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Jie Zheng
Chris Stoeckert
Elisabetta Manduchi
Beta Cell Genomics Ontology (BCGO) is an application ontology built for the Beta Cell Genomics database (http://genomics.betacell.org/gbco/) aiming to support database annotation, complicated semantic queries, and automated cell type classification.
The ontology is built based on OBI Release 2012-07-01 (http://purl.obolibrary.org/obo/obi/2012-07-01/obi.owl)
phalanx number
phalanx number
1
Most land mammals including humans have a 2-3-3-3-3 formula in both the hands (or paws) and feet. Primitive reptiles typically had the formula 2-3-4-4-5, and this pattern, with some modification, remained in many later reptiles and in the mammal-like reptiles. The phalangeal formula in the flippers of cetaceans (marine mammals) is 2-12-8-1
phalanx_number
uberon
x phalanx_number N if and only if (i) x is a phalanx, and (ii) x is phalanx number N in a series of phalanges repeated along an prixomo-distal axis, with phalanx_number 1 being the proximalmost phalanx. Note that in humans, the distalmost phalanx has phlanax_number 3, except in ray_number 1, where the distalmost has phalanx_number 2
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
developmental_classification
derived from the union of EHDAA2 and EMAPA - still to be checked
different_in_magnitude_relative_to
different_in_magnitude_relative_to
different_in_magnitude_relative_to
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.
quality
spatially_disjoint_from
spatially_disjoint_from
1
1
A is spatially_disjoint_from B if they have no parts in common.
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
non_overlapping_with
shares_no_parts_with
spatially_disjoint_from
uberon
loose concept
database_cross_reference
database_cross_reference
Generic GO slim
curator note
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
preceding element is
preceding element is
1
A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates)
preceding_element_is
uberon
Aspergillus GO slim
has_obo_namespace
has_obo_namespace
Prokaryotic GO subset
subset_property
subset_property
A class which has a weakened disjointness axiom, to avoid inconsistency. These are kept separately in the uberon_disjoint_from_strict ontology.
pharyngeal arch number
pharyngeal arch number
1
Note that gill arch N = PA N-2. the term branchial_arch is ambiguous.
pharyngeal_arch_number
uberon
x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch.
Attribute slim
present_in_taxon
present_in_taxon
1
1
S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
applicable for taxon
present_in_taxon
uberon
cell_quality
has_exact_synonym
has_exact_synonym
Subset consisting of classes creating for grouping purposes
Plant GO slim
Candida GO slim
axiom id
increased_in_magnitude_relative_to
increased_in_magnitude_relative_to
This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
increased_in_magnitude_relative_to
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.
quality
derives from
derives from
derives from
sexually_homologous_to
sexually_homologous_to
1
sexually_homologous_to
uberon
homologous_to
homologous_to
1
homologous_to
uberon
has_narrow_synonym
has_narrow_synonym
High-level terms not to be used for direct annotation
is count of
is count of
1
is_count_of
uberon
has_broad_synonym
has_broad_synonym
abstract upper-level terms not directly useful for analysis
Relational slim: types of quality that require an additional entity in order to exist
external_definition
external_definition
1
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.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000001
cl
external_definition
external_definition
uberon
never_in_taxon
never_in_taxon
1
1
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y)
RO:0002161
S never_in_taxon T iff: S SubClassOf in_taxon only not T
never_in_taxon
never_in_taxon
uberon
abstract upper-level terms not directly useful for analysis
shorthand
shorthand
organs, excluding individual muscles and skeletal elements
in_subset
in_subset
Scalar slim
Metagenomics GO slim
has_specified_input
has_specified_input
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Coutot
has_specified_input
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
PERSON: Alan Ruttenberg
see is_input_of example_of_usage
definition
textual definition
textual definition
definition
definition
definition
textual definition
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition
definition
expand expression to
expand expression to
editor note
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
PERSON:Daniel Schober
editor note
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.
has curation status
has curation status
OBI_0000281
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
has curation status
definition source
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
definition source
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
has_specified_output
has_specified_output
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
PERSON: Alan Ruttenberg
term editor
term editor
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
PERSON:Daniel Schober
term editor
ray number
ray number
1
The correct terminology is yet to be established; in tetrapods 'ray' might mean the mereological sum of the phalanges of a manual digit plus a metatarsal bone (or equivalent for hindlimb)
ray_number
uberon
x ray_number N if and only if (i) x is a ray, and (ii) x is ancestrally associated with ray number N in a series of phalanges repeated along a radio-ulnar or equivalent axis, with ray_number 1 being the anteriormost ray.
expand assertion to
expand assertion to
alternative term
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
alternative term
taxon_notes
taxon_notes
1
UBPROP:0000008
taxon_notes
taxon_notes
uberon
has_alternative_id
has_alternative_id
implements_design_pattern
implements_design_pattern
1
UBPROP:0000006
implements_design_pattern
implements_design_pattern
uberon
has_relational_adjective
has_relational_adjective
1
UBPROP:0000007
Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
has_relational_adjective
has_relational_adjective
uberon
editor preferred label
editor preferred term
editor preferred label
editor preferred term
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
editor preferred label
editor preferred term
functional_classification
A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes.
external_comment
external_comment
1
An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000005
external_comment
external_comment
uberon
example of usage
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
example
axiom_lost_from_external_ontology
axiom_lost_from_external_ontology
1
A textual description of an axiom loss in this ontology compared to an external ontology.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000002
axiom_lost_from_external_ontology
axiom_lost_from_external_ontology
cl
uberon
homology_notes
homology_notes
1
Notes on the homology status of this class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000003
homology_notes
homology_notes
uberon
Uberon slim - somewhat arbitrary subset that excludes obscure terms and deep compositional terms
classes that have some inconsistency with FMA
PIR GO slim
Disposition slim
Abnormal/normal slim
abstract class brought in to group ontology classes but not informative
label
has_related_synonym
has_related_synonym
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
dubious_for_taxon
dubious_for_taxon
1
1
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
dubious_for_taxon
this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost
uberon
imported from
imported from
For external terms/classes, the ontology from which the term was imported
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
imported from
Value slim
Pathology slim
Fission yeast GO slim
Yeast GO slim
has_genetic_background_of
strain a has genetic backgroud as strain b is that strain a is derived from strain b and genetic make-up (all its alleles at all loci) of strain a is same to strain b except the mutated gene of interest and a very small amount of other genetic material, generally from one or two other strains. For example, the genetic background of the mutant strains NOD.129S7(B6)-Rag1tm1Mom/J (003729) and NOD.Cg-Rag1tm1Mom Prf1tm1Sdz/SzJ (004848) is NOD.
Person: Jie Zheng
produces_low_amount
Person: Jie Zheng
a produces b if some process that occurs_in a has_output b and amount of b is low relative to normal cases, where a and b are material entities. Examples: defective beta ccell line produces less amount of insulin
produces_high_amount
a produces b if some process that occurs_in a has_output b and amount of b is high relative to generally cases, where a and b are material entities.
Person: Jie Zheng
not_produce
Person: Jie Zheng
a produces_no b if some process that occurs_in a and has_no_output b, where a and b are material entities.
part_of
is part of
BFO:0000050
OBO_REL:part_of
bfo
part_of
part_of
part of
part_of
domain of part of
has_part
has part
BFO:0000051
OBO_REL:has_part
Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2.
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'.
has_part
has_part
quality
has_part
inheres in
inheres_in
bearer of
is bearer of
BFO
BFO:0000053
bearer_of
bearer of
bearer_of
is realized by
realized by
realized_by
realizes
participates in
participates in
BFO:0000056
cl
participates_in
participates_in
has participant
has_participant
is concretized as
concretizes
is immediately preceded by
immediately preceded by
immediately_preceded_by
immediately precedes
immediately_precedes
is preceded by
preceded by
preceded_by
precedes
is course of
course of
course_of
has course
has_course
occurs in
occurs_in
has site of
has_site_of
begins to exist during
begins_to_exist_during
ceases to exist during
ceases_to_exist_during
s depends on
s_depends_on
has granular part
has_granular_part
has granular process part
has_granular_process_part
is granular part of
granular part of
granular_part_of
is granular part of process
granular part of process
granular_part_of_process
is aggregate of
aggregate of
aggregate_of
is fiat part of
fiat part of
fiat_part_of
has participant beginning to exist
has_participant_beginning_to_exist
has participant ceasing to exist
has_participant_ceasing_to_exist
is function of
function of
function_of
is quality of
quality of
quality_of
is role of
role of
role_of
is located in
located in
located_in
is located at
located at
located_at
g depends on
g_depends_on
has function
has_function
has quality
has_quality
has role
has_role
anterior_to
2009-07-31T02:15:46Z
BSPO:0000096
anterior_to
anterior_to
cjm
uberon
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer
distal_to
BSPO:0000097
distal_to
distal_to
uberon
x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
dorsal_to
BSPO:0000098
dorsal_to
dorsal_to
uberon
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
posterior_to
BSPO:0000099
caudal_to
posterior_to
posterior_to
uberon
x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
proximal_to
BSPO:0000100
proximal_to
proximal_to
uberon
x proximal_to y iff x is closer to the point of attachment with the body than y.
ventral_to
BSPO:0000102
uberon
ventral_to
ventral_to
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
in_left_side_of
BSPO:0000120
X left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
http://purl.obolibrary.org/obo/uberon/references/reference_0000014
in_left_side_of
in_left_side_of
uberon
in_right_side_of
BSPO:0000121
X right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
http://purl.obolibrary.org/obo/uberon/references/reference_0000014
in_right_side_of
in_right_side_of
uberon
in_proximal_side_of
BSPO:0000124
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
in_proximal_side_of
in_proximal_side_of
uberon
in_distal_side_of
BSPO:0000125
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
in_distal_side_of
in_distal_side_of
uberon
in_lateral_side_of
BSPO:0000126
X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure
http://purl.obolibrary.org/obo/uberon/references/reference_0000014
in_lateral_side_of
in_lateral_side_of
uberon
preaxial_to
BSPO:1000000
anterior_to (developmentally)
lateral (radial) to
medial (tibial) to
preaxial_to
preaxial_to
uberon
x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the front.
continuous_with
FMA:85972
continuous_with
continuous_with
sourced from FMA
uberon
has measurement unit label
is about
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
We will try to build it back up by elaborating the various subproperties that are more precisely defined.
Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
person:Alan Ruttenberg
denotes
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.
g denotes r =def
r is a portion of reality
there is some c that is a concretization of g
every c that is a concretization of g specifically denotes r
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
person:Alan Ruttenberg
is quality measurement of
8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
Alan Ruttenberg
From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important]
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
--
From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009]
unit of measure is a quality, e.g. the length of a ruler.
[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label]
[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory]
a represents b means either a denotes b or a describes
describe:
a describes b means a is about b and a allows an inference of at least one quality of b
We have had a long discussion about denotes versus describes.
From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully.
a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
From the second meeting on IAO:
An attempt at defining assay using Barry's "reliability" wording
assay:
process and has_input some material entity
and has_output some information content entity
and which is such that instances of this process type reliably generate
outputs that describes the input.
