter non-striated muscle" EXACT [OBOL:automatic] synonym: "pelvis of ureter smooth muscle" EXACT [OBOL:automatic] synonym: "pelvis of ureter smooth muscle tissue" EXACT [OBOL:automatic] synonym: "renal pelvis involuntary muscle" EXACT [OBOL:automatic] synonym: "renal pelvis non-striated muscle" EXACT [OBOL:automatic] synonym: "renal pelvis smooth muscle" EXACT [OBOL:automatic] synonym: "renal pelvis smooth muscle tissue" EXACT [OBOL:automatic] synonym: "smooth muscle of kidney pelvis" EXACT [OBOL:automatic] synonym: "smooth muscle of pelvis of ureter" EXACT [OBOL:automatic] synonym: "smooth muscle of renal pelvis" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of kidney pelvis" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of pelvis of ureter" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of renal pelvis" EXACT [OBOL:automatic] xref: FMA:262022 xref: MA:0002631 is_a: UBERON:0005321 ! mesonephric smooth muscle tissue is_a: UBERON:0009919 ! ureter smooth muscle relationship: part_of UBERON:0001224 ! renal pelvis property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004234 name: iris smooth muscle namespace: uberon def: "A portion of smooth muscle tissue that is part of a iris [Obol]." [OBOL:automatic] synonym: "involuntary muscle of iris" EXACT [OBOL:automatic] synonym: "iris involuntary muscle" EXACT [OBOL:automatic] synonym: "iris non-striated muscle" EXACT [OBOL:automatic] synonym: "iris smooth muscle tissue" EXACT [OBOL:automatic] synonym: "non-striated muscle of iris" EXACT [OBOL:automatic] synonym: "smooth muscle of iris" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of iris" EXACT [OBOL:automatic] xref: BTO:0000655 xref: MA:0001270 is_a: UBERON:0001606 ! muscle of iris is_a: UBERON:0003386 ! smooth muscle of eye relationship: part_of UBERON:0001769 ! iris property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004237 name: blood vessel smooth muscle namespace: uberon alt_id: UBERON:0010508 def: "smooth muscle found within, and composing the majority of the wall of blood vessels." [Wikipedia:Vascular_smooth_muscle] comment: Function notes: Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension. synonym: "blood vessel involuntary muscle" EXACT [OBOL:automatic] synonym: "blood vessel non-striated muscle" EXACT [OBOL:automatic] synonym: "blood vessel smooth muscle tissue" EXACT [OBOL:automatic] synonym: "involuntary muscle of blood vessel" EXACT [OBOL:automatic] synonym: "non-striated muscle of blood vessel" EXACT [OBOL:automatic] synonym: "smooth muscle of blood vessel" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of blood vessel" EXACT [OBOL:automatic] synonym: "vascular smooth muscle" EXACT [ZFA:0005321] synonym: "vascular smooth muscle tissue" EXACT [] xref: BTO:0001431 xref: CALOHA:TS-1107 xref: MA:0000710 xref: MESH:A02.633.570.491 xref: ncithesaurus:Vascular_Smooth_Muscle_Tissue xref: TAO:0005321 xref: UMLS:C1519956 xref: ZFA:0005321 is_a: UBERON:0001135 ! smooth muscle tissue relationship: part_of UBERON:0001981 ! blood vessel property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004277 name: eye muscle namespace: uberon def: "A muscle that is part of the eye region." [OBOL:automatic] xref: AAO:0000156 xref: MA:0000271 xref: OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycB4rvYA8cJwpEbGdrcN5Y29ycA is_a: UBERON:0002376 ! muscle of head is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000019 {source="MA"} ! camera-type eye property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004288 name: skeleton namespace: uberon def: "all the bones and/or cartilaginous elements in the body. Together with the articular system, this comprises the skeletal system." [FMA:23875, UBERON:cjm, Wikipedia:Skeleton] comment: Note that the source FMA definition has been modified here to include cartilage skeletons. We may wish to introduce subclasses for bony/cartilage skeletons. subset: uberon_slim synonym: "set of all bones" EXACT [] synonym: "set of bones of body" EXACT [] xref: AEO:0000168 xref: EFO:0000806 xref: EHDAA2:0001843 xref: EHDAA:5047 xref: EHDAA:8005 xref: EHDAA:8041 xref: FMA:23875 xref: GAID:177 xref: galen:Skeleton xref: MA:0003006 xref: MAT:0000032 xref: MESH:A02.835 xref: MIAA:0000032 xref: OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA xref: SCTID:361378004 xref: VSAO:0000026 xref: XAO:0004053 is_a: UBERON:0000480 ! anatomical group disjoint_from: UBERON:0004770 ! articular system relationship: part_of UBERON:0001434 ! skeletal system property_value: external_definition "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000026", ontology="VSAO", source="GO_REF:0000034"} property_value: has_relational_adjective "skeletal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: seeAlso http://purl.obolibrary.org/obo/uberon/references/reference_0000025 xsd:anyURI [Term] id: UBERON:0004290 name: dermomyotome namespace: uberon def: "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle." [http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768] synonym: "dermamyotome" RELATED [VHOG:0000676] synonym: "dermomyotomes" RELATED PLURAL [VHOG:0000676] xref: AAO:0010572 xref: AEO:0000214 xref: EHDAA2:0003259 xref: ncithesaurus:Dermomyotome xref: TAO:0001513 xref: UMLS:C1511786 xref: VHOG:0000676 xref: ZFA:0001513 is_a: UBERON:0000486 {source="EHDAA2"} ! multilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0002329 {source="EHDAA2", source="ZFA"} ! somite relationship: part_of UBERON:0000926 ! mesoderm property_value: external_definition "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001513", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Portion of somites that gives rise to dermis and muscles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010572", ontology="AAO", source="AAO:EJS"} property_value: homology_notes "Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000676", ontology="VHOG", source="DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004291 name: heart rudiment namespace: uberon def: "a cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube." [GO:0003313] synonym: "heart cone" EXACT [GO:0003313] synonym: "rudimentary heart" EXACT [ZFA:0000115] xref: TAO:0000115 xref: ZFA:0000115 is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0003084 {source="ZFA"} ! heart primordium relationship: develops_from UBERON:0004139 ! cardiogenic plate property_value: external_definition "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000115", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004294 name: glomerular capillary endothelium namespace: uberon def: "An endothelium that is part of a glomerular capillary." [OBOL:automatic] synonym: "renal glomerulus capillary endothelium" EXACT [OBOL:automatic] xref: MA:0001658 xref: ncithesaurus:Endothelium_of_the_Glomerular_Capillary xref: SCTID:243993006 xref: UMLS:C0227647 is_a: UBERON:0001915 ! endothelium of capillary is_a: UBERON:0004189 ! glomerular endothelium is_a: UBERON:0004810 ! nephron tubule epithelium relationship: part_of UBERON:0004212 ! glomerular capillary property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004340 name: allantois namespace: uberon def: "A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG]." [VHOG:0000738, Wikipedia:Allantois] comment: a diverticulum of the hindgut endoderm [ISBN10:0073040584 "Vertebrates, Kardong"]. AO notes: part_of embryo in EHDAA2 - note differences in humans xref: BTO:0000474 xref: EHDAA2:0000113 xref: EMAPA:16084 xref: EMAPA:16107 xref: EMAPA:28547 xref: http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray25.png xref: MESH:A16.254.403.147 xref: ncithesaurus:Allantois xref: RETIRED_EHDAA2:0000114 xref: SCTID:308825007 xref: UMLS:C0002084 xref: VHOG:0000738 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0005631 ! extraembryonic membrane relationship: develops_from UBERON:0000925 {notes="hindgut diverticulum endoderm", source="ISBN10:0073040584"} ! endoderm relationship: develops_from UBERON:0001040 {source="EHDAA2"} ! yolk sac relationship: develops_from UBERON:0004872 {source="ISBN10:0073040584"} ! splanchnic layer of lateral plate mesoderm property_value: external_definition "A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000738", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/allantois"} property_value: has_relational_adjective "allantoic" xsd:string property_value: homology_notes "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000738", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004348 name: optic eminence namespace: uberon def: "the embryonic structure that gives rise to the corneal ectoderm" [MP:0006305] xref: EHDAA:938 xref: EMAPA:16322 xref: EMAPA:17003 xref: RETIRED_EHDAA2:0001308 xref: VHOG:0001296 is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004362 name: pharyngeal arch 1 namespace: uberon def: "First of six branchial arches that develops in fetal life during the fourth week of development.[1] It is located between the stomodeum and the first pharyngeal groove." [Wikipedia:First_pharyngeal_arch] subset: uberon_slim subset: vertebrate_core synonym: "1st arch" RELATED [EHDAA2:0000006] synonym: "1st pharyngeal arch" EXACT [] synonym: "1st visceral arch" RELATED [VHOG:0000296] synonym: "arcus pharyngeus primus" RELATED LATIN [Wikipedia:First_pharyngeal_arch] synonym: "branchial arch 1" EXACT SENSU [] synonym: "first branchial arch" EXACT SENSU [] synonym: "first pharyngeal arch" EXACT [] synonym: "first visceral arch" EXACT SENSU [] synonym: "mandibular arch" EXACT [] synonym: "visceral arch 1" EXACT SENSU [] xref: AAO:0010364 xref: EHDAA2:0000006 xref: EHDAA:573 xref: EMAPA:16118 xref: http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/2d/Gray48.png/200px-Gray48.png xref: ncithesaurus:First_Pharyngeal_Arch xref: SCTID:308767008 xref: TAO:0001595 xref: UMLS:C1517197 xref: VHOG:0000296 xref: XAO:0000097 xref: ZFA:0001612 is_a: UBERON:0002539 ! pharyngeal arch property_value: external_definition "The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010364", ontology="AAO", source="XAO:EJS"} property_value: homology_notes "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000296", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: pharyngeal_arch_number "1" xsd:nonNegativeInteger [Term] id: UBERON:0004363 name: aortic arch namespace: uberon alt_id: UBERON:0004342 def: "One of a series of paired embryological vascular structures which give rise to several major arteries." [MP:0002672, Wikipedia:Aortic_arches] comment: Usage notes: Do not confuse with arch of aorta. Editor notes: add specific artery derivatives. Development notes: The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches. Taxon notes: Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods subset: uberon_slim subset: vertebrate_core synonym: "aa. arcuum pharyngeorum" RELATED LATIN [Wikipedia:Aortic_arches] synonym: "aortic arches" EXACT PLURAL [ZFA:0005004] synonym: "branchial aortic arches " EXACT PLURAL [ZFIN:ZDB-PUB-080512-6] synonym: "branchial arch artery" EXACT [EMAPA:16684] synonym: "embryonic aortic arch artery" EXACT [EMAPA:16684, MP:0002672] synonym: "pharyngeal arch artery" RELATED [VHOG:0000122] xref: AAO:0010414 xref: EFO:0003695 xref: EHDAA2:0000186 xref: EHDAA:398 xref: EHDAA:7327 xref: EMAPA:16684 xref: http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/8/84/Gray473.png/200px-Gray473.png xref: ncithesaurus:Aortic_Arch xref: TAO:0005004 xref: UMLS:C0003489 xref: VHOG:0000122 xref: XAO:0000341 xref: ZFA:0005004 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003351 ! pharyngeal epithelium is_a: UBERON:0003469 ! respiratory system artery is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007497 ! developing epithelial placode is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0002539 ! pharyngeal arch relationship: part_of UBERON:0007303 {source="ZFA"} ! pharyngeal vasculature relationship: part_of UBERON:0008814 ! pharyngeal system property_value: external_definition "Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000122", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/aortic+arches"} property_value: homology_notes "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000122", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004456 name: entire sense organ system namespace: uberon def: "Sum of all sensory systems in an organism." [] comment: note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs subset: uberon_slim synonym: "sense organ system" EXACT [FMA:78499] xref: FMA:78499 is_a: UBERON:0000467 ! anatomical system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004457 name: cavity lining namespace: uberon comment: Editor notes: consider merging with serous membrane. AO notes: in MA this groups pericardium, pleura and periotoneal cavity lining xref: MA:0002448 is_a: UBERON:0004458 {notes="pre-inferred via union_of"} ! body cavity or lining is_a: UBERON:0004923 ! organ component layer property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004458 name: body cavity or lining namespace: uberon comment: Note that this class may be merged into 'serous sac'. See notes for 'cavity lining' xref: EMAPA:16060 xref: MA:0000005 is_a: UBERON:0001062 ! anatomical entity union_of: UBERON:0002323 ! coelemic cavity lumen union_of: UBERON:0004457 ! cavity lining property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004461 name: musculature of head namespace: uberon def: "A musculature that is part of a head [Obol]." [OBOL:automatic] synonym: "head musculature" EXACT [FMA:71287] synonym: "muscle group of head" EXACT [FMA:71287] synonym: "muscles of head" EXACT [FMA:71287] synonym: "musculi capitis" EXACT LATIN [FMA:71287, FMA:TA] synonym: "set of muscles of head" EXACT [FMA:71287] xref: FMA:71287 is_a: UBERON:0008229 ! craniocervical region musculature relationship: part_of UBERON:0000033 ! head property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004490 name: cardiac muscle tissue of atrium namespace: uberon def: "A portion of cardiac muscle tissue that is part of an atrium [Obol]." [OBOL:automatic] xref: FMA:7283 is_a: UBERON:0001133 ! cardiac muscle tissue relationship: part_of UBERON:0002081 ! cardiac atrium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004493 name: cardiac muscle tissue of myocardium namespace: uberon def: "A portion of cardiac muscle tissue that is part of a myocardium [Obol]." [OBOL:automatic] comment: Editors note: Note placement of MA class based on parthood relationship xref: FMA:261726 xref: MA:0002441 is_a: UBERON:0001133 ! cardiac muscle tissue relationship: part_of UBERON:0002349 {source="MA"} ! myocardium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004535 name: cardiovascular system namespace: uberon def: "Anatomical system that has as its parts the heart and blood vessels." [BTO:0000088] comment: Usage notes: we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. subset: uberon_slim subset: vertebrate_core synonym: "CV system" RELATED [BTO:0000088] synonym: "Herz und Gefaesssystem" RELATED [BTO:0000088] xref: AAO:0011001 xref: BILA:0000016 xref: BTO:0000088 xref: EFO:0000791 xref: EHDAA2:0000216 xref: EHDAA:394 xref: EMAPA:16104 xref: EMAPA:16370 xref: EV:0100017 xref: FMA:7161 xref: GAID:467 xref: MA:0000010 xref: MAT:0000016 xref: MESH:A07 xref: MIAA:0000016 xref: ncithesaurus:Cardiovascular_System xref: OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA xref: SCTID:278198007 xref: TAO:0000010 xref: UMLS:C0007226 xref: VHOG:0000302 xref: WikipediaCategory:Cardiovascular_system xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0001009 ! circulatory system property_value: homology_notes "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000302", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004536 name: lymph vasculature namespace: uberon def: "A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep." [ZFA:0005105] subset: vertebrate_core synonym: "lymphatic trunks and ducts" EXACT [FMA:63815] synonym: "lymphatic vasculature" EXACT [] synonym: "lymphatic vessel network" EXACT [] synonym: "lymphatic vessels set" EXACT [FMA:63815] synonym: "set of lymphatic vessels" EXACT [] synonym: "trunci et ductus lymphatici" EXACT LATIN [FMA:63815, FMA:TA] xref: FMA:63815 xref: TAO:0005105 xref: ZFA:0005105 is_a: UBERON:0002049 ! vasculature relationship: part_of UBERON:0002465 ! lymphoid system property_value: external_definition "A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005105", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004537 name: blood vasculature namespace: uberon def: "a vascular network consisting of blood vessels." [UBERON:cjm] synonym: "blood vascular network" EXACT [] synonym: "blood vessels" RELATED [TAO:0001079] synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 is_a: UBERON:0002049 ! vasculature relationship: part_of UBERON:0004535 ! cardiovascular system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004571 name: systemic arterial system namespace: uberon def: "the part of the cardiovascular system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart." [Wikipedia:Systemic_circulation#Arteries] synonym: "systemic arterial circulatory system" EXACT [FMA:45623] xref: FMA:45623 is_a: UBERON:0007798 {source="MA-inferred"} ! vascular system relationship: part_of UBERON:0004572 ! arterial system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004572 name: arterial system namespace: uberon def: "The part of the cardiovascular system consisting of all arteries." [UBERON:cjm] xref: BTO:0004690 xref: EHDAA2:0000143 xref: EHDAA:396 xref: EMAPA:16201 xref: EMAPA:16371 xref: MA:0002719 xref: SCTID:362030008 xref: VHOG:0000273 is_a: UBERON:0007798 {source="MA"} ! vascular system relationship: part_of UBERON:0004535 {source="EHDAA2"} ! cardiovascular system property_value: homology_notes "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000273", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004573 name: systemic artery namespace: uberon def: "Systemic arteries are the arteries of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart." [Wikipedia:Artery#Systemic_arteries] synonym: "systemic arterial subtree" EXACT [FMA:66464] xref: FMA:66464 is_a: UBERON:0001637 ! artery relationship: part_of UBERON:0004571 ! systemic arterial system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004582 name: venous system namespace: uberon def: "The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions." [UBERON:cjm] synonym: "vein system" EXACT [] xref: BTO:0004692 xref: EHDAA2:0002171 xref: EHDAA:486 xref: EMAPA:16240 xref: MA:0002720 xref: ncithesaurus:Venous_System xref: SCTID:362060003 xref: UMLS:C1267406 xref: VHOG:0000277 is_a: UBERON:0007798 {source="MA"} ! vascular system property_value: homology_notes "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000277", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004590 name: sphincter muscle namespace: uberon def: "a structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning." [Wikipedia:Sphincter] comment: AO notes: FMA class is not a subtype of muscle synonym: "circular muscle" RELATED [] synonym: "sphincter" EXACT [] xref: FMA:75004 xref: ncithesaurus:Sphincter xref: UMLS:C1409894 is_a: UBERON:0001630 ! muscle organ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004638 name: blood vessel endothelium namespace: uberon def: "An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart" [UBERON:cjm] subset: vertebrate_core xref: BTO:0000766 xref: MA:0000709 xref: ncithesaurus:Blood_Vessel_Endothelium xref: TAO:0005257 xref: UMLS:C1706972 xref: ZFA:0005257 is_a: UBERON:0004852 ! cardiovascular system endothelium relationship: part_of UBERON:0001981 ! blood vessel property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004639 name: afferent arteriole namespace: uberon def: "The afferent arterioles are a group of blood vessels that supply the nephrons in many excretory systems. They play an important role in the regulation of blood pressure. The afferent arterioles branch from the renal artery which supplies blood to the kidneys. The afferent arterioles later diverge into the capillaries of the glomerulus. When renal blood flow is reduced, the macula densa releases prostaglandins, which cause the juxtaglomerular cells lining the afferent arterioles to release renin, activating the renin-angiotensin-aldosterone system, to increase blood pressure. [WP,unvetted]." [Wikipedia:Afferent_arterioles] subset: vertebrate_core synonym: "afferent glomerular arteriole" EXACT [ZFA:0005307] synonym: "arteriola glomerularis afferens" RELATED LATIN [Wikipedia:Afferent_arterioles] synonym: "kidney afferent arteriole" EXACT [MP:0011312] xref: EMAPA:28230 xref: EMAPA:28266 xref: http://upload.wikimedia.org/wikipedia/commons/2/27/Gray1128.png xref: MA:0002579 xref: MP:0011312 xref: SCTID:67498004 xref: TAO:0002139 xref: ZFA:0005307 is_a: UBERON:0001231 ! nephron tubule is_a: UBERON:0001980 ! arteriole is_a: UBERON:0003644 ! kidney arterial blood vessel relationship: part_of UBERON:0001229 ! renal corpuscle property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004640 name: efferent arteriole namespace: uberon def: "The efferent arterioles are blood vessels that are part of the urinary tract of organisms. The efferent arterioles form from a convergence of the capillaries of the glomerulus. They play an important role in maintaining the glomerular filtration rate despite fluctuations in blood pressure. In the mammalian kidney they follow two markedly different courses, depending on the location of the glomeruli from which they arise. In the mammalian kidney about 15% of glomeruli lie close to the boundary between the renal cortex and renal medulla and are known as juxtamedullary glomeruli. The rest are simply undifferentiated cortical glomeruli. [WP,unvetted]." [Wikipedia:Efferent_arteriole] subset: vertebrate_core synonym: "arteriola glomerularis efferens capsulae renalis" RELATED LATIN [Wikipedia:Efferent_arteriole] synonym: "efferent glomerular arteriole" EXACT [ZFA:0005308] synonym: "kidney efferent arteriole" EXACT [MP:0011313] xref: EMAPA:28233 xref: EMAPA:28275 xref: http://upload.wikimedia.org/wikipedia/commons/2/27/Gray1128.png xref: MA:0002585 xref: SCTID:29926005 xref: TAO:0002140 xref: ZFA:0005308 is_a: UBERON:0001231 ! nephron tubule is_a: UBERON:0001980 ! arteriole is_a: UBERON:0003644 ! kidney arterial blood vessel relationship: part_of UBERON:0001229 ! renal corpuscle property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004645 name: urinary bladder urothelium namespace: uberon def: "An urothelium that is part of a urinary bladder." [OBOL:automatic] synonym: "bladder transitional cell epithelium" EXACT [FMA:15936] synonym: "transitional epithelium" RELATED [MA:0001693] synonym: "transitional epithelium of urinary bladder" EXACT [FMA:15936] synonym: "urinary bladder transitional epithelium" EXACT [FMA:15936] synonym: "urothelium" BROAD [BTO:0001245] synonym: "urothelium of urinary bladder" EXACT [FMA:15936] xref: BTO:0001694 xref: FMA:15936 xref: MA:0001693 xref: ncithesaurus:Transitional_Epithelium xref: SCTID:25631003 xref: UMLS:C0225339 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0000365 ! urothelium is_a: UBERON:0003350 ! epithelium of mucosa is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001259 ! mucosa of urinary bladder property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004647 name: liver lobule namespace: uberon def: "a small division of the liver defined at the histological scale, the functional unit of which is the hepatic acinus." [Wikipedia:Lobules_of_liver] comment: should not be confused with the anatomic lobes of the liver (caudate lobe, quadrate lobe, left lobe, and right lobe), or any of the functional lobe classification systems.[WP] synonym: "hepatic lobule" EXACT [FMA:14471] synonym: "lobules of liver" RELATED PLURAL [Wikipedia:Lobules_of_liver] synonym: "lobuli hepatici" EXACT PLURAL [] synonym: "lobuli hepatis" RELATED LATIN [Wikipedia:Lobules_of_liver] synonym: "lobulus hepaticus" EXACT LATIN [FMA:14471] xref: FMA:14471 xref: MA:0002494 xref: ncithesaurus:Hepatic_Lobule xref: SCTID:362194004 xref: UMLS:C0227518 is_a: UBERON:0000064 {source="FMA"} ! organ part is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0001280 {source="FMA", source="MA"} ! liver parenchyma property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004663 name: aorta wall namespace: uberon def: "An anatomical wall that is part of an aorta [Obol]." [OBOL:automatic] synonym: "Aortic wall" EXACT [FMA:14156] synonym: "wall of aorta" EXACT [FMA:14156] xref: FMA:14156 xref: MA:0002901 is_a: UBERON:0000415 ! artery wall relationship: part_of UBERON:0000947 ! aorta property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004664 name: aorta tunica adventitia namespace: uberon def: "A tunica adventitia that is part of a aorta." [OBOL:automatic] synonym: "tunica adventitia of aorta" EXACT [FMA:14283] xref: FMA:14283 xref: MA:0002902 xref: SCTID:24996002 is_a: UBERON:0007240 ! tunica adventitia of artery relationship: part_of UBERON:0000947 ! aorta relationship: part_of UBERON:0004663 ! aorta wall property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004681 name: vestibular system namespace: uberon def: "The vestibular system, which contributes to our balance and our sense of spatial orientation, is the sensory system that provides the dominant input about movement and equilibrioception. Together with the cochlea, a part of the auditory system, it constitutes the labyrinth of the inner ear, situated in the vestibulum in the inner ear. As our movements consist of rotations and translations, the vestibular system comprises two components: the semicircular canal system, which indicate rotational movements; and the otoliths, which indicate linear accelerations. The vestibular system sends signals primarily to the neural structures that control our eye movements, and to the muscles that keep us upright. The projections to the former provide the anatomical basis of the vestibulo-ocular reflex, which is required for clear vision; and the projections to the muscles that control our posture are necessary to keep us upright." [Wikipedia:Vestibular_system] comment: note that FMA and NIF have no part information for this class. This is a GAT in FMA synonym: "vestibular organ system" EXACT [FMA:7193] synonym: "vestibular system" EXACT [NIF_GrossAnatomy:nlx_anat_090819] xref: BTO:0003381 xref: FMA:7193 xref: NIF_GrossAnatomy:nlx_anat_090819 xref: SCTID:361533001 is_a: UBERON:0001032 ! sensory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004684 name: raphe nuclei namespace: uberon def: "Thin plates of cells in and immediately adjacent to the sagittal plane[NIF]. A moderate-size cluster of nuclei found in the brain stem. Their main function is to release serotonin to the rest of the brain. Selective serotonin reuptake inhibitor (SSRI) antidepressants are believed to act in these nuclei, as well as at their targets. The raphe nuclei are traditionally considered to be the medial portion of the reticular formation, and they appear as a ridge of cells in the center and most medial portion of the brain stem." [https://sourceforge.net/tracker/?func=detail&aid=3248146&group_id=36855&atid=440764, NIF_GrossAnatomy:nlx_anat_20090205, Wikipedia:Raphe_nuclei] comment: we treat NR obscurus, NR magnus etc as parts of the raphe nuclei. This is consistent with treatment in FMA, where the class is 'set of raphe nuclei' subset: vertebrate_core synonym: "nuclei raphes" EXACT LATIN [FMA:84017, FMA:TA] synonym: "nuclei raphes" RELATED LATIN [Wikipedia:Raphe_nuclei] synonym: "raphe cluster" RELATED [Wikipedia:Raphe_nuclei] synonym: "raphe nuclei" EXACT [NIF_GrossAnatomy:nlx_anat_20090205] synonym: "raphe nuclei" EXACT [FMA:84017] synonym: "raphe nuclei set" EXACT [FMA:84017] synonym: "raphe nucleus" RELATED [ZFA:0001429] synonym: "set of raphe nuclei" RELATED [FMA:84017] xref: FMA:84017 xref: http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/9/94/Gray694.png/200px-Gray694.png xref: MESH:A08.186.211.132.659.632 xref: ncithesaurus:Raphe_Nuclei xref: NIF_GrossAnatomy:nlx_anat_20090205 xref: TAO:0001429 xref: UMLS:C0034671 xref: ZFA:0001429 is_a: UBERON:0000073 ! regional part of nervous system relationship: part_of UBERON:0002275 {source="GO", source="Wikipedia"} ! reticular formation property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004695 name: arterial system smooth muscle namespace: uberon def: "A portion of smooth muscle tissue that is part of an arterial system [Obol]." [OBOL:automatic] xref: MA:0000704 is_a: UBERON:0001135 ! smooth muscle tissue relationship: part_of UBERON:0004572 ! arterial system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004700 name: arterial system endothelium namespace: uberon def: "An endothelium that is part of an arterial system [Obol]." [OBOL:automatic] xref: MA:0000703 xref: ncithesaurus:Arterial_System_Endothelium xref: UMLS:C1706849 is_a: UBERON:0004852 ! cardiovascular system endothelium relationship: part_of UBERON:0004572 ! arterial system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004715 name: annulus fibrosus disci intervertebralis namespace: uberon def: "The ring of fibrocartilage and fibrous tissue forming the circumference of the intervertebral disc; surrounds the nucleus pulposus, which is prone to herniation when the annulus fibrosus is compromised." [BTO:0003629, Wikipedia:Annulus_fibrosus_disci_intervertebralis] synonym: "annulus fibrosus" BROAD [MA:0000111] synonym: "annulus fibrosus of intervertebral disc" RELATED [BTO:0003629] synonym: "anulus fibrosus (diskus intervertebralis)" EXACT [FMA:13551] synonym: "anulus fibrosus of intervertebral disk" EXACT [FMA:13551] synonym: "fibrous ring of intervertebral disc" RELATED [BTO:0003629] xref: BTO:0003629 xref: FMA:13551 xref: http://upload.wikimedia.org/wikipedia/commons/d/d9/Cervical_vertebra_english.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/d/d9/Cervical_vertebra_english.png/200px-Cervical_vertebra_english.png xref: MA:0000111 xref: Wikipedia:Annulus_fibrosus_disci_intervertebralis is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006444 ! annulus fibrosus relationship: part_of UBERON:0001066 ! intervertebral disk property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004716 name: conceptus namespace: uberon def: "The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]." [BTO:0003834, Wikipedia:Conceptus] synonym: "embryo plus adnexa" EXACT [] xref: AEO:0000194 xref: BTO:0003834 xref: EHDAA2:0000001 xref: EHDAA2:0003235 xref: ncithesaurus:Conceptus xref: UMLS:C1516779 xref: Wikipedia:Conceptus is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004719 name: arcuate vein namespace: uberon def: "The arcuate vein is a vessel of the renal circulation. It is located at the border of the renal cortex and renal medulla." [Wikipedia:Arcuate_vein] synonym: "arcuate veins" RELATED [Wikipedia:Arcuate_vein] synonym: "venae arcuatae renis" RELATED LATIN [Wikipedia:Arcuate_vein] xref: EMAPA:28221 xref: http://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/7/7e/Kidney_PioM.png/200px-Kidney_PioM.png xref: MA:0002593 xref: Wikipedia:Arcuate_vein is_a: UBERON:0003517 ! kidney blood vessel property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004721 name: crista ampullaris namespace: uberon def: "The crista ampullaris is the sensory organ of rotation located in the semicircular canal of the inner ear. The function of the crista ampullaris is to sense angular acceleration and deceleration." [Wikipedia:Crista_ampullaris] subset: organ_slim synonym: "ampullary crest" RELATED [MA:0002771] synonym: "ampullary crest of semicircular duct" EXACT [FMA:77714] synonym: "cristae ampullares" RELATED [Wikipedia:Crista_ampullaris] xref: FMA:77714 xref: http://upload.wikimedia.org/wikipedia/commons/e/ec/Semicircular_canal_-_ampulla.png xref: MA:0002771 xref: ncithesaurus:Ampullary_Crest xref: SCTID:368953000 xref: UMLS:C0229465 xref: Wikipedia:Crista_ampullaris is_a: UBERON:0000020 ! sense organ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0004043 {source="MA"} ! semicircular canal ampulla property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004723 name: interlobular artery namespace: uberon def: "the branches of the arcuate arteries of the kidney that radiate outward throught the renal columns and supply the glomeruli[MP]. The first set of renal bloodvessels, the interlobular arteries (or cortical radiate arteries, or cortical radial arteries), are given off at right angles from the side of the arcuate arteries looking toward the cortical substance, and pass directly outward between the medullary rays to reach the fibrous tunic, where they end in the capillary network of this part. These vessels do not anastomose with each other, but form what are called end-arteries. In their outward course they give off lateral branches; these are the afferent vessels for the renal corpuscles; they enter the capsule, and end in the glomerulus. From each tuft the corresponding efferent vessel arises, and, having made its egress from the capsule near to the point where the afferent vessel enters, breaks up into a number of branches, which form a dense plexus within Bowman's capsule." [MP:0011316, Wikipedia:Interlobular_arteries] synonym: "arteriae corticales radiatae, arteriae interlobulares renis" RELATED LATIN [Wikipedia:Interlobular_arteries] synonym: "cortical radial arteries" RELATED [Wikipedia:Interlobular_arteries] synonym: "interlobular" RELATED [Wikipedia:Interlobular_arteries] synonym: "interlobular renal artery" EXACT [FMA:70498] synonym: "kidney interlobular artery" EXACT [MP:0011316] xref: EMAPA:28212 xref: FMA:70498 xref: http://upload.wikimedia.org/wikipedia/commons/2/27/Gray1128.