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
m is a quality measurement of q at t when
q is a quality
there is a measurement process p that has specified output m, a measurement datum, that is about q
is duration of
Person:Alan Ruttenberg
relates a process to a time-measurement-datum that represents the duration of the process
is_supported_by_data
Philly 2011 workshop
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
has_specified_input
has_specified_input
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Coutot
has_specified_input
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
PERSON: Alan Ruttenberg
see is_input_of example_of_usage
has_specified_output
has_specified_output
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
PERSON: Alan Ruttenberg
is_manufactured_by
Alan Ruttenberg
Liju Fan
c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
has_make
has_manufacturer
http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
is_manufactured_by
is_specified_output_of
PERSON:Bjoern Peters
is_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
Alan Ruttenberg
achieves_planned_objective
A cell sorting process achieves the objective specification 'material separation objective'
BP, AR, PPPB branch
PPPB branch derived
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
achieves_planned_objective
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
has grain
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
has grain
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
PERSON: Alan Ruttenberg
objective_achieved_by
This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
definition needs clean up to indicate directionality
objective_achieved_by
derives from
derives from
derives from
immediately_preceded_by
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
RO:0002087
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
directly preceded by
http://semanticscience.org/resource/SIO_000251
immediately_preceded_by
immediately_preceded_by
is directly preceded by
is immediately preceded by
starts_at_end_of
uberon
has_plasma_membrane_part
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.
RO
RO:0002104
has_plasma_membrane_part
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)
overlaps
A overlaps B if they share some part in common.
BFO_0000051 some (BFO_0000050 some ?Y)
RO:0002131
overlaps
overlaps
uberon
develops_from
RO
RO:0002202
develops_from
develops_from
uberon
develops_into
RO:0002203
develops_into
develops_into
uberon
directly_develops_from
RO:0002207
directly_develops_from
directly_develops_from
uberon
regulates
RO:0002211
gene_ontology
regulates
regulates
capable_of
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.
CL
http://purl.obolibrary.org/obo/BFO_0000053 some (http://purl.obolibrary.org/obo/BFO_0000054 only ?Y)
surrounded_by
RO:0002219
surrounded_by
surrounded_by
uberon
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
adjacent_to
RO:0002220
adjacent_to
adjacent_to
uberon
x adjacent_to y iff: x and y share a boundary
surrounds
RO:0002221
inverse of surrounded_by
surrounds
surrounds
uberon
starts
RO:0002224
Relation between occurrents, shares a start boundary with.
starts
starts
uberon
develops_from_part_of
RO:0002225
develops_from_part_of
develops_from_part_of
uberon
develops_in
RO:0002226
develops_in
develops_in
uberon
x develops_in y if x is located in x whilst x is developing.
has developmental contribution from
RO:0002254
has_developmental_contribution_from
has_developmental_contribution_from
uberon
developmentally_contributes_to
RO:0002255
developmentally_contributes_to
developmentally_contributes_to
uberon
developmentally_replaces
RO:0002285
developmentally_replaces
developmentally_replaces
uberon
produces
Melissa Haendel
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
produced by
Melissa Haendel
connected to
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
Connection does not imply overlaps.
UBREL:0000001
connected_to
connected_to
http://purl.obolibrary.org/obo/uberon/references/reference_0000004
uberon
composed_primarily_of
UBREL:0000002
composed_primarily_of
composed_primarily_of
uberon
x composed_primarily_of y iff: more than half of the mass of x is made from parts of y
translates_to
Example: codon translates_to amino_acid.
Inverse of translation _of.
Wed Aug 19 00:11:53 PDT 2009
kareneilbeck
translation_of
Example: Polypeptide translation_of CDS.
Wed Aug 19 00:09:59 PDT 2009
X is translation of Y if X is translated by ribosome to create Y.
kareneilbeck
has_high_plasma_membrane_amount
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).
RO
lacks_part
RO
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y
lacks_plasma_membrane_part
RO
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)
different_in_magnitude_relative_to
different_in_magnitude_relative_to
different_in_magnitude_relative_to
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.
quality
has_cross_section
Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.
has_cross_section
quality
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.
increased_in_magnitude_relative_to
increased_in_magnitude_relative_to
This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
increased_in_magnitude_relative_to
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.
quality
anteriorly connected to
anteriorly_connected_to
uberon
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
attaches_to
FMA:85990
attaches_to
uberon
channel for
carries
channel_for
uberon
channels_from
channels_from
uberon
channels_into
channels_into
uberon
connects
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
Editors note: this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)
connects
uberon
distal_part_of
X distal_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y
distal_part_of
uberon
distally connected to
distally_connected_to
uberon
x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
enclosed_by
enclosed_by
uberon
existence_ends_with
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
existence_ends_with
uberon
existence_starts_and_ends_during
existence_starts_and_ends_during
uberon
existence_starts_at
c existence_starts_at e iff c exists_at e and not ( exists e2 : c exists_at e2 and e2 before e)
existence_starts_at
uberon
existence_starts_with
Relation between continuant and occurrent, such that c comes into existence at the start of p.
existence_starts_with
uberon
has_end
has_end
uberon
has_fused_element
A single bone in one species may correspond to the fusion of two or more bones found as distinct elements in another. For example, tibiofibula has_fused_element tibia. A has_fused_element B does not imply that A has_part some B, rather than A has_part some B', where B' is not a subtype of B (because B is a distinct element but B' is a regional part) but has some evolutionary relationship to B.
has_fused_element
uberon
x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat
has_muscle_antagonist
has_muscle_antagonist
m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
uberon
has_muscle_insertion
has_muscle_insertion
m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
uberon
has_muscle_nerve
FMA:85999
has_muscle_nerve
uberon
has_muscle_origin
has_muscle_origin
m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
uberon
has_start
has_start
uberon
in_median_plane_of
X in_median_plane_of Y <=> if X lies on the median plane of Y; i.e. X overlaps o in_left_side_of Y and X overlaps o in_right_side_of Y. X is an unpaired structure
in sagittal plane of
in_median_plane_of
uberon
induced_by
induced_by
sources for induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
t1 induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
uberon
located_in
located_in
uberon
location_of
2009-07-30T10:22:21Z
cjm
location_of
uberon
postaxial_part_of
postaxial_part_of
uberon
posteriorly connected to
posteriorly_connected_to
uberon
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
preaxial_part_of
preaxial_part_of
uberon
proximal_part_of
X proximal_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
proximal_part_of
uberon
proximally connected to
proximally_connected_to
uberon
x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
secreted_by
secreted_by
uberon
secretes
secretes
uberon
start_of
start_of
uberon
subdivision of
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
subdivision_of
uberon
transitively anteriorly connected to
.
transitively_anteriorly_connected_to
uberon
transitively_connected to
transitively_connected_to
uberon
transitively distally connected to
.
transitively_distally_connected_to
uberon
transitively proximally connected to
.
transitively_proximally_connected_to
uberon
transformation_of
http://semanticscience.org/resource/SIO_000657
transformation_of
transformation_of
transforms from
uberon
immediate_transformation_of
direct_transformation_of
http://semanticscience.org/resource/SIO_000658
immediate_transformation_of
immediate_transformation_of
immediately transforms from
uberon
has measurement value
mouse strain
Mus musculus that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organism.
Person: Jie Zheng
rat strain
Person: Jie Zheng
Rattus norvegicus that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organism.
insulin expressing cell
a cell that expresses a gene for insulin.
sequence feature quantification
UPenn Group
Person: Chris Stoeckert, Jie Zheng, Elisabetta Manduchi
A data transformation that attaches quantified values to specific sequence features, e.g. transcript, exon, etc.
high throughput sequence alignment
EFO_0004917 high throughput sequence alignment protocol
a data transformation that aligns sequencing reads to reference sequence.
Person: Chris Stoeckert, Jie Zheng
STOCK Tg(Ins1-EGFP/GH1)14Hara/Mmmh mouse strain
http://www.mmrrc.org/catalog/sds.php?mmrrc_id=438
Person: Jie Zheng, Chris Stoeckert
A mouse strain generated from CD1 and Charles River mouse strains with enhanced green flourescent protein transgene driven by mouse insulin promoter. Genetic background of the strain is CD1. This mouse strain is generally used in development, endocrine deficiency and human disease research.
C57BL/6J mouse strain
A mouse strain that is a laboratory mouse generated from long inbreeding with nearly identical genotype. C57BL/6 mouse has a dark brown, nearly black coat, and an easily irritable temperament. It has a good reproductive performance and is the most widely used "genetic background" for genetically modified mice for use as models of human disease.
black 6
C57
http://en.wikipedia.org/wiki/C57BL/6
Person:Jie Zheng
C57 black 6
functional beta cell like cell
A cell that has all features and genetic signatures as functional beta cell. It may not be part of pancreas.
STOCK Sox17tm2(EGFP/cre)Mgn/Mmnc mouse strain
RES1681 mouse strain
Person: Jie Zheng, Chris Stoeckert
Sox17(GFPCre)Mgn mouse strain
Sox17tm1.3(Cre.GFP)Mgn mouse strain
A mouse strain that was generated by using a novel tag-and-exchange (RMCE) strategy to insert a Cre-GFP (Green fluorescent protein) fusion protein into a Sox17[LCA] allele thereby replacing Sox17 coding sequences. The Sox17-CreGFP mice may be used to track Sox17-expressing cells and their early progeny, or to conditionally inactivate genes in Sox17-expressing cells.
http://www.betacell.org/resource/view/resource_id/1681/
http://www.dkcoin.org/resources/view/id/2096/
http://www.mmrrc.org/catalog/sds.php?mmrrc_id=36463
B6.129S6-Pdx1tm2Mgn/Mmnc mouse strain
Person: Jie Zheng, Chris Stoeckert
RES1301 mouse strain
A mouse strain contains a cyan fluorescent protein (CFP, Cerulean), tagged with 3 copies of an SV40 NLS knocked into the endogenous Pdx1 gene. This mouse strain enables prepancreatic endoderm to be easily identified in the developing mouse embryo and the isolation of Pdx1(+) cells by FACS.
http://www.betacell.org/resource/view/resource_id/1301/
http://www.mmrrc.org/catalog/sds.php?mmrrc_id=36462
Pdx1(CFP)Mgn mouse strain
Pdx1CFP mouse strain
STOCK Ptf1atm1.1Mgn/Mmmh mouse strain
Ptf1atm1Mgn mouse strain
http://www.betacell.org/resource/view/resource_id/236/
http://www.mmrrc.org/catalog/sds.php?mmrrc_id=29175
A mouse strain contains a yellow fluorescent protein (YFP), knocked into the endogenous ptf1a gene. This mouse strain may be used to visualize YFP expression from the ptf1a allele. Ptf1a is expressed in pancreatic buds beginning at E9.5 and plays a vital role in the growth and lineage specification of pancreatic multipotent progenitor cells (MPCs). Ptf1a is also expressed in the neuronal precursors of the cerebellum, spinal cord, and retina where it also performs fate determining roles.
ptf1aYFP mouse strain
RES236 mouse strain
Person: Jie Zheng, Chris Stoeckert
B6.129S-Neurog3tm1(EGFP)Khk/Mmcd mouse strain
http://www.betacell.org/resource/view/resource_id/176/
A mouse strain with targeted mutation at the Neurogenin 3 locus where EGFP replaces entire coding region of Neurogenin3. The basic phenotype is EGFP expression in developing endocrine cells of pancreas and in glandular regions of the stomach.
ngn3-EGFP mouse strain
RES176 mouse strain
Person: Jie Zheng
Insm1tm2Mgn mouse strain
RES661 mouse strain
Person: Jie Zheng, Chris Stoeckert
http://www.betacell.org/resource/view/resource_id/661/
http://www.betacell.org/resource/view/resource_id/661/ provide the definition of 'Insm1tm1.1Mgn mouse strain' which might be the early version of 'Insm1tm2Mgn mouse strain'. However, we are not clear the difference between two strains. We borrowed the definition of 'Insm1tm1.1Mgn mouse strain'. In the webpage, it has strain name 'Mouse Strain RES661' and common name 'lnsm1GFP.Cre mouse strain'. We added 'lnsm1GFP.Cre mouse strain' as alternative term which is true to 'Insm1tm2Mgn mouse strain' too .
A mouse strain contains a GFP-Cre fusion protein which replaces the Insm1 coding sequence. These mice express green fluorescent protein (GFP) under control of the Insm1 gene locus. Insm1 is expressed in pancreatic primordium starting at E9.5. Insm1 is also expressed in neural precursor cells and tumors of may be used for lineage tracing of Insm1-positive cells in both wild-type and Insm1-null mice.
Insm1GFP.Cre mouse strain
STOCK Tg(Tnpo1-EGFP)6729Hara/Mmmh mouse strain
http://www.betacell.org/resource/view/resource_id/188/
RES188 mouse strain
Person: Jie Zheng
MIP-GFP mouse strain
A mouse strain which is hemizygous and shows expression of EGFP in beta lineage cells of the pancreas.
129X1/SvJ mouse strain
A mouse strain that is a laboratory mouse generated from inbreeding. It has white-bellied, pink-eyed, light chinchilla (off-white) or albino or white-bellied, pink-eyed, light chinchilla (light tan). It has a good reproductive performance and is widely used in the production of targeted mutations due to the availability of multiple embryonic stem cell lines derived from them.
Person:Jie Zheng
http://www.informatics.jax.org/mgihome/nomen/strain_129.shtml
http://jaxmice.jax.org/strain/000691.html
129X1
129/SvJ
C3H mouse strain
A mouse strain that Inbred from F130 to F170 depending on substrain original generated from a cross of a Bagg albino female and a DBA male by Strong in 1920. It has Agouti coat color. Most substrains have a good reproductive performance. It is widely used in a wide variety of research areas including cancer, immunology and inflammation, sensorineural, and cardiovascular biology.
Person:Jie Zheng
http://www.informatics.jax.org/external/festing/mouse/docs/C3H.shtml
http://www.criver.com/EN-US/PRODSERV/BYTYPE/RESMODOVER/RESMOD/Pages/C3HMouse.aspx
black swiss mouse strain
Person: Jie Zheng
Sox17-expressing definitive endodermal cell
Person: Chris Stoeckert, Jie Zheng
Chris Stoeckert
Sox17 expressing cell from the embryo body proper
an endodermal cell that is part of the definitive endoderm and expresses a gene for SOX-17
Sox17-expressing Epcam+ pancreatic epithelial cell
an epithelial cell that is part of the ventral pancreatic bud, expresses a gene for SOX-17 and has Epcam in the plasma membrane.
Person: Chris Stoeckert, Jie Zheng
Sox17 expressing cell in ventral pancreatic bud
Chris Stoeckert
Pdx1-expressing foregut endodermal cell
Pdx1-expressing endoderm cell
an endodermal cell that is part of the foregut endoderm and expresses the gene for pancreas/duodenum homeobox protein 1
Person: Chris Stoeckert, Jie Zheng
Chris Stoeckert
Ptf1a-expressing multipotent pancreatic cell
Chris Stoeckert
Person: Chris Stoeckert, Jie Zheng
a non-terminally differentiated cell that is part of the pancreatic bud, participates in pancreas development and expresses the gene for pancreas transcription factor 1 subunit alpha.
Ptf1a-expressing cell
Ptf1a-lacking pancreatic progenitor cell
Ptf1a-null cell
Chris Stoeckert
a non-terminally differentiated cell that is part of the pancreatic bud but lacks pancreas transcription factor 1 subunit alpha.
Person: Chris Stoeckert, Jie Zheng
neurogenin-3-expressing endocrine progenitor cell
Chris Stoeckert
Ngn3-expressing cell
a non-terminally differentiated cell that participates in endocrine pancreas developement and expresses the gene for neurogenin-3.
Person: Chris Stoeckert, Jie Zheng
neurogenin-3-lacking pancreatic progenitor cell
Chris Stoeckert
a non-terminally differentiated cell that is part of the pancreas, participates in pancreas development and lacks neurogenin-3.
Ngn3-null cell
Person: Chris Stoeckert, Jie Zheng
Insm1-expressing endocrine progenitor cell
Chris Stoeckert
a non-terminally differentiated cell that participates in endocrine pancreas development and expresses a gene for insulinoma-associated protein 1
Person: Chris Stoeckert, Jie Zheng
Insm1 expressing pancreatic endocrine cell
Insm1-lacking endocrine progenitor cell
Chris Stoeckert
a non-terminally differentiated cell that is part of the endocrine pancreas and lacks insulinoma-associated protein 1
Person: Chris Stoeckert, Jie Zheng
Non-functional Insm1 expressing pancreatic endocrine cell
insulin-expressing immature beta cell
Chris Stoeckert
a type B pancreatic cell that is immature and expresses a gene for insulin
Person: Chris Stoeckert, Jie Zheng
insulin-expressing nascent beta cells
insulin-expressing mature beta cell
a type B pancreatic cell that is mature and expresses a gene for insulin
Chris Stoeckert
insulin-expressing mature beta cells
Person: Chris Stoeckert, Jie Zheng
Insm1-expressing Pdx1 high-positive pancreatic endocrine progenitor cell
A Insm1-expressing endocrine progenitor cell that expresses the gene for pancreas/duodenum homeobox protein 1 at a high level.
Person: Jie Zheng, Chris Stoeckert
Insm1-expressing Pdx1 low-positive pancreatic endocrine progenitor cell
Person: Jie Zheng, Chris Stoeckert
A Insm1-expressing endocrine progenitor cell that expresses the gene for pancreas/duodenum homeobox protein 1 at a low level.
Insm1tm2(GFP.Cre)Mgn/Pdx1tm2(CFP)Mgn mouse strain
A mouse strain that is the result of mating between a Insm1GFPCre/+ mouse and a Pdx1CFP/+ mouse both on a CD-1 background
Person: Chris Stoeckert, Anna Osipovich
differential expression software
GBCO
A software implementing a higher level analysis protocol of type differential expresssion.
entity
entity
continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
a heart
a person
a symphony orchestra
continuant
endurant
the color of a tomato
the disposition of blood to coagulate
the lawn and atmosphere in front of our building
the mass of a cloud
occurrent
An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
a surgical operation as processual context for a nosocomical infection
occurrent
perdurant
the life of an organism
the most interesting part of Van Gogh's life
the spatiotemporal context occupied by a process of cellular meiosis
the spatiotemporal region occupied by the development of a cancer tumor
independent continuant
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
a chair
a heart
a leg
a person
a symphony orchestra
an organism
independent continuant
substantial entity
the bottom right portion of a human torso
the lawn and atmosphere in front of our building
dependent continuant
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
dependent continuant
process
A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
process
the life of an organism
the process of cell-division
the process of sleeping
temporal region
All instances of occurrent [span:Occurrent] are temporal entities, that is, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant].
An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe, a designated individual, which is thus a temporal region itself.
An occurrent that is part of time.
Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion].
temporal region
the duration of a surgical procedure
the moment of death
the time it takes to run a marathon
disposition
A realizable entity that essentially causes a specific process or transformation in the object in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object has the disposition D to (transform, initiate a process) R under conditions C.
disposition
the disposition of a patient with a weakened immune system to contract disease
the disposition of a vase to brake if dropped
the disposition of blood to coagulate
the disposition of metal to conduct electricity
the disposition of vegetables to decay when not refrigerated
realizable entity
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
realizable entity
the disposition of blood to coagulate
the disposition of metal to conduct electricity
the function of the reproductive organs
the role of being a doctor
quality
A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property).
quality
the ambient temperature of air
the circumference of a waist
the color of a tomato
the mass of a piece of gold
the shape of a nose
the weight of a chimpanzee
specifically dependent continuant
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
mode
property
specifically dependent continuant
the color of a tomato
the disposition of fish to decay
the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
the liquidity of blood
the mass of a cloud
the role of being a doctor
the smell of mozzarella
trope
temporal instant
A connected temporal region comprising a single moment of time.
right now
temporal instant
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death
connected temporal region
A temporal region every point of which is mediately or immediately connected with every other point of which.
connected temporal region
the 1970s years
the time from the beginning to the end of a heart attack
the time taken up by cellular meiosis
role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
role
the role of a biological grandfather as legal guardian in the context of a system of laws
the role of a chemical compound in an experiment
the role of a patient relative as defined by a hospital administrative form
the role of a person as a surgeon
the role of a student in a university
the role of a woman as a legal mother in the context of system of laws
the role of ingested matter in digestion
object boundary
An independent continuant that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object entities that exist at exactly the point where the object is separated off from the rest of the existing entities in the world.
Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.
object boundary
substance boundary
the outer surface of a cell or cell wall
the surface of the earth
the surface of the interior of the stomach
the surface of the skin
site
An independent continuant consisting of a characteristic spatial shape in relation to some arrangement of other continuant entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site entities are entities that can be occupied by other continuant entities.
An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are sites) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class).