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/27/Gray1128.png/200px-Gray1128.png xref: MA:0002584 xref: ncithesaurus:Interlobular_Artery xref: SCTID:76147008 xref: UMLS:C1512856 xref: Wikipedia:Interlobular_arteries is_a: UBERON:0003644 ! kidney arterial blood vessel property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004726 name: vasa recta namespace: uberon def: "In the blood supply of the kidney, the vasa recta renis (or straight arteries of kidney, or straight arterioles of kidney) form a series of straight capillaries in the medulla. They lie parallel to the loop of Henle. These vessels branch off the efferent arterioles of juxtamedullary nephrons (those nephrons closest to the medulla), enter the medulla, and surround the loop of Henle." [Wikipedia:Vasa_recta] comment: TODO - is this a vein or set of veins? in MA it is a venous blood vessel synonym: "arteria recta" RELATED [Wikipedia:Vasa_recta] synonym: "arteriae rectae" RELATED [Wikipedia:Vasa_recta] synonym: "arteriolae rectae renis" EXACT LATIN [FMA:72006, FMA:TA] synonym: "arteriolae rectae renis" RELATED LATIN [Wikipedia:Vasa_recta] synonym: "arteriolae recti" RELATED [Wikipedia:Vasa_recta] synonym: "kidney vasa recta" EXACT [MP:0011324] synonym: "renal medullary capillary" EXACT [EMAPA:30043] synonym: "set of straight arterioles of kidney" EXACT [FMA:72006] synonym: "straight arterioles of kidney" EXACT [FMA:72006] synonym: "vasa recta of kidney" EXACT [FMA:72006] synonym: "vasa recta renis" EXACT LATIN [FMA:72006, FMA:TA] synonym: "vasa rectae" RELATED [Wikipedia:Vasa_recta] xref: EMAPA:30043 xref: FMA:72006 xref: galen:ArteriaeRectae xref: http://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/21/Kidney_nephron.png/200px-Kidney_nephron.png xref: MA:0002595 is_a: UBERON:0001140 ! renal vein property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004732 name: segmental subdivision of nervous system namespace: uberon def: "An organ segment that is part of a nervous system [Obol]." [OBOL:automatic] comment: Editor note: revisit this after CARO is revised and/or we have defined metameric segment synonym: "neuromere" RELATED [FBbt:00005140] xref: FBbt:00005140 is_a: UBERON:0000063 ! organ segment is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001016 ! nervous system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004733 name: segmental subdivision of hindbrain namespace: uberon def: "An organ segment that is part of a hindbrain [Obol]." [OBOL:automatic] synonym: "hindbrain segment" EXACT [FMA:61998] synonym: "segment of hindbrain" EXACT [FMA:61998] xref: FMA:61998 is_a: UBERON:0004732 ! segmental subdivision of nervous system relationship: part_of UBERON:0002028 ! hindbrain property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004734 name: gastrula namespace: uberon alt_id: UBERON:0007012 def: "Organism at the gastrula stage." [Wikipedia:Gastrula, Wikipedia:Trilaminar_blastocyst] comment: We explicitly merge the NCITA terms here synonym: "blastocystis trilaminaris" RELATED [UBERON:cjm] synonym: "gastrula embryo" EXACT [BILA:0000060] synonym: "tri-laminar disc" RELATED [UBERON:cjm] synonym: "tri-laminar disk" RELATED [UBERON:cjm] synonym: "trilaminar blastocyst" RELATED [UBERON:cjm] synonym: "trilaminar blastoderm" RELATED [UBERON:cjm] synonym: "trilaminar disc" RELATED [UBERON:cjm] synonym: "trilaminar disk" RELATED [UBERON:cjm] synonym: "trilaminar germ" RELATED [UBERON:cjm] xref: BILA:0000060 xref: BTO:0001403 xref: FBbt:00005317 xref: GAID:1302 xref: MESH:A16.254.412 xref: MIAA:0000179 xref: ncithesaurus:Gastrula xref: ncithesaurus:Trilaminar_Embryonic_Disc xref: UMLS:C0017199 xref: UMLS:C1284022 is_a: UBERON:0000922 ! embryo relationship: develops_from UBERON:0000307 ! blastula property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004755 name: skeletal tissue namespace: uberon def: "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" [GO_REF:0000034, PSPUB:0000170, VSAO:0000015] comment: Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from synonym: "mineralized tissue" NARROW [] xref: SCTID:309311006 xref: VSAO:0000015 xref: XAO:0004038 xref: ZFA:0005619 is_a: UBERON:0002384 {source="VSAO"} ! connective tissue relationship: part_of UBERON:0004765 ! skeletal element property_value: external_definition "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000015", notes="taken from version of VSAO used in TAO and used directly in Uberon", ontology="VSAO", source="GO_REF:0000034", source="PSPUB:0000170"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004761 name: cartilaginous neurocranium namespace: uberon def: "the primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]." [Wikipedia:Chondrocranium] comment: note that in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain) synonym: "cartilaginous chondocranium" EXACT [] synonym: "cartilaginous skull" RELATED [] synonym: "cartiligionous skeletal structure of skull" EXACT [] synonym: "chondocranium" RELATED [Wikipedia:Chondrocranium] synonym: "embryonic chondocranium" RELATED [] synonym: "neurocranium" RELATED SENSU [] xref: AAO:0000094 xref: AAO:0010153 xref: EHDAA:6031 xref: FMA:76621 xref: ncithesaurus:Chondrocranium xref: SCTID:155540009 xref: UMLS:C1516496 xref: XAO:0003059 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system is_a: UBERON:0004120 ! mesoderm-derived structure relationship: develops_from UBERON:0009617 {source="PMC1571569"} ! head paraxial mesoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004765 name: skeletal element namespace: uberon def: "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles." [UBERON:cjm] comment: TODO - add more general class for other kinds of mineralized tissue subset: organ_slim subset: uberon_slim xref: AAO:0011129 xref: galen:SkeletalStructure xref: TAO:0001890 xref: VSAO:0000128 xref: XAO:0004012 xref: ZFA:0005494 is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0001434 {source="VSAO"} ! skeletal system property_value: external_definition "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000128", ontology="VSAO", source="PSPUB:0000170"} property_value: external_definition "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001890", ontology="TAO", source="TAO:VSAO_workshop"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004770 name: articular system namespace: uberon def: "Anatomical system that consists of all the joints of the body." [VSAO:0000181] synonym: "joint system" EXACT [FMA:23878] synonym: "set of all joints" RELATED [] synonym: "set of all joints of body" EXACT [FMA:23878] synonym: "set of joints of body" RELATED [FMA:23878] xref: FMA:23878 xref: MA:0003007 xref: SCTID:361827000 xref: VSAO:0000181 is_a: UBERON:0000467 {source="VSAO"} ! anatomical system relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004775 name: outer renal medulla vasa recta namespace: uberon def: "A vasa recta that is part of a outer medulla of kidney [Obol]." [OBOL:automatic] synonym: "kidney outer medulla vasa recta" EXACT [MP:0011330] synonym: "kidney outer renal medulla vasa recta" EXACT [MP:0011330] synonym: "outer medulla of kidney vasa recta" EXACT [OBOL:automatic] synonym: "outer zone of medulla of kidney vasa recta" EXACT [OBOL:automatic] synonym: "outer zone of renal medulla vasa recta" EXACT [OBOL:automatic] synonym: "vasa recta of outer medulla of kidney" EXACT [OBOL:automatic] synonym: "vasa recta of outer renal medulla" EXACT [OBOL:automatic] synonym: "vasa recta of outer zone of medulla of kidney" EXACT [OBOL:automatic] synonym: "vasa recta of outer zone of renal medulla" EXACT [OBOL:automatic] xref: MA:0002597 is_a: UBERON:0003517 ! kidney blood vessel is_a: UBERON:0004726 ! vasa recta is_a: UBERON:0013126 ! vein of abdomen relationship: part_of UBERON:0001293 ! outer medulla of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004776 name: inner renal medulla vasa recta namespace: uberon def: "A vasa recta that is part of a inner medulla of kidney [Obol]." [OBOL:automatic] synonym: "inner medulla of kidney vasa recta" EXACT [OBOL:automatic] synonym: "inner zone of medulla of kidney vasa recta" EXACT [OBOL:automatic] synonym: "inner zone of renal medulla vasa recta" EXACT [OBOL:automatic] synonym: "set of inner region of renal pyramids vasa recta" EXACT [OBOL:automatic] synonym: "vasa recta of inner medulla of kidney" EXACT [OBOL:automatic] synonym: "vasa recta of inner renal medulla" EXACT [OBOL:automatic] synonym: "vasa recta of inner zone of medulla of kidney" EXACT [OBOL:automatic] synonym: "vasa recta of inner zone of renal medulla" EXACT [OBOL:automatic] synonym: "vasa recta of set of inner region of renal pyramids" EXACT [OBOL:automatic] xref: MA:0002596 is_a: UBERON:0003517 ! kidney blood vessel is_a: UBERON:0004726 ! vasa recta is_a: UBERON:0013126 ! vein of abdomen relationship: part_of UBERON:0001294 ! inner medulla of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004780 name: gastrointestinal system lamina propria namespace: uberon def: "A lamina propria that is part of a gastrointestinal system." [OBOL:automatic] xref: MA:0001899 xref: ncithesaurus:Gastrointestinal_Tract_Lamina_Propria xref: UMLS:C1708197 is_a: UBERON:0000030 ! lamina propria is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0004786 {source="reference_0000032", is_inferred="true"} ! gastrointestinal system mucosa relationship: part_of UBERON:0005409 ! gastrointestinal system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004782 name: gastrointestinal system serosa namespace: uberon def: "A serous membrane that is part of a digestive system [Obol]." [OBOL:automatic] synonym: "digestive system serosa" EXACT [OBOL:automatic] synonym: "digestive system serous membrane" EXACT [OBOL:automatic] synonym: "gastrointestinal system serous membrane" EXACT [OBOL:automatic] synonym: "serosa of digestive system" EXACT [OBOL:automatic] synonym: "serosa of gastrointestinal system" EXACT [OBOL:automatic] synonym: "serous membrane of digestive system" EXACT [OBOL:automatic] synonym: "serous membrane of gastrointestinal system" EXACT [OBOL:automatic] xref: MA:0001522 is_a: UBERON:0000042 ! serous membrane relationship: part_of UBERON:0005409 ! gastrointestinal system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004785 name: respiratory system mucosa namespace: uberon def: "A mucosa that is part of a respiratory system [Obol]." [OBOL:automatic] comment: TODO - split respiratory tract mucosa from respiratory system mucosa synonym: "apparatus respiratorius mucosa" EXACT [OBOL:automatic] synonym: "apparatus respiratorius mucosa of organ" EXACT [OBOL:automatic] synonym: "apparatus respiratorius mucous membrane" EXACT [OBOL:automatic] synonym: "mucosa of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "mucosa of organ of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "mucosa of organ of respiratory system" EXACT [OBOL:automatic] synonym: "mucosa of respiratory system" EXACT [OBOL:automatic] synonym: "mucous membrane of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "mucous membrane of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory mucosa" RELATED [BTO:0000973] synonym: "respiratory system mucosa of organ" EXACT [OBOL:automatic] synonym: "respiratory system mucous membrane" EXACT [OBOL:automatic] xref: BTO:0000973 xref: EMAPA:18334 xref: GAID:304 xref: MA:0001827 xref: MESH:A04.760 is_a: UBERON:0000344 ! mucosa relationship: part_of UBERON:0001004 ! respiratory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004786 name: gastrointestinal system mucosa namespace: uberon def: "A mucosa that is part of a gastrointestinal system." [OBOL:automatic] comment: The gut mucosa of amphioxus has insulin-secreting cells. PMID:16417468 synonym: "digestive tract mucosa" EXACT [UBERON:cjm] synonym: "gut mucosa" EXACT [BTO:0000546] synonym: "gut mucuous membrane" EXACT [UBERON:cjm] synonym: "mucosa of gut" EXACT [UBERON:cjm] xref: BTO:0000546 xref: MA:0001521 xref: SCTID:410433007 is_a: UBERON:0000344 ! mucosa is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0005409 ! gastrointestinal system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004787 name: urethra urothelium namespace: uberon def: "An urothelium that is part of a urethra [Obol]." [OBOL:automatic] synonym: "urethra Uroepithelium" EXACT [OBOL:automatic] synonym: "uroepithelium of urethra" EXACT [OBOL:automatic] synonym: "urothelium of urethra" EXACT [OBOL:automatic] xref: MA:0001687 xref: ncithesaurus:Urethra_Transitional_Cell_Epithelium xref: UMLS:C1710585 is_a: UBERON:0000365 ! urothelium is_a: UBERON:0002325 ! epithelium of urethra relationship: part_of UBERON:0000057 ! urethra property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004788 name: kidney pelvis urothelium namespace: uberon def: "An urothelium that is part of a renal pelvis [Obol]." [OBOL:automatic] synonym: "kidney pelvis transitional epithelium" EXACT [OBOL:automatic] synonym: "kidney pelvis Uroepithelium" EXACT [OBOL:automatic] synonym: "pelvis of ureter Uroepithelium" EXACT [OBOL:automatic] synonym: "pelvis of ureter urothelium" EXACT [OBOL:automatic] synonym: "renal pelvis transitional epithelium" EXACT [OBOL:automatic] synonym: "renal pelvis Uroepithelium" EXACT [OBOL:automatic] synonym: "renal pelvis urothelium" EXACT [OBOL:automatic] synonym: "transitional epithelium of kidney pelvis" EXACT [OBOL:automatic] synonym: "transitional epithelium of renal pelvis" EXACT [FMA:263264] synonym: "uroepithelium of kidney pelvis" EXACT [OBOL:automatic] synonym: "uroepithelium of pelvis of ureter" EXACT [OBOL:automatic] synonym: "uroepithelium of renal pelvis" EXACT [OBOL:automatic] synonym: "urothelium of kidney pelvis" EXACT [OBOL:automatic] synonym: "urothelium of pelvis of ureter" EXACT [OBOL:automatic] synonym: "urothelium of renal pelvis" EXACT [OBOL:automatic] xref: FMA:263264 xref: MA:0002632 xref: ncithesaurus:Renal_Pelvis_Urothelium xref: UMLS:C1709899 is_a: UBERON:0001254 ! urothelium of ureter is_a: UBERON:0004819 ! kidney epithelium relationship: part_of UBERON:0001224 ! renal pelvis property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004797 name: blood vessel layer namespace: uberon def: "An organ component layer that is part of a blood vessel." [OBOL:automatic] xref: MA:0002854 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004923 ! organ component layer relationship: part_of UBERON:0001981 ! blood vessel property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004801 name: cervix epithelium namespace: uberon def: "An epithelium that is part of a uterine cervix [Obol]." [OBOL:automatic] comment: Histology notes: The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium[http://en.wikipedia.org/wiki/Cervix#Histology] synonym: "cervical canal epithelial tissue" EXACT [OBOL:automatic] synonym: "cervical canal epithelium" EXACT [OBOL:automatic] synonym: "cervical epithelium" EXACT [BTO:0000241] synonym: "cervix epithelial tissue" EXACT [OBOL:automatic] synonym: "epithelium of cervix" EXACT [OBOL:automatic] xref: BTO:0000241 xref: EFO:0001913 xref: MA:0001724 xref: ncithesaurus:Cervix_Epithelium xref: UMLS:C1711358 is_a: UBERON:0006955 ! uterine epithelium relationship: part_of UBERON:0000002 ! uterine cervix property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004802 name: respiratory tract epithelium namespace: uberon def: "An epithelium that is part of a respiratory tract [Obol]." [OBOL:automatic] synonym: "airway epithelium" RELATED [BTO:0000419] synonym: "epithelial tissue of respiratory tract" EXACT [OBOL:automatic] synonym: "epithelium of respiratory tract" EXACT [OBOL:automatic] synonym: "respiratory epithelium" RELATED [BTO:0000419] synonym: "respiratory tract epithelial tissue" EXACT [OBOL:automatic] xref: BTO:0000419 xref: MA:0001480 xref: SCTID:321764001 xref: VHOG:0000981 is_a: UBERON:0004807 ! respiratory system epithelium is_a: UBERON:0005911 ! endo-epithelium relationship: part_of UBERON:0000065 ! respiratory tract relationship: part_of UBERON:0000072 ! segment of respiratory tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004807 name: respiratory system epithelium namespace: uberon def: "An epithelium that is part of a respiratory system [Obol]." [OBOL:automatic] synonym: "apparatus respiratorius epithelial tissue" EXACT [OBOL:automatic] synonym: "apparatus respiratorius epithelium" EXACT [OBOL:automatic] synonym: "epithelial tissue of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "epithelial tissue of respiratory system" EXACT [OBOL:automatic] synonym: "epithelium of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "epithelium of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory system epithelial tissue" EXACT [OBOL:automatic] xref: MA:0001823 xref: VHOG:0000981 is_a: UBERON:0000483 ! epithelium relationship: part_of UBERON:0001004 ! respiratory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004808 name: gastrointestinal system epithelium namespace: uberon def: "An epithelium that is part of a digestive system [Obol]." [OBOL:automatic] synonym: "digestive system epithelial tissue" EXACT [OBOL:automatic] synonym: "digestive system epithelium" EXACT [OBOL:automatic] synonym: "epithelial tissue of digestive system" EXACT [OBOL:automatic] synonym: "epithelial tissue of gastrointestinal system" EXACT [OBOL:automatic] synonym: "epithelium of digestive system" EXACT [OBOL:automatic] synonym: "epithelium of gastrointestinal system" EXACT [OBOL:automatic] synonym: "gastrointestinal system epithelial tissue" EXACT [OBOL:automatic] xref: MA:0001520 is_a: UBERON:0000483 ! epithelium relationship: part_of UBERON:0005409 ! gastrointestinal system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004810 name: nephron tubule epithelium namespace: uberon def: "An epithelium that is part of a nephron tubule [Obol]." [OBOL:automatic] synonym: "epithelial tissue of nephron tubule" EXACT [OBOL:automatic] synonym: "epithelial tissue of renal tubule" EXACT [OBOL:automatic] synonym: "epithelial tissue of tubulus renalis" EXACT [OBOL:automatic] synonym: "epithelium of nephron tubule" EXACT [OBOL:automatic] synonym: "epithelium of renal tubule" EXACT [OBOL:automatic] synonym: "epithelium of tubulus renalis" EXACT [OBOL:automatic] synonym: "kidney tubule epithelium" EXACT [MA:0001681] synonym: "nephron tubule epithelial tissue" EXACT [OBOL:automatic] synonym: "nephron tubule epithelium" EXACT [OBOL:automatic] synonym: "renal tubule epithelial tissue" EXACT [OBOL:automatic] synonym: "tubulus renalis epithelial tissue" EXACT [OBOL:automatic] synonym: "tubulus renalis epithelium" EXACT [OBOL:automatic] xref: MA:0001681 xref: ncithesaurus:Renal_Tubule_Epithelium xref: UMLS:C1709902 is_a: UBERON:0004211 ! nephron epithelium relationship: part_of UBERON:0001231 ! nephron tubule property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004813 name: seminiferous tubule epithelium namespace: uberon def: "The epithelium lining the seminiferous tubules composed of primary male germ cells (spermatogonia) and supporting sertoli cells. As spermatogenesis proceeds, the developing germ cells migrate toward the lumen. The adluminal compartment, the inner two thirds of the tubules, contains spermatocytes and the more advanced germ cells[GAID]." [Wikipedia:Germinal_epithelium_(male)] synonym: "epithelial tissue of seminiferous tubule" EXACT [OBOL:automatic] synonym: "epithelial tissue of seminiferous tubule of testis" EXACT [OBOL:automatic] synonym: "epithelium of seminiferous tubule" EXACT [OBOL:automatic] synonym: "epithelium of seminiferous tubule of testis" EXACT [OBOL:automatic] synonym: "germinal epithelium (male)" EXACT [Wikipedia:Germinal_epithelium_(male)] synonym: "male germinal epithelium" EXACT [Wikipedia:Germinal_epithelium_(male)] synonym: "seminiferous epithelium" EXACT [BTO:0001811] synonym: "seminiferous tubule epithelial tissue" EXACT [OBOL:automatic] synonym: "testis germinal epithelium" EXACT [VHOG:0000631] synonym: "wall of seminiferous tubule" EXACT [Wikipedia:Germinal_epithelium_(male)] xref: BTO:0001811 xref: EHDAA:8148 xref: FMA:19885 xref: GAID:401 xref: MA:0001748 xref: MESH:A05.360.444.849.700.700 xref: ncithesaurus:Seminiferous_Epithelium xref: RETIRED_EHDAA2:0002009 xref: UMLS:C0036629 xref: VHOG:0000631 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0001136 ! mesothelium is_a: UBERON:0004910 ! epithelium of male gonad is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0010371 ! ecto-epithelium relationship: part_of UBERON:0001343 ! seminiferous tubule of testis property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004815 name: lower respiratory tract epithelium namespace: uberon def: "An epithelium that is part of a lower respiratory tract [Obol]." [OBOL:automatic] synonym: "epithelial tissue of lower respiratory tract" EXACT [OBOL:automatic] synonym: "epithelium of lower respiratory tract" EXACT [OBOL:automatic] synonym: "lower respiratory tract epithelial tissue" EXACT [OBOL:automatic] xref: MA:0001481 is_a: UBERON:0004802 ! respiratory tract epithelium relationship: part_of UBERON:0001558 ! lower respiratory tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004819 name: kidney epithelium namespace: uberon def: "An epithelium that is part of a kidney [Obol]." [OBOL:automatic] synonym: "epithelial tissue of kidney" EXACT [OBOL:automatic] synonym: "epithelium of kidney" EXACT [OBOL:automatic] synonym: "kidney epithelial tissue" EXACT [OBOL:automatic] xref: BTO:0000059 xref: MA:0002846 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0002113 ! kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004820 name: bile duct epithelium namespace: uberon def: "Epithelium of the gallbladder and the intrahepatic and extrahepatic bile ducts." [BTO:0001513] comment: todo - check if BTO terms need merged synonym: "bile duct epithelial tissue" EXACT [OBOL:automatic] synonym: "biliary duct epithelial tissue" EXACT [OBOL:automatic] synonym: "biliary duct epithelium" EXACT [OBOL:automatic] synonym: "biliary epithelium" EXACT [BTO:0001513] synonym: "epithelial tissue of bile duct" EXACT [OBOL:automatic] synonym: "epithelial tissue of biliary duct" EXACT [OBOL:automatic] synonym: "epithelium of bile duct" EXACT [OBOL:automatic] synonym: "epithelium of biliary duct" EXACT [OBOL:automatic] xref: BTO:0000417 xref: BTO:0001513 xref: MA:0001629 xref: ncithesaurus:Bile_Duct_Epithelium xref: UMLS:C1711208 is_a: UBERON:0005911 ! endo-epithelium relationship: part_of UBERON:0002394 ! bile duct property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004821 name: pulmonary alveolus epithelium namespace: uberon def: "the epithelial layer of the alveoli[MP]. The layer of cells covering the lining of the tiny air sacs at the end of the bronchioles[BTO]." [BTO:0003511, MP:0010898] synonym: "alveolus epithelial tissue" EXACT [OBOL:automatic] synonym: "alveolus epithelium" EXACT [MA:0001771] synonym: "epithelial tissue of alveolus" EXACT [OBOL:automatic] synonym: "epithelium of alveolus" EXACT [OBOL:automatic] synonym: "epithelium of pulmonary alveolus" EXACT [FMA:63915] synonym: "pulmonary alveolar epithelium" EXACT [FMA:63915] synonym: "pulmonary alveolus epithelium" EXACT [MP:0010898] xref: BTO:0003511 xref: FMA:63915 xref: MA:0001771 is_a: UBERON:0000115 ! lung epithelium is_a: UBERON:0000487 {source="FMA"} ! simple squamous epithelium relationship: part_of UBERON:0002299 ! alveolus of lung relationship: part_of UBERON:0004894 {source="FMA"} ! alveolar wall property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004823 name: intrahepatic bile duct epithelium namespace: uberon def: "An epithelium that is part of a intrahepatic bile duct [Obol]." [OBOL:automatic] synonym: "epithelial tissue of intrahepatic bile duct" EXACT [OBOL:automatic] synonym: "epithelium of intrahepatic bile duct" EXACT [OBOL:automatic] synonym: "intrahepatic bile duct epithelial tissue" EXACT [OBOL:automatic] xref: MA:0002662 xref: ncithesaurus:Intrahepatic_Bile_Duct_Epithelium xref: UMLS:C1708552 is_a: UBERON:0004820 ! bile duct epithelium relationship: part_of UBERON:0003704 ! intrahepatic bile duct property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004852 name: cardiovascular system endothelium namespace: uberon def: "An endothelium that is part of the cardiovascular system." [UBERON:cjm] comment: consider merging with 'endothelium' subset: vertebrate_core xref: BTO:0001853 xref: GAID:519 xref: MA:0000717 xref: MESH:A07.231.330 xref: TAO:0002171 xref: VHOG:0001217 xref: XAO:0000356 xref: ZFA:0001639 is_a: UBERON:0001986 ! endothelium relationship: part_of UBERON:0004535 ! cardiovascular system property_value: homology_notes "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001217", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004854 name: gastrointestinal system mesentery namespace: uberon def: "A mesentery that is part of a digestive system [Obol]." [OBOL:automatic] synonym: "digestive system mesentery" EXACT [OBOL:automatic] synonym: "mesentery of digestive system" EXACT [OBOL:automatic] synonym: "mesentery of gastrointestinal system" EXACT [OBOL:automatic] xref: MA:0001900 is_a: UBERON:0002095 ! mesentery is_a: UBERON:0004782 ! gastrointestinal system serosa relationship: part_of UBERON:0005409 ! gastrointestinal system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004872 name: splanchnic layer of lateral plate mesoderm namespace: uberon def: "Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]." [Wikipedia:Lateral_plate_mesoderm#Division_into_layers] comment: AO notes: We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors synonym: "inner layer of lateral plate mesoderm" EXACT [] synonym: "splanchnic mesoderm" RELATED [ISBN:9780878932504] synonym: "visceral mesoderm" BROAD [BILA:0000044, http://www.drugs.com/dict/visceral-mesoderm.html, http://www.stedmans.com/] xref: AAO:0011102 xref: BILA:0000044 xref: XAO:0000276 is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0003081 ! lateral plate mesoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004874 name: somatopleure namespace: uberon def: "a structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]." [Wikipedia:Somatopleure] comment: todo - check relationship to LPM xref: EHDAA2:0001847 xref: EHDAA:381 xref: EMAPA:16180 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/28/Gray16.png/200px-Gray16.png xref: ncithesaurus:Somatopleure xref: UMLS:C1519423 xref: VHOG:0000557 is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0003081 {source="EHDAA2"} ! lateral plate mesoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004875 name: nephrogenic cord namespace: uberon def: "a portion of the urogenital ridge which is the source of much of the urinary system[WP]." [Wikipedia:Nephrogenic_cord] comment: part_of or develops_from urogenital ridge? synonym: "chorda nephrogenica" RELATED LATIN [Wikipedia:Nephrogenic_cord] xref: FMA:72168 xref: ncithesaurus:Nephrogenic_Cord xref: SCTID:361405003 xref: UMLS:C1283944 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0004876 ! urogenital ridge relationship: part_of UBERON:0000922 ! embryo property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004876 name: urogenital ridge namespace: uberon def: "One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP]." [MP:0011835, MP:anna, Wikipedia:Urogenital_folds] comment: Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP] synonym: "urethral fold" EXACT [] synonym: "urogenital fold" EXACT [EHDAA2:0004022] xref: BTO:0001402 xref: EHDAA2:0004022 xref: EMAPA:30888 xref: EMAPA:30899 xref: ncithesaurus:Urogenital_Ridge xref: SCTID:308801004 xref: UMLS:C0231047 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0003064 {source="Wikipedia"} ! intermediate mesoderm relationship: develops_from UBERON:0012292 {source="EHDAA2"} ! embryonic cloacal fold relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0009196 {source="EHDAA2"} ! indifferent external genitalia property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004880 name: chordamesoderm namespace: uberon def: "The central region of trunk mesoderm. This tissue forms the notochord" [UBERON:cjm] comment: note that WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. synonym: "axial chorda mesoderm" EXACT [ZFA:0000091] synonym: "chorda mesoderm" EXACT [] synonym: "dorsal mesoderm" EXACT [UBERONREF:0000002] synonym: "presumptive notochord" EXACT [ZFA:0000091] xref: AAO:0000478 xref: EFO:0003426 xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0003068 ! axial mesoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004894 name: alveolar wall namespace: uberon def: "A wall that contains the alveoli" [LG:0012626] synonym: "pulmonary alveolar wall" EXACT [FMA:14117] synonym: "pulmonary interalveolar septum" EXACT [FMA:14117] synonym: "wall of pulmonary alveolus" EXACT [FMA:14117] xref: BTO:0002543 xref: FMA:14117 xref: MA:0002568 xref: ncithesaurus:Alveolar_Wall xref: SCTID:361965008 xref: UMLS:C0225695 is_a: UBERON:0000060 ! anatomical wall is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0002299 ! alveolus of lung property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004902 name: urogenital sinus epithelium namespace: uberon def: "The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra" [PMID:18977204] comment: we follow EHDAA2 in dividing the UGS into epithelium and lumen synonym: "epithelium of urogenital sinus" EXACT [OBOL:automatic] synonym: "UGE" EXACT [PMID:18977204] xref: EHDAA2:0004061 is_a: UBERON:0009846 ! embryonic cloacal epithelium relationship: develops_from UBERON:0009846 {source="EHDAA2"} ! embryonic cloacal epithelium relationship: part_of UBERON:0000164 ! primitive urogenital sinus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004905 name: articulation namespace: uberon def: "anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts." [] subset: grouping_class xref: FBbt:00005811 is_a: UBERON:0000477 ! anatomical cluster property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004906 name: ectodermal gut namespace: uberon def: "A portion of the gut that is derived from ectoderm." [GO:0007439] is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004185 ! endodermal gut relationship: develops_from UBERON:0000924 ! ectoderm relationship: part_of UBERON:0001555 ! digestive tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004907 name: lower digestive tract namespace: uberon def: "the region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]." [Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract] comment: WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L subset: uberon_slim synonym: "gut" BROAD [GO:0048565] synonym: "lower gastrointestinal tract" EXACT [] synonym: "lower GI tract" EXACT [] xref: EHDAA2:0000726 xref: FMA:49179 xref: galen:LowerGastrointestinalTract xref: MA:0000917 xref: ncithesaurus:Lower_Gastrointestinal_Tract xref: SCTID:279973004 xref: UMLS:C0226875 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: develops_from UBERON:0001046 ! hindgut relationship: part_of UBERON:0005409 ! gastrointestinal system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004909 name: epithelium of gonad namespace: uberon def: "An epithelium surrounding a gonad." [OBOL:automatic] comment: Note that after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts synonym: "gonad epithelium" EXACT [OBOL:automatic] synonym: "gonadal epithelium" EXACT [OBOL:automatic] xref: EHDAA:4032 xref: EHDAA:5931 xref: FBbt:00004859 xref: ncithesaurus:Germinal_Epithelium xref: UMLS:C1517534 is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0000991 ! gonad property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004910 name: epithelium of male gonad namespace: uberon def: "An epithelium surrounding a testis." [OBOL:automatic] comment: Note that after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts synonym: "testis epithelium" EXACT [OBOL:automatic] synonym: "testis sheath" NARROW SENSU [FBbt:00004955] xref: BTO:0001364 xref: EMAPA:17973 xref: FBbt:00004955 is_a: UBERON:0004909 ! epithelium of gonad relationship: part_of UBERON:0000473 ! testis property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004911 name: epithelium of female gonad namespace: uberon def: "An epithelium surrounding an ovary." [OBOL:automatic] comment: Note that after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts synonym: "ovarian epithelium" EXACT [OBOL:automatic] synonym: "ovarian sheath" NARROW SENSU [FBbt:00004896] synonym: "ovary epithelium" EXACT [OBOL:automatic] xref: BTO:0003661 xref: FBbt:00004896 is_a: UBERON:0004909 ! epithelium of gonad relationship: part_of UBERON:0000992 ! female gonad property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004912 name: biliary bud namespace: uberon synonym: "hepatic diverticulum" RELATED [EMAPA:16561] xref: EHDAA2:0000171 xref: EMAPA:16561 xref: EMAPA:16565 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/4/4f/Gray1088.png/200px-Gray1088.png xref: VHOG:0001351 is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0009497 ! epithelium of foregut-midgut junction relationship: develops_from UBERON:0004161 {source="EHDAA2-modified"} ! septum transversum relationship: part_of UBERON:0006235 {source="EMAPA"} ! foregut-midgut junction property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004921 name: subdivision of digestive tract namespace: uberon comment: intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. subset: non_informative synonym: "alimentary system subdivision" RELATED [FMA:71131] synonym: "subdivision of alimentary system" RELATED [FMA:71131] xref: FBbt:00100315 xref: FMA:71131 is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0011216 {source="FMA"} ! organ system subdivision relationship: part_of UBERON:0001555 ! digestive tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004923 name: organ component layer namespace: uberon subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000060 ! anatomical wall property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004996 name: mucosa of cardia of stomach namespace: uberon def: "A mucosa that is part of a cardia of stomach [Obol]." [OBOL:automatic] synonym: "cardia of stomach mucosa" EXACT [OBOL:automatic] synonym: "cardia of stomach mucosa of organ" EXACT [OBOL:automatic] synonym: "cardia of stomach mucous membrane" EXACT [OBOL:automatic] synonym: "cardia of stomach organ mucosa" EXACT [OBOL:automatic] synonym: "cardial part of stomach mucosa" EXACT [OBOL:automatic] synonym: "cardial part of stomach mucosa of organ" EXACT [OBOL:automatic] synonym: "cardial part of stomach mucous membrane" EXACT [OBOL:automatic] synonym: "cardial part of stomach organ mucosa" EXACT [OBOL:automatic] synonym: "gastric cardia mucosa" EXACT [OBOL:automatic] synonym: "gastric cardia mucosa of organ" EXACT [OBOL:automatic] synonym: "gastric cardia mucous membrane" EXACT [OBOL:automatic] synonym: "gastric cardia organ mucosa" EXACT [OBOL:automatic] synonym: "mucosa of cardial part of stomach" EXACT [OBOL:automatic] synonym: "mucosa of gastric cardia" EXACT [OBOL:automatic] synonym: "mucosa of organ of cardia of stomach" EXACT [OBOL:automatic] synonym: "mucosa of organ of cardial part of stomach" EXACT [OBOL:automatic] synonym: "mucosa of organ of gastric cardia" EXACT [OBOL:automatic] synonym: "mucosa of organ of pars cardiaca (gaster)" EXACT [OBOL:automatic] synonym: "mucosa of organ of stomach cardiac region" EXACT [OBOL:automatic] synonym: "mucosa of pars cardiaca (gaster)" EXACT [OBOL:automatic] synonym: "mucosa of stomach cardiac region" EXACT [OBOL:automatic] synonym: "mucous membrane of cardia of stomach" EXACT [OBOL:automatic] synonym: "mucous membrane of cardial part of stomach" EXACT [OBOL:automatic] synonym: "mucous membrane of gastric cardia" EXACT [OBOL:automatic] synonym: "mucous membrane of pars cardiaca (gaster)" EXACT [OBOL:automatic] synonym: "mucous membrane of stomach cardiac region" EXACT [OBOL:automatic] synonym: "organ mucosa of cardia of stomach" EXACT [OBOL:automatic] synonym: "organ mucosa of cardial part of stomach" EXACT [OBOL:automatic] synonym: "organ mucosa of gastric cardia" EXACT [OBOL:automatic] synonym: "organ mucosa of pars cardiaca (gaster)" EXACT [OBOL:automatic] synonym: "organ mucosa of stomach cardiac region" EXACT [OBOL:automatic] synonym: "pars cardiaca (gaster) mucosa" EXACT [OBOL:automatic] synonym: "pars cardiaca (gaster) mucosa of organ" EXACT [OBOL:automatic] synonym: "pars cardiaca (gaster) mucous membrane" EXACT [OBOL:automatic] synonym: "pars cardiaca (gaster) organ mucosa" EXACT [OBOL:automatic] synonym: "stomach cardiac region mucosa" EXACT [OBOL:automatic] synonym: "stomach cardiac region mucosa of organ" EXACT [OBOL:automatic] synonym: "stomach cardiac region mucous membrane" EXACT [OBOL:automatic] synonym: "stomach cardiac region organ mucosa" EXACT [OBOL:automatic] xref: FMA:17456 is_a: UBERON:0001199 ! mucosa of stomach relationship: part_of UBERON:0001162 ! cardia of stomach property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0004998 name: mucosa of pylorus namespace: uberon def: "A mucosa that is part of a pylorus [Obol]." [OBOL:automatic] synonym: "antropyloric mucosa" RELATED [BTO:0002984] synonym: "mucosa of organ of pyloric part of stomach" EXACT [OBOL:automatic] synonym: "mucosa of organ of pylorus" EXACT [OBOL:automatic] synonym: "mucosa of organ of stomach pyloric region" EXACT [OBOL:automatic] synonym: "mucosa of pyloric part of stomach" EXACT [OBOL:automatic] synonym: "mucosa of stomach pyloric region" EXACT [OBOL:automatic] synonym: "mucous membrane of pyloric part of stomach" EXACT [OBOL:automatic] synonym: "mucous membrane of pylorus" EXACT [OBOL:automatic] synonym: "mucous membrane of stomach pyloric region" EXACT [OBOL:automatic] synonym: "organ mucosa of pyloric part of stomach" EXACT [OBOL:automatic] synonym: "organ mucosa of pylorus" EXACT [OBOL:automatic] synonym: "organ mucosa of stomach pyloric region" EXACT [OBOL:automatic] synonym: "pyloric part of stomach mucosa" EXACT [OBOL:automatic] synonym: "pyloric part of stomach mucosa of organ" EXACT [OBOL:automatic] synonym: "pyloric part of stomach mucous membrane" EXACT [OBOL:automatic] synonym: "pyloric part of stomach organ mucosa" EXACT [OBOL:automatic] synonym: "pylorus mucosa" EXACT [OBOL:automatic] synonym: "pylorus mucosa of organ" EXACT [OBOL:automatic] synonym: "pylorus mucous membrane" EXACT [OBOL:automatic] synonym: "pylorus organ mucosa" EXACT [OBOL:automatic] synonym: "stomach pyloric region mucosa" EXACT [OBOL:automatic] synonym: "stomach pyloric region mucosa of organ" EXACT [OBOL:automatic] synonym: "stomach pyloric region mucous membrane" EXACT [OBOL:automatic] synonym: "stomach pyloric region organ mucosa" EXACT [OBOL:automatic] xref: BTO:0002984 xref: EMAPA:27199 xref: EMAPA:27499 xref: FMA:17461 is_a: UBERON:0001199 ! mucosa of stomach relationship: part_of UBERON:0001166 ! pylorus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005039 name: mucosa of bronchiole namespace: uberon def: "A mucosa that is part of a bronchiole [Obol]." [OBOL:automatic] synonym: "bronchiole mucosa" EXACT [OBOL:automatic] synonym: "bronchiole mucosa of organ" EXACT [OBOL:automatic] synonym: "bronchiole mucous membrane" EXACT [OBOL:automatic] synonym: "bronchiole organ mucosa" EXACT [OBOL:automatic] synonym: "lobular bronchiole mucosa" EXACT [OBOL:automatic] synonym: "lobular bronchiole mucosa of organ" EXACT [OBOL:automatic] synonym: "lobular bronchiole mucous membrane" EXACT [OBOL:automatic] synonym: "lobular bronchiole organ mucosa" EXACT [OBOL:automatic] synonym: "mucosa of lobular bronchiole" EXACT [OBOL:automatic] synonym: "mucosa of organ of bronchiole" EXACT [OBOL:automatic] synonym: "mucosa of organ of lobular bronchiole" EXACT [OBOL:automatic] synonym: "mucous membrane of bronchiole" EXACT [OBOL:automatic] synonym: "mucous membrane of lobular bronchiole" EXACT [OBOL:automatic] synonym: "organ mucosa of bronchiole" EXACT [OBOL:automatic] synonym: "organ mucosa of lobular bronchiole" EXACT [OBOL:automatic] xref: FMA:263230 xref: FMA:62774 xref: SCTID:10887006 is_a: UBERON:0000410 ! bronchial mucosa relationship: part_of UBERON:0002186 ! bronchiole property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005057 name: immune organ namespace: uberon def: "An organ that is part of a immune system [Obol]." [OBOL:automatic] subset: organ_slim is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0002405 ! immune system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005058 name: hemolymphoid system gland namespace: uberon def: "A gland that is part of a hemolymphoid system [Obol]." [OBOL:automatic] subset: organ_slim synonym: "hemopoietic or lymphoid gland" EXACT [GOC:cjm] synonym: "hemopoietic or lymphoid organ" BROAD [GO:0048534] xref: MA:0002962 is_a: UBERON:0002530 ! gland relationship: part_of UBERON:0002193 ! hemolymphoid system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005062 name: neural fold namespace: uberon def: "One of the two elevated edges of the neural groove[GO,MP]." [GO:0001842, MP:0011256, Wikipedia:Neural_fold] synonym: "medullary fold" EXACT [MP:0011256] xref: EHDAA2:0001249 xref: EMAPA:16093 xref: EMAPA:16142 xref: EMAPA:16146 xref: EMAPA:16151 xref: EMAPA:16155 xref: EMAPA:16159 xref: EMAPA:16162 xref: EMAPA:16288 xref: EMAPA:16292 xref: EMAPA:16295 xref: EMAPA:16299 xref: EMAPA:16303 xref: EMAPA:16307 xref: EMAPA:16528 xref: ncithesaurus:Neural_Fold xref: SCTID:361461009 xref: UMLS:C0814993 xref: XAO:0004087 is_a: UBERON:0005157 ! epithelial fold is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0003075 ! neural plate property_value: external_definition "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." xsd:string {source="Wikipedia:Neural_fold"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005068 name: neural rod namespace: uberon def: "a solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]." [GO:0014024, ZFA:0000133] xref: EFO:0003498 xref: TAO:0000133 xref: ZFA:0000133 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0002346 ! neurectoderm relationship: develops_from UBERON:0007135 ! neural keel relationship: part_of UBERON:0000922 ! embryo property_value: external_definition "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000133", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005081 name: ureter ureteric bud namespace: uberon def: "The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]." [GO:0035503] is_a: UBERON:0000084 ! ureteric bud is_a: UBERON:0007497 ! developing epithelial placode property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005085 name: ectodermal placode namespace: uberon def: "An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]" [GO:0060788] comment: Homology: With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates. Editor notes: consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm // AO notes: in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous is_a: UBERON:0001048 ! primordium relationship: part_of UBERON:0000924 ! ectoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005086 name: hair follicle placode namespace: uberon def: "An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud[GO]." [GO:0060789] synonym: "hair gem" RELATED [ISBN:9780878932504] synonym: "hair peg" RELATED [ISBN:9780878932504] synonym: "vibrissa placode" NARROW [] is_a: UBERON:0011817 ! follicle placode relationship: develops_from UBERON:0001003 ! epidermis relationship: develops_from UBERON:0011272 {source="Wikipathways:WP2062"} ! embryonic skin basal layer property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005087 name: tooth placode namespace: uberon def: "An tooth placode is a thickening of the ectoderm that will give rise to the tooth bud[GO]." [GO:0060790] comment: Location notes: In mammals this may be located in the alveolar ridges, but note that some