Maria's nostril or her intestines for a variety of bacteria
a particular room in a particular hospital
site
generically dependent continuant
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
a certain PDF file that exists in different and in several hard drives
generically dependent continuant
scattered temporal region
A temporal region every point of which is not mediately or immediately connected with every other point of which.
scattered temporal region
the time occupied by the individual games of the World Cup
the time occupied by the individual liaisons in a romantic affair
function
A realizable entity the manifestation of which is an essentially end-directed activity of a continuant entity in virtue of that continuant entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
function
the digestive function of the stomach to nutriate the body
the function of a birth canal to enable transport
the function of a computer program to compute mathematical equations
the function of a hammer to drive in nails
the function of a judge in a court of law
the function of an automobile to provide transportation
the function of reproduction in the transmission of genetic material
the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
process boundary
A processual entity that is the fiat or bona fide instantaneous temporal process boundary.
birth
death
process boundary
the detaching of a finger in an industrial accident
the final separation of two cells at the end of cell-division
the forming of a synapse
the incision at the beginning of a surgery
the onset of REM sleep
temporal interval
A connected temporal region lasting for more than a single moment of time.
any continuous temporal duration during which a process occurs
temporal interval
material entity
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
Examples: collection of random bacteria, a chair, dorsal surface of the body
Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
material entity
lymphoblastoid cell line
lymphoblastoid cell line
embryonic stem cell line
embryonic stem cell line
CCE cell
CCE cell
gross anatomical part
Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells.
gross anatomical part
biotin
An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins.
biotin
polynucleotide
A nucleobase-containing molecular entity with an oligomeric structure comprised of a linear sequence of 13 or more nucleotide residues.
polynucleotide
peptide
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid.
peptide
deoxyribonucleic acid
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
deoxyribonucleic acid
hydrogensulfite
A sulfur oxoanion that has formula HO3S.
hydrogensulfite
polysaccharide
A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues.
polysaccharide
benzopyrrole
benzopyrrole
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
molecular entity
chemical entity
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
chemical entity
organic heterocyclic compound
A cyclic compound having as ring members atoms of carbon and at least of one other element.
organic heterocyclic compound
hydroxides
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
hydroxides
indoles
Any compound containing an indole skeleton.
indoles
ion
A molecular entity having a net electric charge.
ion
agarose
A polysaccharide that has formula C24H38O19.
agarose
oxide
An oxide is a chemical compound of oxygen with other chemical elements.
oxide
oxygen molecular entity
oxygen molecular entity
sulfur molecular entity
sulfur molecular entity
organic heterobicyclic compound
organic heterobicyclic compound
phosphorus atom
A pnictogen that has formula P.
phosphorus atom
atom
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
atom
primary amide
A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
primary amide
organosulfur compound
An organosulfur compound is a compound containing at least one carbon-sulfur bond.
organosulfur compound
polyatomic anion
An anion consisting of more than one atom.
polyatomic anion
heteroorganic entity
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
heteroorganic entity
chalcogen molecular entity
Any p-block molecular entity containing a chalcogen.
chalcogen molecular entity
main group element atom
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
main group element atom
sulfur oxoacid derivative
sulfur oxoacid derivative
sulfur oxoanion
sulfur oxoanion
chalcogen oxoanion
chalcogen oxoanion
organosulfonic acid
An organic derivative of sulfonic acid in which the sulfo group is linked directly to carbon.
organosulfonic acid
carboxylic acid
A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.
carboxylic acid
main group molecular entity
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.
main group molecular entity
cyclic compound
cyclic compound
organic aromatic compound
organic aromatic compound
heteropolycyclic compound
heteropolycyclic compound
heterobicyclic compound
A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom.
heterobicyclic compound
p-block molecular entity
A p-block molecular entity is a molecular entity containing one or more atoms of a p-block element.
p-block molecular entity
biomacromolecule
A macromolecule formed by a living organism.
biomacromolecule
nucleic acid
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
nucleic acid
ribonucleic acid
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
ribonucleic acid
organic cyclic compound
organic cyclic compound
heteroarene
A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2).
heteroarene
organonitrogen compound
Any heteroorganic entity containing at least one carbon-nitrogen bond.
organonitrogen compound
oxoanion
An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
oxoanion
carbon oxoacid
carbon oxoacid
polyatomic entity
Any molecular entity consisting of more than one atom.
polyatomic entity
polyatomic ion
An ion consisting of more than one atom.
polyatomic ion
carbonyl compound
Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.
carbonyl compound
organochalcogen compound
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
organochalcogen compound
organooxygen compound
An organochalcogen compound containing at least one carbon-oxygen bond.
organooxygen compound
heteroatomic molecular entity
A molecular entity consisting of two or more chemical elements.
heteroatomic molecular entity
cyanine dye
Cyanine dyes are synthetic dyes with the general formula R2N[CH=CH]nCH=N(+)R2 <-> R2N(+)=CH[CH=CH]nNR2 (n is a small number) in which the nitrogen and part of the conjugated chain usually form part of a heterocyclic system, such as imidazole, pyridine, pyrrole, quinoline and thiazole.
cyanine dye
phosphorus-32 atom
The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days.
phosphorus-32 atom
phosphorus-33 atom
The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2.
phosphorus-33 atom
Cy3 dye
Cy3 dye
Cy5 dye
Cy5 dye
organonitrogen heterocyclic compound
Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms.
organonitrogen heterocyclic compound
organosulfur heterocyclic compound
organosulfur heterocyclic compound
organic heteropentacyclic compound
organic heteropentacyclic compound
organic heteropolycyclic compound
organic heteropolycyclic compound
azabicycloalkane
azabicycloalkane
thiabicycloalkane
thiabicycloalkane
double-stranded DNA
double-stranded DNA
organic amino compound
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
organic amino compound
organic molecular entity
Any molecular entity that contains carbon.
organic molecular entity
nitrogen molecular entity
nitrogen molecular entity
biotins
Compounds containing a biotin (5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid) skeleton.
biotins
Alexa Fluor 532
Alexa Fluor 532
An organosulfonic acid that has formula C34H33N3O11S2.
Alexa Fluor 546
Alexa Fluor 546
An organic heteropentacyclic compound that has formula C44H46Cl3N4NaO14S3.
heterocyclic compound
A cyclic compound having as ring members atoms of at least two different elements.
heterocyclic compound
nucleobase-containing molecular entity
Any compound that has a nucleobase as a part.
nucleobase-containing molecular entity
cell line cell
cell line cell
A cell line cell is a cultured cell that is part of a stable and homogeneous population of cells of common biological origin, derived through the passaging of primary cultured cells or the alteration of existing cell line cells
immortal cell line cell
immortal cell line cell
a cell line that can be passaged in an infinite number of generations (i.e., immortalized).
permanent stem cell line cell
a cell line that is derived from stem cell
permanent stem cell line cell
permanent neuron cell line cell
a permanent electrically responsive cell line that is derived from neuron
permanent neuron cell line cell
permanent animal cell line cell
a permanent eukaryotic cell line that is derived from animal cell
permanent animal cell line cell
permanent hematopoietic cell line cell
a permanent animal cell line that is derived from hematopoietic cell
permanent hematopoietic cell line cell
permanent neural cell line cell
a permanent animal cell line that is derived from neural cell
permanent neural cell line cell
permanent somatic cell line cell
a cell line that is derived from somatic cell
permanent somatic cell line cell
3T3-L1 cell
3T3-L1 cell
Ainv15 cell
Ainv15 cell
BETA-TC-3 cell
BETA-TC-3 cell
CGR8 cell
CGR8 cell
Daudi cell
Daudi cell
H9 cell
H9 cell
JURKAT cell
JURKAT cell
K 562 cell
K 562 cell
PANC-1 cell
PANC-1 cell
Raji cell
Raji cell
SW480 cell
SW480 cell
cell
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.
FMA:68646
GO:0005623
KUPO:0000002
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).
VHOG:0001533
WBbt:0004017
XAO:0003012
cell
native cell
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:0000013
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).
cell
cell in vivo
cultured cell
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
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.
cell
cell line cell
female germ cell
Female germ cell is a germ cell that supports female gamete production.
MA:0000388
VHOG:0001530
cell
ncithesaurus:Egg
oocyte
A female germ cell that has entered meiosis.
BTO:0000964
FBbt:00004886
FMA:18644
WBbt:0006797
cell
oogonium
stem cell
A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
FMA:63368
cell
hematopoietic stem cell
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.
BTO:0000725
FMA:70337
FMA:86475
HSC
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.
VHOG:0001485
blood forming stem cell
cell
colony forming unit hematopoietic
hemopoietic stem cell
erythroid progenitor cell
A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative).
BFU-E
BTO:0004911
CFU-E
blast forming unit erythroid
burst forming unit erythroid
cell
colony forming unit erythroid
erythroid stem cell
germ line cell
A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring.
Originally this term had some plant germ line cell children.
cell
monoblast
A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus.
CFU-M
FMA:83553
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.
cell
colony forming unit macrophage
colony forming unit monocyte
monocyte stem cell
multi fate stem cell
A stem cell that can give rise to multiple lineages of cells.
FMA:84789
cell
multi-fate stem cell
multifate stem cell
multipotent cell
multipotent stem cell
common myeloid progenitor
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.
BTO:0004730
CFU-GEMM
CFU-S
CMP
CMP are reportedly CD16-positive, CD32-positive, CD38-positive, CD45RA-negative, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative.
cell
colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte
common myeloid precursor
multipotential myeloid stem cell
myeloid stem cell
pluripotent stem cell (bone marrow)
megakaryocyte-erythroid progenitor cell
A progenitor cell committed to the megakaryocyte and erythroid lineages.
CFU-EM
CFU-MegE
MEP
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.
Meg/E progenitor
cell
colony forming unit erythroid megakaryocyte
megakaryocyte/erythrocyte progenitor
megakaryocyte/erythroid progenitor cell
common lymphoid progenitor
A oligopotent progenitor cell committed to the lymphoid lineage.
CL:0000044
CLP
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.
ELP
cell
committed lymphopoietic stem cell
common lymphocyte precursor
common lymphocyte progenitor
common lymphoid precursor
early lymphocyte progenitor
lymphoid stem cell
lymphopoietic stem cell
non-terminally differentiated cell
A precursor cell with a limited number of potential fates.
BTO:0000125
FMA:84782
blast cell
cell
define using PATO mulit-potent or oligopotent?
myoblast
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.
BTO:0000222
FBbt:00005083
FMA:70335
VHOG:0001529
cell
fibroblast
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.
BTO:0000452
FMA:63877
These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative.
VHOG:0001482
cell
epithelial cell
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.
BTO:0000414
CARO:0000077
FBbt:00000124
FMA:66768
WBbt:0003672
cell
epitheliocyte
blood vessel endothelial cell
An endothelial cell that lines the vasculature.
cell
cuboidal endothelial cell of vascular tree
columnar/cuboidal epithelial cell
cell
squamous epithelial cell
cell
blood cell
A cell found predominately in the blood.
FMA:62844
cell
epithelial cell of pancreas
An epithelial cell of the pancreas.
BTO:0000028
cell
T cell
A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
BTO:0000782
CL:0000804
CL:0000812
FMA:62870
T lymphocyte
T-cell
T-lymphocyte
VHOG:0001479
cell
immature T cell
mature T cell
granulocyte
A leukocyte with abundant granules in the cytoplasm.
BTO:0000539
BTO:0001026
FMA:62854
cell
granular leucocyte
granular leukocyte
polymorphonuclear leukocyte
endothelial cell
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.
BTO:0001176
FMA:66772
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].
cell
endotheliocyte
neurectodermal cell
Ectoderm destined to be nervous tissue.
cell
neurectoderm cell
mesenchymal cell
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.
BMSC
BTO:0002625
BTO:0003298
CFU-F
CL:0002452
FMA:70546
MSC
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.
bone marrow stromal cells
cell
colony-forming unit-fibroblast
marrow stromal cells
mesenchymal precursor cell
mesenchymal progenitor cells
mesenchymal stem cell
mesenchymal stromal cell
mesenchymal stromal cells
stem cells, mesenchymal
fat cell
A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides.
BTO:0000443
CL:0000450
FMA:63880
adipocyte
adipose cell
cell
pigment cell
A pigment cell is a cell that contains pigment granules.
VHOG:0001678
cell
chromatocyte
chromatophore
melanocyte
A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance.
BTO:0000847
CL:0000572
FMA:70545
VHOG:0001679
cell
melanophore
glandular epithelial cell
A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules.
FMA:86494
cell
secretory cell
A cell that specializes in controlled release of one or more substances.
BTO:0003659
FMA:86916
cell
exocrine cell
A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct.
FMA:16014
cell
protein secreting cell
cell
endocrine cell
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.
FMA:83809
cell
endocrinocyte
enteroendocrine cell
An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas.
BTO:0003865
FMA:62930
cell
peptide hormone secreting cell
cell
insulin secreting cell
BTO:0000783
cell
type B pancreatic cell
A cell that secretes insulin and is located towards the center of the islets of Langerhans.
B-cell of pancreatic islet
BTO:0000783
EV:0200009
FMA:70586
MA:0002419
Pancreatic beta cells are also reportedly CD284-positive. Upon activation, they upregulate their CD14 expression.
beta cell
beta cell islet
beta cell of pancreatic islet
cell
insulin-secreting cell
ncithesaurus:Beta_Cell
pancreatic B cell
pancreatic B-cell
pancreatic beta cell
pancreatic islet core
type B enteroendocrine cell
glucagon secreting cell
A cell that secretes glucagon.
FMA:84045
cell
glucagon-secreting cell
pancreatic A cell
A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon.
BTO:0000990
FMA:70585
alpha cell of iselt of Langerhans
cell
pancreatic alpha cell
somatostatin secreting cell
cell
pancreatic D cell
A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin.
BTO:0000803
D-cell of pancreatic islet
FMA:70587
cell
delta cell of islet
delta cell of pancreatic islet
pancreatic D-cell
pancreatic delta cell
somatostatin-secreting pancreatic cell
metabolising cell
A cell whose primary function is intermediary metabolism.
cell
hepatocyte
BTO:0000575
FMA:14515
Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive.
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.
cell
contractile cell
A cell whose primary function is to shorten.
cell
muscle cell
A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
BTO:0000888
BTO:0000902
FBbt:00005074
FMA:67328
WBbt:0003675
cell
muscle fiber
myocyte
electrically active cell
A cell whose function is determined by the generation or the reception of an electric signal.
cell
lining cell
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.
boundary cell
cell
barrier cell
A cell whose primary function is to prevent the transport of stuff across compartments.
cell
motile cell
A cell that moves by its own activities.
cell
ectodermal cell
A cell of the outer of the three germ layers of the embryo.
FMA:72549
cell
ectoderm cell
mesodermal cell
A cell of the middle germ layer of the embryo.
FMA:72554
cell
mesoblast
mesoderm cell
endodermal cell
A cell of the inner of the three germ layers of the embryo.
FMA:72555
cell
endoderm cell
anucleate cell
A cell that lacks a nucleus.
FMA:68647
cell
non-nucleated cell
single nucleate cell
A cell with a single nucleus.
cell
erythrocyte
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
BTO:0000424
FMA:81100
RBC
cell
red blood cell
platelet
A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation.
BTO:0000132
FMA:62851
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.
anucleate thrombocyte
blood platelet
cell
enucleate thrombocyte
B cell
A lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
B lymphocyte
B-cell
B-lymphocyte
BTO:0000776
FMA:62869
VHOG:0001480
cell
eukaryotic cell
cell
stuff accumulating cell
A cell that is specialised to accumulate a particular substance(s).
cell
oxygen accumulating cell
cell
migratory neural crest cell
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.
FMA:86667
cell
muscle stem cell
A multifate stem cell found in skeletal muscle than can differentiate into many different cell types. Distinct cell type from satellite cell.
FMA:86767
cell
electrically responsive cell
A cell whose function is determined by its response to an electric signal.
cell
polyploid cell
A cell whose nucleus, or nuclei, each contain more than two haploid genomes.
cell
endopolyploid cell
cell
white fat cell
FMA:83434
Fat cells with light coloration and few mitochondria. They contain a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole.
cell
white adipocyte
white adipose cell
white fat cell
dendritic cell
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).
BTO:0002042
FMA:83036
cell
interdigitating cell
veiled cell
biogenic amine secreting cell
cell
serotonin secreting cell
5-HT secreting cell
5-Hydroxytryptamine secreting cell
A cell type that secretes 5-Hydroxytryptamine (serotonin).
cell
type D enteroendocrine cell
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.
D cell
FMA:62935
cell
cardiac muscle myoblast
A precursor cell destined to differentiate into cardiac muscle cell.
CL:0000714
FMA:84797
cell
melanoblast
A cell that originates from the neural crest and differentiates into a pigment cell.
BTO:0003217
Derived from UBERON:0002342 neural crest.
FMA:83377
cell
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.
BTO:0000775
Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)
FMA:62863
VHOG:0001535
cell
proerythroblast
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.
FMA:83518
cell
pronormoblast
rubriblast
animal cell
cell
basophilic erythroblast
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.
FMA:83505
basophilic normoblast
cell
early erythroblast
early normoblast
prorubricyte
polychromatophilic erythroblast
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.
FMA:83506
cell
intermediate erythroblast
intermediate normoblast
polychromatic erythroblast
polychromatic normoblast
polychromatophilic normoblast
rubricyte
orthochromatic erythroblast
FMA:84646
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.
acidophilic erythroblast
cell
eosinophilic erythroblast
late erythoblast
orthochromatic normoblast
pyknotic eto enrythroblast
megakaryocyte progenitor cell
BTO:0001164
CFU-Meg
FMA:84235
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.
Meg-CFC
MkP
The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative).
cell
colony-forming unit-megakaryocyte
megacaryoblast
megacaryocyte progenitor cell
megakaryoblast
megakaryocytic progenitor cell
promegacaryocyte
promegakaryocyte
megakaryocyte
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.
BTO:0000843
FMA:83555
Megakaryocytes are reportedly CD181-positive and CD182-positive.
cell
megacaryocyte
megalocaryocyte
megalokaryocyte
granulocyte monocyte progenitor cell
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.
CFU-C , Colony forming unit in culture
CFU-GM
GMP
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.
cell
colony forming unit granulocyte macrophage
granulocyte-macrophage progenitor
granulocyte/monocyte precursor
granulocyte/monocyte progenitor
reticulocyte
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.
BTO:0001173
cell
promonocyte
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.
BTO:0004657
FMA:83551
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.
cell
angioblastic mesenchymal cell
A mesenchymal stem cell capable of developing into blood vessel endothelium.
These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive.
angioblast
cell
chondroplast
monocyte
BTO:0000876
FMA:62864
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.
Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
cell
experimentally modified cell in vitro
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
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
cell
germ cell
BTO:0000535
The reproductive cell in multicellular organisms.
VHOG:0001534
WBbt:0006796
cell
acinar cell
A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus).
FMA:83625
acinic cell
acinous cell
cell
natural killer cell
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.
BTO:0000914
BTO:0004716
FMA:63147
FMA:83601
NK cell
VHOG:0001697
cell
large granular lymphocyte
null cell
muscle precursor cell
cell
PP cell
A cell that stores and secretes pancreatic polypeptide hormone.
FMA:62938
FMA:83409
cell
type F enteroendocrine cell
neurecto-epithelial cell
BTO:0004301
Epithelial cells derived from neural plate and neural crest.
FMA:70557
The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098).
cell
neuroepithelial cell
somatic stem cell
A stem cell that can give rise to cell types of the body other than those of the germ-line.
FMA:63368
cell
striated muscle cell
BTO:0002916
FMA:86936
Muscle cell which has as its direct parts myofilaments organized into sarcomeres.
cell
leukocyte
An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
BTO:0000751
FMA:62852
cell
immune cell
leucocyte
white blood cell
cardiac muscle cell
BTO:0001539
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.
FMA:14067
FMA:83808
cardiac muscle fiber
cardiac myocyte
cardiocyte
cardiomyocyte
cell
heart muscle cell
myeloid cell
A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
BTO:0001441
cell
erythroid lineage cell
A immature or mature cell in the lineage leading to and including erythrocytes.
CL:0002156
FMA:62845
FMA:83516
Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes.
cell
erythropoietic cell
erythroblast
A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.
BTO:0001571
FMA:83504
cell
normoblast
myeloid leukocyte
A cell of the monocyte, granulocyte, or mast cell lineage.
cell
basophil
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.
BTO:0000129
FMA:62862
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.
basophilic leucocyte
basophilic leukocyte
cell
polymorphonuclear leucocyte
polymorphonuclear leukocyte
eosinophil
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.
BTO:0000399
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.
FMA:62861
cell
eosinocyte
eosinophilic granulocyte
eosinophilic leucocyte
eosinophilic leukocyte
polymorphonuclear leucocyte
polymorphonuclear leukocyte
neutrophil
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.
BTO:0000130
FMA:62860
PMN
cell
neutrocyte
neutrophil leucocyte
neutrophil leukocyte
neutrophilic leucocyte
neutrophilic leukocyte
poly
polymorphonuclear leucocyte
polymorphonuclear leukocyte
polymorphonuclear neutrophil
polynuclear neutrophilic leucocyte
polynuclear neutrophilic leukocyte
pro-NK cell
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.
Most markers only described for human pro NK cells.
NKP
cell
natural killer cell progenitor
null cell
preNK cell
pro-natural killer cell
pro-B cell
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.
BTO:0003104
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.
cell
pre-B cell (Philadelphia nomenclature)
pre-pro B cell
pro-B lymphocyte
pro-B-cell
pro-B-lymphocyte
progenitor B cell
progenitor B lymphocyte
progenitor B-cell
progenitor B-lymphocyte
pro-T cell
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.
DN1 cell
DN1 thymocyte
TN1 cell
cell
pro-T lymphocyte
progenitor T cell
myeloblast
BTO:0000187
FMA:83524
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.
cell
promyelocyte
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.
FMA:83530
cell
hematopoietic multipotent progenitor cell
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.
BTO:0000725
MPP
Markers differ between mouse and human.
cell
hemopoietic progenitor cell
lymphoid lineage restricted progenitor cell
A progenitor cell restricted to the lymphoid lineage.
BTO:0004731
FMA:70338
Note that this is a class of cell types, not an identified single cell type.
cell
lymphoid progenitor cell
myeloid lineage restricted progenitor cell
A progenitor cell restricted to the myeloid lineage.
BTO:0004730
FMA:70339
Note that this is a class of cell types, not an identified single cell type.
cell
myeloid progenitor cell
mononuclear cell
A leukocyte with a single non-segmented nucleus in the mature form.
BTO:0000878
FMA:86713
cell
peripheral blood mononuclear cell
lymphocyte of B lineage
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.
Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells).
cell
hematopoietic cell
A cell of a hematopoietic lineage.
BTO:0000574
FMA:70366
FMA:83598
cell
haematopoietic cell
haemopoietic cell
hemopoietic cell
cell in vitro
'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.