species such as zebrafish have ceratobranchial teeth. Sharks have dermal denticles that share developmental origins. Currently we don't include location information due to this diversity, but in future we may include specific subclasses and/or taxon GCIs. synonym: "dental placode" EXACT [Obol:automatic] synonym: "dental primordium" EXACT [ZFA:0001153] synonym: "odontogenic placode" EXACT [Obol:automatic] synonym: "tooth germ" RELATED [ZFA:0001153] xref: BTO:0001511 xref: TAO:0001153 xref: ZFA:0001153 is_a: UBERON:0011814 {source="NBK53175"} ! non-neurogenic ectodermal placode property_value: external_definition "Placode that develops into a tooth. The placode is a thickening of the pharyngeal epithelium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001153", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005088 name: sebaceous gland placode namespace: uberon def: "A sebaceous gland placode is a thickening of the ectoderm that will give rise to the sebaceous gland bud[GO]." [GO:0060791] comment: todo - add bud is_a: UBERON:0011814 {source="NBK53175"} ! non-neurogenic ectodermal placode relationship: develops_from UBERON:0011272 {source="Wikipathways:WP2062"} ! embryonic skin basal layer property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005089 name: sweat gland placode namespace: uberon def: "An sweat gland placode is a thickening of the ectoderm that will give rise to the sweat gland bud[GO]." [GO:0060793] comment: todo - add bud is_a: UBERON:0011814 {source="NBK53175"} ! non-neurogenic ectodermal placode relationship: develops_from UBERON:0011272 {source="Wikipathways:WP2062"} ! embryonic skin basal layer property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005090 name: muscle structure namespace: uberon def: "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]." [GO:0061061] comment: Usage notes: in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila synonym: "muscle" RELATED [] synonym: "muscle element" RELATED [] xref: FBbt:00005073 is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005095 name: kidney rudiment namespace: uberon def: "." [GO:0072003] comment: Editor notes: class added for consistency with GO - consider merging with kidney mesenchyme. synonym: "kidney anlage" RELATED [GOC:mtg_kidney_jan10] is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0007687 {source="GO"} ! kidney field relationship: part_of UBERON:0000922 ! embryo property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005096 name: descending thin limb namespace: uberon alt_id: UBERON:0005165 def: "The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle[GO]." [GO:0072022, Wikipedia:Descending_limb_of_loop_of_Henle] subset: uberon_slim synonym: "descending limb of henle%27s loop" RELATED [Wikipedia:Descending_limb_of_loop_of_Henle] synonym: "descending limb of loop of henle" RELATED [Wikipedia:Descending_limb_of_loop_of_Henle] synonym: "descending thin limb of loop of Henle" EXACT [] synonym: "loop of Henle descending thin limb" EXACT [] synonym: "loop of henle thin descending limb" EXACT [MA:0002625] synonym: "pars descendens (tubulus attenuatus)" EXACT [FMA:17719] synonym: "thin descending limb" EXACT [] synonym: "thin descending limb of loop of henle" RELATED [Wikipedia:Descending_limb_of_loop_of_Henle] synonym: "thin descending limb of the loop of henle" RELATED [Wikipedia:Descending_limb_of_loop_of_Henle] synonym: "thin descending loop of henle" RELATED [Wikipedia:Descending_limb_of_loop_of_Henle] xref: EMAPA:28325 xref: EMAPA:28355 xref: EMAPA:29681 xref: FMA:17719 xref: http://upload.wikimedia.org/wikipedia/commons/2/27/Gray1128.png xref: MA:0002625 is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0001288 ! loop of Henle relationship: part_of UBERON:0004136 ! intermediate tubule property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005097 name: renal connecting tubule namespace: uberon def: "The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO]." [GO:0072027, Wikipedia:Connecting_tubule] synonym: "connecting tubule" EXACT [MA:0002610] synonym: "kidney connecting tubule" EXACT [MA:0002610] synonym: "tubulus renalis arcuatus" RELATED LATIN [Wikipedia:Connecting_tubule] xref: BTO:0004539 xref: EMAPA:27758 xref: EMAPA:27790 xref: EMAPA:27865 xref: EMAPA:28011 xref: http://upload.wikimedia.org/wikipedia/commons/2/27/Gray1128.png xref: MA:0002610 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0007685 ! region of nephron tubule is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0003220 {source="Wikipedia"} ! metanephric mesenchyme property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005103 name: mesonephric epithelium namespace: uberon def: "An epithelium that is part of a mesonephros [Obol]." [OBOL:automatic] is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0004819 ! kidney epithelium is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0000080 ! mesonephros property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005153 name: epithelial bud namespace: uberon def: "A bud is a protrusion that forms from an epithelial sheet by localized folding." [GO:0060572] xref: BTO:0001639 is_a: UBERON:0005157 ! epithelial fold property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005154 name: epithelial cord namespace: uberon comment: TODO - add superclass of developing structure xref: AEO:0000216 xref: EHDAA2:0004052 is_a: UBERON:0000483 ! epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005156 name: reproductive structure namespace: uberon def: "An anatomical structure that is part of the reproductive system." [GOC:cjm] synonym: "reproductive system structure" EXACT [] is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0000990 ! reproductive system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005157 name: epithelial fold namespace: uberon def: "An epithelial sheet bent on a linear axis." [GO:0060571] is_a: UBERON:0000483 ! epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005162 name: multi cell component structure namespace: uberon def: "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." [CARO:0001000] comment: AO notes: we go with the FMA classification rather than the CARO one. FMA def: "Anatomical cluster which has as direct parts cell parts from two or more cells." subset: upper_level synonym: "cell part cluster" RELATED [FMA:83115] synonym: "multi-cell-component structure" EXACT [CARO:0001000] xref: AAO:0011000 xref: CARO:0001000 xref: FBbt:00007060 xref: FMA:83115 is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005164 name: ascending limb of loop of Henle namespace: uberon def: "the distal part of the loop of Henle that is impermeable to water and actively pumps sodium out of the filtrate to generate the hypertonic interstitium that drives countercurrent exchange; it consists of an initial very thin segment lined by simple squamous epithelium followed by a distal thick segment lined by simple cuboidal epithelium[MP]." [MP:0011342, Wikipedia:Ascending_limb_of_loop_of_Henle] comment: TODO: thick/thin check. Also relationship to distal tubule. We need a home for MA:0002634-renal straight tubule subset: uberon_slim synonym: "ascending limb" BROAD [] synonym: "ascending limb of Henle's loop" EXACT [] synonym: "distal straight tubule" RELATED [] synonym: "loop of Henle ascending limb" EXACT [MP:0011342] xref: FMA:17717 xref: MA:0001676 xref: ncithesaurus:Ascending_Limb_of_the_Henle_s_Loop xref: SCTID:245434005 xref: UMLS:C0227658 is_a: UBERON:0004135 ! distal tubule relationship: part_of UBERON:0001288 ! loop of Henle property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005167 name: papillary duct namespace: uberon def: "The terminal portions of the medullary collecting ducts are the papillary ducts, which end at the renal papilla and empty into a minor calyx." [Encyclopedia:http\://encyclopedia.thefreedictionary.com/] synonym: "Bellini's duct" RELATED [MP:0011331] synonym: "duct of Bellini" RELATED [] synonym: "papillary duct of kidney" EXACT [SCTID:110623009] xref: BTO:0004540 xref: MA:0001646 xref: SCTID:110623009 is_a: UBERON:0001232 ! collecting duct of renal tubule property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005168 name: interlobular vein namespace: uberon def: "The venae stellatae join to form the interlobular veins, which pass inward between the rays, receive branches from the plexuses around the convoluted tubules, and, having arrived at the bases of the renal pyramids, join with the venae rectae" [Wikipedia:Interlobular_veins] synonym: "interlobular veins of kidney" RELATED [FMA:71634] synonym: "set of interlobular veins of kidney" RELATED [FMA:71634] synonym: "venae interlobulares renis" EXACT LATIN [FMA:71634, FMA:TA] synonym: "venae interlobulares renis" RELATED LATIN [Wikipedia:Interlobular_veins] xref: EMAPA:28218 xref: FMA:71634 xref: http://upload.wikimedia.org/wikipedia/commons/2/27/Gray1128.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/27/Gray1128.png/200px-Gray1128.png xref: MA:0002594 is_a: UBERON:0005269 ! renal cortex vein relationship: part_of UBERON:0001225 ! cortex of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005169 name: interstitial tissue namespace: uberon def: "connective tissue between the cellular elements of a structure." [http://medical-dictionary.thefreedictionary.com/tissue] comment: Editors note: specify differentia from stroma synonym: "interstitium" EXACT [] xref: FMA:86301 xref: SCTID:85293002 is_a: UBERON:0003891 {source="FMA"} ! stroma property_value: has_relational_adjective "interstital" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005171 name: hepatic duct namespace: uberon def: "The hepatic duct is the duct that leads from the liver to the bile duct[GO]. A duct that carries bile from the liver to the small intestine[ZFA]." [GO:0061011] comment: TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same subset: vertebrate_core xref: EHDAA2:0000741 xref: EHDAA:3049 xref: EMAPA:16843 xref: EMAPA:18672 xref: galen:HepaticDuct xref: MA:0000357 xref: ncithesaurus:Hepatic_Duct xref: OpenCyc:Mx4rvWo8WJwpEbGdrcN5Y29ycA xref: SCTID:245399002 xref: TAO:0001100 xref: UMLS:C0917710 xref: VHOG:0000219 xref: ZFA:0001100 is_a: UBERON:0002394 ! bile duct relationship: part_of UBERON:0001173 ! biliary tree property_value: external_definition "A duct that carries bile from the liver to the small intestine.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001100", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "The excretory duct of the liver or one of its branches in the lobes of the liver. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000219", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/hepatic+duct"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005172 name: abdomen organ namespace: uberon def: "An organ that is part of an abdomen [Obol]." [OBOL:automatic] subset: non_informative xref: MA:0000522 xref: SCTID:272631008 is_a: UBERON:0005173 ! abdominal segment organ relationship: part_of UBERON:0000916 ! abdomen property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005173 name: abdominal segment organ namespace: uberon def: "An organ that is part of a abdominal segment of trunk." [OBOL:automatic] comment: Includes abdomen organ and pelvis organ subset: non_informative xref: MA:0000529 is_a: UBERON:0005177 ! trunk organ relationship: part_of UBERON:0002417 ! abdominal segment of trunk property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005174 name: back organ namespace: uberon def: "An organ that is part of a back [Obol]." [OBOL:automatic] subset: non_informative subset: organ_slim xref: MA:0001901 is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0001137 ! dorsum property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005176 name: tooth enamel organ namespace: uberon def: "." [https://sourceforge.net/tracker/?func=detail&aid=3556489&group_id=76834&atid=994726, Wikipedia:Enamel_organ] comment: Editor notes: some sources treat the dental organ as epithelium - we treat it as the mereological sum of dentail epithelium plus dental papilla (consistent with treatment in many AOs), but this may be revised.Development notes: NOT develeops_from NC[UBERONREF:0000002]. Alternate definitioon: A cellular aggregation seen in histologic sections of a developing tooth. It lies above a condensation of ectomesenchymal cells called the odontogenic papilla. Historically, enamel organ has been the term to describe this structure, but it was attempted unsuccessfully in recent years to change the name to dental organ in order to better represent its multiple functions apart from enamel formation[WP] subset: vertebrate_core synonym: "dental organ" EXACT [ZFA:0005138] synonym: "enamel organ" EXACT [MP:0010747] synonym: "odontogenic organ" RELATED [] synonym: "organum enameleum" RELATED LATIN [Wikipedia:Enamel_organ] xref: BTO:0001722 xref: MA:0001604 xref: MESH:A14.254.900.720.265 xref: SCTID:362863002 xref: TAO:0005138 xref: ZFA:0005138 is_a: UBERON:0000481 {source="ZFA"} ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0005087 {source="ZFA"} ! tooth placode relationship: part_of UBERON:0001091 {source="MA-abduced"} ! calcareous tooth property_value: external_definition "A structure that is involved in tooth formation. A bell shape two layer epithelial structure that descends toward the ceratobranchial 5 bone, enclosing the dental mesenchyme. At later times in tooth development the cells at the apex of the bell may be involved in enameloid formation. This structure remains at the base of the erupted tooth and is the source of replacement teeth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005138", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:8782 [Term] id: UBERON:0005177 name: trunk organ namespace: uberon def: "An organ that is part of a trunk [Obol]." [OBOL:automatic] subset: non_informative subset: organ_slim xref: MA:0000516 is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0002100 ! trunk property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005178 name: thoracic cavity organ namespace: uberon def: "An organ that is part of a thoracic cavity [Obol]." [OBOL:automatic] subset: non_informative xref: MA:0000557 is_a: UBERON:0000062 ! organ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005179 name: pelvis organ namespace: uberon def: "An organ that is part of the pelvic region[Obol]." [OBOL:automatic] subset: non_informative subset: organ_slim xref: MA:0000543 is_a: UBERON:0005173 ! abdominal segment organ relationship: part_of UBERON:0002355 ! pelvis property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005185 name: renal medulla collecting duct namespace: uberon def: "A collecting duct of renal tubule that is part of a renal medulla [Obol]." [OBOL:automatic] synonym: "kidney medulla collecting duct" EXACT [MA:0002935] synonym: "medullary collecting duct" EXACT [EMAPA:28061] xref: EMAPA:28061 xref: MA:0002935 is_a: UBERON:0001232 ! collecting duct of renal tubule relationship: part_of UBERON:0000362 ! renal medulla property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005186 name: outer renal medulla collecting duct namespace: uberon def: "A collecting duct of renal tubule that is part of a outer medulla of kidney [Obol]." [OBOL:automatic] synonym: "kidney outer medulla collecting duct" EXACT [MA:0002599] xref: MA:0002599 is_a: UBERON:0005185 ! renal medulla collecting duct relationship: part_of UBERON:0001293 ! outer medulla of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005187 name: inner renal medulla collecting duct namespace: uberon def: "A collecting duct of renal tubule that is part of a inner medulla of kidney [Obol]." [OBOL:automatic] synonym: "kidney inner medulla collecting duct" EXACT [MA:0002598] synonym: "papillary collecting duct" RELATED [MA:0002598] xref: MA:0002598 is_a: UBERON:0005185 ! renal medulla collecting duct relationship: part_of UBERON:0001294 ! inner medulla of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005211 name: renal medulla interstitium namespace: uberon def: "tissue surrounding the loop of Henle in the renal medulla.." [Wikipedia:Bone_marrow_of_ovaryry_interstitium] comment: Function notes: It functions in renal water reabsorption by building up a high hypertonicity, which draws water out of the thin descending limb of the loop of Henle and the collecting duct system. This hypertonicity, in turn, is created by an efflux of urea from the inner medullary collecting duct. synonym: "kidney medulla interstitium" EXACT [MA:0002619] synonym: "renal medullary interstitium" EXACT [EMAPA:18326] xref: EMAPA:18326 xref: MA:0002619 is_a: UBERON:0005215 ! kidney interstitium relationship: part_of UBERON:0000362 ! renal medulla relationship: part_of UBERON:0005215 {source="MA"} ! kidney interstitium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005212 name: testis interstitial tissue namespace: uberon def: "The male gonad containing two functional parts: the SEMINIFEROUS TUBULES for the production and transport of male germ cells (SPERMATOGENESIS) and the interstitial compartment containing LEYDIG CELLS that produce ANDROGENS.." [MESH:A05.360.444.849] synonym: "interstitium of testis" EXACT [UBERON:cjm] synonym: "interstitium of the testis" EXACT [EMAPA:18687] synonym: "testis - interstitial" EXACT [UBERON:cjm] synonym: "testis interstitium" EXACT [UBERON:cjm] xref: EMAPA:18687 xref: MA:0002713 xref: SCTID:362280005 is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0005169 ! interstitial tissue relationship: part_of UBERON:0000473 ! testis property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005213 name: outer renal medulla interstitium namespace: uberon def: "A portion of interstitial tissue that is part of a outer medulla of kidney [Obol]." [OBOL:automatic] synonym: "kidney outer medulla interstitium" EXACT [MA:0002621] synonym: "outer medullary interstitium" EXACT [EMAPA:28337] xref: EMAPA:28337 xref: MA:0002621 is_a: UBERON:0005211 ! renal medulla interstitium relationship: part_of UBERON:0001293 {source="MA"} ! outer medulla of kidney relationship: part_of UBERON:0005211 {source="MA"} ! renal medulla interstitium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005214 name: inner renal medulla interstitium namespace: uberon def: "A portion of interstitial tissue that is part of a inner medulla of kidney [Obol]." [OBOL:automatic] synonym: "inner medullary interstitium" EXACT [EMAPA:28364] synonym: "kidney inner medulla interstitium" EXACT [MA:0002620] xref: EMAPA:28364 xref: MA:0002620 is_a: UBERON:0005211 ! renal medulla interstitium relationship: part_of UBERON:0001294 {source="MA"} ! inner medulla of kidney relationship: part_of UBERON:0005211 {source="MA"} ! renal medulla interstitium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005215 name: kidney interstitium namespace: uberon def: "The interstitium of the kidney comprises the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances. As we define it here, the interstitium is bounded on all sides by tubular and vascular basement membranes." [doi:10.1038/ki.1991.49] synonym: "renal interstitium" EXACT [FMA:70983] synonym: "renal stroma" EXACT [FMA:70983] synonym: "stroma of kidney" EXACT [FMA:70983] xref: EMAPA:27690 xref: FMA:70983 xref: MA:0002616 is_a: UBERON:0003567 ! abdomen connective tissue is_a: UBERON:0005169 ! interstitial tissue is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0002113 ! kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005253 name: head mesenchyme namespace: uberon def: "Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells." [ISBN:0683400088, MP:0011260] subset: vertebrate_core synonym: "cephalic mesenchyme" EXACT [MP:0011260] xref: EFO:0003492 xref: EHDAA2:0000732 xref: EHDAA:179 xref: EMAPA:16098 xref: EMAPA:16269 xref: TAO:0000113 xref: VHOG:0000332 xref: ZFA:0000113 is_a: UBERON:0003104 {source="ZFA"} ! mesenchyme relationship: part_of UBERON:0000033 ! head property_value: external_definition "Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000113", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005256 name: trunk mesenchyme namespace: uberon def: "Mesenchyme that is part of a trunk." [OBOL:automatic] subset: vertebrate_core xref: EFO:0003485 xref: EHDAA2:0002092 xref: EHDAA:377 xref: EMAPA:16177 xref: TAO:0000081 xref: VHOG:0000281 xref: ZFA:0000081 is_a: UBERON:0003104 ! mesenchyme relationship: part_of UBERON:0002100 ! trunk property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005267 name: renal cortex collecting duct namespace: uberon def: "A collecting duct of renal tubule that is part of a cortex of kidney [Obol]." [OBOL:automatic] synonym: "kidney cortex collecting duct" EXACT [MA:0002600] xref: MA:0002600 is_a: UBERON:0001232 ! collecting duct of renal tubule relationship: part_of UBERON:0001225 ! cortex of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005268 name: renal cortex artery namespace: uberon def: "Artery that supplies renal cortex." [OBOL:automatic] synonym: "kidney cortex artery" EXACT [MP:0011314] synonym: "renal cortex arterial system" RELATED [MA:0002582] synonym: "renal cortex artery" EXACT [MA:0002582] xref: EMAPA:28035 xref: MA:0002582 is_a: UBERON:0001637 ! artery is_a: UBERON:0003644 ! kidney arterial blood vessel relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005269 name: renal cortex vein namespace: uberon def: "Artery that receives blood from the renal cortex[MP, modified]" [MGI:csmith] synonym: "kidney cortex vein" RELATED [MP:0011322] synonym: "renal cortex venous system" RELATED [MA:0002592] xref: EMAPA:28152 xref: MA:0002592 is_a: UBERON:0003517 ! kidney blood vessel is_a: UBERON:0013126 ! vein of abdomen relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005270 name: renal cortex interstitium namespace: uberon def: "A portion of interstitial tissue that is part of a cortex of kidney [Obol]." [OBOL:automatic] synonym: "cortical stroma" RELATED [EMAPA:28136] synonym: "kidney cortex interstitium" EXACT [MA:0002608] xref: EMAPA:28136 xref: MA:0002608 is_a: UBERON:0005215 ! kidney interstitium relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney relationship: part_of UBERON:0005215 {source="MA"} ! kidney interstitium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005271 name: juxtamedullary cortex namespace: uberon def: "the part of the renal cortex nearest to the medulla." [http://medical-dictionary.thefreedictionary.com/juxtamedullary+cortex] synonym: "inner cortex of kidney" EXACT [FMA:74288] synonym: "inner renal cortex" EXACT [KUPO:0001008] synonym: "juxtamedullary cortex of kidney" EXACT [FMA:74288] xref: FMA:74288 xref: KUPO:0001008 xref: MA:0001648 is_a: UBERON:0000064 ! organ part is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0001225 {source="FMA", source="KUPO"} ! cortex of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005272 name: peritubular capillary namespace: uberon def: "In the renal system, peritubular capillaries are tiny blood vessels that travel alongside nephrons allowing reabsorption and secretion between blood and the inner lumen of the nephron. Ions and minerals that need to be saved in the body are reabsorbed into the peritubular capillaries through active transport, secondary active transport, or transcytosis. The ions that need to be excreted as waste are secreted from the capillaries into the nephron to be sent towards the bladder and out of the body. The majority of exchange through the peritubular capillaries occurs because of chemical gradients, osmosis and Na+ pumps[WP]." [Wikipedia:Peritubular_capillaries] xref: MA:0002588 is_a: UBERON:0003527 ! kidney capillary property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005281 name: ventricular system of central nervous system namespace: uberon def: "a set of structures containing cerebrospinal fluid in the brain. It is continuous with the central canal of the spinal cord[WP]." [Wikipedia:Ventricular_system] comment: todo - resolve space vs structure conflation. We follow FMA in making this and the various ventricles a structure - it follows from this that strutures such as the tela choroidea and choroid plexuses can be part of the ventricles and ventricular system. Note: see also the class 'neuraxis cavity' subset: vertebrate_core synonym: "CNS ventricular system" EXACT [EHDAA2:0004362] synonym: "ventricle system" RELATED [Wikipedia:Ventricular_system] synonym: "ventricular system" EXACT [ZFA:0001261] synonym: "ventricular system of neuraxis" EXACT [FMA:242675] synonym: "ventriculi cerebri" RELATED LATIN [Wikipedia:Ventricular_system] xref: EFO:0003650 xref: EHDAA2:0004362 xref: EV:0100306 xref: FMA:242675 xref: http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/7/7d/Gray734.png/200px-Gray734.png xref: TAO:0001261 xref: ZFA:0001261 is_a: UBERON:0000467 {source="ZFA"} ! anatomical system is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001017 ! central nervous system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005282 name: ventricular system of brain namespace: uberon synonym: "brain ventricular system" EXACT [VHOG:0000005] xref: FMA:242787 xref: VHOG:0000005 is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0005281 ! ventricular system of central nervous system property_value: homology_notes "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000005", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005283 name: tela choroidea namespace: uberon def: "A structure found in the walls of the ventricles of the brain, consisting of part of the meninges (pia mater in mammals) plus ependyma[cjm]." [http://isc.temple.edu/neuroanatomy/lab/embryo_new/choroid/, ISBN10:0471888893, Wikipedia:Tela_chorioidea] comment: Vascularized tela choroidea is choroid plexus. AO notes: Note that the structure in ZFA may be different. subset: vertebrate_core synonym: "tela chorioidea" RELATED [FMA:242849] xref: FMA:242849 xref: TAO:0000447 xref: ZFA:0000447 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 ! organ component layer relationship: part_of UBERON:0005358 {source="FMA"} ! ventricle of nervous system property_value: external_definition "Portion of tissue that is part of the primitive meninx which forms a fold, roofing a ventricle of the brain and supporting the choroid plexus[ZFA:0000447]." xsd:string {source="ZFA:0000447"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005284 name: brain vasculature namespace: uberon def: "A vasculature that is part of a brain [Obol]." [OBOL:automatic] subset: vertebrate_core synonym: "vasculature of brain" EXACT [FMA:242007] xref: EFO:0003491 xref: FMA:242007 xref: TAO:0000099 xref: ZFA:0000099 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0006876 ! vasculature of organ relationship: part_of UBERON:0000955 ! brain property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005291 name: embryonic tissue namespace: uberon def: "A portion of tissue that is part of an embryo." [OBOL:automatic] subset: upper_level synonym: "developing tissue" RELATED [] synonym: "portion of embryonic tissue" EXACT [OBOL:automatic] is_a: UBERON:0000479 ! tissue is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0002050 ! embryonic structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005292 name: extraembryonic tissue namespace: uberon def: "Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo." [UBERON:cjm] synonym: "extra-embryonic tissue" EXACT [] xref: BTO:0003360 xref: EFO:0001406 xref: MAT:0000061 xref: MIAA:0000061 is_a: UBERON:0000478 ! extraembryonic structure is_a: UBERON:0000479 ! tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005294 name: genital ridge namespace: uberon def: "The precursor to the gonads." [Wikipedia:Gonadal_ridge] comment: TODO - check developmental relationships. merge with urogenital ridge? synonym: "crista gonadalis" RELATED LATIN [Wikipedia:Gonadal_ridge] synonym: "gonadal ridge" EXACT [Wikipedia:Gonadal_ridge] xref: AAO:0011047 xref: EFO:0001414 xref: EHDAA2:0004044 xref: http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1106.png xref: http://upload.wikimedia.org/wikipedia/commons/thumb/3/30/Gray1106.png/200px-Gray1106.png xref: ncithesaurus:Gonadal_Ridge xref: SCTID:361399001 xref: UMLS:C1512243 xref: XAO:0000018 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0004876 ! urogenital ridge relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0004122 ! genitourinary system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005295 name: sex cord namespace: uberon def: "Cordlike masses of epithelial tissue that invaginate from germinal epithelium of the gonad and give rise to seminiferous tubules and rete testes in the male, and primary ovarian follicles and rete ovarii in the female." [http://www.answers.com/topic/sex-cord, Wikipedia:Sex_cords] synonym: "gonad cord" RELATED [] synonym: "gonadal cord" RELATED [] synonym: "primitive sex cord" RELATED [] xref: EHDAA2:0004051 xref: ncithesaurus:Gonadal_Cord xref: RETIRED_EHDAA2:0001523 xref: SCTID:343823004 xref: UMLS:C1512242 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0005154 {source="EHDAA2"} ! epithelial cord is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0005294 ! genital ridge relationship: part_of UBERON:0000922 ! embryo property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005296 name: ovary sex cord namespace: uberon def: "structures that develop from sex cords in the female. After further development they become the ovarian follicles." [Wikipedia:Cortical_cords] comment: TODO check secondary vs cortical vs ovary synonym: "cortical cord" RELATED [] synonym: "cortical sex cord" RELATED [] synonym: "ovary primitive sex cord" RELATED [] synonym: "ovigerous cord" EXACT [] synonym: "ovigerous cords" EXACT PLURAL [VHOG:0001339] synonym: "secondary cord" RELATED [] xref: EHDAA2:0001363 xref: EHDAA:8130 xref: ncithesaurus:Cortical_Cord xref: UMLS:C1511527 xref: VHOG:0001339 is_a: UBERON:0004911 ! epithelium of female gonad is_a: UBERON:0005295 ! sex cord relationship: develops_from UBERON:0010141 ! primitive sex cord of indifferent gonad relationship: part_of UBERON:0000992 ! female gonad property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005297 name: testis sex cord namespace: uberon def: "The testis cords are precursors to the rete testis. They play several different roles in the development of the male genitals[WP]." [Wikipedia:Testis_cords] comment: check primary vs testis synonym: "primary sex cord" RELATED [] synonym: "testis cord" EXACT [MP:0006424] synonym: "testis primary sex cords" EXACT [EHDAA2:0002011] synonym: "testis primitive sex cord" RELATED [] xref: EHDAA2:0002011 xref: EHDAA:8152 xref: EMAPA:29098 xref: VHOG:0001321 is_a: UBERON:0004910 ! epithelium of male gonad is_a: UBERON:0005295 ! sex cord relationship: develops_from UBERON:0010141 ! primitive sex cord of indifferent gonad relationship: part_of UBERON:0000473 ! testis property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005311 name: mammary placode namespace: uberon def: "The mammary placode is a transient lens shaped structure that will give rise to the mammary bud proper[GO]." [GO:0060596] comment: TODO develops_from is_a: UBERON:0011814 {source="NBK53175"} ! non-neurogenic ectodermal placode relationship: develops_from UBERON:0008425 {source="Stedmans"} ! mammary ridge property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005317 name: pulmonary artery endothelium namespace: uberon def: "An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]." [GO:0061155] synonym: "pulmonary artery endothelial tube" EXACT [GO:0061155] xref: BTO:0000137 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0001917 ! endothelium of artery is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0002012 ! pulmonary artery property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005321 name: mesonephric smooth muscle tissue namespace: uberon def: "." [GO:0061214] is_a: UBERON:0001135 ! smooth muscle tissue is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0002113 ! kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005333 name: mammary bud namespace: uberon alt_id: UBERON:0004181 def: "Mammary gland buds form by an outpocketing of the mammary placodes and grow to invade the mammary fat, when they form the mammary cord[GO]. produced along the length of the embryonic mammary ridge these buds represent the future locations of the mammary glands. Invagination of ectoderm at each bud leads to the development of epithelial diverticula, later maturing as lactiferous ducts[TFD]." [GO:0060648, http://medical-dictionary.thefreedictionary.com/mammary+bud] synonym: "mammary gland bud" EXACT [GO:0060648] synonym: "milk bud" RELATED [] is_a: UBERON:0005153 ! epithelial bud is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium relationship: develops_from UBERON:0005311 ! mammary placode relationship: part_of UBERON:0000076 {source="PMID:20484386"} ! external ectoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005358 name: ventricle of nervous system namespace: uberon synonym: "region of wall of ventricular system of neuraxis" RELATED [FMA:242770] xref: FMA:242770 is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001016 ! nervous system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005366 name: olfactory lobe namespace: uberon def: "Olfactory apparatus on the lower surface of the frontal lobe of the brain. It consists of the olfactory bulb, tract, and trigone[BTO]." [BTO:0001362] xref: BTO:0001362 xref: EFO:0000108 xref: EHDAA2_RETIRED:0001294 xref: EHDAA:5480 xref: EMAPA:17778 xref: MA:0002413 xref: MIAA:0000116 xref: ncithesaurus:Olfactory_Lobe xref: UMLS:C0178780 xref: VHOG:0000833 is_a: UBERON:0002791 ! regional part of telencephalon relationship: part_of UBERON:0001893 ! telencephalon property_value: external_definition "Part of the telencephalon, comprised of paired anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits. In Xenopus,the olfactory bulbs begin to fuse at NF stage 50, fusion is complete around NF stage 58. The cerebral vein loops around the olfactory bulb by NF stage 43[XAO:0004180]." xsd:string {source="XAO:0004180"} property_value: homology_notes " (In mammals) Odorant detection is mediated by millions of olfactory sensory neurons located in the olfactory epithelium lining the nasal cavity. These neurons transmit sensory signals to the olfactory bulb of the brain, which in turn sends signals to the olfactory cortex.