2012-01-12T09:58:38Z
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.
cell
haendel
bone cell
2011-11-16T04:28:16Z
A connective tissue cell found in bone.
adiehl
cell
macrophage dendritic cell progenitor
2010-01-19T02:51:58Z
A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages.
MDP
cell
tmeehan
hematopoietic lineage restricted progenitor cell
2010-01-06T03:43:20Z
A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells.
cell
tmeehan
hematopoietic oligopotent progenitor cell
2010-01-06T03:43:27Z
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.
cell
tmeehan
type A enterocrine cell
2010-09-10T10:48:54Z
An enterocrine cell that produces glucagon.
FMA:62939
cell
tmeehan
endo-epithelial cell
2010-06-29T03:38:14Z
An epithelial cell derived from endoderm.
FMA:69075
cell
tmeehan
ecto-epithelial cell
2010-06-29T03:38:22Z
An epithelial cell derived from ectoderm.
FMA:69074
cell
tmeehan
meso-epithelial cell
2010-06-29T03:49:14Z
Epithelial cell derived from mesoderm or mesenchyme.
FMA:69076
cell
epithelial mesenchymal cell
tmeehan
nongranular leukocyte
2010-07-22T11:30:33Z
A leukocyte that lacks granules.
FMA:62855
agranular leukocyte
cell
tmeehan
bone marrow cell
2010-07-22T04:48:15Z
A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells.
BTO:0004850
FMA:83621
MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense.
cell
tmeehan
endothelial cell of vascular tree
2010-08-24T02:06:40Z
An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels.
BTO:0001854
FMA:67755
These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive.
cell
cubodial endothelial cell of vascular tree
tmeehan
vascular endothelial cell
granulocytopoietic cell
2010-08-30T12:54:27Z
A cell involved in the formation of a granulocyte.
FMA:83519
cell
tmeehan
myelocyte
2010-08-30T01:08:19Z
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.
BTO:0000734
FMA:83525
cell
tmeehan
monopoietic cell
2010-08-30T01:27:48Z
A cell involved in the formation of a monocyte (monopoiesis).
FMA:83552
cell
tmeehan
epithelial cell of tracheobronchial tree
2010-09-02T02:09:14Z
An epithelial cell of the tracheobronchial tree.
CL:1000407
FMA:66816
cell
tmeehan
nucleate cell
2010-09-07T03:32:33Z
A cell containing at least one nucleus.
FMA:67513
cell
tmeehan
epithelial cell of thymus
2010-09-13T02:34:22Z
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.
CL:1000459
FMA:72208
cell
epithelial cell of thymus gland
epithelial reticular cell
epithelial reticular cell of thymus
thymic epithelial cell
tmeehan
connective tissue cell
2010-09-15T03:01:54Z
A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.
CL:1000406
FMA:63875
cell
tmeehan
embryonic cell
2010-09-15T03:39:21Z
A cell of the embryo.
FMA:82840
FMA:82841
WBbt:0007028
cell
tmeehan
embryonic stem cell
2010-09-15T03:44:35Z
A stem cell of embryonic origin.
BTO:0001086
ESC
FMA:82841
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.
cell
tmeehan
bronchial epithelial cell
2010-09-20T02:00:00Z
An epithelial cell of the bronchus.
BTO:0002922
cell
tmeehan
preadipocyte
2010-09-20T02:31:53Z
An undifferentiated fibroblast that can be stimulated to form a fat cell.
BTO:0001107
cell
tmeehan
progenitor cell of endocrine pancreas
2010-09-21T04:41:06Z
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.
cell
pancreatic endocrine progenitor
pancreatic islet progenitor cell
tmeehan
medullary thymic epithelial cell
2010-09-23T03:17:14Z
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.
BTO:0004563
cell
mTEC
tmeehan
respiratory epithelial cell
2010-09-23T04:38:49Z
An endo-epithelial cell of the respiratory tract.
BTO:0004533
airway epithelial cell
cell
tmeehan
somatic cell
2010-09-24T09:44:42Z
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).
BTO:0001268
FMA:72300
WBbt:0008378
cell
tmeehan
cardiocyte
2010-12-07T09:37:22Z
A cell located in the heart, including both muscle and non muscle cells.
BTO:0001539
FMA:83808
FMA:84791
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.
cell
heart cell
tmeehan
aortic endothelial cell
2011-02-28T03:54:42Z
An arterial endothelial cell that is part of the aorta endothelium.
BTO:0003245
cell
tmeehan
embryonic blood vessel endothelial progenitor cell
2011-02-28T04:20:39Z
An endothelial progenitor cell that participates in angiogenesis during development.
See CL:0002619.
cell
tmeehan
epithelial cell of lower respiratory tract
2011-06-21T12:29:31Z
cell
tmeehan
ghrelin secreting cell
A cell that secretes ghrelin, the peptide hormone that stimulates hunger.
cell
pancreatic epsilon cell
Ghrelin secreting cells found in the found in the exocrine pancreas.
In mammals the endocrine pancreas is called the Islets of Langerhans.
cell
pancreatic e cell
premigratory neural crest cell
2012-06-27T08:27:35Z
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.
cell
haendel
endothelial cell of artery
A blood vessel endothelial cell that is part of an arterial endothelium.
BTO:0004758
CL:0002542
FMA:67761
KUPO:0001095
arterial endothelial cell
cell
epithelial cell of gall bladder
An epithelial cell that is part of the gallbladder.
FMA:67780
cell
neutrophillic cytoplasm
2010-05-25T01:36:34Z
Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions.
cell
tmeehan
acidophilic cytoplasm
2009-12-22T04:23:25Z
Cytoplasm that exhibits molecular interaction for acidic dyes under specific pH conditions.
cell
eosinophilic
tmeehan
basophilic cytoplasm
2009-12-22T04:24:54Z
Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions.
cell
tmeehan
polychromatophilic cytoplasm
2009-12-28T04:25:23Z
Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions.
cell
tmeehan
increased nucleus size
2009-12-23T10:53:24Z
A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell.
cell
tmeehan
soil
Any material within 2 m from the Earth's surface that is in contact with the atmosphere, with the exclusion of living organisms, areas with continuous ice not covered by other material, and water bodies deeper than 2 m.
soil
environmental material
Material in or on which organisms may live.
environmental material
massively parallel signature sequencing
A DNA sequencing by ligation technique that involves a bead-based method that uses a complex approach of adapter ligation followed by adapter decoding, reading the sequence in increments of four nucleotides; this method made it susceptible to sequence-specific bias or loss of specific sequences.
massively parallel signature sequencing
biopsy
Specimen creation of a sample of tissue from a living body for diagnostic purposes.
biopsy
Fetus
Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus.
Fetus
geographical location
A reference to a place on the Earth, by its name or by its geographical location.
chromatin
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
chromatin
euchromatin
A dispersed and relatively uncompacted form of chromatin.
euchromatin
heterochromatin
A compact and highly condensed form of chromatin.
heterochromatin
osteoblast differentiation
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.
osteoblast differentiation
ameboidal cell migration
Cell migration that is accomplished by extension and retraction of a pseudopodium.
ameboidal cell migration
cytokine production
The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
cytokine production
serotonin secretion
The regulated release of serotonin by a cell. 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.
serotonin secretion
somatic diversification of immune receptors
The somatic process allowing for the production of immune receptors whose specificity is not encoded in the germline genomic sequences.
somatic diversification of immune receptors
natural killer cell mediated immunity
The promotion of an immune response by natural killer cells through direct recognition of target cells or through the release of cytokines.
natural killer cell mediated immunity
hematopoietic progenitor cell differentiation
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.
hematopoietic progenitor cell differentiation
immune system process
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
immune system process
lymphocyte mediated immunity
Any process involved in the carrying out of an immune response by a lymphocyte.
lymphocyte mediated immunity
T cell mediated immunity
Any process involved in the carrying out of an immune response by a T cell.
T cell mediated immunity
adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
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.
adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
leukocyte differentiation
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.
leukocyte differentiation
somatic diversification of immune receptors via germline recombination within a single locus
The process in which immune receptor genes are diversified through recombination of the germline genetic elements within a single genetic locus.
somatic diversification of immune receptors via germline recombination within a single locus
myeloid leukocyte differentiation
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage.
myeloid leukocyte differentiation
regulation of immune system process
Any process that modulates the frequency, rate, or extent of an immune system process.
regulation of immune system process
regulation of leukocyte activation
Any process that modulates the frequency, rate, or extent of leukocyte activation.
regulation of leukocyte activation
peptide secretion
The controlled release of a peptide from a cell or a tissue.
peptide secretion
molecular_function
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.
molecular_function
catalytic activity
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
catalytic activity
RNA-directed DNA polymerase activity
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
RNA-directed DNA polymerase activity
cellular_component
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.
cellular_component
nucleus
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.
nucleus
nucleolus
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.
nucleolus
cytoplasm
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
cytoplasm
vacuole
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.
vacuole
ribosome
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.
ribosome
nucleobase-containing compound metabolic process
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
nucleobase-containing compound metabolic process
DNA metabolic process
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.
DNA metabolic process
DNA packaging
Any process in which DNA and associated proteins are formed into a compact, orderly structure.
DNA packaging
chromatin remodeling
Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
chromatin remodeling
cellular aromatic compound metabolic process
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.
cellular aromatic compound metabolic process
transport
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.
transport
ion transport
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.
ion transport
serotonin transport
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.
serotonin transport
immune response
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
immune response
organelle organization
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.
organelle organization
cell cycle
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.
cell cycle
endomitotic cell cycle
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.
endomitotic cell cycle
meiosis
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.
meiosis
female meiosis
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.
female meiosis
gamete generation
The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell.
gamete generation
blood coagulation
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.
blood coagulation
blood circulation
The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
blood circulation
biological_process
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.
biological_process
metabolic process
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.
metabolic process
protein secretion
The controlled release of proteins from a cell.
protein secretion
detection of chemical stimulus
The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal.
detection of chemical stimulus
detection of carbohydrate stimulus
The series of events in which a carbohydrate stimulus is received by a cell and converted into a molecular signal.
detection of carbohydrate stimulus
detection of hexose stimulus
The series of events in which a stimulus from a hexose is received and converted into a molecular signal.
detection of hexose stimulus
response to carbohydrate stimulus
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 carbohydrate stimulus.
response to carbohydrate stimulus
response to hexose stimulus
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 hexose stimulus.
response to hexose stimulus
hormone transport
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.
hormone transport
cellular process
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.
cellular process
gene expression
The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
gene expression
protein transport
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.
protein transport
oxygen transport
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.
oxygen transport
peptide transport
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.
peptide transport
monoamine transport
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.
monoamine transport
cytoplasmic membrane-bounded vesicle
A membrane-bounded vesicle found in the cytoplasm of the cell.
cytoplasmic membrane-bounded vesicle
cellular component organization
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organization
somatic recombination of immunoglobulin gene segments
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.
somatic recombination of immunoglobulin gene segments
cell migration
The orderly movement of a cell from one site to another, often during the development of a multicellular organism or multicellular structure.
cell migration
stem cell division
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.
stem cell division
regulation of nucleobase-containing compound metabolic process
Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
regulation of nucleobase-containing compound metabolic process
regulation of metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
regulation of metabolic process
B cell mediated immunity
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.
B cell mediated immunity
immunoglobulin complex
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.
immunoglobulin complex
B cell receptor complex
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.
B cell receptor complex
antigen processing and presentation
The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
antigen processing and presentation
reproductive process
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.
reproductive process
signal release
The process in which a signal is secreted or discharged into the extracellular medium from a cellular source.
signal release
peptide hormone secretion
The regulated release of a peptide hormone from a cell.
peptide hormone secretion
insulin secretion
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.
insulin secretion
lymphocyte differentiation
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.
lymphocyte differentiation
myeloid cell differentiation
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.
myeloid cell differentiation
secretory granule
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.
secretory granule
cell differentiation
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.
cell differentiation
neuron differentiation
The process in which a relatively unspecialized cell acquires specialized features of a neuron.
neuron differentiation
T cell differentiation
T cell differentiation
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.
erythrocyte differentiation
The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
erythrocyte differentiation
megakaryocyte differentiation
The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte.
megakaryocyte differentiation
monocyte differentiation
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte.
monocyte differentiation
macrophage differentiation
The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage.
macrophage differentiation
chromosome condensation
The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
chromosome condensation
apoptotic chromosome condensation
The compaction of chromatin during apoptosis.
apoptotic chromosome condensation
osteoclast differentiation
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.
osteoclast differentiation
ribonucleoprotein complex
A macromolecular complex containing both protein and RNA molecules.
ribonucleoprotein complex
granulocyte differentiation
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.
granulocyte differentiation
epithelial cell differentiation
The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
epithelial cell differentiation
pancreas development
The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes.
pancreas development
endocrine pancreas development
The process whose specific outcome is the progression of the endocrine pancreas over time, from its formation to the mature structure. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin.
endocrine pancreas development
regulation of cellular metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
regulation of cellular metabolic process
cytoplasmic vesicle
A vesicle formed of membrane or protein, found in the cytoplasm of a cell.
cytoplasmic vesicle
vesicle
Any small, fluid-filled, spherical organelle enclosed by membrane or protein.
vesicle
developmental process
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.
developmental process
secretion by cell
The controlled release of a substance by a cell.
secretion by cell
macromolecular complex
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together.
macromolecular complex
immunoglobulin V(D)J recombination
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.
immunoglobulin V(D)J recombination
response to monosaccharide stimulus
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 monosaccharide stimulus.
response to monosaccharide stimulus
detection of monosaccharide stimulus
The series of events in which a stimulus from a monosaccharide is received and converted into a molecular signal.
detection of monosaccharide stimulus
cellular nitrogen compound metabolic process
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
cellular nitrogen compound metabolic process
ghrelin secretion
The regulated release of ghrelin from a cell. Ghrelin is a 28 amino acid hunger-stimulating peptide hormone.
ghrelin secretion
regulation of molecular function, epigenetic
Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya.
regulation of molecular function, epigenetic
T cell receptor complex
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.
T cell receptor complex
response to chemical stimulus
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.
response to chemical stimulus
melanosome
A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
melanosome
immunoglobulin complex, circulating
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.
immunoglobulin complex, circulating
DNA polymerase complex
A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
DNA polymerase complex
azurophil granule
Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid.
azurophil granule
MHC protein complex
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.
MHC protein complex
MHC class II protein complex
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.
MHC class II protein complex
amide transport
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.
amide transport
myeloid dendritic cell differentiation
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.
myeloid dendritic cell differentiation
macromolecule metabolic process
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.
macromolecule metabolic process
organelle
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.
organelle
intracellular organelle
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.
intracellular organelle
intracellular membrane-bounded organelle
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.
intracellular membrane-bounded organelle
intracellular non-membrane-bounded organelle
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.
intracellular non-membrane-bounded organelle
protein complex
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.
protein complex
receptor complex
Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
receptor complex
sequence-specific DNA binding
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
sequence-specific DNA binding
regulation of DNA methylation
Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
regulation of DNA methylation
cellular metabolic process
The chemical reactions and pathways by which individual cells transform chemical substances.
cellular metabolic process
primary metabolic process
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.
primary metabolic process
cellular macromolecule metabolic process
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.
cellular macromolecule metabolic process
intracellular part
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.
intracellular part
membrane part
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.
membrane part
cytoplasmic part
Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
cytoplasmic part
intracellular organelle part
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.
intracellular organelle part
plasma membrane part
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.
plasma membrane part
cell part
Any constituent part of a cell, the basic structural and functional unit of all organisms.
cell part
single-organism process
A biological process that involves only one organism.
single-organism process
single organism reproductive process
A biological process that directly contributes to the process of producing new individuals, involving a single organism.
single organism reproductive process
single-multicellular organism process
A biological process occurring within a single, multicellular organism.
single-multicellular organism process
single-organism cellular process
Any process that is carried out at the cellular level, occurring within a single organism.
single-organism cellular process
single-organism transport
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, involving a single organism.
single-organism transport
single-organism developmental process
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, involving only one organism.
single-organism developmental process
innate immune response
Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
innate immune response
leukocyte activation
A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor.
leukocyte activation
fat cell differentiation
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.
fat cell differentiation
regulation of T cell differentiation
Any process that modulates the frequency, rate or extent of T cell differentiation.
regulation of T cell differentiation
regulation of cell differentiation
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.
regulation of cell differentiation
regulation of lymphocyte differentiation
Any process that modulates the frequency, rate or extent of lymphocyte differentiation.
regulation of lymphocyte differentiation
heterocycle metabolic process
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).
heterocycle metabolic process
lymphocyte activation
A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor.
lymphocyte activation
hormone secretion
The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells.
hormone secretion
secretion
The controlled release of a substance by a cell or a tissue.
secretion
somatic stem cell division
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.
somatic stem cell division
oogenesis
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.
oogenesis
multicellular organismal reproductive process
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.
multicellular organismal reproductive process
anatomical structure development
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.
anatomical structure development
cellular developmental process
A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
cellular developmental process
cell motility
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
cell motility
regulation of immune response
Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
regulation of immune response
regulation of biological process
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.
regulation of biological process
regulation of developmental process
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).
regulation of developmental process
regulation of cellular process
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.
regulation of cellular process
regulation of body fluid levels
Any process that modulates the levels of body fluids.
regulation of body fluid levels
response to stimulus
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.
response to stimulus
regulation of DNA metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA.
regulation of DNA metabolic process
regulation of nitrogen compound metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
regulation of nitrogen compound metabolic process
establishment of localization
The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location.
establishment of localization
regulation of lymphocyte activation
Any process that modulates the frequency, rate or extent of lymphocyte activation.
regulation of lymphocyte activation
chromosome organization
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.
chromosome organization
detection of glucose
The series of events in which a glucose stimulus is received by a cell and converted into a molecular signal.
detection of glucose
cardiac muscle cell differentiation
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.
cardiac muscle cell differentiation
chondroblast differentiation
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.
chondroblast differentiation
biological regulation
Any process that modulates a measurable attribute of any biological process, quality or function.
biological regulation
regulation of biological quality
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.
regulation of biological quality
glucagon secretion
The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans).
glucagon secretion
somatostatin secretion
The regulated release of somatostatin from secretory granules in the D cells of the pancreas.
somatostatin secretion
organic substance transport
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.
organic substance transport
organic substance metabolic process
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
organic substance metabolic process
nitrogen compound transport
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.
nitrogen compound transport
extracellular vesicular exosome assembly
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.
extracellular vesicular exosome assembly
regulation of primary metabolic process
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.
regulation of primary metabolic process
nucleic acid metabolic process
Any cellular metabolic process involving nucleic acids.
nucleic acid metabolic process
organic cyclic compound metabolic process
The chemical reactions and pathways involving organic cyclic compound.
organic cyclic compound metabolic process
regulation of leukocyte differentiation
Any process that modulates the frequency, rate or extent of leukocyte differentiation.
regulation of leukocyte differentiation
regulation of multicellular organismal development
Any process that modulates the frequency, rate or extent of multicellular organismal development.
regulation of multicellular organismal development
measurement unit label
2009-03-16: provenance: a term measurement unit was
proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and
Cristian Cocos, and subsequently moved to IAO where the objective for
which the original term was defined was satisfied with the definition
of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
Examples of measurement unit labels are liters, inches, weight per volume.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
measurement unit label
objective specification
2009-03-16: original definition when imported from OBI read: "objective is an
non realizable information entity which can serve as that proper part
of a plan towards which the realization of the plan is directed."
Answers the question, why did you do this experiment?
OBI Plan and Planned Process/Roles Branch
OBI_0000217
PERSON: Alan Ruttenberg
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
objective specification
purpose of a study; support of hypothesis, discovery of new information
action specification
Alan Ruttenberg
OBI Plan and Planned Process branch
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
datum label
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
GROUP: IAO
datum label
http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n
software
GROUP: OBI
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Chris Stoeckert
PERSON: Melanie Courtot
Software is a plan specification composed of a series of instructions that can be
interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
software
data item
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
Data items include counts of things, analyte concentrations, and statistical summaries.
JAR: datum -- well, this will be very tricky to define, but maybe some
information-like stuff that might be put into a computer and that is
meant, by someone, to denote and/or to be interpreted by some
process... I would include lists, tables, sentences... I think I might
defer to Barry, or to Brian Cantwell Smith
JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
data
data item
symbol
20091104, MC: this needs work and will most probably change
PERSON: Jonathan Rees
a smallish, word-like datum...
symbol
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
OBI_0000142
PERSON: Chris Stoeckert
an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
information content entity
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).
Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
scalar measurement datum
1
1
10 feet. 3 ml.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in
this case we explicitly refer to the singular form
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
directive information entity
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be
concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
curation status specification
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
PERSON:Bill Bug
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
curation status specification
data set
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
OBI_0000042
data set
group:OBI
person:Allyson Lister
person:Chris Stoeckert
image
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
OBI_0000030
group:OBI
image
person:Alan Ruttenberg
person:Allyson
person:Chris Stoeckert
data about an ontology part
Person:Alan Ruttenberg
data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
2/3/2009 Comment from OBI review.
Action specification not well enough specified.
Conditional specification not well enough specified.
Question whether all plan specifications have objective specifications.
Request that IAO either clarify these or change definitions not to use them
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
Alan Ruttenberg
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
OBI Plan and Planned Process branch
OBI_0000344
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
plan specification
measurement datum
2/2/2009 is_specified_output of some assay?
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
OBI_0000305
group:OBI
measurement datum
person:Chris Stoeckert
conclusion textual entity
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
2009/10/23 Alan Ruttenberg: We need to work on the definition still
A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
Person:Alan Ruttenberg
conclusion textual entity
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
textual entity
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
PERSON: Lawrence Hunter
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
text
textual entity
figure
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
Any picture, diagram or table
PERSON: Lawrence Hunter
figure
document
A collection of information content entities intended to be understood together as a whole
A journal article, patent application, laboratory notebook, or a book
PERSON: Lawrence Hunter
document
time measurement datum
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
A scalar measurement datum that is the result of measuring a temporal interval
Person:Alan Ruttenberg
documenting
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
Bjoern Peters
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
a planned process in which a document is created or added to by including the specified input in it.
wikipedia http://en.wikipedia.org/wiki/Documenting
CRID symbol
A symbol that is part_of a CRID and that is sufficient to look up a record from the CRID's registry.