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000833", ontology="VHOG", source="DOI:10.1111/j.1753-4887.2004.tb00097.x Buck LB, Olfactory receptors and odor coding in mammals. Nutrition Reviews (2008)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005376 name: olfactory bulb external plexiform layer namespace: uberon def: "Cytoarchitectural part of the olfactory bulb, lying superior to the mitral cell layer and inferior to the glomerular layer. The EPL is mostly neuropil composed almost entirely of mitral and tulfted cell dendrites and granule cell dendrites and their synaptic inputs." [NIF_GrossAnatomy:nlx_anat_20090403] synonym: "external plexiform layer" BROAD [BTO:0001319] xref: BTO:0001319 xref: MA:0000969 xref: NIF_GrossAnatomy:nlx_anat_20090403 is_a: UBERON:0009950 ! olfactory bulb plexiform layer property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005377 name: olfactory bulb glomerular layer namespace: uberon def: "The glomerular layer is the most superficial layer, consisting of mitral cell dendritic arborizations (glomeruli), olfactory nerve fibers, and periglomerular cells. Periglomerular cells contact multiple mitral cell dendrites within the glomeruli and provide lateral inhibition of neighboring glomeruli while allowing excitation of a specific mitral cell dendritic tree. Each mitral cell is contacted by at least 1000 olfactory nerve fibers[BTO]. Portion of tissue which is located in between the primary olfactory fiber layer and the external cellular layer of the olfactory bulb[ZFA]." [BTO:0001317] subset: vertebrate_core synonym: "glomerular layer" BROAD [BTO:0001317, ZFA:0000357] synonym: "stratum glomerulosum bulbi olfactorii" EXACT [ZFA:0000357] xref: ABA:MOBgl xref: BTO:0001317 xref: MA:0000970 xref: TAO:0000357 xref: ZFA:0000357 is_a: UBERON:0004001 ! olfactory bulb layer property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005384 name: nasal cavity epithelium namespace: uberon def: "An epithelium that is part of a nasal cavity." [OBOL:automatic] synonym: "nasal epithelium" EXACT [FMA:63140] synonym: "nasal mucosa" RELATED [] xref: EHDAA2:0001227 xref: EHDAA:6803 xref: EMAPA:17605 xref: FMA:63140 xref: MA:0001324 xref: ncithesaurus:Nasal_Cavity_Epithelium xref: UMLS:C1709151 xref: VHOG:0000501 is_a: UBERON:0003350 ! epithelium of mucosa is_a: UBERON:0004807 ! respiratory system epithelium is_a: UBERON:0010371 ! ecto-epithelium relationship: part_of UBERON:0001826 {source="FMA"} ! nasal cavity mucosa property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005388 name: photoreceptor array namespace: uberon def: "An array of photoreceptors and any supporting cells found in an eye." [UBERON:cjm] synonym: "light-sensitive tissue" EXACT [] xref: FBbt:00004200 is_a: UBERON:0000479 ! tissue relationship: part_of UBERON:0000970 ! eye property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005389 name: transparent eye structure namespace: uberon comment: transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array synonym: "lens" NARROW [] is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000970 ! eye property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005396 name: carotid artery segment namespace: uberon def: "One of: the common carotid artery, or its branches, the external and internal carotid arteries." [https://sourceforge.net/tracker/?func=detail&aid=3486870&group_id=76834&atid=994764, Wikipedia:Carotid_artery] comment: Editor/usage notes: This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries subset: grouping_class subset: vertebrate_core synonym: "carotid artery" EXACT [MA:0001925] synonym: "common carotid arterial subdivision" RELATED [FMA:70504] synonym: "subdivision of common carotid artery" EXACT [FMA:70504] xref: BTO:0000168 xref: EFO:0000818 xref: EHDAA:6385 xref: EMAPA:18609 xref: EV:0100379 xref: FMA:70504 xref: GAID:478 xref: galen:CarotidArtery xref: MA:0001925 xref: MAT:0000501 xref: MESH:A07.231.114.186 xref: ncithesaurus:Carotid_Artery xref: OpenCyc:Mx4rvg7rcJwpEbGdrcN5Y29ycA xref: SCTID:362040006 xref: SCTID:69105007 xref: TAO:0000097 xref: UMLS:C0007272 xref: VHOG:0000266 xref: ZFA:0000097 is_a: UBERON:0004573 {source="FMA"} ! systemic artery property_value: external_definition "Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000097", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005398 name: female reproductive gland namespace: uberon def: "A sex gland that is part of a female reproductive system." [OBOL:automatic] subset: organ_slim xref: BTO:0000254 xref: MA:0000383 is_a: UBERON:0003937 ! sex gland relationship: part_of UBERON:0000474 ! female reproductive system relationship: part_of UBERON:0003134 ! female reproductive organ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005399 name: male reproductive gland namespace: uberon def: "A sex gland that is part of a male reproductive system." [OBOL:automatic] subset: organ_slim xref: BTO:0000080 xref: MA:0000399 is_a: UBERON:0003937 ! sex gland relationship: part_of UBERON:0000079 ! male reproductive system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005406 name: perirenal fat namespace: uberon def: "The adipose capsule of kidney (or perinephric fat or perirenal fat) is a structure between the renal fascia and renal capsule, and may be regarded as a part of the latter. A different structure, the pararenal fat, is the adipose tissue superficial to the renal fascia." [Wikipedia:Adipose_capsule_of_kidney] comment: TODO - split perinephric / perirenal synonym: "adipose capsule of kidney" RELATED [MA:0002975] synonym: "capsula adiposa renis" RELATED LATIN [Wikipedia:Adipose_capsule_of_kidney] synonym: "fatty capsule of kidney" RELATED [MA:0002975] synonym: "perinephric fat" RELATED [MA:0002975] synonym: "periphrenic fascia" RELATED [MA:0002975] synonym: "perirenal fascia" EXACT [FMA:20502] synonym: "perirenal fascia" RELATED [MA:0002975] synonym: "perirenal fat capsule" RELATED ATTRIBUTION_REQUIRED [MA:0002975] xref: FMA:15876 xref: FMA:20502 xref: http://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg xref: MA:0002975 xref: SCTID:246901006 is_a: UBERON:0001013 ! adipose tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005409 name: gastrointestinal system namespace: uberon comment: note that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla synonym: "alimentary system" RELATED [MA:0000323] synonym: "alimentary tract" RELATED [MA:0000323] synonym: "gastro-intestinal system" RELATED [FMA:71132] synonym: "gastrointestinal (GI) tract" RELATED [GAID:294] synonym: "gastrointestinal system" RELATED [FMA:71132] synonym: "gastrointestinal tract" RELATED INCONSISTENT [FMA:71132] synonym: "GI tract" RELATED [GAID:294] xref: BTO:0000058 xref: EHDAA2:0000110 xref: EHDAA:514 xref: EMAPA:16246 xref: EV:0100056 xref: FMA:71132 xref: GAID:294 xref: galen:GastrointestinalTract xref: MA:0000323 xref: MESH:A03.492 xref: ncithesaurus:Gastrointestinal_System xref: SCTID:373871007 xref: UMLS:C0012240 xref: VHOG:0000412 is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0001007 ! digestive system property_value: homology_notes "All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000412", ontology="VHOG", source="ISBN:978-0721676685 Sherwood Romer A and Parsons T, Vertebrate body (1977) p.3", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005423 name: developing anatomical structure namespace: uberon synonym: "developing structure" RELATED [] synonym: "developmental structure" RELATED [] synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 xref: FBbt:00007006 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005424 name: presumptive retinal pigmented epithelium namespace: uberon def: "Portion of tissue that is the outer layer of the optic cup and will become the retinal pigmented epithelium." [ZFIN:curator] subset: vertebrate_core synonym: "optic cup outer layer" EXACT [EHDAA2:0001306] synonym: "outer layer optic cup" EXACT [ZFA:0000064] synonym: "presumptive pigmented epithelia" EXACT PLURAL [ZFA:0000064] synonym: "presumptive pigmented epithelium" RELATED [TAO:0000064] xref: EHDAA2:0001306 xref: EMAPA:16677 xref: TAO:0000064 xref: VHOG:0000492 xref: ZFA:0000064 is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0010312 ! immature eye relationship: part_of UBERON:0003072 ! optic cup property_value: homology_notes " (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000492", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005426 name: lens vesicle namespace: uberon def: "Portion of tissue that gives rise to the lens." [https://sourceforge.net/tracker/?func=detail&atid=994726&aid=3514998&group_id=76834, ZFIN:curator] comment: Development notes: the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals[ZFA] subset: vertebrate_core synonym: "hollow lens vesicle" NARROW SENSU [] synonym: "solid lens vesicle" NARROW SENSU [ZFA:0001679] xref: EHDAA2:0000983 xref: EHDAA:4737 xref: EMAPA:17163 xref: SCTID:361510002 xref: TAO:0002205 xref: VHOG:0001163 xref: ZFA:0001679 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0003073 ! lens placode property_value: external_definition "A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001163", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/lens+vesicle"} property_value: homology_notes " (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001163", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005427 name: corneal primordium namespace: uberon def: "Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea." [ZFIN:ZDB-PUB-061010-3] xref: TAO:0002188 xref: ZFA:0001688 is_a: UBERON:0000479 {source="ZFA"} ! tissue is_a: UBERON:0001048 {source="Obol"} ! primordium is_a: UBERON:0010312 ! immature eye is_a: UBERON:0010313 ! neural crest-derived structure relationship: develops_from UBERON:0002342 ! neural crest relationship: part_of UBERON:0000019 {source="ZFA"} ! camera-type eye property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005428 name: vagal neural crest namespace: uberon def: "Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA]." [ZFIN:curator] subset: vertebrate_core synonym: "post-otic neural crest" EXACT [ZFA:0000818] xref: EHDAA2:0002156 xref: EHDAA:669 xref: TAO:0000818 xref: VHOG:0001208 xref: XAO:0004191 xref: ZFA:0000818 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0002342 ! neural crest property_value: external_definition "Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000818", ontology="TAO", source="ZFIN:curator"} property_value: homology_notes "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001208", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005432 name: aortic sac namespace: uberon def: "the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD]." [http://medical-dictionary.thefreedictionary.com/aortic+sac] xref: EHDAA2:0004145 xref: EHDAA:9826 xref: FMA:71008 xref: RETIRED_EHDAA2:0000133 xref: SCTID:361527005 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0001637 {source="EHDAA2"} ! artery is_a: UBERON:0003498 ! heart blood vessel is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0004363 {source="EHDAA2"} ! aortic arch relationship: part_of UBERON:0004145 ! outflow tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005497 name: non-neural ectoderm namespace: uberon comment: Development notes: After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm. Editor note: todo - epidermis? todo - track down EHDAA2 class in new release // Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998) subset: vertebrate_core synonym: "epidermal ectoderm" NARROW [UBERONREF:0000002] synonym: "epithelial ectoderm" NARROW [UBERONREF:0000002] synonym: "non neural ectoderm" EXACT [ZFA:0001178] synonym: "surface ectoderm" RELATED [UBERONREF:0000002] synonym: "ventral ectoderm" EXACT [ZFA:0001178] xref: EFO:0003643 xref: EHDAA:257 xref: EMAPA:16074 xref: RETIRED_EHDAA2:0001273 xref: TAO:0001178 xref: VHOG:0001372 xref: XAO:0004091 xref: ZFA:0001178 is_a: UBERON:0000479 {source="ZFA"} ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0000924 {source="UBERONREF:0000002"} ! ectoderm property_value: homology_notes "In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001372", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0002346 [Term] id: UBERON:0005498 name: primitive heart tube namespace: uberon def: "Multi-tissue structure that arises from the heart rudiment and will become the heart tube." [ZFA:0000149] subset: vertebrate_core xref: EHDAA2:0001512 xref: EHDAA:436 xref: EMAPA:16215 xref: SCTID:361522004 xref: TAO:0000149 xref: ZFA:0000149 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure relationship: develops_from UBERON:0004291 {source="ZFA"} ! heart rudiment property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005562 name: thymus primordium namespace: uberon def: "A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID]." [ZFA:0001077] comment: Editor notes: we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Development notes: Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution. Taxon notes: variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals[ISBN-10:0781714125] subset: vertebrate_core synonym: "thymic primordium" EXACT [Obol:automatic] synonym: "thymic rudiment" EXACT [ZFA:0001077] xref: EFO:0003622 xref: EHDAA2:0002023 xref: EHDAA:2969 xref: EMAPA:17523 xref: EMAPA:18536 xref: TAO:0001077 xref: ZFA:0001077 is_a: UBERON:0001048 ! primordium is_a: UBERON:0003351 ! pharyngeal epithelium relationship: develops_from UBERON:0007690 {source="ZFA"} ! early pharyngeal endoderm relationship: part_of UBERON:0000974 {source="EHDAA2"} ! neck relationship: part_of UBERON:0002405 {source="ZFA"} ! immune system relationship: part_of UBERON:0003295 {source="EHDAA2"} ! pharyngeal gland property_value: external_definition "A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001077", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005564 name: gonad primordium namespace: uberon def: "Portion of tissue that gives rise to the immature gonad." [ZFA:0001262] comment: Taxon notes: this is a very broad grouping class subset: grouping_class subset: vertebrate_core synonym: "gonadal primordium" EXACT [ZFA:0001262] synonym: "undifferentiated gonad" EXACT [ZFA:0001262] xref: EFO:0003651 xref: EHDAA:5927 xref: EMAPA:17204 xref: RETIRED_EHDAA2:0002148 xref: TAO:0001262 xref: WBbt:0008366 xref: ZFA:0001262 is_a: UBERON:0000479 {source="ZFA"} ! tissue is_a: UBERON:0001048 {source="Obol"} ! primordium is_a: UBERON:0005156 ! reproductive structure relationship: part_of UBERON:0000990 {source="ZFA"} ! reproductive system property_value: external_definition "Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001262", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005597 name: lung primordium namespace: uberon def: "A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum." [XAO:0001002] synonym: "lateral diverticula" RELATED [XAO:0001002] synonym: "lung endoderm" RELATED [EFO:0002578] xref: AAO:0011059 xref: EFO:0002578 xref: XAO:0001002 is_a: UBERON:0001048 {source="XAO"} ! primordium relationship: develops_from UBERON:0001041 {source="XAO"} ! foregut relationship: part_of UBERON:0008947 ! respiratory primordium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005602 name: dorsal mesogastrium namespace: uberon def: "The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum." [Wikipedia:Dorsal_mesentery] synonym: "dorsal mesentery" RELATED [Wikipedia:Dorsal_mesentery] xref: EHDAA2:0000416 xref: EHDAA:3001 xref: EMAPA:17025 xref: EMAPA:18903 xref: MA:0001618 xref: ncithesaurus:Dorsal_Mesogastrium xref: UMLS:C1512038 xref: VHOG:0000352 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0003281 {source="MA"} ! mesentery of stomach relationship: part_of UBERON:0002296 {source="EHDAA2"} ! dorsal mesentery relationship: part_of UBERON:0003281 {source="EHDAA2"} ! mesentery of stomach property_value: external_definition "The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000352", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/mesogastrium"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005629 name: vascular plexus namespace: uberon def: "a vascular network formed by frequent anastomoses between the blood vessels (arteries or veins) of a part." [http://www.medilexicon.com/medicaldictionary.php?t=70052] synonym: "plexus vasculosus" EXACT LATIN [] xref: AEO:0000219 xref: EHDAA2:0004112 xref: FMA:5900 xref: XAO:0004143 is_a: UBERON:0002049 ! vasculature relationship: part_of UBERON:0001009 ! circulatory system property_value: external_definition "In a vascular plexus, the contents of the vessels mix. A plexus allows blood to flow via multiple routes. If one branch of the plexus is obstructed, the blood may flow via the open branches[Wikipedia:Plexus#Circulatory_system]." xsd:string {source="Wikipedia:Plexus#Circulatory_system"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005631 name: extraembryonic membrane namespace: uberon def: "Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo." [ISBN10:0073040584] comment: AO notes: EHDAA2 is a mereological sum. Taxon notes: stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN10:0073040584 "Vertebrates, Kardong"] xref: EHDAA2:0004714 xref: SCTID:362840007 is_a: UBERON:0000158 ! membranous layer is_a: UBERON:0000478 ! extraembryonic structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: seeAlso http://purl.obolibrary.org/obo/uberon/references/reference_0000010 xsd:anyURI [Term] id: UBERON:0005721 name: pronephric mesoderm namespace: uberon def: "A mesoderm that develops_into a pronephros." [OBOL:automatic] comment: the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney synonym: "pronephric anlage" RELATED [XAO:0000264] synonym: "pronephric bulge" RELATED [XAO:0000264] synonym: "pronephric mesenchyme" RELATED [XAO:0000264] synonym: "pronephric primordium" RELATED [XAO:0000264] xref: AAO:0011090 xref: EFO:0003479 xref: TAO:0000067 xref: VHOG:0001239 xref: XAO:0000264 xref: ZFA:0000067 is_a: UBERON:0000926 ! mesoderm is_a: UBERON:0004120 ! mesoderm-derived structure relationship: develops_from UBERON:0007297 {evidence="definitional"} ! presumptive pronephric mesoderm relationship: part_of UBERON:0003064 {source="ZFA"} ! intermediate mesoderm property_value: external_definition "Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011090", ontology="AAO", source="XAO:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005725 name: olfactory system namespace: uberon def: "The olfactory system is the sensory system used for olfaction, or the sense of smell. Most mammals and reptiles have two distinct parts to their olfactory system: a main olfactory system and an accessory olfactory system. The main olfactory system detects volatile, airborne substances, while the accessory olfactory system senses fluid-phase stimuli. Behavioral evidence indicates that most often, the stimuli detected by the accessory olfactory system are pheromones. The olfactory system is often spoken of along with the gustatory system as the chemosensory senses because both transduce chemical signals into perception[WP]." [Wikipedia:Olfactory_system] comment: In mammals, the main olfactory system detects odorants that are inhaled through the nose, where they contact the main olfactory epithelium, which contains various olfactory receptors. These olfactory receptors are membrane proteins of bipolar olfactory receptor neurons in the olfactory epithelium. Rather than binding specific ligands like most receptors, olfactory receptors display affinity for a range of odor molecules. Olfactory neurons transduce receptor activation into electrical signals in neurons. The signals travel along the olfactory nerve, which belongs to the peripheral nervous system. This nerve terminates in the olfactory bulb, which belongs to the central nervous system. The complex set of olfactory receptors on different olfactory neurons can distinguish a new odor from the background environmental odors and determine the concentration of the odor // Editor note: consider splitting into main and accessory. See also: vomeronasal organ // note we make the relationship to nervous system 'overlaps', as the olfactory system includes e.g. apertures in the cranium that are not part of the nervous system subset: vertebrate_core xref: AAO:0000334 xref: AAO:0000978 xref: BILA:0000144 xref: EFO:0001973 xref: FMA:7190 xref: MA:0002445 xref: ncithesaurus:Olfactory_System xref: NIF_GrossAnatomy:nlx_anat_090806 xref: OpenCyc:Mx4rvViw75wpEbGdrcN5Y29ycA xref: SCTID:362290002 xref: TAO:0001149 xref: UMLS:C0228065 xref: XAO:0003196 xref: ZFA:0001149 is_a: UBERON:0001032 ! sensory system property_value: external_definition "The sensory system used for olfaction (the sense of smell).[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000978", ontology="AAO", source="AAO:EJS"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005728 name: extraembryonic mesoderm namespace: uberon def: "." [http://www.ana.ed.ac.uk/database/humat/notes/extraemb/mesoder.htm] synonym: "extra-embryonic mesoderm" EXACT [] synonym: "extraembryonic mesenchyme" EXACT [] xref: EHDAA2:0000474 xref: VHOG:0000616 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005292 ! extraembryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: develops_from UBERON:0003081 ! lateral plate mesoderm relationship: develops_from UBERON:0008780 {source="EHDAA2"} ! inner cell mass derived epiblast property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005734 name: tunica adventitia of blood vessel namespace: uberon def: "The outermost layer of a blood vessel, composed mainly of fibrous tissue." [ISBN10:0073040584, Wikipedia:Tunica_externa_%28vessels%29] comment: TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings synonym: "adventitia externa" EXACT [Wikipedia:Tunica_externa_%28vessels%29] synonym: "external coat" RELATED [Wikipedia:Tunica_externa_%28vessels%29] synonym: "tunica adventitia" EXACT [Wikipedia:Tunica_externa_%28vessels%29] synonym: "tunica adventitia of vessel" EXACT [Wikipedia:Tunica_externa_%28vessels%29] synonym: "tunica adventitia vasorum" RELATED LATIN [Wikipedia:Tunica_externa_%28vessels%29] synonym: "tunica externa vasorum" RELATED LATIN [Wikipedia:Tunica_externa_%28vessels%29] xref: http://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg xref: ncithesaurus:Tunica_Adventitia xref: SCTID:61066005 xref: UMLS:C0225342 is_a: UBERON:0004797 {source="cjm"} ! blood vessel layer is_a: UBERON:0005742 ! adventitia property_value: external_definition "The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_%28vessels%29]." xsd:string {source="Wikipedia:Tunica_externa_%28vessels%29"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005742 name: adventitia namespace: uberon def: "An outermost connective tissue covering of an organ, vessel, or other structure[WP]." [Wikipedia:Adventitia] subset: grouping_class synonym: "tunica advetitia" NARROW [Wikipedia:Adventitia] synonym: "tunica externa" NARROW [FMA:45635] xref: FMA:45635 xref: http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg xref: SCTID:30180000 is_a: UBERON:0004923 ! organ component layer property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005744 name: cranial conduit namespace: uberon def: "Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves." [TAO:curator, Wikipedia:Foramina_of_the_skull] comment: AO notes: in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper). subset: vertebrate_core synonym: "foramen" BROAD [ZFA:0005386] synonym: "foramen of skull" RELATED [Wikipedia:Foramina_of_the_skull] synonym: "foramens@fr" RELATED [TAO:0001736] synonym: "foramina@fr" RELATED [TAO:0001736] xref: AAO:0010438 xref: FMA:53165 xref: http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png xref: SCTID:276742007 xref: TAO:0001736 xref: VHOG:0001760 xref: ZFA:0005386 is_a: UBERON:0004111 ! anatomical conduit relationship: part_of UBERON:0003129 ! skull property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005749 name: glomerular tuft namespace: uberon def: "the capillary loops of the kidney that normally function as a filtration unit[MP]. ...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus[GudMap]." [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron, MP:0005325, Wikipedia:Glomerulus] synonym: "glomerular capillary tuft" RELATED [] synonym: "glomerulus" RELATED INCONSISTENT [EMAPA:28239] xref: EMAPA:28239 xref: SCTID:362217000 is_a: UBERON:0000064 ! organ part is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0006554 ! urinary system structure relationship: develops_from UBERON:0003220 {source="Wikipedia"} ! metanephric mesenchyme relationship: part_of UBERON:0001230 ! glomerular capsule property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005750 name: glomerular parietal epithelium namespace: uberon def: "A single layer of simple squamous epithelium in the glomerular capsule. Does not function in filtration[UBERON]. outer layer of the glomerular capsule composed of a single layer of simple squamous epithelium[MP]" [MP:0011498, UBERON:cjm] comment: TODO - check this. BTO has podocytes under here subset: vertebrate_core synonym: "Bowman's parietal epithelium" EXACT [MP:0011498] synonym: "capsular epithelium" EXACT [BTO:0002296] synonym: "glomerular capsule parietal layer" EXACT [FMA:74272] synonym: "outer layer of glomerular capsule" EXACT [FMA:74272] synonym: "parietal capsular epithelium" EXACT [MP:0011498] synonym: "parietal epithelial layer" EXACT [ZFA:0005253] synonym: "parietal epithelium of Bowman's capsule" EXACT [MP:0011498] synonym: "parietal layer of Bowman capsule" EXACT [] synonym: "parietal layer of Bowman's capsule" EXACT [MP:0011498] synonym: "parietal layer of glomerular capsule" EXACT [MP:0011498] synonym: "parietal layer of glomerular capsule" EXACT [FMA:74272] synonym: "renal glomerular capsule epithelium" EXACT [ZFA:0005253] xref: BTO:0002296 xref: EMAPA:27979 xref: EMAPA:28260 xref: FMA:74272 xref: MA:0002605 xref: ncithesaurus:Parietal_Layer_of_Bowman_s_Capsule xref: SCTID:362218005 xref: TAO:0005253 xref: UMLS:C0227645 xref: ZFA:0005253 is_a: UBERON:0000487 ! simple squamous epithelium is_a: UBERON:0004188 ! glomerular epithelium relationship: part_of UBERON:0001230 ! glomerular capsule property_value: external_definition "Simple squamous epithelium that lines the capsule of the renal glomerulus.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005253", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005751 name: visceral layer of glomerular capsule namespace: uberon def: "The inner, or visceral, layer of the renal glomerular capsule, overlying the capillaries, composed of podocytes, and separated from the outer, or parietal, layer by the capsular (Bowman's) space[BTO]. Lies just above the thickened glomerular basement membrane and is made of podocytes. Beneath the visceral layer lie the glomerular capillaries[WP]. inner layer of the glomerular capsule surrounding the capillary endothelial cells and composed of highly specialized epithelial cells (podocytes) that are separated by filtration slits; the visceral layer is separated from the outer parietal layer by the urinary space (also known as the Bowman's or capsular space)[MP]" [BTO:0001515, MP:0011497] comment: TODO - check - the BTO class 'glomerular epithelium' is the visceral layer. But GO uses 'glomerular epithelium' as the mereological sum of P+V layers subset: inconsistent_with_fma synonym: "Bowman's visceral epithelium" EXACT [MP:0011497] synonym: "glomerular capsule visceral layer" EXACT [MP:0011497] synonym: "inner epithelial layer of Bowman's capsule" EXACT [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] synonym: "podocyte layer of Bowman's capsule" EXACT [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] synonym: "visceral epithelium of Bowman's capsule" EXACT [MP:0011497] synonym: "visceral epithelium of Bowman's capsule" EXACT [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] synonym: "visceral layer of Bowman's capsule" EXACT [MP:0011497] synonym: "visceral layer of glomerular capsule" EXACT [MP:0011497] xref: FMA:74273 xref: ncithesaurus:Visceral_Layer_of_Bowman_s_Capsule xref: SCTID:244093000 xref: UMLS:C0227644 is_a: UBERON:0004211 ! nephron epithelium relationship: part_of UBERON:0001230 ! glomerular capsule property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005754 name: rostral part of nephrogenic cord namespace: uberon def: "The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros." [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0004875 ! nephrogenic cord property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005760 name: urorectal septum namespace: uberon def: "The ridge of mesoderm covered with endoderm that in the early developing embryo partitions the endodermal cloaca into the primary urogenital sinus (ventrally) and the anorectal canal of the hindgut (dorsally); the urorectal septum eventually fuses with the cloacal membrane, dividing it into a dorsal anal membrane and a larger ventral urogenital membrane - this area of fusion is represented in the adult by the perineal body[MP]." [MP:anna, Wikipedia:Urorectal_septum] comment: Editor notes: todo - use to define cloacal septation in GO synonym: "cloacal septum" RELATED [VHOG:0000018] synonym: "septum urorectale" EXACT LATIN [Wikipedia:Urorectal_septum] synonym: "urorectal fold" EXACT [MP:anna] synonym: "urorectal membrane" EXACT [MP:anna] xref: EHDAA2:0002152 xref: EHDAA:5921 xref: EMAPA:17212 xref: EMAPA:17380 xref: http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray992.png xref: ncithesaurus:Urorectal_Septum xref: UMLS:C1519838 xref: VHOG:0000018 xref: Wikipedia:Urorectal_septum is_a: UBERON:0003037 ! septum is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0001008 ! excretory system relationship: part_of UBERON:0012361 {source="EHDAA2"} ! internal anal region property_value: external_definition "A ridge of mesoderm covered with endoderm that in the early developing embryo divides the endodermal cloaca into the urogenital sinus and the rectum. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000018", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/urorectal+septum"} property_value: homology_notes "In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000018", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.388-89 and Figure 300", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005795 name: embryonic uterus namespace: uberon synonym: "fetal uterus" EXACT [FMA:72173] xref: FMA:72173 xref: SCTID:255782009 is_a: UBERON:0002050 ! embryonic structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005800 name: segment of aorta namespace: uberon synonym: "aortic segment" EXACT [FMA:13087] xref: FMA:13087 xref: ncithesaurus:Aortic_Segment xref: SCTID:119203005 xref: UMLS:C0506947 is_a: UBERON:0000063 ! organ segment is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0000947 ! aorta property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005856 name: developing mesenchymal condensation namespace: uberon def: "A delimited region of dense mesenchyme within looser mesenchyme." [AEO:0000148] synonym: "mesenchyme condensation" EXACT [EMAPA:25351] xref: AEO:0000148 xref: EHDAA2_RETIRED:0003148 xref: EHDAA:8979 xref: EMAPA:25351 is_a: UBERON:0007524 {source="AEO"} ! dense mesenchyme tissue is_a: UBERON:0011585 {source="cjm"} ! cell condensation property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005863 name: cartilaginous condensation namespace: uberon def: "Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes." [GO:curator] comment: AO notes: isa cell condensation in VSAO synonym: "cartilage condensation" EXACT [EMAPA:25353] synonym: "cartilagenous condensation" EXACT [EHDAA2:0003147] synonym: "chondrogenic condensation" EXACT [VSAO:0000092] xref: AEO:0000147 xref: EHDAA2:0003147 xref: EMAPA:25353 xref: VSAO:0000092 xref: XAO:0004022 is_a: UBERON:0005856 {source="AEO"} ! developing mesenchymal condensation relationship: develops_from UBERON:0005866 ! pre-cartilage condensation relationship: part_of UBERON:0004288 {source="AEO"} ! skeleton property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005866 name: pre-cartilage condensation namespace: uberon def: "A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage." [http://dictionary.reference.com/browse/precartilage] synonym: "pre-chondrogenic condensation" EXACT [] synonym: "precartilage condensation" EXACT [] synonym: "precartilagenous condensation" EXACT [] synonym: "prechondrogenic condensation" EXACT [] xref: AEO:0000150 xref: EHDAA2:0003150 is_a: UBERON:0005856 {source="AEO"} ! developing mesenchymal condensation relationship: part_of UBERON:0004288 {source="AEO"} ! skeleton property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005872 name: 1st arch pharyngeal cleft namespace: uberon def: "A groove that is situated between the 1st and 2nd pharyngeal arch." [VHOG:OG] subset: vertebrate_core synonym: "1st arch branchial groove" EXACT [EHDAA2:0000008] synonym: "1st arch groove ectoderm" EXACT [EHDAA2:0000009] synonym: "1st pharyngeal cleft" RELATED [VHOG:0000969] synonym: "1st pharyngeal groove" EXACT [VHOG:0000969] synonym: "1st pharyngeal groove ectoderm" EXACT [VHOG:0000554] synonym: "branchial groove of 1st arch" EXACT [EMAPA:16119] xref: EHDAA2:0000009 xref: EHDAA:575 xref: EMAPA:16119 xref: VHOG:0000554 xref: VHOG:0000969 is_a: UBERON:0005879 ! pharyngeal cleft property_value: external_definition "A groove that is situated between the 1st and 2nd pharyngeal arch. [The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.70, see_Kaufman_MH_and_Bard_JBL][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000969", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000969", ontology="VHOG", source="DOI:10.1016/j.semcdb.2010.01.022 Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005879 name: pharyngeal cleft namespace: uberon def: "the counterpart of a branchial pouch on the ectodermal side. The first pharyngeal groove produces the external auditory meatus.[2] The rest (2, 3, and 4) are overlapped by the growing 2nd pharyngeal arch, and form the floor of the depression termed the cervical sinus, which opens ventrally, and finally obliterated[WP]." [Wikipedia:Pharyngeal_groove] comment: AO notes: some ontologies distringuish between cleft and cleft ectoderm, we merge these here. Editor notes: consider adding location (precursor) - i.e. external (ectodermal). Note we use overlaps as the relationship to the arches synonym: "branchial cleft" RELATED [Wikipedia:Pharyngeal_groove] synonym: "branchial groove" RELATED [AAO:0010623, Wikipedia:Pharyngeal_groove] synonym: "gill cleft" NARROW [] synonym: "Kiemenspalten" RELATED [] synonym: "pharyngeal groove" EXACT [Wikipedia:Pharyngeal_groove] synonym: "pharyngeal groove ectoderm" EXACT [UBERON:cjm] synonym: "sulcus pharyngei" RELATED LATIN [Wikipedia:Pharyngeal_groove] xref: AAO:0010623 xref: http://upload.wikimedia.org/wikipedia/commons/2/20/Kiemenbogen.jpg xref: ncithesaurus:Pharyngeal_Groove xref: UMLS:C1280559 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006846 {source="EHDAA2"} ! groove is_a: UBERON:0010371 ! ecto-epithelium relationship: develops_from UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0000922 ! embryo property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005891 name: coelomic epithelium namespace: uberon def: "The epithelial lining of the surface of the coelom." [Wikipedia:Coelomic_epithelium, XAO:0000329] comment: AO notes: EHDAA2:0004049 used to be called "coelomic epithelium" but is now "gonadal ridge mesothelium" synonym: "celomic epithelium" EXACT [] synonym: "germinal epithelium of Waldeyer" EXACT [Wikipedia:Coelomic_epithelium] xref: XAO:0000329 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0011997 ! coelom property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005904 name: duct of male reproductive system namespace: uberon def: "A duct that is part of a male reproductive system." [OBOL:automatic] comment: groups the individual ducts in a variety of species subset: grouping_class is_a: UBERON:0000058 ! duct is_a: UBERON:0005156 ! reproductive structure relationship: part_of UBERON:0000079 ! male reproductive system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005906 name: serous sac namespace: uberon def: "Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]" [FMA:9689] comment: See notes for serous membrane xref: FMA:9689 xref: SCTID:362890006 is_a: UBERON:0000062 ! organ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005908 name: conjunctival sac namespace: uberon def: "Serous sac, which has as parts the conjunctiva and the cavity of conjunctiva. Examples: There are only two conjunctival sacs, the right and the left.[FMA]" [FMA:20291] xref: EMAPA:18233 xref: FMA:20291 xref: SCTID:362531001 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005906 {source="FMA"} ! serous sac relationship: part_of UBERON:0000019 {source="FMA"} ! camera-type eye relationship: part_of UBERON:0001801 {source="MA"} ! anterior segment of eyeball property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005910 name: transitional epithelium namespace: uberon def: "Multilaminar epithelium, which of consists of more than one layer of epithelial cells, in contact with a basement membrane, that can undergo distention and contraction without losing its integrity and consistency. Examples: urothelium.[FMA]" [FMA:63914, FMA:FMA, Wikipedia:Transitional_epithelium] comment: see comments for urothelium synonym: "epithelium transitionale" EXACT [FMA:63914] synonym: "urothelium" NARROW [EMAPA:28089, Wikipedia:Transitional_epithelium] xref: BTO:0003906 xref: FMA:63914 xref: http://upload.wikimedia.org/wikipedia/commons/9/91/Harnblase_Urothel.png xref: MESH:A10.272.850 xref: ncithesaurus:Transitional_Epithelium xref: SCTID:30117005 xref: UMLS:C0225339 is_a: UBERON:0000486 ! multilaminar epithelium is_a: UBERON:0005911 ! endo-epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005911 name: endo-epithelium namespace: uberon def: "Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]" [FMA:69065] xref: FMA:69065 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0000925 ! endoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005913 name: zone of bone organ namespace: uberon synonym: "bone organ zone" EXACT [FMA:10483] xref: FMA:10483 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004765 ! skeletal element relationship: part_of UBERON:0001474 ! bone property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005932 name: bulb of hair follicle namespace: uberon comment: see https://sourceforge.net/tracker/?func=detail&aid=3213510&group_id=76834&atid=1205376 synonym: "coat hair bulb" NARROW SENSU [MA:0000161] synonym: "hair bulb" EXACT [FMA:70666] synonym: "hair follicle bulb" EXACT [FMA:70666] xref: EMAPA:18770 xref: FMA:70666 xref: MA:0000161 xref: ncithesaurus:Hair_Bulb xref: SCTID:361360009 xref: UMLS:C0221962 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0002073 ! hair follicle property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005933 name: hair root sheath namespace: uberon comment: AO notes: see https://sourceforge.net/tracker/?func=detail&aid=3213510&group_id=76834&atid=1205376 xref: EMAPA:18772 xref: MA:0000162 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0005932 ! bulb of hair follicle property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005941 name: hair inner root sheath namespace: uberon def: "A multilayered tube composed of terminally differentiated hair follicle keratinocytes that is surrounded by the outer root sheath; the layers of the inner root sheath include the companion layer, Henle's layer, Huxley's layer and the inner root sheath cuticle[MP]." [https://sourceforge.net/tracker/?func=detail&aid=3213510&group_id=76834&atid=1205376, MP:0010685] synonym: "hair follicle inner root sheath" EXACT [MP:0010685] synonym: "inner root sheath" RELATED [BTO:0003971] synonym: "inner root sheath of hair follicle" EXACT [FMA:70935] synonym: "inner sheath of hair follicle" EXACT [FMA:70935] synonym: "internal root sheath of hair follicle" EXACT [FMA:70935] xref: BTO:0003971 xref: FMA:70935 xref: MA:0000779 is_a: UBERON:0005933 ! hair root sheath property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005942 name: hair outer root sheath namespace: uberon def: "It surrounds the hair follicle like a sleeve all the way to the bulb. The outer root sheath is essentially a stratified epithelium that is contiguous with the epidermis." [https://sourceforge.net/tracker/?func=detail&aid=3213510&group_id=76834&atid=1205376, Keratin.com:http\://www.keratin.com/] synonym: "external root sheath of hair follicle" EXACT [FMA:70943] synonym: "hair follicle outer root sheath" EXACT [BTO:0003969] synonym: "ORS" RELATED [BTO:0003969] synonym: "outer root sheath" RELATED [BTO:0003969] synonym: "outer root sheath of hair follicle" EXACT [FMA:70943] xref: BTO:0003969 xref: FMA:70943 xref: MA:0000780 xref: SCTID:319224003 is_a: UBERON:0005933 ! hair root sheath property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005969 name: reticulum trabeculare namespace: uberon alt_id: UBERON:0004028 def: "a fenestrated endothelial-like tissue situated at the intersection of the cornea and the iris[GO]. The trabecular meshwork is an area of tissue in the eye located around the base of the cornea, near the ciliary body, and is responsible for draining the aqueous humor from the eye via the anterior chamber (the chamber on the front of the eye covered by the cornea). The tissue is spongy and lined by trabeculocytes; it allows fluid to drain into a set of tubes called Schlemm's canal flowing into the blood system[WP]. A porelike structure surrounding the entire circumference of the anterior chamber through which aqueous humor circulates to the canal of Schlemm.