IAO call, 20101124: 12345 is not a CRID symbol. To be a CRID symbol you need to have some information about the registry within which the CRID is recorded.
Original proposal from Bjoern, discussions at IAO calls
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
PMID:12345, 12345 in a database column which has header "pubmedID"
obese
a status with body weight that is grossly above the average, acceptable or desirable weight, usually due to accumulation of excess fat tissue in the body
Mus musculus
Mus musculus
Rattus
Rattus
Rattus norvegicus
Rattus norvegicus
Viruses
Viruses
Euteleostomi
Euteleostomi
Bacteria
Bacteria
Archaea
Archaea
Eukaryota
Eukaryota
Euarchontoglires
Euarchontoglires
Teleostei
Teleostei
Amniota
Amniota
Sauria
Sauria
Murinae
Murinae
Vertebrata <Metazoa>
Vertebrata <Metazoa>
Gnathostomata <vertebrate>
Gnathostomata <vertebrate>
Danio rerio
Danio rerio
Serpentes
Serpentes
Aves
Aves
Homo sapiens
Homo sapiens
planned process
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
6/11/9: Edited at workshop. Used to include: is initiated by an agent
Bjoern Peters
Injecting mice with a vaccine in order to test its efficacy
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some
objectives is a planned process.
branch derived
A processual entity that realizes a plan which is the concretization of a plan specification.
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
planned process
biological feature identification objective
Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
Jennifer Fostel
biological feature identification objective
material supplier role
Jackson Labs is an organization which provide mice as experimental material
Supplier role is a special kind of service, e.g. biobank
material provider role
material supplier role
supplier
PERSON:Jennifer Fostel
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
reference substance role
reference substance
reference substance role
Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html
OBI
Person:Jennifer Fostel
a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.
waiting
BP: I have doubts about the utility of this.
OBI branch derived
PERSON:Alan Ruttenberg
We need a better handling/modeling of time (January 2008)
not actively doing anything to a material for a duration of time.
waiting
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
PERSON: Alan Ruttenberg
processed material
microarray platform
OBI Instrument branch
OBI Instrument branch
A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI.
microarray platform
investigation
Could add specific objective specification
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
Bjoern Peters
OBI branch derived
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
investigation
evaluant role
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
GROUP: Role Branch
OBI
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role.
a role that inheres in an entity that is realized in an assay in which data is generated about the bearer of the evaluant role
evaluant role
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
reporting party role
MO:submitter mapped to this term. So, alternative term 'submitter' was added.
Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress.
reporting party
reporting party role
submitter
Jennifer Fostel
OBI
The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm
a study personnel role played by a party who reports the outcome of a study component
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about some evaluant
OBI branch derived
PlanAndPlannedProcess Branch
assay
measuring
scientific observation
diagnosis textual entity
Jennifer Fostel
diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
diagnosis textual entity
culture medium
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178
Modification made by JZ.
culture medium
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
OBI
Person: Jennifer Fostel, Jie Zheng
reagent role
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
reagent
reagent role
www.answers.com/topic/reagent; November 2008
Buffer, dye, a catalyst, a solvating agent.
GROUP: Role Branch
a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances
material processing
A cell lysis, production of a cloning vector, creating a buffer.
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca Serra
material processing
A planned process which results in physical changes in a specified input material
OBI branch derived
PERSON: Bjoern Peters
material transformation
protocol testing objective
Jennifer Fostel
Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols.
protocol testing objective
study subject role
Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study.
Parasite example
people infected, then extract parasite which are then tested = observation study of the parasite
1 study in which we observe people and 1 study in which subject is parasite is one way to split this. the true definition will come from the study design specification.
OBI
study subject role inheres in an entity and realized through the execution of a study design in which the entity participates by being that which the results are about.
GROUP: Role Branch
study subject role
measured expression level
OBI Data Transformation branch
A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts.
Examples are quantified data from an expression microarray experiment, PCR measurements, etc.
measured expression level
person:Chris Stoeckert
biological vector role
6/12/2009 Alan made this a material to be added role, because it was, and because this speeded up reasoning
Feb 20, 2009. The material transmitted can be genetic information (as in cloning vector) or a pathogen (as in a disease vector)
GROUP: Role Branch
OBI and Wikipedia
a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission.
biological vector role
1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.
Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280
specimen role
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
GROUP: Role Branch
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
OBI
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
specimen role
a role borne by a material entity that is gained during a specimen creation process and that can be realized by use of the specimen in an investigation
blood taken from animal: animal continues in study, whereas blood has role specimen.
something taken from study subject, leaves the study and becomes the specimen.
parasite example
- when parasite in people we study people, people are subjects and parasites are specimen
- when parasite extracted, they become subject in the following study
specimen can later be subject.
sequence feature identification objective
Jennifer Fostel
Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
sequence feature identification objective
intervention design
An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
OBI branch derived
PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
Philppe Rocca-Serra
intervention design
worker role
"executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
worker
worker role
OBI
Person:Jennifer Fostel
Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html
a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
molecular feature identification objective
Jennifer Fostel
Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.
molecular feature identification objective
label role
OBI
label
Label role is a role which inheres in a material entity and which is realized in a detection of label assay
Nucleotides synthesized with the incorporation of biotin were used to synthesize cDNA, which was then detected by adding fluorochrome-conjugated anti-biotin antibody. the fluorochrome bears label role, the antibody bears detector role, the biotin bears reporter role. may need to change the terms following discussion
Role Branch
label role
need to add a restriction that the material entity has the disposition / quality that permits it to be detected, and one way to say this (BP) is that the entity is such that an assay exists that detects the presence of the material entity
we need to sort out probe, detector and reporter. See https://sourceforge.net/tracker/index.php?func=detail&aid=1866458&group_id=177891&atid=886178
complete nutrient role
A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment.
complete nutrient
complete nutrient role
Person: Jennifer Fostel
Rat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htm
cDNA library
GROUP: PSI
Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.
ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications.
PERSON: Luisa Montecchi
PERSON: Philippe Rocca-Serra
PMID:6110205. collection of cDNA derived from mouse splenocytes.
PRS: 22022008. class moved under population,
modification of definition and replacement of biomaterials in previous definition with 'material'
addition of has_role restriction
cDNA library
imaging assay
An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
OBI branch derived
PlanAndPlannedProcess Branch
imaging assay
protocol optimization objective
Jennifer Fostel
Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol.
protocol optimization objective
biological replicate role
a reference participant role realized by equivalent treatment of participants
biological replicate
biological replicate role
A member of a dose-time group; a patient in a given arm of a trial
OBI
Person:Jennifer Fostel
investigation agent role
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
investigation agent role
investigator
GROUP: Role Branch
Investigation agent role is a role borne by a person or organization which is realized in a process that is part of an investigation in which an objective is achieved. These processes include: planning, overseeing, funding, reviewing.
OBI
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
nutrient role
19 Feb 2009; old def: A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment.
nutrient
nutrient role
GROUP: Role branch
Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia.
Wikipedia, feb 29, 2008
a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment.
methodology testing objective
Jennifer Fostel
Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies.
methodology testing objective
cellular feature identification objective
Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation.
Jennifer Fostel
cellular feature identification objective
reference subject role
reference participant
reference subject role
Jennifer Fostel
OBI
Saline treated rat; one of three identically-treated subjects
a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference
software testing objective
Jennifer Fostel
Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software.
software testing objective
organization
GROUP: OBI
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Philippe Rocca-Serra
PERSON: Susanna Sansone
An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:
1) there are organization_member_roles (president, treasurer, branch
editor), with individual persons as bearers
2) there are organization_roles (employer, owner, vendor, patent holder)
3) an organization has a charter / rules / bylaws, which specify what roles
there are, how they should be realized, and how to modify the
charter/rules/bylaws themselves.
It is debatable what the organization itself is (some kind of dependent
continuant or an aggregate of people). This also determines who/what the
bearer of organization_roles' are. My personal favorite is still to define
organization as a kind of 'legal entity', but thinking it through leads to
all kinds of questions that are clearly outside the scope of OBI.
Interestingly enough, it does not seem to matter much where we place
organization itself, as long as we can subclass it (University, Corporation,
Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,
W3C, University of Oklahoma), and have it play roles.
This leads to my proposal: We define organization through the statements 1 -
3 above, but without an 'is a' statement for now. We can leave it in its
current place in the is_a hierarchy (material entity) or move it up to
'continuant'. We leave further clarifications to BFO, and close this issue
for now.
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
organization
feed role
a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment.
feed
feed role
OBI
Person: Jennifer Fostel
Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008
technical replicate role
technical replicate
technical replicate role
technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay
Aliquots of a tissue subjected to parallel assays
Person: Jennifer Fostel
DNA extraction
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
DNA extraction
OBI branch derived
PlanAndPlannedProcess Branch
organism feature identification objective
Jennifer Fostel
Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
organism feature identification objective
protocol
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
PMID: 18388943.Nat Protoc. 2008;3(4):612-8.Protocol for the induction of arthritis in C57BL/6 mice.
PlanAndPlannedProcess Branch
a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process.
protocol
adding a material entity into a target
BP
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
adding a material entity into a target
branch derived
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
analyte role
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
GROUP: Role Branch
Glucose in blood (measured in an assay to determine the concentration of glucose).
OBI
analyte role
interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
qualities such as weight, color are not assayed but measured, so they do not fall into this category.
Analyte role is a role borne by a molecular entity and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role
disease stage
PERSON: Bjoern peters
disease stage
Stage II breast cancer, The timepoint of recovery from a disease
a part of an occurrence of a disease process which is associated with position in the normal progression of the disease
intraperitoneal injection
BP
intraperitoneal injection
is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe
material to be added role
9 March 09 from discussion with PA branch
OBI
Role Branch
drug added to a buffer contained in a tube; substance injected into an animal;
material to be added role
material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
interpreting data
Bjoern Peters
Identifiying and removing outliers from data by eye. Examining data to and deriving a new hypothesis.
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
interpreting data
the process of evaluating the data gathered in an investigation in the context of literature knowledge with the objective to generate more general conclusions or to identify what additional data is necessary to draw conclusions
planning
7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
Bjoern Peters
Bjoern Peters
PPPB branch
planning
the process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment.
a process of creating or modifying a plan.
histological sample preparation
OBI branch derived
PERSON:Bjoern Peters
histological sample preparation
histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay
light emission function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
light emission function
contain function
A syringe, a beaker
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A contain function is a function to constrain a material entities location in space
contain function
heat function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A heat function is a function that increases the internal kinetic energy of a material
heat function
material separation function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
material separation function
excitation function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
excitation function
synthesizing function
A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
synthesizing function
perturb function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function.
http://en.wikipedia.org/wiki/