[GAID] the pore-like structure surrounding the entire circumference of the anterior chamber through which aqueous humor circulates[MP]." [GO:0002930, MP:0005203, Wikipedia:Trabecular_meshwork] comment: TODO check syns - ligaments synonym: "cribiform ligament" RELATED [Wikipedia:Trabecular_meshwork] synonym: "Hueck's ligament" RELATED [BTO:0001605] synonym: "iridis" RELATED [Wikipedia:Trabecular_meshwork] synonym: "ligamentum peactin-tum iridis" RELATED [Wikipedia:Trabecular_meshwork] synonym: "ligamentum pectinatum" RELATED [Wikipedia:Trabecular_meshwork] synonym: "ligamentum pectinatum anguli iridocornealis" RELATED [BTO:0001605] synonym: "ligamentum pectinatum iridis" RELATED [Wikipedia:Trabecular_meshwork] synonym: "pectinate ligament" RELATED [BTO:0001605] synonym: "pectinate ligament of iris" RELATED [BTO:0001605] synonym: "reticulum trabeculare sclerae" RELATED LATIN [Wikipedia:Trabecular_meshwork] synonym: "scleral trabeculae" RELATED [Wikipedia:Trabecular_meshwork] synonym: "scleral trabecular" RELATED [Wikipedia:Trabecular_meshwork] synonym: "scleral trabecule" RELATED [Wikipedia:Trabecular_meshwork] synonym: "scribiform ligament" RELATED [Wikipedia:Trabecular_meshwork] synonym: "trabecular mesh" RELATED [Wikipedia:Trabecular_meshwork] synonym: "trabecular meshwork" RELATED [BTO:0001605, GO:0002930] synonym: "trabecular meshwork of the eye" EXACT [Wikipedia:Trabecular_meshwork] xref: BTO:0001605 xref: EFO:0003077 xref: EV:0100352 xref: GAID:897 xref: http://upload.wikimedia.org/wikipedia/commons/2/22/Gray870.png xref: MESH:A09.371.060.932 xref: ncithesaurus:Trabecular_Meshwork xref: SCTID:280694002 xref: UMLS:C0040573 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0003956 ! aqueous drainage system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005971 name: amniotic fold namespace: uberon def: "A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong]." [ISBN10:0073040584] xref: EMAPA:16076 is_a: UBERON:0000478 ! extraembryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure relationship: develops_from UBERON:0004874 {source="Kardong"} ! somatopleure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005983 name: heart layer namespace: uberon def: "the laminar structure of the heart" [MP:0010545] is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004923 ! organ component layer relationship: part_of UBERON:0000948 ! heart property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005985 name: coronary vessel namespace: uberon def: "any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation" [MP:0010551] comment: TODO - change relation from part_of xref: MESH:A07.231.114.269 is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0000948 ! heart property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005986 name: left branch of atrioventricular bundle namespace: uberon def: "Subdivision of conducting system of heart which enters the septal myocardium of left ventricle and is continuous with the anterior, septal and posterior divisions of the left branch of the atrioventricular bundle[FMA]. the left branch of the atrioventricular bundle that separates at the bundle of His, descends the septal wall of the left ventricle and connects to the terminal Purkinje fiber[MP]." [FMA:9487, MP:0010566] synonym: "crus sinistrum (fasciculi atrioventricularis)" EXACT [FMA:9487] synonym: "left bundle branch" EXACT [MP:0010566] synonym: "left bundle branch of bundle of His" EXACT [HP:0005172] synonym: "left bundle of atrioventricular bundle" EXACT [MP:0010566] synonym: "left crus of atrioventricular bundle" EXACT [MP:0010566] synonym: "left posterior branch" EXACT [MP:0010566] synonym: "left posterior bundle" EXACT [MP:0010566] xref: FMA:9487 xref: galen:LeftBundleBranch xref: SCTID:277690001 is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0002350 {source="FMA"} ! conducting system of heart property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0005987 name: right branch of atrioventricular bundle namespace: uberon def: "Subdivision of conducting system of heart which enters the septal myocardium of right ventricle to reach the anterior papillary muscle and then subendocardially to the apex of the heart[FMA]. the right branch of the atrioventricular bundle that separates just below the bundle of His, descends the septal wall of the right ventricle and connects to the terminal Purkinje fibers[MP]." [FMA:9486, MP:0010567] synonym: "crus dextrum (fasciculi atrioventricularis)" EXACT [FMA:9486] synonym: "right bundle" EXACT [FMA:9486, MP:0010567] synonym: "right bundle branch" EXACT [FMA:9486] synonym: "right bundle branch of bundle of His" EXACT [] synonym: "right right crus of atrioventricular bundle" EXACT [MP:0010567] synonym: "right ventricular bundle" EXACT [MP:0010567] xref: FMA:9486 xref: galen:RightBundleBranch xref: SCTID:277689005 is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0002350 {source="FMA"} ! conducting system of heart property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006003 name: skin adnexa namespace: uberon def: "the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails" [http://code.google.com/p/caro2/issues/detail?id=5, MP:0010678, Wikipedia:Skin_appendage] comment: editor note - add subclasses based on resolution of CARO tracker item. Also check: adnexal gland synonym: "adnexae cutis" RELATED LATIN [Wikipedia:Skin_appendage] is_a: UBERON:0000061 ! anatomical structure relationship: part_of UBERON:0002416 ! integumental system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006004 name: hair follicle matrix region namespace: uberon def: "the bulb region adjacent to the dermal papilla that contains rapidly proliferating matrix cells that give rise to the various cell lineages of the hair shaft and inner root sheath" [MP:0010686] synonym: "germinal matrix of hair bulb" EXACT [FMA:70772] synonym: "lower part of bulb of hair follicle" EXACT [FMA:70772] synonym: "lower zone of bulb of hair follicle" EXACT [FMA:70772] xref: FMA:70772 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0005932 ! bulb of hair follicle property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006082 name: fundus of urinary bladder namespace: uberon def: "The base or posterior surface of the urinary bladder contains the trigone of the bladder and the outlet where urine empties through the internal urethral orifice." [MP:0011785, Wikipedia:Fundus_of_the_urinary_bladder#Fundus] synonym: "base of urinary bladder" EXACT [FMA:15908] synonym: "fundus of bladder" BROAD [FMA:15908] synonym: "fundus vesicae" EXACT LATIN [FMA:15908, FMA:TA] synonym: "urinary bladder base" EXACT [MP:0011785] synonym: "urinary bladder fundus" EXACT [FMA:15908] synonym: "urinary bladder fundus region" EXACT [MA:0001694] xref: EHDAA2:0000582 xref: EHDAA:9330 xref: EMAPA:18322 xref: FMA:15908 xref: MA:0001694 xref: ncithesaurus:Bladder_Fundus xref: SCTID:362226002 xref: UMLS:C0447584 xref: VHOG:0001184 is_a: UBERON:0000064 ! organ part is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0006554 ! urinary system structure relationship: develops_from UBERON:0005760 {source="EHDAA2-modified"} ! urorectal septum relationship: develops_from UBERON:0009845 {source="EHDAA2"} ! urogenital sinus mesenchyme relationship: part_of UBERON:0001255 ! urinary bladder property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006215 name: rhombic lip namespace: uberon def: "Rhombic lips are a posterior section of the developing metencephalon within an embryo. They extend posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cells and contain cerebellar precursor cells, among others" [Wikipedia:Rhombic_lips] subset: vertebrate_core synonym: "cerebellum primordium" RELATED [EMAPA:17074] synonym: "dorsal part of alar plate of metencephalon" RELATED [EMAPA:17074] xref: TAO:0001440 xref: XAO:0004135 xref: ZFA:0001440 is_a: UBERON:0001048 ! primordium relationship: part_of UBERON:0002028 {source="ZFA"} ! hindbrain relationship: part_of UBERON:0010092 {source="Wikipedia"} ! future metencephalon property_value: external_definition "The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001440", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006235 name: foregut-midgut junction namespace: uberon def: "An anatomical boundary that adjacent_to a foregut and adjacent_to a midgut." [OBOL:automatic] subset: emapa_ehdaa2 xref: EHDAA2:0000569 xref: EHDAA:526 xref: EMAPA:16363 xref: VHOG:0000291 is_a: UBERON:0000015 ! anatomical boundary relationship: part_of UBERON:0001555 ! digestive tract property_value: homology_notes "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000291", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006238 name: future brain namespace: uberon comment: Usage notes: this class is restricted to neural-tube derived brains subset: emapa_ehdaa2 subset: vertebrate_core synonym: "brain rudiment" EXACT [TAO:0000146] synonym: "presumptive brain" EXACT [ZFA:0000146] xref: EFO:0003431 xref: EHDAA:300 xref: EHDAA:830 xref: EMAPA:16089 xref: EMAPA:16471 xref: RETIRED_EHDAA2:0000591 xref: TAO:0000146 xref: ZFA:0000146 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0001049 ! neural tube relationship: part_of UBERON:0000922 ! embryo property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006242 name: gall bladder primordium namespace: uberon subset: emapa_ehdaa2 xref: EHDAA2:0000700 xref: EHDAA:3047 xref: EMAPA:16713 xref: EMAPA:16842 xref: XAO:0004205 is_a: UBERON:0001048 ! primordium relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0002423 ! hepatobiliary system relationship: part_of UBERON:0004912 ! biliary bud property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006266 name: nasolacrimal groove namespace: uberon def: "Groove between maxillary prominence and lateral nasal process." [http://www.indiana.edu/~anat550/hnanim/face/face.html, Wikipedia:Lacrimal_groove] comment: On the nasal surface of the body of the maxilla, in front of the opening of the sinus is a deep groove, the lacrimal groove (or lacrimal sulcus), which is converted into the nasolacrimal canal, by the lacrimal bone and inferior nasal concha; this canal opens into the inferior meatus of the nose and transmits the nasolacrimal duct[WP] See also: oblique facial cleft subset: emapa_ehdaa2 synonym: "naso-lacrimal groove" EXACT [EMAPA:16679] synonym: "s. lacrimalis maxillae" RELATED LATIN [Wikipedia:Lacrimal_groove] xref: EHDAA2:0001238 xref: EHDAA:4770 xref: EMAPA:16679 xref: http://upload.wikimedia.org/wikipedia/commons/3/3f/Gray163.png xref: ncithesaurus:Nasolacrimal_Groove xref: UMLS:C1513875 xref: VHOG:0001307 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0004807 ! respiratory system epithelium is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010371 ! ecto-epithelium relationship: develops_from UBERON:0012313 {source="EHDAA2"} ! 1st arch maxillary ectoderm relationship: part_of UBERON:0000004 {source="EHDAA2"} ! olfactory apparatus relationship: part_of UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0000922 ! embryo property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006267 name: notochordal plate namespace: uberon def: "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord." [VHOG:0001212] comment: TODO - check ordering; awaiting confirmation from JB subset: emapa_ehdaa2 xref: EHDAA2:0001278 xref: EHDAA:264 xref: EMAPA:16101 xref: ncithesaurus:Notochordal_Plate xref: UMLS:C1518429 xref: VHOG:0001212 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium relationship: develops_from UBERON:0006268 {source="EHDAA2"} ! notochordal process relationship: part_of UBERON:0000922 ! embryo property_value: external_definition "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001212", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006268 name: notochordal process namespace: uberon def: "a midline cellular cord formed from the migration of mesenchymal cells from the primitive knot" [http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/05embryonicperiod.htm] comment: The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. subset: emapa_ehdaa2 synonym: "chordamesoderm" RELATED [] synonym: "presumptive notochord" RELATED [] xref: EHDAA2:0001279 xref: EHDAA:224 xref: EMAPA:16102 xref: ncithesaurus:Notochordal_Process xref: UMLS:C1518430 xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0000924 {source="EHDAA2"} ! ectoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006293 name: spleen primordium namespace: uberon alt_id: UBERON:0009750 def: "A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP]." [ISBN:0123747295, MP:0011263] comment: AO notes: check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme synonym: "left spleen primordium" NARROW [XAO:0000326] synonym: "spleen mesenchyme" EXACT [MP:0011263] synonym: "splenic mesenchyme" EXACT [UBERON:cjm] synonym: "splenic primordium" EXACT [EHDAA2:0001904] xref: EHDAA2:0001904 xref: EHDAA:3003 xref: EMAPA:18535 xref: EMAPA:18659 xref: XAO:0000326 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0001048 {source="XAO"} ! primordium is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0005291 ! embryonic tissue relationship: develops_from UBERON:0004872 {source="XAO"} ! splanchnic layer of lateral plate mesoderm relationship: part_of UBERON:0005602 {source="EHDAA2-modified"} ! dorsal mesogastrium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006311 name: chamber of eyeball namespace: uberon def: "Chamber of eyeball[FMA]" [FMA:58071] synonym: "eye chamber" EXACT [MA:0002459] synonym: "eyeball chamber" EXACT [FMA:58071] xref: BTO:0002085 xref: FMA:58071 xref: MA:0002459 xref: ncithesaurus:Chamber_of_the_Eye xref: SCTID:280540004 xref: UMLS:C0459556 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000019 ! camera-type eye property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006341 name: outer renal medulla peritubular capillary namespace: uberon def: "A peritubular capillary that is part of a outer medulla of kidney." [OBOL:automatic] synonym: "kidney outer medulla peritubular capillary" EXACT [MA:0002589] xref: MA:0002589 is_a: UBERON:0005272 ! peritubular capillary relationship: part_of UBERON:0001293 ! outer medulla of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006376 name: premacula segment of distal straight tubule namespace: uberon def: "." [https://sourceforge.net/tracker/?func=detail&aid=3123600&group_id=76834&atid=1205376, PMID:14595018] synonym: "distal straight tubule premacula segment" EXACT [MA:0002628] synonym: "kidney medulla loop of Henle ascending limb thick segment" EXACT [MA:th] synonym: "medullary thick ascending limb of Henle's loop" EXACT [MA:th] synonym: "renal medulla loop of Henle ascending limb thick segment" EXACT [MA:th] synonym: "renal medulla thick ascending limb" EXACT [MA:th] xref: EMAPA:28331 xref: EMAPA:29683 xref: EMAPA:31379 xref: MA:0002628 is_a: UBERON:0007685 ! region of nephron tubule is_a: UBERON:0008408 ! distal tubular epithelium relationship: part_of UBERON:0001291 {source="MA"} ! thick ascending limb of loop of Henle relationship: part_of UBERON:0006541 {source="MA"} ! outer medulla inner stripe loop of henle relationship: part_of UBERON:0006542 {source="MA"} ! outer medulla outer stripe loop of henle property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006444 name: annulus fibrosus namespace: uberon def: "A ring of fibrous or fibrocartilaginous tissue (as of an intervertebral disk or surrounding an orifice of the heart)." [BTO:0003627] subset: grouping_class synonym: "anulus fibrosus" EXACT [FMA:76704] synonym: "fibrous ring" RELATED [BTO:0003627] xref: BTO:0003627 xref: FMA:76704 is_a: UBERON:0001995 ! fibrocartilage property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006524 name: alveolar system namespace: uberon def: "System pertaining to a bronchus and alveoli." [BTO:0000136] synonym: "bronchoalveolar system" RELATED [BTO:0000136] synonym: "pulmonary alveolar system" EXACT [MP:0010899] xref: BTO:0000136 xref: EMAPA:19003 xref: EMAPA:19005 xref: EMAPA:19007 xref: EMAPA:19009 xref: MA:0000416 is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0002048 ! lung property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006534 name: renal convoluted tubule namespace: uberon synonym: "convoluted tubule" EXACT [] synonym: "kidney convoluted tubule" EXACT [MA:0001665] xref: MA:0001665 xref: ncithesaurus:Convoluted_Tubule xref: SCTID:361333002 xref: UMLS:C1707510 is_a: UBERON:0007685 ! region of nephron tubule property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006541 name: outer medulla inner stripe loop of henle namespace: uberon def: "A loop of Henle that is part of a kidney outer medulla inner stripe." [OBOL:automatic] xref: EMAPA:29679 xref: MA:0002627 is_a: UBERON:0001288 ! loop of Henle relationship: part_of UBERON:0004201 ! kidney outer medulla inner stripe property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006542 name: outer medulla outer stripe loop of henle namespace: uberon def: "A loop of Henle that is part of a kidney outer medulla outer stripe." [OBOL:automatic] xref: EMAPA:29665 xref: MA:0002630 is_a: UBERON:0001288 ! loop of Henle relationship: part_of UBERON:0004202 ! kidney outer medulla outer stripe property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006544 name: kidney vasculature namespace: uberon def: "A vasculature that is part of a kidney." [OBOL:automatic] subset: vertebrate_core xref: EMAPA:28457 xref: TAO:0005305 xref: ZFA:0005305 is_a: UBERON:0002201 ! vasculature of trunk is_a: UBERON:0006554 ! urinary system structure is_a: UBERON:0006876 ! vasculature of organ relationship: part_of UBERON:0002113 ! kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006553 name: renal duct namespace: uberon def: "A tube in the kidney that collect and transport urine." [ZFIN:ZDB-PUB-071029-9] comment: in ZFA this is defined as part of mesonephros xref: TAO:0005289 xref: ZFA:0005289 is_a: UBERON:0000058 ! duct is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0002113 ! kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006554 name: urinary system structure namespace: uberon def: "An anatomical structure that is part of a excretory system." [OBOL:automatic] comment: editor note: note that we do not explicitly exclude entities such as WBbt:0005777 (excretory duct) here, but they will be automatically classified under this class after reasoning xref: SCTID:122489005 is_a: UBERON:0000061 ! anatomical structure relationship: part_of UBERON:0001008 ! excretory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006555 name: excretory tube namespace: uberon def: "A tube that is part of a excretory system." [OBOL:automatic] is_a: UBERON:0000025 ! tube is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0001008 ! excretory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006558 name: lymphatic part of lymphoid system namespace: uberon def: "." [Wikipedia:Lymphatic_system] comment: AO notes: in FMA this is part of the cardiovascular system, but here we treat the CV system as a separate component of the circulatory system from the lymphatic system synonym: "lymphatic system" EXACT [FMA:7162, MA:0002435] synonym: "lymphatic tree system" EXACT [FMA:7162] synonym: "lymporeticular system" RELATED [VHOG:0001761] xref: AAO:0010522 xref: EFO:0000870 xref: EMAPA:18248 xref: FMA:7162 xref: MA:0002961 xref: MESH:A15.382.520 xref: SCTID:362597000 xref: VHOG:0001761 is_a: UBERON:0000477 ! anatomical cluster relationship: part_of UBERON:0001009 ! circulatory system relationship: part_of UBERON:0002465 ! lymphoid system relationship: part_of UBERON:0007798 {source="MA"} ! vascular system property_value: external_definition "Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010522", ontology="AAO", source="AAO:BJB"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006561 name: non-lymphatic part of lymphoid system namespace: uberon synonym: "non-lymphatic lymphoid system" EXACT [FMA:74623] xref: FMA:74623 is_a: UBERON:0000477 ! anatomical cluster relationship: part_of UBERON:0002465 ! lymphoid system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006562 name: pharynx namespace: uberon def: "The pharynx is the part of the digestive system immediately posterior to the mouth[GO]." [GO:0060465] comment: Taxon notes: This is a dubious grouping class that collects structures as diverse as the chordate pharynx (which is a subclass - UBERON:0001042) and the nematode pharynx. This portion of the ontology should be revised, but this should be done in sync with GO, from which this grouping arises subset: grouping_class subset: uberon_slim synonym: "pharyngeal tube" EXACT [] xref: FBbt:00005380 xref: MAT:0000049 xref: MIAA:0000049 xref: WBbt:0003681 is_a: UBERON:0004921 ! subdivision of digestive tract property_value: external_definition "A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]" xsd:string {date_retrieved="2012-07-02", ontology="FEED", url="http://www.feedexp.org"} property_value: has_relational_adjective "branchial" xsd:string property_value: has_relational_adjective "pharyngeal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006568 name: hypothalamic nucleus namespace: uberon def: "A nucleus of brain that is part of a hypothalamus." [OBOL:automatic] synonym: "nucleus of hypothalamus" EXACT [FMA:258762] xref: BTO:0002449 xref: FMA:258762 xref: MA:0002426 xref: SCTID:279304003 is_a: UBERON:0003048 ! regional part of hypothalamus is_a: UBERON:0006569 ! diencephalic nucleus relationship: part_of UBERON:0001898 ! hypothalamus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006569 name: diencephalic nucleus namespace: uberon def: "A nucleus of brain that is part of a diencephalon." [OBOL:automatic] xref: TAO:0002191 xref: ZFA:0001659 is_a: UBERON:0002308 ! nucleus of brain is_a: UBERON:0002784 ! regional part of diencephalon relationship: part_of UBERON:0001894 ! diencephalon property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006595 name: presumptive endoderm namespace: uberon xref: AAO:0000471 xref: EFO:0003437 xref: TAO:0000416 xref: ZFA:0000416 is_a: UBERON:0006598 ! presumptive structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006598 name: presumptive structure namespace: uberon synonym: "presumptive structures" EXACT [ZFA:0001116] xref: AAO:0000479 xref: TAO:0001116 xref: ZFA:0001116 is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0000922 ! embryo property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006601 name: presumptive ectoderm namespace: uberon comment: Editors note: requires review. ZFA def: Presumptive structure at the animal poll of the blastula that will develop into ectoderm via the epiblast. Determined by fate mapping synonym: "presumptive epidermis" RELATED [ZFA:0001376] xref: AAO:0000470 xref: EFO:0003466 xref: TAO:0001376 xref: XAO:0004132 xref: ZFA:0001376 is_a: UBERON:0006598 ! presumptive structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006603 name: presumptive mesoderm namespace: uberon comment: Editors note: requires review xref: AAO:0000476 xref: EFO:0003467 xref: TAO:0001377 xref: ZFA:0001377 is_a: UBERON:0006598 ! presumptive structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006660 name: muscle layer namespace: uberon def: "A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis." [Wikipedia:Muscular_layer] comment: AO notes: NCITA class appears to be defined more generally synonym: "muscular coat" RELATED [Wikipedia:Muscularis_externa] synonym: "muscular layer" EXACT [OBOL:automatic] synonym: "muscularis" RELATED [] synonym: "muscularis externa" RELATED [BTO:0004838] synonym: "muscularis layer" EXACT [FMA:45634] synonym: "muscularis propria" RELATED [Wikipedia:Muscularis_externa] synonym: "transverse muscular fibers" RELATED [Wikipedia:Muscularis_externa] synonym: "tunica externa" RELATED [BTO:0004838] synonym: "tunica muscularis" EXACT LATIN [BTO:0004838] synonym: "tunica muscularis" RELATED [Wikipedia:Muscularis_externa] xref: BTO:0004838 xref: FMA:45634 xref: ncithesaurus:Muscle_Layer xref: SCTID:86915006 xref: UMLS:C0225358 is_a: UBERON:0004923 {source="FMA"} ! organ component layer property_value: external_definition "An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO]." xsd:string {source="BTO:0004838"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: spatially_disjoint_from UBERON:0000009 property_value: spatially_disjoint_from UBERON:0006676 [Term] id: UBERON:0006725 name: spiral ligament namespace: uberon def: "A spiral thickening of the fibrous lining of the cochlear wall. Spiral ligament secures the membranous cochlear duct to the bony spiral canal of the cochlea. Its spiral ligament fibrocytes function in conjunction with the stria vascularis to mediate cochlear ion homeostasis." [https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=3557974&group_id=76834, MESH:MESH, Wikipedia:Spiral_ligament] comment: Note that this is not classified as a ligament in FMA synonym: "ligamentum spirale ductus cochlearis" EXACT LATIN [Wikipedia:Spiral_ligament] synonym: "spiral cochlear ligament" EXACT LATIN [] synonym: "spiral ligament of cochlear duct" EXACT [FMA:77834] xref: A09.246.631.246.965 xref: FMA:77834 xref: MA:0001192 xref: SCTID:279840005 is_a: UBERON:0000211 ! ligament is_a: UBERON:0003566 ! head connective tissue is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0001855 ! cochlear duct of membranous labyrinth property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006799 name: glandular epithelium namespace: uberon def: "Epithelium composed of secretory cells." [Online_Medical_Dictionary:http\://cancerweb.ncl.ac.uk/] comment: Editor notes: consider splitting epithelium from epithelial tissue xref: BTO:0002991 xref: ncithesaurus:Glandular_Epithelial_Tissue xref: ncithesaurus:Glandular_Epithelium xref: UMLS:C0682578 xref: UMLS:C1708242 is_a: UBERON:0000483 ! epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006800 name: anatomical line namespace: uberon def: "Non-material anatomical entity of one dimension, which forms a boundary of an anatomical surface or is a modulation of an anatomical surface." [CARO:MAH] subset: upper_level xref: AAO:0010267 xref: AEO:0000008 xref: BILA:0000008 xref: CARO:0000008 xref: EHDAA2:0003008 xref: FMA:9657 xref: HAO:0000008 xref: TAO:0001837 xref: TGMA:0001828 xref: XAO:0004003 xref: ZFA:0001689 is_a: UBERON:0000015 ! anatomical boundary property_value: external_definition "Non-material anatomical entity of one dimension, whiVSAO forms a boundary of an anatomical surface or is a modulation of an anatomical surface.[CARO]" xsd:string {date_retrieved="2012-08-14", external_class="CARO:0000008", ontology="CARO", source="CARO:MAH", source="FMA:9657"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006815 name: areolar connective tissue namespace: uberon def: "Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand.[FMA]" [FMA:63897, FMA:FMA] synonym: "loose areolar connective tissue" EXACT [FMA:63897] synonym: "loose connective tissue" RELATED [AAO:0000027] xref: AAO:0000027 xref: FMA:63897 xref: SCTID:68477002 is_a: UBERON:0011825 {source="FMA"} ! loose connective tissue relationship: part_of UBERON:0000030 ! lamina propria property_value: axiom_lost_from_external_ontology "relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000027", ontology="AAO"} property_value: external_definition "Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000027", ontology="AAO", source="AAO:LAP"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006846 name: groove namespace: uberon def: "Anatomical line that delineates a furrow or depression in an organ or tissue." [ZFA:0001690] subset: grouping_class xref: AAO:0010276 xref: AEO:0000161 xref: EHDAA2:0003161 xref: FMA:75037 xref: TAO:0001838 xref: ZFA:0001690 is_a: UBERON:0006800 ! anatomical line property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006851 name: renal cortex peritubular capillary namespace: uberon def: "A peritubular capillary that is part of a cortex of kidney." [OBOL:automatic] synonym: "kidney cortex peritubular capillary" EXACT [MA:0002590] xref: MA:0002590 is_a: UBERON:0005272 ! peritubular capillary relationship: part_of UBERON:0001225 ! cortex of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006853 name: renal cortex tubule namespace: uberon def: "A region of nephron tubule that is part of a cortex of kidney." [OBOL:automatic] synonym: "cortical tubule" RELATED [MA:0002609] synonym: "kidney cortex tubule" EXACT [MA:0002609] xref: EMAPA:18976 xref: MA:0002609 is_a: UBERON:0007685 ! region of nephron tubule relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006854 name: distal straight tubule postmacula segment namespace: uberon def: "." [https://sourceforge.net/tracker/?func=detail&aid=3123598&group_id=76834&atid=1205376] synonym: "cortical thick ascending limb of Henle's loop" EXACT [MA:th] synonym: "kidney cortex loop of Henle ascending limb thick segment" EXACT [MA:th] synonym: "renal cortex loop of Henle ascending limb thick segment" EXACT [MA:th] synonym: "renal cortex thick ascending limb" EXACT [MA:th] xref: EMAPA:28402 xref: MA:0002615 is_a: UBERON:0006853 ! renal cortex tubule is_a: UBERON:0008408 ! distal tubular epithelium relationship: part_of UBERON:0001291 {source="MA"} ! thick ascending limb of loop of Henle relationship: part_of UBERON:0006853 {source="MA"} ! renal cortex tubule property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006855 name: ureter muscle layer namespace: uberon def: "A muscle layer that is part of a ureter." [OBOL:automatic] synonym: "muscular coat of ureter" EXACT [FMA:15893] synonym: "muscular layer of ureter" EXACT [FMA:15893] synonym: "muscularis of ureter" EXACT [FMA:15893] synonym: "tunica muscularis (ureter)" EXACT LATIN [FMA:TA] synonym: "tunica muscularis ureteris" EXACT LATIN [FMA:TA] synonym: "ureteral smooth muscle layer" RELATED [EMAPA:28567] xref: EMAPA:28567 xref: FMA:15893 xref: MA:0002654 xref: SCTID:3563003 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0006554 ! urinary system structure is_a: UBERON:0006660 ! muscle layer relationship: part_of UBERON:0000056 ! ureter relationship: part_of UBERON:0009916 {source="FMA"} ! wall of ureter property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006858 name: adrenal/interrenal gland namespace: uberon def: "This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO]" [GO:0030325] comment: Editor notes: keep this grouping class so long as it is required for GO subset: grouping_class subset: organ_slim synonym: "adrenal - interrenal gland" RELATED [VHOG:0001141] synonym: "adrenal gland - interrenal gland" EXACT [VHOG:0001141] synonym: "adrenal gland/interrenal tissue" EXACT [] synonym: "suprarenal gland - interrenal gland" RELATED [VHOG:0001141] xref: VHOG:0001141 is_a: UBERON:0002368 ! endocrine gland is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005172 ! abdomen organ relationship: develops_from UBERON:0003064 ! intermediate mesoderm relationship: part_of UBERON:0000916 ! abdomen property_value: homology_notes "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001141", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006866 name: terminal part of digestive tract namespace: uberon comment: Usage notes: this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future. synonym: "rectal part of digestive tract" RELATED [] synonym: "rectum" RELATED [FBbt:00005756] synonym: "terminal section of digestive tract" RELATED [] xref: FBbt:00005756 xref: WBbt:0005773 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: develops_from UBERON:0001046 ! hindgut property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006876 name: vasculature of organ namespace: uberon def: "A vasculature that is part of a organ." [OBOL:automatic] subset: non_informative synonym: "organ vasculature" EXACT [FMA:74612] synonym: "set of blood vessels of organ" EXACT [FMA:74612] xref: FMA:74612 is_a: UBERON:0002049 ! vasculature relationship: part_of UBERON:0000062 ! organ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006877 name: vasculature of liver namespace: uberon def: "A vasculature that is part of a liver." [OBOL:automatic] comment: the EHDAA2 term and the FMA term may not be exact equivalents - check synonym: "hepatic vasculature" EXACT [FMA:73748] synonym: "liver vascular system" RELATED [EHDAA2:0003454] xref: EHDAA2:0003454 xref: FMA:73748 is_a: UBERON:0002201 ! vasculature of trunk is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0006876 ! vasculature of organ relationship: part_of UBERON:0002107 ! liver property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006904 name: head mesenchyme from mesoderm namespace: uberon def: "A head mesenchyme that develops_from a mesoderm." [OBOL:automatic] comment: Editor note: merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements UBERONREF:0000002 NC meeting scheme subset: vertebrate_core synonym: "cranial mesoderm" RELATED [UBERON:0005280] synonym: "head mesenchyme derived from mesoderm" EXACT [] synonym: "head mesenchyme from head mesoderm" EXACT [EHDAA2:0001118] synonym: "head mesenchyme from mesoderm" EXACT [] synonym: "head mesoderm" RELATED [AAO:0011051, UBERON:0005280] synonym: "mesenchyme derived from head mesoderm" EXACT [EHDAA:1057] synonym: "mesenchyme from head mesoderm" EXACT [] xref: AAO:0011051 xref: EFO:0003337 xref: EFO:0003603 xref: EHDAA2:0001118 xref: EHDAA:655 xref: EMAPA:16099 xref: EMAPA:16270 xref: TAO:0000998 xref: VHOG:0000185 xref: XAO:0000053 xref: ZFA:0000998 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005253 {source="ZFA"} ! head mesenchyme relationship: develops_from UBERON:0000926 {source="EHDAA2"} ! mesoderm relationship: develops_from UBERON:0003063 {source="EHDAA2", source="XAO"} ! prechordal plate property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006914 name: squamous epithelium namespace: uberon def: "an epithelium characterised by its most superficial layer consisting of squamous epithelial cells." [Wikipedia:Squamous_epithelium] comment: consider FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium xref: BTO:0002072 xref: ncithesaurus:Squamous_Epithelium xref: SCTID:40118003 xref: UMLS:C0221909 is_a: UBERON:0000483 ! epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006915 name: stratified squamous epithelium namespace: uberon def: "Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA]" [FMA:45563, Wikipedia:Stratified_squamous_epithelium] synonym: "epithelium stratificatum squamosum" EXACT [FMA:45563] xref: FMA:45563 xref: ncithesaurus:Stratified_Squamous_Epithelium xref: UMLS:C0836131 is_a: UBERON:0000486 ! multilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006924 name: stomach glandular epithelium namespace: uberon def: "A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands." [ISBN10:0073040584] comment: Editor notes: we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland. Consider also: stomach glandular region as a part-of parent synonym: "epithelium of gastric gland" NARROW [FMA:63458] synonym: "gastric gland epithelium" RELATED [FMA:63458] xref: EMAPA:17623 xref: FMA:63458 xref: MA:0002784 is_a: UBERON:0001276 ! epithelium of stomach is_a: UBERON:0006929 {source="FMA"} ! glandular columnar epithelium relationship: part_of UBERON:0000945 ! stomach relationship: part_of UBERON:0006931 ! stomach glandular region mucosa property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006925 name: digestive gland namespace: uberon def: "A gland, such as the liver or pancreas, that secretes into the alimentary canal substances necessary for digestion." [The_American_Heritage_Dictionary_of_the_English_Language:Fourth_Edition._2000.] subset: organ_slim synonym: "digestive system gland" EXACT [AAO:0000130] xref: AAO:0000130 xref: BTO:0000345 is_a: UBERON:0002368 ! endocrine gland relationship: part_of UBERON:0001007 ! digestive system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006929 name: glandular columnar epithelium namespace: uberon def: "Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA]" [FMA:64800] xref: FMA:64800 xref: ncithesaurus:Columnar_Epithelium xref: UMLS:C0225337 is_a: UBERON:0000485 ! simple columnar epithelium is_a: UBERON:0006799 ! glandular epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006931 name: stomach glandular region mucosa namespace: uberon def: "A mucosa of stomach that is part of a stomach glandular region." [OBOL:automatic] xref: MA:0001614 is_a: UBERON:0001199 ! mucosa of stomach relationship: part_of UBERON:0011953 ! stomach glandular region property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006932 name: vestibular epithelium namespace: uberon def: "An epithelium that is part of a vestibular labyrinth." [OBOL:automatic] synonym: "epithelium of vestibular labyrinth" EXACT [OBOL:automatic] synonym: "inner ear vestibular component epithelium" EXACT [RETIRED_EHDAA2:0000834] synonym: "vestibular sensory epithelium" EXACT [FMA:75606] xref: FMA:75606 xref: MA:0002892 xref: RETIRED_EHDAA2:0000834 is_a: UBERON:0006934 ! sensory epithelium is_a: UBERON:0006937 ! inner ear epithelium is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0001862 ! vestibular labyrinth property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006934 name: sensory epithelium namespace: uberon def: "Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue." [BTO:0000314] comment: note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical synonym: "neuroepithelium" RELATED INCONSISTENT [BTO:0000314] xref: FMA:62410 xref: SCTID:309045006 is_a: UBERON:0000488 ! atypical epithelium is_a: UBERON:0010371 ! ecto-epithelium relationship: part_of UBERON:0000010 ! peripheral nervous system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006935 name: crista ampullaris neuroepithelium namespace: uberon def: "An epithelium that is part of a crista ampullaris." [OBOL:automatic] synonym: "ampullary crest neuroepithelium" RELATED [MA:0002870] synonym: "epithelium of crista of ampulla of semicircular duct of membranous labyrinth" EXACT [FMA:75636] xref: FMA:75636 xref: MA:0002870 is_a: UBERON:0006932 {source="FMA"} ! vestibular epithelium relationship: part_of UBERON:0004721 {source="MA"} ! crista ampullaris property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006937 name: inner ear epithelium namespace: uberon def: "An epithelium that is part of a internal ear." [OBOL:automatic] xref: MA:0001189 is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010371 ! ecto-epithelium relationship: part_of UBERON:0001846 ! internal ear property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006955 name: uterine epithelium namespace: uberon def: "An epithelium that is part of a uterus." [OBOL:automatic] synonym: "uterus epithelium" RELATED [BTO:0003082] xref: BTO:0003082 is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0000995 ! uterus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0006965 name: vascular cord namespace: uberon def: "The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]." [GO:0072360, ZFA:0005077] xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0004535 ! cardiovascular system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007005 name: cardiac mesoderm namespace: uberon def: "the splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]." [http://www.drugs.com/dict/cardiogenic-mesoderm.html, XAO:0000235] comment: consider FBbt:00005541 synonym: "cardiogenic mesoderm" RELATED [http://www.drugs.com/dict/cardiogenic-mesoderm.html] synonym: "heart primordia" RELATED [XAO:0000235] xref: AAO:0011021 xref: BILA:0000051 xref: EFO:0000315 xref: EHDAA:385 xref: SCTID:360387000 xref: VHOG:0001641 xref: XAO:0000235 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm relationship: part_of UBERON:0004140 ! heart field relationship: part_of UBERON:0009881 ! anterior lateral plate mesoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007010 name: cleaving embryo namespace: uberon def: "Organism at the cleavage stage." [OBOL:automatic] xref: BILA:0000058 is_a: UBERON:0000922 ! embryo property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007026 name: primitive gut namespace: uberon comment: The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis[NBK10107] xref: BILA:0000084 xref: ncithesaurus:Primordial_Gut xref: SCTID:360394002 xref: UMLS:C1514442 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0000925 ! endoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007100 name: circulatory organ namespace: uberon def: "A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood[GO]." [GO:0007507] comment: editor note: we need to find the appropriate GO process to use for the definition - 'blood circulation' may not apply to invertebrates; 'circulatory system process' is circular. Note we cannot use a part_of-based definition as this results in the iris and all vascular elements being categorized as circulatory organs. Taxon notes: note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. "The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian". Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis. Gene notes: Bmp, Nkx, Gata subset: grouping_class synonym: "adult heart" RELATED [FBbt:00003154] synonym: "cardiac pump" EXACT [] synonym: "cardiac structure" RELATED [] synonym: "dorsal tube" NARROW [Wikipedia:Heart] synonym: "heart" NARROW [GO:0007507] synonym: "heart or heart like organ" EXACT [] xref: ANISEED:1235302 xref: FBbt:00003154 xref: http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg xref: TADS:0000147 is_a: UBERON:0003103 ! compound organ relationship: part_of UBERON:0001009 ! circulatory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: present_in_taxon NCBITaxon:7718 {source="PMID:20959416"} [Term] id: UBERON:0007123 name: pharyngeal pouch 2 namespace: uberon alt_id: UBERON:0005715 def: "The second pouch between the second and third arches. Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve[WP]" [PMID:16313389, Wikipedia:Pharyngeal_pouch_(embryology)#Second_pouch] subset: vertebrate_core synonym: "2nd arch branchial pouch" EXACT [RETIRED_EHDAA2:0000060] synonym: "2nd arch branchial pouch endoderm" EXACT [EHDAA2:0000061] synonym: "2nd arch pouch endoderm" EXACT [EHDAA2:0000058] synonym: "2nd pharyngeal pouch endoderm" EXACT [VHOG:0000561] synonym: "pharyngeal pouches 2" EXACT PLURAL [ZFA:0001130] synonym: "second arch pharyngeal pouch" EXACT [OBOL:automatic] synonym: "second pharyngeal pouch" RELATED [VHOG:0000967] synonym: "second visceral pouch" EXACT [XAO:0000247] synonym: "visceral pouch 2" EXACT [XAO:0000247] xref: AAO:0011115 xref: EFO:0003633 xref: EHDAA2:0000058 xref: EMAPA:16275 xref: EMAPA:16276 xref: ncithesaurus:Second_Pharyngeal_Pouch xref: RETIRED_EHDAA2:0000060 xref: SCTID:345349000 xref: TAO:0001130 xref: UMLS:C0231069 xref: VHOG:0000561 xref: VHOG:0000967 xref: XAO:0000247 xref: ZFA:0001130 is_a: UBERON:0004117 ! pharyngeal pouch property_value: external_definition "A pouch that is situated between the 2nd and 3rd pharyngeal arch. [The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.72, see_Kaufman_MH_and_Bard_JBL][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000967", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: external_definition "Second of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011115", ontology="AAO", source="ISBN:0-226-55763-4"} property_value: homology_notes "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000967", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007135 name: neural keel namespace: uberon def: "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section." [ZFIN:ZDB-PUB-961014-576] synonym: "presumptive central nervous system" RELATED [ZFA:0000131] xref: EFO:0003497 xref: TAO:0000131 xref: ZFA:0000131 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0003075 ! neural plate property_value: external_definition "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000131", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007196 name: tracheobronchial tree namespace: uberon alt_id: UBERON:0004102 def: "the structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells." [Wikipedia:Tracheobronchial_tree] subset: organ_slim synonym: "tracheobronchial system" RELATED [HP:0005607] xref: FMA:7393 xref: SCTID:361384001 is_a: UBERON:0000062 ! organ is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0001558 ! lower respiratory tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007204 name: brachiocephalic vasculature namespace: uberon is_a: UBERON:0002049 ! vasculature property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007213 name: mesenchyme derived from head neural crest namespace: uberon def: "Mesenchyme that develops_from a cranial neural crest." [OBOL:automatic] subset: vertebrate_core synonym: "head mesenchyme from cranial neural crest" EXACT [] synonym: "head mesenchyme from neural crest" EXACT [EHDAA2:0000735] xref: EFO:0003572 xref: EHDAA2:0000735 xref: EMAPA:16100 xref: EMAPA:16169 xref: EMAPA:16271 xref: EMAPA_RETIRED:16271 xref: TAO:0000787 xref: ZFA:0000787 is_a: UBERON:0005253 {source="ZFA"} ! head mesenchyme is_a: UBERON:0010313 ! neural crest-derived structure relationship: develops_from UBERON:0003099 ! cranial neural crest property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007238 name: 1st arch maxillary component namespace: uberon comment: Editors note: relationship to palatoquadrate to be added xref: EHDAA2:0000038 xref: EHDAA:595 xref: EMAPA:16388 xref: VHOG:0000511 is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0004362 {source="EHDAA2"} ! pharyngeal arch 1 property_value: homology_notes "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000511", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007240 name: tunica adventitia of artery namespace: uberon def: "A tunica adventitia that is part of a artery." [OBOL:automatic] synonym: "arterial adventitia" EXACT [EV:0100030] synonym: "tunica externa (adventitia)(arteriae)" EXACT [FMA:14274] xref: EV:0100030 xref: FMA:14274 xref: SCTID:113261001 is_a: UBERON:0005734 ! tunica adventitia of blood vessel relationship: part_of UBERON:0000415 ! artery wall relationship: part_of UBERON:0001637 ! artery property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007245 name: nuclear complex of neuraxis namespace: uberon def: "Internal gray matter component which consists of an assemblage of nuclei of neuraxis. Example: cerebellar nuclear complex, Vestibular nuclear complex.[FMA]" [FMA:84059, FMA:FMA] comment: todo - move existing complex classes currently under nucleus to be under this class synonym: "cluster of neural nuclei" RELATED [] synonym: "neural nuclei" RELATED [] synonym: "nuclear complex" RELATED [] xref: FMA:84059 is_a: UBERON:0002020 ! gray matter of neuraxis property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007277 name: presumptive hindbrain namespace: uberon def: "The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, \"rhombencephalosynapsis\" is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure." [Wikipedia:Rhombencephalon] comment: TODO - unify naming conventions synonym: "embryonic rhombencephalon" RELATED [CALOHA:TS-2118] synonym: "future hindbrain" RELATED [UBERON:cjm] synonym: "rhombencephalon" RELATED [EHDAA2:0001630] xref: CALOHA:TS-2118 xref: EFO:0003440 xref: EHDAA2:0001630 xref: TAO:0000569 xref: ZFA:0000569 is_a: UBERON:0006598 ! presumptive structure relationship: part_of UBERON:0006238 ! future brain property_value: external_definition "The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]." xsd:string {source="NPX:PDR"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007280 name: presumptive endocardium namespace: uberon def: "A presumptive structure that develops_into a endocardium." [OBOL:automatic] xref: TAO:0002233 xref: ZFA:0001724 is_a: UBERON:0006598 ! presumptive structure property_value: external_definition "Portion of tissue that is part of the heart tube and will become the endocardium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002233", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007282 name: presumptive segmental plate namespace: uberon def: "A presumptive structure that develops_into a presomitic mesoderm." [OBOL:automatic] xref: EFO:0003421 xref: TAO:0000053 xref: ZFA:0000053 is_a: UBERON:0006598 ! presumptive structure relationship: develops_from UBERON:0009618 {consistent_with="UBERONREF:0000002", source="EDHAA2"} ! trunk paraxial mesoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007284 name: presumptive neural plate namespace: uberon def: "A presumptive structure that develops_into a neural plate." [OBOL:automatic] xref: EFO:0003424 xref: TAO:0000063 xref: ZFA:0000063 is_a: UBERON:0006598 ! presumptive structure property_value: external_definition "Region of the gastrula which gives rise to the neural plate.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000063", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007285 name: presumptive paraxial mesoderm namespace: uberon def: "A presumptive structure that develops_into a paraxial mesoderm." [OBOL:automatic] xref: EFO:0003443 xref: TAO:0000591 xref: XAO:0004134 xref: ZFA:0000591 is_a: UBERON:0006598 ! presumptive structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007297 name: presumptive pronephric mesoderm namespace: uberon def: "A presumptive structure that develops_into a pronephric mesoderm." [OBOL:automatic] synonym: "nephron primordium" EXACT [ZFA:0001070] xref: EFO:0003619 xref: TAO:0001070 xref: ZFA:0001070 is_a: UBERON:0006598 ! presumptive structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007303 name: pharyngeal vasculature namespace: uberon def: "A vasculature that is part of a chordate pharynx." [OBOL:automatic] synonym: "branchial vasculature" EXACT [ZFA:0005003] xref: TAO:0005003 xref: ZFA:0005003 is_a: UBERON:0002049 ! vasculature is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0001042 ! chordate pharynx property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007324 name: pancreatic lobe namespace: uberon comment: todo - check synonym: "lobulus pancreaticus" EXACT [FMA:16012] synonym: "pancreas lobe" EXACT [MA:0000721] synonym: "pancreatic lobule" EXACT [FMA:16012] xref: FMA:16012 xref: MA:0000721 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0000017 ! exocrine pancreas property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007329 name: pancreatic duct namespace: uberon def: "A duct that is part of the pancreas and connected to the duodenum." [UBERON:cjm, Wikipedia:Pancreatic_duct] comment: note that this class groups together accessory (dorsal) and main (ventral) pancreatic ducts. AO notes: in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms subset: vertebrate_core synonym: "duct of pancreas" EXACT [OBOL:accepted] synonym: "ductus pancreaticus" RELATED LATIN [Wikipedia:Pancreatic_duct] synonym: "pancreas duct" EXACT [OBOL:accepted] xref: EHDAA:9194 xref: FMA:10419 xref: http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png xref: MA:0000124 xref: SCTID:181278006 xref: TAO:0001372 xref: VHOG:0000254 xref: ZFA:0001372 is_a: UBERON:0003928 {source="ZFA"} ! digestive system duct is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0003922 ! pancreatic bud relationship: part_of UBERON:0000017 {source="MA"} ! exocrine pancreas property_value: external_definition "Duct connecting the pancreas with the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000254", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: homology_notes "These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000254", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007376 name: outer epithelial layer namespace: uberon def: "The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. The epidermis of a more complex invertebrate is just one-layer deep, and may be protected by a non-cellular cuticle. The epidermis of a higher vertebrate has many layers, and the outer layers are reinforced with keratin and then die[WP]." [Wikipedia:Epidermis_(zoology)] comment: Editor's note: this grouping class exists primarily to align with GO - see GO:0008544. subset: grouping_class synonym: "epidermis" NARROW [GO:0008544] synonym: "hypodermis" RELATED INCONSISTENT [GO:0008544, WBbt:0005733] synonym: "outer epidermal layer" EXACT [] xref: FBbt:00004993 xref: HAO:0000298 xref: TADS:0000109 xref: WBbt:0005733 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0003102 ! surface structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007383 name: enveloping layer of ectoderm namespace: uberon def: "Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Originallu this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm." [ISBN:9780878932504, ZFIN:ZDB-PUB-961014-576] synonym: "enveloping layer" EXACT [ZFIN:ZDB-PUB-961014-576] synonym: "EVL" EXACT [ZFA:0000086] xref: EFO:0003425 xref: TAO:0000086 xref: ZFA:0000086 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0000924 ! ectoderm relationship: part_of UBERON:0000922 ! embryo property_value: axiom_lost_from_external_ontology "relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000086", ontology="TAO"} property_value: external_definition "Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000086", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007497 name: developing epithelial placode namespace: uberon alt_id: EHDAA2:0003112 def: "A domain of columnar epithelium in an embryo that represents the early stage of the development of the epithelial component of a new anatomical structure." [AEO:0000218, JB:DEF] comment: Consider merging with ectodermal placode? In EHDAA2 this includes lens, nasal, otic epibranchial and trigeminal placodes synonym: "epithelial placode" EXACT [AEO:0000112] xref: AEO:0000218 xref: AEO_RETIRED:0000112 xref: EHDAA2_RETIRED:0003112 is_a: UBERON:0000485 {source="AEO"} ! simple columnar epithelium is_a: UBERON:0001048 ! primordium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007499 name: epithelial sac namespace: uberon def: "An epithelial tube that is open at one end only." [AEO:JB, UBERONREF:0000001] xref: AEO:0000115 xref: EHDAA2:0003115 is_a: UBERON:0003914 {source="AEO"} ! epithelial tube is_a: UBERON:0009856 ! sac property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007500 name: epithelial tube open at both ends namespace: uberon def: "An epithelial tube open at both ends that allows fluid flow." [AEO:JB, UBERONREF:0000001] xref: AEO:0000116 xref: RETIRED_EHDAA2:0003116 is_a: UBERON:0003914 {source="AEO"} ! epithelial tube property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007503 name: epithelial vesicle namespace: uberon alt_id: EHDAA2:0003119 def: "A closed epithelium with a lumen." [AEO:JB] xref: AEO:0000119 xref: EHDAA2:0003119 is_a: UBERON:0000483 {source="AEO"} ! epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007521 name: smooth muscle sphincter namespace: uberon def: "A ring of smooth muscle cells whose contraction closes the opening of the ring." [AEO:JB] xref: AEO:0000143 xref: EHDAA2:0003143 xref: SCTID:362915001 is_a: UBERON:0001135 {source="AEO"} ! smooth muscle tissue is_a: UBERON:0004590 ! sphincter muscle property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007524 name: dense mesenchyme tissue namespace: uberon alt_id: EHDAA2:0003146 def: "Mesenchyme with little extracellular matrix." [AEO:JB] xref: AEO:0000146 xref: EHDAA2:0003146 is_a: UBERON:0003104 {source="AEO"} ! mesenchyme property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007530 name: migrating mesenchyme population namespace: uberon alt_id: EHDAA2:0003152 def: "Mesenchymal cells that are migrating." [AEO:JB] comment: Editors note: this class will be an important part of the NC reorganization xref: AEO:0000152 xref: EHDAA2:0003152 is_a: UBERON:0003104 ! mesenchyme property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007592 name: ciliated columnar epithelium namespace: uberon def: "Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]" [FMA:64798] xref: FMA:64798 is_a: UBERON:0000485 {source="FMA"} ! simple columnar epithelium is_a: UBERON:0007601 ! ciliated epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007601 name: ciliated epithelium namespace: uberon def: "Epithelium bearing vibratile cilia on the free surface." [http://medical-dictionary.thefreedictionary.com/ciliated+epithelium] is_a: UBERON:0000483 ! epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007616 name: layer of synovial tissue namespace: uberon def: "A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]." [BTO:0001338, http://www.britannica.com/EBchecked/topic/578563/synovial-tissue] synonym: "stratum synoviale" NARROW [FMA:TA] synonym: "synovial layer" NARROW [FMA:66762] synonym: "synovial membrane" NARROW [FMA:66762] synonym: "synovial tissue" RELATED [BTO:0001338] xref: BTO:0001338 xref: FMA:66762 is_a: UBERON:0000042 ! serous membrane is_a: UBERON:0002384 {source="BTO"} ! connective tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007625 name: pigment epithelium of eye namespace: uberon def: "epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules." [MP:0005200] synonym: "eye pigment epithelium" RELATED [MESH:A09.371.670] xref: GAID:907 xref: MESH:A09.371.670 is_a: UBERON:0000483 ! epithelium relationship: part_of UBERON:0000970 ! eye property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007645 name: future meninx namespace: uberon comment: The zebrafish primitive meninx develops from neural crest[UBERONREF:0000002]. In EHDAA2 the meninges are divided by layer and location, each has differing developmental origins - mesenchyme from mesoderm/endoderm, mesenchyme from NC synonym: "primitive meninx" RELATED [] is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0000922 ! embryo property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007647 name: ectomeninx namespace: uberon def: "the layer of mesoderm from which the dura mater and much of the membrane bone of the skull develop in the higher vertebrate embryo." [http://www.merriam-webster.com/medical/ectomeninx] is_a: UBERON:0007645 ! future meninx relationship: develops_from UBERON:0000926 ! mesoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007684 name: uriniferous tubule namespace: uberon def: "functional unit of the kidney that forms urine, consisting of two parts, the nephron and the collecting tubule." [ISBN10:0073040584] xref: FMA:17691 is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0004819 ! kidney epithelium is_a: UBERON:0006555 ! excretory tube relationship: part_of UBERON:0002113 {source="FMA"} ! kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007685 name: region of nephron tubule namespace: uberon comment: note - consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts synonym: "region of renal tubule" RELATED [FMA:17692] synonym: "renal tubule region" EXACT [FMA:17692] xref: FMA:17692 is_a: UBERON:0001231 ! nephron tubule is_a: UBERON:0004810 ! nephron tubule epithelium relationship: part_of UBERON:0001231 ! nephron tubule property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007687 name: kidney field namespace: uberon def: "region of the embryo into the area in which the kidney rudiment will develop." [GO:0072004, GOC:mtg_kidney_jan10] synonym: "kidney anlage" RELATED [GOC:mtg_kidney_jan10] is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0000922 ! embryo property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007689 name: thyroid diverticulum namespace: uberon def: "endodermal bud derived from the endodermal epithelium of the embryonic pharyngeal floor[MP]. The thyroid diverticulum is the embryological structure from which thyroid follicular cells derive. It grows from the floor of the pharnyx[WP]." [MP:0004662, Wikipedia:Thyroid_diverticulum] synonym: "saccus thyroideus; diverticulum thyroideum" RELATED LATIN [Wikipedia:Thyroid_diverticulum] is_a: UBERON:0001048 ! primordium relationship: develops_from UBERON:0003091 ! thyroid primordium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007690 name: early pharyngeal endoderm namespace: uberon def: "." [http://dev.biologists.org/content/128/22/4573.full] comment: relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm' synonym: "early pharyngeal arch endoderm" EXACT [EHDAA2:0001457] synonym: "pharyngeal arch endoderm" RELATED [] synonym: "pharyngeal endoderm" RELATED [ZFA:0001104] synonym: "pharyngeal region endoderm" RELATED [EHDAA2:0001456] xref: EFO:0003626 xref: EHDAA2:0001457 xref: EHDAA:962 xref: TAO:0001104 xref: ZFA:0001104 is_a: UBERON:0000925 {source="ZFA"} ! endoderm is_a: UBERON:0004119 ! endoderm-derived structure relationship: develops_from UBERON:0000925 {source="EHDAA2"} ! endoderm relationship: part_of UBERON:0008814 ! pharyngeal system relationship: part_of UBERON:0009722 {source="cjm"} ! entire pharyngeal arch endoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007771 name: epidermis gland namespace: uberon def: "A gland that is part of a epidermis." [OBOL:automatic] subset: grouping_class synonym: "epidermal gland" EXACT [] synonym: "gland of epidermis" EXACT [FMA:59153] xref: FMA:59153 is_a: UBERON:0002419 ! skin gland relationship: part_of UBERON:0001003 ! epidermis property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007798 name: vascular system namespace: uberon comment: in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system xref: BTO:0001085 xref: EHDAA2:0004520 xref: MA:0002718 xref: ncithesaurus:Vascular_System xref: UMLS:C0489903 is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0004535 {source="MA"} ! cardiovascular system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007806 name: connecting stalk namespace: uberon def: "A bridge of mesoderm connecting the caudal end of the young embryo with the trophoblastic tissues; the precursor of the umbilical cord." [Medical_Dictionary:http\://medical-dictionary.thefreedictionary.com/] comment: todo - this is currently defined as a bridge of mesoderm, but in EHDAA2 is extraembryonic structure split into mesoderm and blood vessels xref: BTO:0004705 xref: ncithesaurus:Connecting_Stalk xref: UMLS:C1516792 is_a: UBERON:0000478 {source="EHDAA2"} ! extraembryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure relationship: develops_from UBERON:0005728 {source="EHDAA2"} ! extraembryonic mesoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007811 name: craniocervical region namespace: uberon def: "The anteriormost subdivision of the body that includes the head and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae." [UBERON:cjm] synonym: "head and neck" EXACT [FMA:280881] synonym: "head or neck" RELATED [] xref: CALOHA:TS-2356 xref: EV:0100009 xref: FMA:280881 xref: galen:HeadAndNeck xref: MA:0000006 xref: ncithesaurus:Head_and_Neck xref: SCTID:361355005 xref: UMLS:C0460004 xref: WikipediaCategory:Head_and_neck is_a: UBERON:0000475 {source="MA"} ! organism subdivision relationship: part_of UBERON:0000153 ! anterior region of body property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007844 name: cartilaginous element namespace: uberon def: "Skeletal element that is composed of cartilage tissue and may be permanent or transient." [VSAO:curator] comment: AO notes: TAO still mixes tissue and element subset: organ_slim synonym: "cartilage" RELATED [VSAO:0000000] synonym: "cartilage element" EXACT [] synonym: "cartilage organ" EXACT [FMA:55107] synonym: "chondrogenic element" EXACT [VSAO:0000000] xref: AAO:0011130 xref: FMA:55107 xref: VSAO:0000000 xref: XAO:0004013 xref: ZFA:0001501 is_a: UBERON:0004765 {source="VSAO"} ! skeletal element relationship: develops_from UBERON:0005863 {source="VSAO"} ! cartilaginous condensation property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007845 name: regular connective tissue namespace: uberon def: "Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue." [FMA:20103] comment: Editor notes: the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification). xref: FMA:20103 is_a: UBERON:0002384 {source="FMA"} ! connective tissue disjoint_from: UBERON:0011821 ! irregular connective tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007846 name: dense regular connective tissue namespace: uberon def: "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts)[VSAO]" [VSAO:0000050, Wikipedia:Dense_regular_connective_tissue] synonym: "dense fibrous connective tissue" EXACT [FMA:64781] synonym: "dense regular collagenous connective tissue" EXACT [FMA:64781] synonym: "dense regular collagenous tissue" EXACT [FMA:64781] synonym: "regular dense connective tissue" EXACT [] synonym: "typus regularis (textus connectivus collagenosus compactus)" EXACT [FMA:64781] xref: FMA:64781 xref: ncithesaurus:Regular_Dense_Connective_Tissue xref: SCTID:22560007 xref: UMLS:C0225333 xref: VSAO:0000050 xref: XAO:0004030 is_a: UBERON:0007845 {source="FMA"} ! regular connective tissue is_a: UBERON:0011823 {source="ncithesaurus"} ! dense connective tissue property_value: external_definition "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000050", ontology="VSAO", source="GO_REF:0000034", source="PSPUB:0000170"} property_value: external_definition "Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]" xsd:string {date_retrieved="2012-08-29", external_class="FMA:64781", ontology="FMA"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0007914 name: head or neck bone namespace: uberon def: "A bone that is part of a craniocervical region." [OBOL:automatic] xref: MA:0000569 is_a: UBERON:0001474 {source="MA"} ! bone relationship: part_of UBERON:0007811 {source="MA"} ! craniocervical region property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008001 name: irregular bone namespace: uberon def: "The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid." [Wikipedia:Irregular_bone] synonym: "os irregulare" EXACT [] synonym: "os irregulare" RELATED LATIN [Wikipedia:Irregular_bone] xref: FMA:7477 xref: ncithesaurus:Irregular_Bone xref: SCTID:421560006 xref: UMLS:C0502414 is_a: UBERON:0001474 {source="FMA"} ! bone property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008193 name: pneumatized bone namespace: uberon def: "a bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]. Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]." [http://www.medilexicon.com/medicaldictionary.php?t=11303, Wikipedia:Skeletal_pneumaticity] comment: editor note: subclasses of this should be checked for taxonomic consistency synonym: "hollow bone" RELATED [] synonym: "os pneumaticum" EXACT [FMA:7478] synonym: "pneumatic bone" EXACT [FMA:7478] xref: FMA:7478 xref: galen:PneumaticBone xref: SCTID:333008005 is_a: UBERON:0008001 {source="FMA"} ! irregular bone property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008229 name: craniocervical region musculature namespace: uberon def: "A musculature that is part of a craniocervical region." [OBOL:automatic] synonym: "head or neck muscle" EXACT [MA:0000571] synonym: "head or neck muscle" RELATED [MA:0000571] xref: MA:0000571 is_a: UBERON:0001015 {source="MA"} ! musculature relationship: part_of UBERON:0007811 {source="MA"} ! craniocervical region property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008404 name: proximale tubular epithelium namespace: uberon def: "The cells lining the proximal tubule are cuboidal epithelial cells with deep basal membrane invaginations that provide a large basal surface area. The long microvilli (the brush border) lining the tubule lumen, maximize luminal surface area and make these cells ideally suited for both reabsorptive and secretory functions." [Renal_Physiology:Section_7\,_Chapter_3] synonym: "proximale tubule epithelium" RELATED [BTO:0003576] xref: BTO:0003576 is_a: UBERON:0004810 ! nephron tubule epithelium relationship: part_of UBERON:0004134 {source="BTO"} ! proximal tubule property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008408 name: distal tubular epithelium namespace: uberon def: "An epithelium that is part of a distal tubule." [OBOL:automatic] synonym: "distal tubule epithelium" RELATED [BTO:0003948] xref: BTO:0003948 is_a: UBERON:0004810 ! nephron tubule epithelium relationship: part_of UBERON:0004135 {source="BTO"} ! distal tubule property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008425 name: mammary ridge namespace: uberon def: "A bandlike thickening of ectoderm in the embryo extending from just below the axilla to the inguinal region and giving rise to the mammary glands[Stedmans]. One of two parallel lines, formed by thickenings of the epidermis (the mammary ridge) along the ventral surface of mammals of both sexes. They extend from the upper limbs (arms) to the lower limbs (legs) and are developed in the embryo. They give rise to the mammary glands and nipples but are otherwise usually not visible in the adult. The first manifestation of the mammary gland in many mammals is an elevated ridge or milk line, which then fragments into individual buds in specific regions lateral of the dorsal midline. These buds are either located in the thoracic region in primates, in the inguinal area in ungulates or along the entire length of the trunk in rodents and pigs. In humans, milk lines appear in the seventh week of embryonic development. After initial development of the milk lines they go into remission. Nipples develop on the milk lines of mammals. Most humans have two nipples, but in some cases more than two will develop. In most cases, these 'third nipples'—and sometimes fourth nipple—grow along the milk line[WP]." [http://dictionary.reference.com/browse/mammary%20ridge, Wikipedia:Milk_line] comment: split ridge and milk line? synonym: "mammary fold" EXACT [http://dictionary.reference.com/browse/mammary+ridge] synonym: "milk line" RELATED [Wikipedia:Milk_line] xref: EMAPA:18541 is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000924 ! ectoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008780 name: inner cell mass derived epiblast namespace: uberon def: "An epiblast (generic) that develops_from a inner cell mass." [OBOL:automatic] subset: early_development synonym: "embryonic epiblast" RELATED [MP:0003886] xref: EHDAA2:0000444 xref: EHDAA:42 xref: EHDAA:75 xref: EMAPA:16050 xref: ncithesaurus:Epiblast xref: UMLS:C1516906 is_a: UBERON:0002532 ! epiblast (generic) relationship: develops_from UBERON:0000087 {source="Wikipedia"} ! inner cell mass relationship: part_of UBERON:0000091 ! bilaminar disc property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008814 name: pharyngeal system namespace: uberon def: "A transient embryonic complex that is specific to vertebrates. It comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming: the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear." [GO:0060037, GOC:dph] synonym: "pharyngeal apparatus" EXACT [] synonym: "pharyngeal arch region" EXACT [EHDAA2:0000187] synonym: "pharyngeal arches and clefts" RELATED [] xref: EHDAA2:0000187 xref: ncithesaurus:Pharyngeal_Apparatus xref: UMLS:C1519038 is_a: UBERON:0002050 ! embryonic structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008816 name: embryonic head namespace: uberon def: "A head that is part of a embryo." [OBOL:automatic] xref: FBbt:00000155 is_a: UBERON:0000033 ! head is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000922 ! embryo property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008835 name: hepatic diverticulum namespace: uberon def: "The first morphological sign of the embryonic liver is the formation of the hepatic diverticulum, an out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile duct." [http://www.stembook.org/node/512, Wikipedia:Hepatic_diverticulum] synonym: "diverticulum hepaticum" RELATED LATIN [Wikipedia:Hepatic_diverticulum] synonym: "liver diverticulum" EXACT [XAO:0000101] xref: AAO:0011057 xref: EHDAA2:0000740 xref: EHDAA:1530 xref: http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png xref: ncithesaurus:Hepatic_Diverticulum xref: UMLS:C1512407 xref: XAO:0000101 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac is_a: UBERON:0009497 ! epithelium of foregut-midgut junction is_a: UBERON:0009854 ! digestive tract diverticulum relationship: develops_from UBERON:0003894 {source="EHDAA2"} ! liver primordium relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0006235 {source="EHDAA2"} ! foregut-midgut junction property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008836 name: liver bud namespace: uberon xref: BTO:0001642 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0008835 {source="http://www.stembook.org/node/512"} ! hepatic diverticulum property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008859 name: cardiac gastric gland namespace: uberon def: "A gastric gland in the cardiac region of the stomach; cardiac glands are fewer in number than in the fundus and body, and secrete mucin which coats the stomach and protects it[MP]" [MP:0010795, Wikipedia:Cardiac_glands] comment: Consistency note: Kardong places this in the glandular epithelium, FMA more generally in the mucosa subset: organ_slim synonym: "cardiac gland" RELATED [FMA:14920] synonym: "gardiac gland" EXACT [ISBN10:0073040584] synonym: "gastric cardiac gland" EXACT [FMA:14920] synonym: "gastric gland of cardia" EXACT [FMA:14920] synonym: "glandula cardiaca (gaster)" EXACT [FMA:14920] xref: FMA:14920 xref: SCTID:8894005 is_a: UBERON:0000325 ! gastric gland relationship: part_of UBERON:0001162 ! cardia of stomach relationship: part_of UBERON:0004996 {source="FMA"} ! mucosa of cardia of stomach property_value: external_definition "The cardiac glands of the stomach secrete primarily mucus. They are few in number and occur close to the cardiac orifice where the esophagus joins the stomach. In general, they are more shallow than those in the other parts of the stomach. They are of two kinds: (1) simple tubular glands resembling those of the pyloric end of the stomach, but with short ducts. (2) compound racemose glands resembling the duodenal glands. The cardiac gland is both innervated by the parasympathetic and symapthetic nerve fibres of the autonomic nervous system[Wikipedia:Cardiac_glands]." xsd:string {source="Wikipedia:Cardiac_glands"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008861 name: pyloric gastric gland namespace: uberon def: "the gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP]." [MP:0010797, Wikipedia:Pyloric_gland] comment: Editors note: check relationship to pylorus vs antrum synonym: "glandula pylorica" EXACT [FMA:14922] synonym: "pyloric antrum gland" EXACT [OBOL:automatic] synonym: "pyloric gland" EXACT [FMA:14922] xref: FMA:14922 xref: http://upload.wikimedia.org/wikipedia/commons/b/bf/Gray1054.png xref: ncithesaurus:Pyloric_Gland xref: SCTID:70710007 xref: UMLS:C0227239 is_a: UBERON:0000325 ! gastric gland relationship: part_of UBERON:0001166 ! pylorus relationship: part_of UBERON:0004998 ! mucosa of pylorus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008874 name: pulmonary acinus namespace: uberon def: "the part of the airway consisting of a respiratory bronchiole and all of its branches" [MP:0010911, Wikipedia:Acinus#The_Lungs] synonym: "primary pulmonary lobule" EXACT [FMA:7313] xref: FMA:7313 xref: ncithesaurus:Pulmonary_Acinus xref: SCTID:361365004 xref: UMLS:C0225696 is_a: UBERON:0010368 {source="FMA"} ! pulmonary lobule relationship: part_of UBERON:0002048 ! lung property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008883 name: osteoid namespace: uberon def: "Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue" [VSAO:0000046, Wikipedia:Osteoid] comment: AO notes: Note that in VSAO this was classified both as tissue and acellular extracellular matrix. Consider also the AEO class 'bone condensation'. is_a intercellular matrix in FMA. synonym: "pre-bone" EXACT [PSPUB:0000170] synonym: "prebone" EXACT [VSAO:curator] synonym: "prebone tissue" EXACT [FMA:66830] xref: FMA:66830 xref: galen:Osteoid xref: http://upload.wikimedia.org/wikipedia/commons/9/9c/Active_osteoblasts.jpg xref: ncithesaurus:Osteoid xref: SCTID:39365008 xref: UMLS:C0682561 xref: VSAO:0000046 xref: XAO:0004035 is_a: UBERON:0002481 {source="VSAO"} ! bone tissue property_value: axiom_lost_from_external_ontology "relationship loss: subclass proteinaceous extracellular matrix (VSAO:0000021)[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000046", ontology="VSAO"} property_value: external_definition "Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000046", ontology="VSAO", source="GO_REF:0000034", source="PSPUB:0000170"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008886 name: pulmonary vascular system namespace: uberon def: "The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins." [ISBN10:0073040584, Wikipedia:Pulmonary_circulation] synonym: "pulmonary system" EXACT [ISBN10:0073040584] synonym: "pulmonary circulatory system" EXACT [FMA:45621] xref: FMA:45621 is_a: UBERON:0007798 {source="Obol"} ! vascular system relationship: part_of UBERON:0004535 {source="FMA"} ! cardiovascular system property_value: external_definition "Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA]" xsd:string {ontology="FMA", source="FMA:45621"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008947 name: respiratory primordium namespace: uberon xref: EHDAA2:0004069 xref: ncithesaurus:Respiratory_Primordium xref: UMLS:C1514898 is_a: UBERON:0001048 {source="Obol"} ! primordium relationship: part_of UBERON:0003258 ! endoderm of foregut property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0008987 name: renal parenchyma namespace: uberon def: "The functional tissue of the kidney, consisting of the nephrons." [BTO:0003604] synonym: "kidney parenchyma" RELATED [BTO:0003604] synonym: "parenchyma of kidney" EXACT [FMA:15574] xref: BTO:0003604 xref: FMA:15574 xref: SCTID:29704000 is_a: UBERON:0000353 {source="FMA"} ! parenchyma is_a: UBERON:0006554 {source="BTO"} ! urinary system structure relationship: part_of UBERON:0002113 {source="FMA"} ! kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009034 name: stomach region namespace: uberon def: "An organ part that is part of a stomach." [OBOL:automatic] xref: MA:0002561 xref: SCTID:245415005 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0000945 ! stomach property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009089 name: inner medulla vasa recta descending limb namespace: uberon comment: This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medullar parallel to the descending limb xref: KUPO:0001003 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0004776 {source="KUPO"} ! inner renal medulla vasa recta property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009090 name: outer medulla vasa recta descending limb namespace: uberon comment: This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medullar parallel to the descending limb xref: KUPO:0001004 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0004775 {source="KUPO"} ! outer renal medulla vasa recta property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009091 name: vasa recta ascending limb namespace: uberon comment: This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the ascending limb xref: KUPO:0001005 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0004726 {source="KUPO"} ! vasa recta property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009092 name: inner medulla vasa recta ascending limb namespace: uberon comment: This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medulla parallel to the ascending limb xref: KUPO:0001006 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0004776 {source="KUPO"} ! inner renal medulla vasa recta property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009093 name: outer medulla vasa recta ascending limb namespace: uberon comment: This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medulla parallel to the ascending limb xref: KUPO:0001007 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0004775 {source="KUPO"} ! outer renal medulla vasa recta property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009095 name: tip of renal papilla namespace: uberon synonym: "papillary tip" EXACT [KUPO:0001009] synonym: "papillary tips" EXACT PLURAL [KUPO:0001009] xref: KUPO:0001009 is_a: UBERON:0000064 ! organ part is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0001228 {source="KUPO"} ! renal papilla property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009113 name: thymic region namespace: uberon is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0000153 ! anterior region of body property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009117 name: indifferent gonad namespace: uberon def: "A gonad prior to differentiating into a definitive testis or ovary." [http://www.medterms.com/script/main/art.asp?articlekey=8981] comment: typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321] subset: organ_slim xref: EHDAA2:0000716 xref: ncithesaurus:Indifferent_Gonad xref: UMLS:C1512703 is_a: UBERON:0000991 ! gonad relationship: part_of UBERON:0009196 ! indifferent external genitalia property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009122 name: adenohypophyseal placode namespace: uberon def: "The adenohypophyseal placode forms the anterior lobe of the pituitary gland and gives rise to the endocrine secretory cells of the pituitary" [http://www.ncbi.nlm.nih.gov/books/NBK53175/] comment: Editor notes: consider adding more detailed spatial placement - e.g. oral ectoderm and/or rostal ectoderm. Addtional notes: Fate-mapping studies in amphibian, chick and mouse embryos (Eagleson et al., 1986; 1995; Couly and Le Douarin, 1985; Cobos et al., 2001; Osumi-Yamachita et al., 1994; Kawamura et al., 2002) have shown that the cells contributing to the adenohypophysis develop at the midline of the anterior neural ridge, which delineates the rostral boundary of the neural plate, a region devoid of neural crest. The anterior neural ridge also gives rise to the olfactory placodes and some forebrain tissues including the olfactory bulbs (reviewed in Papalopulu, 1995). Ablation of this region in chick embryos at the 2-4 somite stage confirmed these lineage analyses as it prevented formation of Rathke’s pouch and any further pituitary development (elAmraoui and Dubois, 1993). Upon head folding, the oral ectoderm cells of the adenohypophyseal placode invaginate towards the prospective ventral diencephalon to form Rathke’s pouch, the anlage of the adenohypophysis. Rathke’s pouch starts as an invagination of the oral ectoderm in response to inductive signals from the prospective diencephalon. The region of the diencephalon above the pouch is known as the infundibulum and forms the posterior lobe of the pituitary or neurohypohysis (Figure 3). While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke’s pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head (reviewed in Pogoda and Hammerschmidt; 2009) synonym: "pituitary placode" RELATED [ZFA:0001198] xref: EFO:0000229 xref: TAO:0001198 xref: XAO:0004208 xref: ZFA:0001198 is_a: UBERON:0002546 ! cranial placode is_a: UBERON:0011814 {source="NBK53175"} ! non-neurogenic ectodermal placode relationship: develops_from UBERON:0005497 {source="ZFA"} ! non-neural ectoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009123 name: otic cup namespace: uberon is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0003069 {source="NBK53175"} ! otic placode property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009142 name: entire mesenchyme namespace: uberon alt_id: UBERON:0003313 comment: consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) xref: EHDAA2:0001113 xref: EHDAA:177 xref: EMAPA:16097 is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009143 name: developing esophageal region namespace: uberon comment: consider merging into esophagus synonym: "esophageal region" BROAD [] synonym: "oesophageal region" BROAD [EMAPA:16700] synonym: "oesophageal region" EXACT [RETIRED_EHDAA2:0000654] xref: EMAPA:16700 xref: RETIRED_EHDAA2:0000654 xref: SCTID:245404000 is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0001041 {source="EHDAA2"} ! foregut property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009145 name: pharyngeal region namespace: uberon xref: EMAPA:16549 xref: RETIRED_EHDAA2:0001454 is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0001041 {source="EHDAA2"} ! foregut relationship: part_of UBERON:0001557 {source="EHDAA2"} ! upper respiratory tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009196 name: indifferent external genitalia namespace: uberon subset: organ_slim xref: EHDAA2:0004021 is_a: UBERON:0004176 {source="cjm"} ! external reproductive organ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009201 name: nephric duct namespace: uberon def: "A nephric duct is a tube that drains a primitive kidney[GO]." [GO:0072176] comment: pronephric duct or mesonephric duct is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0004819 ! kidney epithelium is_a: UBERON:0006553 ! renal duct is_a: UBERON:0006555 ! excretory tube relationship: part_of UBERON:0002113 ! kidney property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009202 name: vasa recta descending limb namespace: uberon comment: This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the descending limb xref: KUPO:0001002 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0004726 {source="KUPO"} ! vasa recta property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009210 name: pharyngeal membrane namespace: uberon def: "a thin fold of ectoderm and endoderm that separates the pharyngeal pouches from the branchial clefts in a developing embryo." [http://musom.marshall.edu/anatomy/grosshom/z_devbranc.html] synonym: "pharyngeal membrane" EXACT [] xref: ncithesaurus:Pharyngeal_Membrane xref: UMLS:C1519040 is_a: UBERON:0002050 ! embryonic structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009213 name: pharyngeal membrane of 1st arch namespace: uberon def: "separates the first pharyngeal groove from the first pharyngeal pouch." [ISBN10:1416037055] comment: check EMAPA - 3 terms appear to match. We follow EMAPA in making each membrane part of the arch with the same number, though in fact it is between these arches synonym: "1st branchial membrane" EXACT [EMAPA:16992] synonym: "1st pharyngeal membrane" EXACT [VHOG:0001427] synonym: "future tympanic membrane" EXACT [EMAPA:17281] synonym: "tympanic membrane primordium" EXACT [ISBN10:1416037055] xref: EHDAA:3788 xref: EMAPA:16121 xref: EMAPA:16992 xref: EMAPA:17281 xref: VHOG:0001427 is_a: UBERON:0009210 ! pharyngeal membrane relationship: part_of UBERON:0004362 {source="EMAPA"} ! pharyngeal arch 1 property_value: homology_notes "In all vertebrates, the endodermal epithelium lining each pouch contacts the surface ectoderm of the clefts to form a series of bilayered branchial membranes, that break down in fish to form the gill openings.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001427", ontology="VHOG", source="ISBN:978-0124020603 Kaufman MH, Bard JBL, The anatomical basis of mouse development (1999) p.72", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009497 name: epithelium of foregut-midgut junction namespace: uberon def: "An epithelium that is part of a foregut-midgut junction." [OBOL:automatic] subset: emapa_ehdaa2 xref: EHDAA2:0000573 xref: EMAPA:16564 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0003929 ! gut epithelium relationship: part_of UBERON:0006235 ! foregut-midgut junction property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009550 name: endoderm of foregut-midgut junction namespace: uberon def: "An endoderm that is part of a foregut-midgut junction." [OBOL:automatic] subset: emapa_ehdaa2 xref: EHDAA2:0000572 xref: EMAPA:18403 is_a: UBERON:0000925 ! endoderm is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0006235 ! foregut-midgut junction property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009566 name: intestinal submucosa namespace: uberon def: "A submucosa that is part of a intestine." [OBOL:automatic] synonym: "submucosa of intestine" EXACT [FMA:15696] xref: FMA:15696 is_a: UBERON:0000009 ! submucosa is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0001262 {source="FMA"} ! wall of intestine property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009569 name: subdivision of trunk namespace: uberon subset: non_informative synonym: "region of trunk" EXACT [FMA:25054] synonym: "trunk subdivision" EXACT [FMA:25054] xref: FMA:25054 xref: SCTID:22943007 is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0002100 ! trunk property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009616 name: presumptive midbrain namespace: uberon def: "A presumptive structure that develops_into a midbrain." [OBOL:automatic] comment: TODO - unify naming conventions synonym: "early midbrain" RELATED [UBERON:cjm] synonym: "future midbrain" RELATED [UBERON:cjm] synonym: "mesencephalon" RELATED [EHDAA2:0000615] synonym: "presumptive mesencephalon" EXACT [ZFA:0000148] xref: EFO:0003432 xref: EHDAA2:0000615 xref: TAO:0000148 xref: ZFA:0000148 is_a: UBERON:0006598 ! presumptive structure relationship: develops_from UBERON:0003080 ! anterior neural tube relationship: develops_from UBERON:0010286 {source="ZFA"} ! midbrain neural tube relationship: part_of UBERON:0006238 {source="ZFA"} ! future brain property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009617 name: head paraxial mesoderm namespace: uberon def: "Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles." [PMID:21610022] synonym: "cephalic paraxial mesoderm" EXACT [UBERON:cjm] synonym: "head paraxial mesenchyme" EXACT [EHDAA2:0000736] xref: EHDAA2:0000736 xref: EHDAA:364 xref: EMAPA:16171 is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: develops_from UBERON:0000926 {source="EHDAA2"} ! mesoderm relationship: part_of UBERON:0003077 ! paraxial mesoderm relationship: part_of UBERON:0005253 {source="EHDAA2"} ! head mesenchyme property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009618 name: trunk paraxial mesoderm namespace: uberon synonym: "trunk and cervical paraxial mesenchyme" EXACT [EHDAA2:0002094] synonym: "trunk paraxial mesenchyme" RELATED [] xref: EHDAA2:0002094 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005256 ! trunk mesenchyme is_a: UBERON:0005291 ! embryonic tissue relationship: develops_from UBERON:0000926 {source="EHDAA2"} ! mesoderm relationship: part_of UBERON:0003077 ! paraxial mesoderm relationship: part_of UBERON:0005256 {source="EHDAA2"} ! trunk mesenchyme property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009623 name: spinal nerve root namespace: uberon def: "The paired bundles of nerve fibers entering and leaving the spinal cord at each segment. The dorsal and ventral nerve roots join to form the mixed segmental spinal nerves. The dorsal roots are generally afferent, formed by the central projections of the spinal (dorsal root) ganglia sensory cells, and the ventral roots efferent, comprising the axons of spinal motor and autonomic preganglionic neurons. There are, however, some exceptions to this afferent/efferent rule." [MESH:A08.800.800.720.725] comment: ZFA has part_of to spinal cord but this causes spatial disjointness violations (CNS/PNS) synonym: "root of spinal nerve" EXACT [FMA:14060] synonym: "spinal neural root" EXACT [FMA:14060] xref: FMA:14060 xref: GAID:717 xref: MESH:A08.800.800.720.725 xref: ncithesaurus:Spinal_Nerve_Root xref: SCTID:362436008 xref: UMLS:C0037940 xref: ZFA:0005578 is_a: UBERON:0002211 {source="FMA"} ! nerve root is_a: UBERON:0004732 ! segmental subdivision of nervous system relationship: part_of UBERON:0001780 {source="FMA"} ! spinal nerve property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009661 name: midbrain nucleus namespace: uberon def: "Nucleus located in the midbrain." [ZFIN:curator] xref: SCTID:279285003 xref: TAO:0002209 xref: ZFA:0001665 is_a: UBERON:0002308 ! nucleus of brain is_a: UBERON:0002950 ! regional part of midbrain relationship: part_of UBERON:0001891 ! midbrain property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009663 name: telencephalic nucleus namespace: uberon def: "A nucleus of brain that is part of a telencephalon." [OBOL:automatic] xref: TAO:0002178 xref: ZFA:0001660 is_a: UBERON:0002308 ! nucleus of brain is_a: UBERON:0002791 ! regional part of telencephalon relationship: part_of UBERON:0001893 ! telencephalon property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009664 name: gut mesentery namespace: uberon xref: EHDAA2:0004566 is_a: UBERON:0000477 {source="EHDAA2"} ! anatomical cluster property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009722 name: entire pharyngeal arch endoderm namespace: uberon synonym: "pharyngeal arch endoderm" RELATED [EHDAA2:0004621] xref: EHDAA2:0004621 is_a: UBERON:0000477 {source="EHDAA2"} ! anatomical cluster is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0003929 {source="EHDAA2"} ! gut epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009753 name: adrenal gland cortex zone namespace: uberon synonym: "adrenal cortical region" EXACT [FMA:69086] synonym: "region of adrenal cortex" RELATED [FMA:69086] xref: FMA:69086 xref: MA:0001887 xref: SCTID:68594002 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0001235 {source="MA"} ! adrenal cortex property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009773 name: renal tubule namespace: uberon def: "A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis." [GO:0061333, GOC:dph, GOC:mtg_kidney_jan10] subset: grouping_class synonym: "renal tubule (generic)" EXACT [UBERON:cjm] synonym: "tubule of excretory system" EXACT [OBOL:automatic, UBERON:cjm] is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0006555 ! excretory tube relationship: part_of UBERON:0001008 ! excretory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009778 name: pleural sac namespace: uberon def: "Serous sac, which has as parts the pleura and the pleural cavity. Examples: There are only two canonical instances, right and left pleural sacs." [FMA:9690] xref: FMA:9690 xref: SCTID:361996004 is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0005906 {source="FMA"} ! serous sac relationship: part_of UBERON:0001558 {source="FMA"} ! lower respiratory tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009842 name: acinus namespace: uberon def: "An acinus refers to any cluster of cells that resembles a many-lobed \"berry,\" such as a raspberry (acinus is Latin for berry). The berry-shaped termination of an exocrine gland, where the secretion is produced is acinar in form, as is the alveolar sac containing multiple alveoli in the lungs." [Wikipedia:Acinus] synonym: "acini" RELATED PLURAL [Wikipedia:Acinus] synonym: "glandular acinus" RELATED [] xref: FMA:55588 xref: http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png is_a: UBERON:0000064 ! organ part property_value: has_relational_adjective "acinar" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009843 name: prostate epithelial cord namespace: uberon def: "A solid cord of prostate epithelium." [GO:0060527, OBOL:automatic, PMID:18977204] comment: Complexity is conferred on the prostate during a postnatal development phase known as branching morphogenesis. Solid cords of prostate epithelium formed in utero elongate postnatally and their tips are bifurcated into primary, secondary, and tertiary branches in a pattern that is unique for each prostate lobe. Branching morphogenesis proceeds differentially for each of the three mouse prostate lobes (ventral, dorsolateral, and anterior) and is completed by about postnatal day 20 in mice, providing each lobe with unique glandular architecture [5]. It is important to note that the developing human prostate undergoes a similar series of morphogenetic events especially during prostatic bud formation, but gives rise to a mature glandular prostate that is unique from the rodent and features peripheral, central, and transitional zones[PMID:18977204] synonym: "cord of prostate epithelium" EXACT [PMID:18977204] synonym: "epithelial cord of prostate" EXACT [] is_a: UBERON:0000428 ! prostate epithelium is_a: UBERON:0005154 ! epithelial cord relationship: part_of UBERON:0002367 ! prostate gland property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009845 name: urogenital sinus mesenchyme namespace: uberon def: "Mesenchyme that is part of a primitive urogenital sinus." [OBOL:automatic] comment: Androgen receptor (AR) activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth synonym: "UGM" EXACT [PMID:18977204] xref: EHDAA2:0004061 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0000164 ! primitive urogenital sinus property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009846 name: embryonic cloacal epithelium namespace: uberon def: "An epithelium that is part of a embryonic cloaca." [OBOL:automatic] synonym: "cloacal epithelium" BROAD [EHDAA2:0004585] xref: EHDAA2:0004585 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006554 ! urinary system structure is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0012481 ! cloacal epithelium relationship: develops_from UBERON:0003353 {source="EHDAA2"} ! epithelium of hindgut relationship: part_of UBERON:0000163 ! embryonic cloaca relationship: part_of UBERON:0003929 {source="EHDAA2"} ! gut epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009847 name: prostate field namespace: uberon def: "a specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop." [GO:0060515, GOC:dph, PMID:18977204] synonym: "prostate primordium" EXACT [] is_a: UBERON:0004902 ! urogenital sinus epithelium relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0004902 {source="PMID:18977204"} ! urogenital sinus epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009854 name: digestive tract diverticulum namespace: uberon def: "Branch or outpocketing of the digestive tract." [UBERON:cjm] synonym: "diverticulum of gut" RELATED [FBbt:00100316] synonym: "intestinal pouch" RELATED [] xref: FBbt:00100316 is_a: UBERON:0004921 ! subdivision of digestive tract is_a: UBERON:0009856 ! sac relationship: part_of UBERON:0001555 ! digestive tract property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009856 name: sac namespace: uberon synonym: "diverticulum" RELATED [] synonym: "pouch" EXACT [] xref: galen:Diverticulum is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009859 name: endosteum namespace: uberon def: "a thin layer of connective tissue that lines the surface of the bony tissue that forms the medullary cavity of long bones" [Wikipedia:Endosteum] xref: FMA:32692 xref: http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg xref: ncithesaurus:Endosteum xref: SCTID:57487002 xref: UMLS:C0222658 is_a: UBERON:0000158 ! membranous layer relationship: part_of UBERON:0002495 ! long bone property_value: has_relational_adjective "endosteal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009870 name: zone of stomach namespace: uberon def: "A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland." [ISBN10:0073040584, Wikipedia:Stomach#Sections] comment: Editor notes: We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach synonym: "gastric zone" EXACT [FMA:14558] synonym: "region of stomach" EXACT [] synonym: "section of stomach" EXACT [] xref: FMA:14558 xref: http://upload.wikimedia.org/wikipedia/commons/thumb/2/29/Regions_of_stomach.svg/500px-Regions_of_stomach.svg.png xref: SCTID:245415005 is_a: UBERON:0009034 ! stomach region relationship: part_of UBERON:0000945 {source="Obol"} ! stomach property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009881 name: anterior lateral plate mesoderm namespace: uberon synonym: "ALPM" EXACT [ZFA:0005041] xref: EFO:0003704 xref: TAO:0005041 xref: ZFA:0005041 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009889 name: secondary heart field namespace: uberon def: "extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract." [PMID:17276708] comment: Taxon notes: "In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11–14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested" [PMID:17276708] synonym: "anterior heart field" EXACT [PMID:17276708] synonym: "anterior/second heart field" EXACT [Geisha:syn, NCBITaxon:8782] synonym: "second heart field" EXACT [XAO:0004186] synonym: "SHF" RELATED [XAO:0004186] xref: XAO:0004186 is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0000926 ! mesoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009911 name: lobule namespace: uberon subset: upper_level xref: FMA:45737 xref: ncithesaurus:Lobule xref: UMLS:C0921005 is_a: UBERON:0000064 ! organ part property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009916 name: wall of ureter namespace: uberon def: "An anatomical wall that is part of a ureter." [OBOL:automatic] synonym: "ureteral wall" EXACT [FMA:15888] xref: FMA:15888 xref: SCTID:279397004 is_a: UBERON:0000060 ! anatomical wall is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0000056 ! ureter property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009919 name: ureter smooth muscle namespace: uberon def: "the smooth muscle tissue surrounding the epithelium of the ureter" [MP:0011426] synonym: "ureteral smooth muscle" EXACT [MP:0011426] synonym: "ureteral smooth muscle layer" EXACT [EMAPA:28844] xref: EMAPA:28844 is_a: UBERON:0000078 ! mixed ectoderm/mesoderm/endoderm-derived structure is_a: UBERON:0001135 ! smooth muscle tissue is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0000056 ! ureter relationship: part_of UBERON:0006855 ! ureter muscle layer property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009950 name: olfactory bulb plexiform layer namespace: uberon comment: check if the NIF class is actually a grouping class synonym: "plexiform layer" BROAD [NIF_GrossAnatomy:nlx_anat_20090405] xref: NIF_GrossAnatomy:nlx_anat_20090405 is_a: UBERON:0004001 {source="NIF_GrossAnatomy"} ! olfactory bulb layer property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009954 name: vomeronasal system namespace: uberon def: "a vertebrate nasal chemosensory system that is responsible for detecting intraspecific pheromonal cues as well as environmental odorants" [] comment: Editor note: check relationship to olfactory system. Evolution: The morphological components of the VNS are found only in tetrapods, but the genetic components of the system have been found in teleost fish, in addition to tetrapods. In tetrapods, the VNS was thought to be the olfactory system for detecting pheromones, while the main olfactory system detected general odorants (Scalia and Winans 1975). However, experimental evidence suggests that there is not such a clear functional distinction (Restrepo et al. 2004; Baxi, Dorries, and Eisthen 2006; Spehr et al. 2006; Kelliher 2007). Sea lampreys produce unique bile acids which act as pheromones both in migration and mate finding (Li, Sorensen, and Gallaher 1995; Li et al. 2002; Siefkes and Li 2004). However, bile acids in teleost fish are known to require components of the main olfactory signal transduction pathway (Hansen et al. 2003), and interruption of the VNS signal transduction pathway had no effect on bile acid olfactory response (Hansen et al. 2003)[Grus - EVOLUTION OF THE VOMERONASAL SYSTEM VIEWED THROUGH SYSTEM-SPECIFIC GENES] is_a: UBERON:0001032 ! sensory system relationship: part_of UBERON:0005725 ! olfactory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0009955 name: neurogenic placode namespace: uberon def: "Cranial placode with neurogenic potential[cjm]. Neurogenic placodes are transient ectodermal thickenings that form at the border of the neural plate and epidermis and give rise to sensory neurons of the cranial ganglia[ZFA]. The neurogenic placodes give rise to parts of various nerves and ganglia, the olfactory organ, parietal eye, parts of the inner ear, and the lateral line. There are 2 major series of neurogenic placodes, the dorsolateral and ventrolateral or epibranchial[PMID]" [PMID:11523831, Wikipedia:Neurogenic_placodes, ZFA:0001309] comment: Includes: trigeminal, otic, lateral line and epibranchial placodes. Taxon notes: While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000)[NBK53171] synonym: "neurogenic placodes" EXACT PLURAL [ZFA:0001309] synonym: "placodae neurogenicae" RELATED LATIN [Wikipedia:Neurogenic_placodes] xref: EFO:0003460 xref: TAO:0001309 xref: ZFA:0001309 is_a: UBERON:0002546 {source="cjm"} ! cranial placode disjoint_from: UBERON:0011814 ! non-neurogenic ectodermal placode property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010009 name: aggregate regional part of brain namespace: uberon def: "A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF]." [NIF_GrossAnatomy:nlx_anat_20090509] synonym: "set of nuclei of neuraxis" EXACT [FMA:256381] xref: FMA:256381 xref: NIF_GrossAnatomy:nlx_anat_20090509 is_a: UBERON:0002616 {source="NIF"} ! regional part of brain property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010011 name: collection of basal ganglia namespace: uberon comment: Editor note: it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the collection of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done. synonym: "basal ganglia" EXACT [FMA:84013] synonym: "basal ganglia set" EXACT [FMA:84013] synonym: "set of basal ganglia" EXACT [FMA:84013] xref: BM:Tel-BG xref: FMA:84013 xref: GAID:617 xref: MA:0000184 xref: MESH:A08.186.211.730.885.105 xref: ncithesaurus:Basal_Ganglia xref: NIF_GrossAnatomy:birnlex_826 xref: UMLS:C0004781 xref: VHOG:0001696 is_a: UBERON:0002791 ! regional part of telencephalon is_a: UBERON:0010009 {source="FMA"} ! aggregate regional part of brain relationship: part_of UBERON:0000454 {source="FMA"} ! cerebral subcortex relationship: part_of UBERON:0001893 {source="NIF"} ! telencephalon property_value: homology_notes "All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001696", ontology="VHOG", source="DOI:10.1016/j.cub.2011.05.001 Stephenson-Jones M, Samuelsson E, Ericsson J, Robertson B, Grillner S, Evolutionary conservation of the basal ganglia as a common vertebrate mechanism for action selection. Current Biology (2011)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010039 name: food storage organ namespace: uberon def: "An organ of the digestive tract that is capable of retaining and storing food" [UBERON:cjm] comment: This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates subset: functional_classification subset: grouping_class xref: TADS:0000172 xref: TGMA:0001041 is_a: UBERON:0000062 ! organ is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0005409 ! gastrointestinal system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010047 name: oral gland namespace: uberon alt_id: UBERON:0003293 def: "Gland of the epithelium lining the oral cavity. The most common are the salivary glands." [ISBN10:0073040584] comment: Note that Kardong classifies lacrimal glands here synonym: "buccal gland" EXACT [] synonym: "gland of oral opening" EXACT [OBOL:automatic] synonym: "gland of oral part of face" EXACT [OBOL:automatic] synonym: "gland of subdivision of mouth" EXACT [OBOL:automatic] synonym: "oral cavity gland" RELATED [OBOL:automatic] synonym: "oral opening gland" EXACT [OBOL:automatic] synonym: "oral part of face gland" EXACT [OBOL:automatic] synonym: "oral region gland" EXACT [OBOL:automatic] synonym: "subdivision of mouth gland" EXACT [OBOL:automatic] xref: EHDAA2:0001327 xref: EHDAA:2181 xref: EMAPA:16572 xref: EMAPA:16723 xref: SCTID:25421004 xref: VHOG:0000652 is_a: UBERON:0002365 ! exocrine gland is_a: UBERON:0003408 ! gland of gut is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000165 ! mouth property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010077 name: cuboidal epithelium namespace: uberon def: "An epithelium consisting of cuboidal epithelial cells." [Wikipedia:Cuboidal_epithelium] comment: AO notes: in NCIT this is glandular. Editor notes: TODO - coordinate with CL, add cuboidal cell xref: ncithesaurus:Cuboidal_Epithelium xref: UMLS:C0682577 is_a: UBERON:0000483 ! epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010092 name: future metencephalon namespace: uberon def: "A developing anatomical structure that develops_into a metencephalon." [OBOL:automatic] xref: EHDAA2:0000623 is_a: UBERON:0002616 ! regional part of brain is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0002028 ! hindbrain property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010131 name: conducting tissue of heart namespace: uberon synonym: "specialized conducting tissue of heart" EXACT [FMA:83378] synonym: "specialized muscle tissue of heart" EXACT [FMA:83378] xref: EHDAA2:0004528 xref: FMA:83378 is_a: UBERON:0001133 {source="FMA"} ! cardiac muscle tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010133 name: neuroendocrine gland namespace: uberon def: "An endocrine gland that is part of a nervous system." [OBOL:automatic] xref: MA:0000720 is_a: UBERON:0002368 ! endocrine gland is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001016 ! nervous system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010141 name: primitive sex cord of indifferent gonad namespace: uberon def: "A sex cord that is part of a indifferent gonad." [OBOL:automatic] comment: Usage notes: note that this represents the indifferent structure. synonym: "indifferent sex cord" EXACT [] synonym: "primitive sex cords" EXACT [EHDAA2:0004051] xref: EHDAA2:0004051 is_a: UBERON:0004909 ! epithelium of gonad is_a: UBERON:0005295 ! sex cord relationship: develops_from UBERON:0005891 {source="EHDAA2"} ! coelomic epithelium relationship: part_of UBERON:0009117 ! indifferent gonad property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010147 name: male accessory sex gland namespace: uberon def: "Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male." [BTO:0004798] xref: BTO:0004798 is_a: UBERON:0005399 {source="BTO"} ! male reproductive gland relationship: part_of UBERON:0000079 ! male reproductive system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010188 name: protuberance namespace: uberon def: "A roughly circular bulge in a surface." [EHDAA2:0003250] xref: AEO:0000205 xref: EHDAA2:0003250 xref: FMA:82506 is_a: UBERON:0003102 {source="EHDAA2"} ! surface structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010191 name: aortic system namespace: uberon xref: EHDAA2:0004512 is_a: UBERON:0000480 {source="EHDAA2"} ! anatomical group property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010226 name: future cardiac ventricle namespace: uberon def: "Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle." [ZFA:0001719] synonym: "presumptive cardiac ventricle heart tube" EXACT [ZFA:0001719] synonym: "primordial cardiac ventricle" EXACT [FMA:71006] synonym: "primordial ventricle" EXACT [FMA:71006] xref: FMA:71006 xref: TAO:0002231 xref: ZFA:0001719 is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0004141 {source="ZFA"} ! heart tube property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010227 name: future cardiac atrium namespace: uberon def: "Multi-tissue structure that is part of the heart tube and will become the cardiac atrium." [ZFA:0001718] synonym: "presumptive atrium heart tube" EXACT [ZFA:0001718] synonym: "primordial atrium" EXACT [FMA:71005] synonym: "primordial cardiac atrium" EXACT [FMA:71005] xref: FMA:71005 xref: TAO:0002228 xref: ZFA:0001718 is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0004141 {source="ZFA"} ! heart tube property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010230 name: eyeball of camera-type eye namespace: uberon def: "The camera-type eye apart from its appendages/adnexa." [Wikipedia:Globe_(human_eye)] comment: See notes for camera-type eye synonym: "bulbus oculi" EXACT [] synonym: "eye" RELATED INCONSISTENT [] synonym: "eye globe" EXACT [VHOG:0001616] synonym: "eyeball" EXACT [FMA:12513] synonym: "globe" RELATED [HP:0100886, MIAA:0000283] xref: FMA:12513 xref: MIAA:0000283 xref: SCTID:244486005 xref: VHOG:0001616 is_a: UBERON:0000020 ! sense organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000019 {source="FMA"} ! camera-type eye property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010260 name: umbilical blood vessel namespace: uberon def: "A blood vessel that overlaps a umbilical cord." [OBOL:automatic] synonym: "umbilical cord blood vessel" EXACT [] xref: SCTID:408728001 is_a: UBERON:0001981 ! blood vessel property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010286 name: midbrain neural tube namespace: uberon def: "Portion of neural tube that gives rise to the midbrain." [ZFA:0007039] xref: TAO:0007039 xref: ZFA:0007039 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0003080 {source="ZFA"} ! anterior neural tube property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010302 name: amnioserosa namespace: uberon def: "a single extraembryonic epithelium, which closes the germband dorsally." [doi:10.1073/pnas.0709145105] comment: Editor's notes: May be obsoleted once added to insect ontology. Coordinate with cell type in CL synonym: "amnion-serosa" RELATED [BTO:0004800] xref: BTO:0004800 xref: EFO:0000250 xref: FBbt:00000095 is_a: UBERON:0010303 {source="doi:10.1073/pnas.0709145105"} ! extraembryonic epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010303 name: extraembryonic epithelium namespace: uberon def: "An epithelium that is part of a extraembryonic structure." [OBOL:automatic] synonym: "extra-embryonic epithelium" EXACT [] is_a: UBERON:0000483 ! epithelium relationship: part_of UBERON:0000478 ! extraembryonic structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010312 name: immature eye namespace: uberon def: "Developing anatomical structure that develops into the eyeball and associated structures." [ZFA:0001678] synonym: "future eye" EXACT [] xref: TAO:0002201 xref: ZFA:0001678 is_a: UBERON:0005423 ! developing anatomical structure relationship: develops_from UBERON:0003071 {evidence="definitional"} ! eye primordium property_value: external_definition "Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002201", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010313 name: neural crest-derived structure namespace: uberon def: "An anatomical structure that develops from the neural crest." [UBERON:cjm] comment: Grouping term for query purposes subset: grouping_class is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0002342 ! neural crest property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010314 name: structure with developmental contribution from neural crest namespace: uberon def: "An anatomical structure that has some part that develops from the neural crest." [UBERON:cjm] comment: Grouping term for query purposes subset: grouping_class is_a: UBERON:0000061 ! anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010316 name: germ layer / neural crest namespace: uberon is_a: UBERON:0005291 ! embryonic tissue relationship: develops_from UBERON:0002532 ! epiblast (generic) property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010323 name: cranial skeletal system namespace: uberon def: "Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus." [VSAO:0000049] comment: Note that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium. Editor notes: we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints) synonym: "cranial skeleton" NARROW [] synonym: "cranium" RELATED INCONSISTENT [ZFA:0000737] synonym: "osteocranium" NARROW [] xref: AAO:0000109 xref: AAO:0000971 xref: AAO:0010185 xref: TAO:0000737 xref: VSAO:0000049 xref: XAO:0003075 xref: ZFA:0000737 is_a: UBERON:0000075 ! subdivision of skeletal system relationship: part_of UBERON:0011137 ! axial skeletal system property_value: external_definition "Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000109", ontology="AAO", source="AAO:LAP"} property_value: external_definition "Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000737", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010363 name: endochondral element namespace: uberon def: "A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification." [VSAO:0000139] synonym: "endochondral replacement element" EXACT [VSAO:0000139] xref: VSAO:0000139 xref: XAO:0004017 xref: ZFA:0005620 is_a: UBERON:0004765 {source="VSAO"} ! skeletal element property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: seeAlso http://purl.obolibrary.org/obo/uberon/references/reference_0000009 xsd:anyURI [Term] id: UBERON:0010364 name: dermal skeleton namespace: uberon def: "Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements." [VSAO:0000035] comment: This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO synonym: "dermal skeletal system" RELATED [VSAO:curator] synonym: "dermoskeleton" RELATED [VSAO:curator] synonym: "desmoskeleton" RELATED [VSAO:curator] synonym: "exoskeleton" BROAD INCONSISTENT [VSAO:curator] xref: VSAO:0000035 xref: XAO:0004025 is_a: UBERON:0010912 {source="VSAO"} ! subdivision of skeleton property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010365 name: odontoid tissue namespace: uberon def: "Skeletal tissue that is part of the exoskeleton and derived from an odontogenic papilla." [VSAO:0000063] synonym: "dental tissue" RELATED [VSAO:curator] synonym: "odontogenic tissue" EXACT [VSAO:curator] synonym: "tooth tissue" RELATED [] xref: ncithesaurus:Tooth_Tissue xref: UMLS:C1519551 xref: VSAO:0000063 xref: XAO:0004046 xref: ZFA:0005623 is_a: UBERON:0004755 ! skeletal tissue is_a: UBERON:0010313 ! neural crest-derived structure relationship: develops_from UBERON:0001763 ! odontogenic papilla relationship: part_of UBERON:0010364 ! dermal skeleton property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010368 name: pulmonary lobule namespace: uberon xref: FMA:75739 xref: ncithesaurus:Pulmonary_Lobule is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0009911 {source="FMA"} ! lobule relationship: part_of UBERON:0002048 ! lung property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010371 name: ecto-epithelium namespace: uberon def: "Epithelium that derives from the ectoderm. Examples: epithelium of acinus of lactiferous duct, subscapular lens epithelium, epithelium of posterior surface of cornea." [FMA:69064] synonym: "ectoderm-derived epithelium" EXACT [] xref: FMA:69064 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0000924 ! ectoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010375 name: pancreas dorsal primordium namespace: uberon comment: Consider merging with dorsal pancreatic bud. Starts at CS12 in human (EHDAA2, embryology.ch 'bud anlagen') synonym: "dorsal pancreas" RELATED INCONSISTENT [FMA:79793] xref: EHDAA2:0001384 xref: FMA:79793 is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure is_a: UBERON:0001048 {source="EHDAA2"} ! primordium is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0002365 {source="EHDAA2"} ! exocrine gland is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0003921 {source="EHDAA2"} ! pancreas primordium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010376 name: pancreas ventral primordium namespace: uberon comment: Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen') synonym: "ventral pancreas" RELATED INCONSISTENT [FMA:79794] xref: EHDAA2:0001387 xref: FMA:79794 is_a: UBERON:0001048 {source="EHDAA2"} ! primordium is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0002365 {source="EHDAA2"} ! exocrine gland is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0003921 {source="EHDAA2"} ! pancreas primordium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010409 name: eye surface namespace: uberon xref: MA:0002486 is_a: UBERON:0003102 ! surface structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000019 ! camera-type eye property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010422 name: primary nodular lymphoid tissue namespace: uberon def: "A lymphoid follicle containing naive B cells" [CL:tm] comment: Location notes: The cortex of lymph nodes, the white pulp of spleen, and mucosa associated lymphoid tissue all have these primary follicles synonym: "primary follicle" RELATED [] synonym: "primary lymphoid follicle" EXACT [] synonym: "primary lymphoid nodule" EXACT [FMA:55223] xref: FMA:55223 is_a: UBERON:0000444 {source="FMA"} ! lymphoid follicle property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010498 name: pseudostratified columnar epithelium namespace: uberon def: "A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels." [http://medical-dictionary.thefreedictionary.com/pseudostratified+epithelium, Wikipedia:Pseudostratified_columnar_epithelium] comment: AO notes: glandular in NCIT; we consider the two NCIT terms synonymous. Function notes: Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia. xref: FMA:45572 xref: ncithesaurus:Pseudostratified_Columnar_Epithelium xref: ncithesaurus:Pseudostratified_Epithelium xref: UMLS:C0836138 xref: UMLS:C1514590 is_a: UBERON:0000485 {source="FMA"} ! simple columnar epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010499 name: pseudostratified ciliated columnar epithelium namespace: uberon def: "Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile." [NCIT:NCIT] synonym: "epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)" EXACT [FMA:13146] xref: FMA:13146 xref: ncithesaurus:Pseudostratified_Columnar_Ciliated_Epithelium xref: UMLS:C0506992 is_a: UBERON:0007592 ! ciliated columnar epithelium is_a: UBERON:0010498 ! pseudostratified columnar epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010523 name: microcirculatory vessel namespace: uberon def: "A portion of tissue that consists of a tube composed of epithelial cells that connects larger vessels." [ZFA:0005251] synonym: "microcirculatory vessels" RELATED PLURAL [TAO:0005251] xref: TAO:0005251 xref: ZFA:0005251 is_a: UBERON:0000055 ! vessel relationship: part_of UBERON:0002049 {source="ZFA"} ! vasculature property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010532 name: primitive nephron namespace: uberon synonym: "developing nephron" BROAD [] synonym: "primitive nephron" BROAD [] is_a: UBERON:0001285 {source="ZFA-inferred"} ! nephron is_a: UBERON:0003914 {source="EHDAA2-inferred"} ! epithelial tube is_a: UBERON:0004819 ! kidney epithelium is_a: UBERON:0006555 ! excretory tube relationship: develops_from UBERON:0004209 {source="EHDAA2"} ! renal vesicle relationship: part_of UBERON:0003918 ! kidney mesenchyme property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010743 name: meningeal cluster namespace: uberon def: "The collection of all meningeal layers that line a central nervous system." [UBERON:cjm] comment: In some primitive organisms, the meningeal cluster includes only the primitive meninx synonym: "cluster of meninges" EXACT [FMA:231572] synonym: "meninges" EXACT [FMA:231572] xref: EHDAA2:0004661 xref: FMA:231572 xref: SCTID:362879001 is_a: UBERON:0000477 ! anatomical cluster is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001017 ! central nervous system property_value: has_relational_adjective "meningeal" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010912 name: subdivision of skeleton namespace: uberon def: "Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints." [UBERON:cjm, UBERONREF:0000003] comment: AO notes: VSAO def logically wrong subset: non_informative synonym: "skeletal subdivision" EXACT [VSAO:0000042] synonym: "subdivision of skeleton (in vivo)" RELATED [FMA:23879] xref: FMA:23879 xref: SCTID:129140006 xref: VSAO:0000042 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0000075 {source="UBERONREF:0000003"} ! subdivision of skeletal system relationship: part_of UBERON:0004288 {source="VSAO"} ! skeleton property_value: external_definition "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000042", ontology="VSAO", source="VSAO:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010913 name: vertebral element namespace: uberon def: "Skeletal element that forms around the notochord and is part of the vertebral column." [VSAO:0000184] comment: Note that Uberon includes a distinct subclass for bony vertebra xref: VHOG:0001143 xref: VSAO:0000184 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004765 {source="VSAO"} ! skeletal element relationship: develops_from UBERON:0003089 {source="cjm"} ! sclerotome relationship: part_of UBERON:0001130 {source="VSAO"} ! vertebral column property_value: has_relational_adjective "vertebral" xsd:string property_value: homology_notes "In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001143", ontology="VHOG", source="DOI:10.1016/j.cub.2011.07.014 Janvier P, Comparative anatomy: all vertebrates do have vertebrae. Current Biology (2011)", source="http://bgee.unil.ch/"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010959 name: craniocervical muscle namespace: uberon def: "A muscle organ that is part of a craniocervical region." [OBOL:automatic] synonym: "muscle of head and neck" RELATED [] synonym: "muscle of head or neck" EXACT [] xref: ncithesaurus:Head_and_Neck_Muscle xref: UMLS:C0448281 is_a: UBERON:0001630 ! muscle organ relationship: part_of UBERON:0007811 ! craniocervical region property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0010996 name: articular cartilage of joint namespace: uberon def: "A thin layer of cartilage, usually hyaline, on the articular surface of bones in synovial joints." [BTO:0001572] subset: uberon_slim subset: vertebrate_core synonym: "articular cartilage" EXACT [MA:0000487] synonym: "cartilago articularis" EXACT [FMA:12264] synonym: "hyaline cartilage" RELATED [BTO:0001572] xref: BTO:0001572 xref: EFO:0001902 xref: FMA:12264 xref: GAID:101 xref: galen:ArticularCartilage xref: MA:0000487 xref: MESH:A02.165.165 xref: ncithesaurus:Articular_Cartilage xref: SCTID:305026006 xref: UMLS:C0007303 is_a: UBERON:0001994 {source="MA"} ! hyaline cartilage relationship: part_of UBERON:0002217 {source="Wikipedia"} ! synovial joint property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011094 name: vertebra cartilaginous condensation namespace: uberon def: "A cartilaginous condensation that is part of a vertebral column." [OBOL:automatic] comment: AO notes: This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups synonym: "vertebral cartilage condensation" EXACT [VHOG:0000584] xref: VHOG:0000584 is_a: UBERON:0005863 ! cartilaginous condensation is_a: UBERON:0010913 ! vertebral element relationship: develops_from UBERON:0011095 ! vertebra pre-cartilage condensation relationship: part_of UBERON:0001130 ! vertebral column property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011095 name: vertebra pre-cartilage condensation namespace: uberon def: "A pre-cartilage condensation that is part of a vertebral column." [OBOL:automatic] synonym: "vertebral pre-cartilage condensation" EXACT [VHOG:0000582] xref: VHOG:0000582 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005866 ! pre-cartilage condensation relationship: develops_from UBERON:0003089 {source="EHDAA2-abduced"} ! sclerotome relationship: part_of UBERON:0001130 ! vertebral column property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011134 name: nonsynovial joint namespace: uberon def: "Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis." [FMA:7491] synonym: "solid joint" EXACT [FMA:7491] xref: FMA:7491 is_a: UBERON:0000982 {source="FMA"} ! skeletal joint property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011135 name: intervertebral cartilage namespace: uberon def: "A cartilage element that lies between two successive vertebral centra." [ISBN10:0073040584] xref: AAO:0000795 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0007844 ! cartilaginous element relationship: part_of UBERON:0001468 {source="FMA", source="MA"} ! intervertebral joint property_value: external_definition "Block of cartilage, which usually ossifies, that lies between successive vertebral centra.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000795", ontology="AAO", source="AAO:Trueb_1973"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011137 name: axial skeletal system namespace: uberon def: "Subdivision of the skeletal system which consists of the axial skeleton plus associated joints." [UBERON:cjm] xref: FMA:7483 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011138 name: post-cranial axial skeletal system namespace: uberon def: "Subdivision of the skeletal system which consists of the post-cranial axial skeleton plus associated joints." [UBERON:cjm] synonym: "axial skeletal system" BROAD [http://purl.obolibrary.org/obo/uberon/references/reference_0000008] is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system is_a: UBERON:0004120 ! mesoderm-derived structure relationship: develops_from UBERON:0003089 {source="cjm"} ! sclerotome property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: seeAlso http://purl.obolibrary.org/obo/uberon/references/reference_0000003 xsd:anyURI [Term] id: UBERON:0011143 name: upper urinary tract namespace: uberon def: "Subdivision of urinary system which consists of the kidney and the ureters." [FMA:45658] xref: FMA:45658 xref: galen:UpperUrinaryTract xref: SCTID:181413006 is_a: UBERON:0000477 ! anatomical cluster is_a: UBERON:0006554 ! urinary system structure relationship: part_of UBERON:0001008 {source="FMA"} ! excretory system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011148 name: submucosal gland namespace: uberon def: "Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue." [BTO:0003751, Wikipedia:Submucosal_glands] xref: BTO:0003751 is_a: UBERON:0000414 ! mucous gland relationship: part_of UBERON:0000009 ! submucosa property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011156 name: facial skeleton namespace: uberon def: "Subdivision of skull that consists of the facial bones." [http://www.bartleby.com/107/37.html, MP:0005274, UBERON:cjm, Wikipedia:Facial_skeleton] synonym: "facial bone" RELATED [MA:0000318] synonym: "facial skeleton" EXACT [FMA:53673] synonym: "ossa facialia" RELATED LATIN [Wikipedia:Facial_skeleton] synonym: "ossa faciei" RELATED LATIN [Wikipedia:Facial_skeleton] synonym: "viscerocranium" RELATED INCONSISTENT [MA:0000318] xref: EHDAA2:0002206 xref: EHDAA:8361 xref: EMAPA:18022 xref: FMA:53673 xref: http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg xref: MA:0000318 is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0011158 {source="FMA"} ! primary subdivision of skull relationship: develops_from UBERON:0002342 {source="PMID:11523816"} ! neural crest relationship: part_of UBERON:0001456 {source="FMA"} ! face property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011158 name: primary subdivision of skull namespace: uberon def: "The skull can be divided into two: the neurocranium and the facial skeleton" [] subset: non_informative synonym: "skull subdivision" EXACT [FMA:54964] synonym: "subdivision of skull" EXACT [FMA:54964] xref: FMA:54964 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system relationship: part_of UBERON:0003129 ! skull property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011159 name: primary subdivision of cranial skeletal system namespace: uberon subset: non_informative is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system relationship: part_of UBERON:0010323 ! cranial skeletal system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011216 name: organ system subdivision namespace: uberon def: "Anatomical structure, which consists of a specific set of the members of (predominantly) one organ or organ part subclass interconnected by zones of continuity or body substances; is demarcated from other subdivisions of the same organ system by one or more zones of continuity or anatomical lines; together with other subdivisions of the same organ system, it constitutes an organ system. Examples: rib cage, facial skeleton, portal system, central nervous system, upper respiratory tract, muscle group of back." [FMA:67509] subset: upper_level xref: FBbt:00007330 xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0000477 ! anatomical cluster relationship: part_of UBERON:0000467 ! anatomical system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011222 name: intra-ocular muscle namespace: uberon synonym: "intrinsic muscle of eyeball" EXACT [] synonym: "intrinsic ocular muscle" EXACT [EMAPA:18808] xref: AAO:0010038 xref: EMAPA:18808 xref: FMA:49150 is_a: UBERON:0004277 ! eye muscle relationship: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0003386 {source="EMAPA"} ! smooth muscle of eye property_value: external_definition "Muscles within the eye (bulbus oculi).[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010038", ontology="AAO", source="AAO:EJS"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011249 name: appendicular skeletal system namespace: uberon def: "Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints." [UBERON:cjm] xref: FMA:7484 xref: VHOG:0001666 xref: VSAO:0000306 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system property_value: external_definition "Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000306", ontology="VSAO", source="UBERON:cjm"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011272 name: embryonic skin basal layer namespace: uberon comment: Editor notes: compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm' synonym: "basal cell layer of skin" RELATED [] synonym: "outer epithelium of body" RELATED [Wikipathways:WP2062] xref: EHDAA2:0001845 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0010371 ! ecto-epithelium relationship: develops_from UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0002199 {source="EHDAA2"} ! integument property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011300 name: gray matter of telencephalon namespace: uberon def: "A portion of gray matter of neuraxis that is part of a telencephalon." [OBOL:automatic] xref: FMA:83911 is_a: UBERON:0003528 ! brain grey matter relationship: part_of UBERON:0001893 ! telencephalon property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011362 name: cranial blood vasculature namespace: uberon def: "A blood vasculature that is part of a head." [OBOL:automatic] synonym: "cranial blood vessels" RELATED PLURAL [TAO:0005297] synonym: "set of blood vessels of head" EXACT [] xref: TAO:0005297 xref: ZFA:0005297 is_a: UBERON:0002200 ! vasculature of head is_a: UBERON:0004537 ! blood vasculature relationship: part_of UBERON:0000033 ! head property_value: external_definition "Blood vessel part of cranial vasculature.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005297", ontology="TAO", source="ZFIN:curator"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011585 name: cell condensation namespace: uberon def: "Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995)." [VSAO:0000006] comment: Editor notes: consider obsoleting, coordinate with VSAO xref: VSAO:0000006 xref: XAO:0004021 is_a: UBERON:0000061 {source="VSAO"} ! anatomical structure property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011587 name: pre-dentine namespace: uberon def: "Odontogenic tissue that is collagen-rich and characteristic of vertebrate teeth and tooth-like structures (e.g., odontodes) deposited by preodontoblasts and odontoblasts that are typically excluded from the matrix[VSAO]." [VSAO:0000071] synonym: "pre-dentine tissue" EXACT [VSAO:curator] synonym: "predentin" EXACT [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3360947] synonym: "predentine tissue" EXACT [VSAO:curator] xref: VSAO:0000071 xref: XAO:0004052 is_a: UBERON:0010365 {source="VSAO"} ! odontoid tissue relationship: develops_from UBERON:0000924 ! ectoderm relationship: develops_from UBERON:0002342 {source="UBERONREF:0000002"} ! neural crest property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011588 name: pre-enamel namespace: uberon def: "Odontogenic tissue that is avascular non-mineralized matrix that is deposited by preameloblast and ameloblasts that are excluded from the matrix." [VSAO:0000066] synonym: "pre-enamel tissue" EXACT [VSAO:curator] synonym: "preenamel tissue" EXACT [VSAO:curator] xref: VSAO:0000066 xref: XAO:0004202 is_a: UBERON:0010365 {source="VSAO"} ! odontoid tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011595 name: jaw region namespace: uberon comment: there are two jaw regions: the upper and lower. Each jaw region can be subdivided into left and right halves is_a: UBERON:0000477 ! anatomical cluster is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000165 ! mouth property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: seeAlso http://eol.org/collections/11578 xsd:anyURI [Term] id: UBERON:0011676 name: axial subdivision of organism namespace: uberon def: "A major subdivision of an organism that divides an organism along its anterio-posterior axis. In vertebrates, this is based on the vertebral column." [UBERON:cjm] subset: upper_level is_a: UBERON:0000475 ! organism subdivision property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011814 name: non-neurogenic ectodermal placode namespace: uberon is_a: UBERON:0005085 {source="cjm"} ! ectodermal placode property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011817 name: follicle placode namespace: uberon comment: Includes hair and feather follicles is_a: UBERON:0011814 {source="NBK53175"} ! non-neurogenic ectodermal placode property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011821 name: irregular connective tissue namespace: uberon def: "Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium." [FMA:20107] xref: FMA:20107 is_a: UBERON:0002384 {source="FMA"} ! connective tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011823 name: dense connective tissue namespace: uberon def: "Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets" [Wikipedia:Dense_connective_tissue] xref: AAO:0000121 xref: ncithesaurus:Dense_Connective_Tissue xref: UMLS:C1511770 is_a: UBERON:0002384 ! connective tissue disjoint_from: UBERON:0011825 ! loose connective tissue property_value: external_definition "Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]" xsd:string {date_retrieved="2012-08-29", external_class="ncithesaurus:Dense_Connective_Tissue", ontology="NCIT"} property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011825 name: loose connective tissue namespace: uberon def: "Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue." [FMA:19783, Wikipedia:Loose_connective_tissue] xref: FMA:19783 xref: ncithesaurus:Loose_Connective_Tissue xref: UMLS:C1253917 is_a: UBERON:0011821 {source="FMA"} ! irregular connective tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011892 name: anterior uvea namespace: uberon def: "Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris." [MP:0005194] synonym: "anterior part of uveal tract" EXACT [] synonym: "anterior uveal tract" EXACT [] synonym: "anterior vascular layer of the eyeball" EXACT [] synonym: "anterior vascular tunic of the eye" EXACT [] synonym: "ciliary body and iris" RELATED [] synonym: "Haller tunica vascula" EXACT [MP:0005194] synonym: "tunica vasculosa bulbosa" EXACT [MP:0005194] synonym: "vasculosa oculi" RELATED [MP:0005194] synonym: "ventral uveal tract" EXACT [] xref: SCTID:280656002 is_a: UBERON:0000481 {source="ZFA"} ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001768 {source="MP"} ! uvea relationship: part_of UBERON:0001801 ! anterior segment of eyeball property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011932 name: pilosebaceous unit namespace: uberon def: "An epidermal invagination that has as parts a hair follicle, a sebaceous gland, and arrector pili muscle" [PMC:PMC3130146, Wikipedia:Pilosebaceous_unit] synonym: "fabrica pilosebacea" EXACT [Wikipedia:Pilosebaceous_unit] synonym: "pilo-sebaceous apparatus" EXACT [FMA:70661] synonym: "pilo-sebaceous unit" EXACT [] synonym: "pilosebaceous apparatus" EXACT [] xref: FMA:70661 is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster relationship: part_of UBERON:0002416 ! integumental system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011953 name: stomach glandular region namespace: uberon def: "A stomach region that has_part a stomach glandular epithelium." [OBOL:automatic] synonym: "glandular stomach" RELATED [] xref: MA:0001613 xref: ncithesaurus:Glandular_Stomach xref: SCTID:27633001 xref: UMLS:C0227197 is_a: UBERON:0009034 ! stomach region property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0011997 name: coelom namespace: uberon def: "The structure that contains the coelemic cavity." [Wikipedia:Body_cavity, Wikipedia:Coelom] comment: Editor notes: EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. synonym: "coelem" RELATED [] synonym: "coelomic cavity" RELATED [EHDAA2:0004731] xref: EHDAA2:0004731 is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000922 {source="EHDAA2"} ! embryo property_value: has_relational_adjective "coelomic" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} [Term] id: UBERON:0012069 name: epithelium-associated lymphoid tissue namespace: uberon xref: FMA:62811 is_a: UBERON:0001744 {source="FMA"} ! lymphoid tissue property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0012274 name: columnar epithelium namespace: uberon def: "An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]" [Wikipedia:Columnar_epithelium] is_a: UBERON:0000483 ! epithelium property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0012275 name: meso-epithelium namespace: uberon def: "Epithelium that derives from the mesoderm. [Obol]" [Obol:automatic] xref: FMA:86452 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004120 ! mesoderm-derived structure relationship: develops_from UBERON:0000926 ! mesoderm property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0012292 name: embryonic cloacal fold namespace: uberon def: "One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly" [MP:0011836, MP:anna] comment: We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts synonym: "cloacal fold" BROAD [EHDAA2:0004009] xref: EHDAA2:0004009 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0012469 {source="EHDAA2"} ! external anal region property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0012313 name: 1st arch maxillary ectoderm namespace: uberon synonym: "ectoderm of maxillary component" EXACT [EMAPA:16389] xref: EHDAA2:0000039 xref: EMAPA:16389 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium relationship: develops_from UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0007238 {source="EHDAA2"} ! 1st arch maxillary component property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0012344 name: holocrine gland namespace: uberon def: "A gland whose discharged secretion contains entire secreting cells." [BTO:0002325, Wikipedia:Holocrine, Wikipedia:Holocrine_glands] xref: BTO:0002325 is_a: UBERON:0002530 {source="BTO"} ! gland property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0012361 name: internal anal region namespace: uberon xref: EHDAA2:0004588 is_a: UBERON:0000477 {source="EHDAA2"} ! anatomical cluster is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001353 {source="EHDAA2"} ! anal region property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0012429 name: hemopoietic tissue namespace: uberon def: "Blood-forming tissue, consisting of reticular fibers and cells. Also known as hemopoietic tissue" [http://encyclopedia2.thefreedictionary.com/hematopoietic+tissue] comment: Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue synonym: "haemopoietic tissue" EXACT [FMA:14073] synonym: "hematopoietic tissue" EXACT [FMA:14073] synonym: "textus haemopoieticus" EXACT [FMA:14073] xref: CALOHA:TS-2142 xref: FMA:14073 xref: ncithesaurus:Hematopoietic_Tissue xref: UMLS:C0229619 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0002390 ! hematopoietic system property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0012430 name: tunica fibrosa of eyeball namespace: uberon synonym: "fibrous layer of eyeball" EXACT [FMA:58102] synonym: "tunica fibrosa" BROAD [] xref: FMA:58102 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer relationship: part_of UBERON:0010230 ! eyeball of camera-type eye property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl property_value: present_in_taxon NCBITaxon:7955 {source="doi:10.1177/0192623311409597"} [Term] id: UBERON:0012469 name: external anal region namespace: uberon xref: EHDAA2:0004589 is_a: UBERON:0000477 {source="EHDAA2"} ! anatomical cluster is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001353 {source="EHDAA2"} ! anal region property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0012481 name: cloacal epithelium namespace: uberon def: "An epithelium that is part of a cloaca." [] is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003929 ! gut epithelium is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0000162 ! cloaca property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0013126 name: vein of abdomen namespace: uberon comment: This class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein. TODO: mirror representation of abdominal aorta subset: grouping_class synonym: "abdominal vein" EXACT [] xref: SCTID:281473003 is_a: UBERON:0001638 ! vein is_a: UBERON:0003497 ! abdomen blood vessel relationship: part_of UBERON:0000916 ! abdomen property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:1000023 name: spleen pulp namespace: uberon synonym: "malpighian corpuscles" EXACT [FMA:15845] synonym: "pulp of spleen" EXACT [] synonym: "splenic pulp" EXACT [] xref: FMA:15845 xref: MA:0002487 xref: ncithesaurus:Splenic_Pulp xref: SCTID:13515001 xref: UMLS:C0229691 is_a: UBERON:0000064 ! organ part is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure relationship: part_of UBERON:0002106 {source="MA"} ! spleen relationship: part_of UBERON:1000024 {source="FMA"} ! parenchyma of spleen property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:1000024 name: parenchyma of spleen namespace: uberon def: "A parenchyma that is part of a spleen." [OBOL:automatic] synonym: "splenic parenchyma" EXACT [FMA:16029] xref: FMA:16029 is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0000353 ! parenchyma relationship: part_of UBERON:0002106 ! spleen property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:2005260 name: fenestrated capillary namespace: uberon def: "Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse" [Wikipedia:Capillary#Types, Wikipedia:Fenestra_(histology)] comment: Editor notes: the ZFA class from which this was derived is not explicitly classified as a capillary - need to verify for taxon histology differences synonym: "fenestrated blood vessel endothelium" BROAD [ZFA:0005260] xref: FMA:63196 xref: ncithesaurus:Fenestrated_Capillary xref: TAO:0005260 xref: UMLS:C1179615 xref: ZFA:0005260 is_a: UBERON:0001982 {source="FMA"} ! capillary is_a: UBERON:0003915 ! endothelial tube is_a: UBERON:0004638 {source="ZFA"} ! blood vessel endothelium property_value: external_definition "Blood vessel endothelium that has pores that allow passage small molecules and proteins[ZFA]." xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: snap:MaterialEntity name: material_entity namespace: protein [Term] id: snap:Object name: object namespace: protein is_a: snap:MaterialEntity ! material_entity [Typedef] id: RO:0002131 name: overlaps xref: RO:0002131 [Typedef] id: UBPROP:0000001 name: external_definition def: "An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class." [UBERON:cjm] xref: UBPROP:0000001 is_metadata_tag: true [Typedef] id: UBPROP:0000002 name: axiom_lost_from_external_ontology def: "A textual description of an axiom loss in this ontology compared to an external ontology." [UBERON:cjm] xref: UBPROP:0000002 is_metadata_tag: true [Typedef] id: adjacent_to name: adjacent_to [Typedef] id: bearer_of name: bearer of namespace: BFO xref: BFO:0000053 [Typedef] id: capable_of name: capable_of namespace: CL def: "A relation between a material entity (such as a cell) and a process. This is a shortcut relation, translation rule for which is: capable_of P <-> bearer_of (some realized_by only P). Example: osteoclast capable of bone resorption." [GOC:cjm] expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000053 some (http://purl.obolibrary.org/obo/BFO_0000054 only ?Y)" [] [Typedef] id: decreased_in_magnitude_relative_to name: decreased_in_magnitude_relative_to namespace: quality def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM] comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl domain: PATO:0000001 ! quality range: PATO:0000001 ! quality is_transitive: true is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to [Typedef] id: derives_from name: derives_from (UNDECLARED) [Typedef] id: develops_from name: develops_from namespace: RO xref: RO:0002202 [Typedef] id: different_in_magnitude_relative_to name: different_in_magnitude_relative_to namespace: quality def: "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM] property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl domain: PATO:0000001 ! quality range: PATO:0000001 ! quality [Typedef] id: directly_associated_with name: directly_associated_with namespace: quality def: "q1 directly_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 increases if the magnitude of q2 is increased, or the magnitude of q1 decreases if the magnitude of q2 is decreased. The relationship is not necessarily linear." [PATOC:cjm, Wikipedia:Association_(statistics)] comment: Example: 'Lewy bodies increased number related to dystrophic neurite increased number' (from annotation of PMID:8740227 in http://ccdb.ucsd.edu/1.0/NDPO.owl#ndpo_404). Here the increase in the number of lewy bodies is directly_associated_with the increase in the number of dystrophic neurites.\nAssociation is weaker than correlation or proportionality. These relations may be later added to PATO. property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl domain: PATO:0000001 ! quality range: PATO:0000001 ! quality created_by: cjm creation_date: 2009-08-26T02:50:08Z [Typedef] id: has_completed name: has_completed [Typedef] id: has_cross_section name: has_cross_section namespace: quality def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM] comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Typedef] id: has_dividend_quality name: has_dividend_quality namespace: quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl range: PATO:0000001 ! quality is_a: has_ratio_quality ! has_ratio_quality [Typedef] id: has_divisor_quality name: has_divisor_quality namespace: quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl range: PATO:0000001 ! quality is_a: has_ratio_quality ! has_ratio_quality [Typedef] id: has_high_plasma_membrane_amount name: has_high_plasma_membrane_amount namespace: RO def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al *PMID:19243617)." [PMID:19243617] [Typedef] id: has_low_plasma_membrane_amount name: has_low_plasma_membrane_amount namespace: RO def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al *PMID:19243617)." [PMID:19243617] [Typedef] id: has_modification name: has_modification namespace: RO [Typedef] id: has_not_completed name: has_not_completed namespace: RO [Typedef] id: has_part name: has_part namespace: bfo def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM] comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. xref: BFO:0000051 xref: OBO_REL:has_part property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl/cl-relations.owl property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl is_transitive: true inverse_of: part_of ! part_of [Typedef] id: has_plasma_membrane_part name: has_plasma_membrane_part namespace: RO def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [PMID:19243617] xref: RO:0002104 expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" [] [Typedef] id: has_quality name: has_quality namespace: RO alt_id: OBO_REL:0000029 xref: OBO_REL:has_quality [Typedef] id: has_ratio_quality name: has_ratio_quality namespace: quality property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl range: PATO:0000001 ! quality [Typedef] id: increased_in_magnitude_relative_to name: increased_in_magnitude_relative_to namespace: quality def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM] comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl domain: PATO:0000001 ! quality range: PATO:0000001 ! quality is_transitive: true is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to [Typedef] id: inversely_associated_with name: inversely_associated_with namespace: quality def: "q1 inversely_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 decreases if the magnitude of q2 is increased, or the magnitude of q1 increases if the magnitude of q2 is decreased. The relationship is not necessarily linear." [PATOC:cjm, Wikipedia:Association_(statistics)] comment: Association is weaker than correlation or proportionality. These relations may be later added to PATO. property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl domain: PATO:0000001 ! quality range: PATO:0000001 ! quality created_by: cjm creation_date: 2009-08-26T02:50:24Z [Typedef] id: lacks_modification name: lacks_modification namespace: RO [Typedef] id: lacks_part name: lacks_part namespace: RO expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" [] [Typedef] id: lacks_plasma_membrane_part name: lacks_plasma_membrane_part namespace: RO expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" [] [Typedef] id: located_in name: located_in [Typedef] id: negatively_regulates name: negatively_regulates namespace: gene_ontology xref: RO:0002212 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl is_a: regulates ! regulates [Typedef] id: occurs_in name: occurs in namespace: gene_ontology xref: BFO:0000066 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl transitive_over: part_of ! part_of [Typedef] id: part_of name: part_of namespace: bfo xref: BFO:0000050 xref: OBO_REL:part_of property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl/cl-relations.owl property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl is_transitive: true [Typedef] id: participates_in name: participates in xref: BFO:0000056 [Typedef] id: positively_regulates name: positively_regulates namespace: gene_ontology xref: RO:0002213 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl is_a: regulates ! regulates [Typedef] id: produces name: produces namespace: RO xref: RO:0003000 [Typedef] id: realized_by name: realized by xref: BFO:0000054 [Typedef] id: reciprocal_of name: reciprocal_of namespace: quality def: "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e." [PATOC:CJM] comment: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Typedef] id: regulates name: regulates namespace: gene_ontology xref: RO:0002211 property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl transitive_over: part_of ! part_of [Typedef] id: results_in name: results_in namespace: gene_ontology comment: This relation is currently used to connect two regulation processes p1 and p2, such that if r1 regulates p1 and r2 regulates p2, and r1 results_in r2 then the regulation of p1 is required for the regulation of p2. For an example of use, see GO:0035958 'regulation of glyoxylate cycle by regulation of transcription from RNA polymerase II promoter'. Note that a precise definition of this relation is under discussion. After it has been formalized it will be added to RO, where it will have a RO ID. Note that the existing identifier and label are subject to change. property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Typedef] id: secretes name: secretes [Typedef] id: similar_in_magnitude_relative_to name: similar_in_magnitude_relative_to namespace: quality def: "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM] property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl domain: PATO:0000001 ! quality range: PATO:0000001 ! quality [Typedef] id: spatially_disjoint_from name: spatially_disjoint_from def: "A is spatially_disjoint_from B if they have no parts in common." [SO:cjm] synonym: "non_overlapping_with" EXACT [] synonym: "shares_no_parts_with" EXACT [] expand_assertion_to: "Class: EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)" [] is_metadata_tag: true is_class_level: true [Typedef] id: towards name: towards namespace: quality comment: Relation binding a relational quality or disposition to the relevant type of entity. property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl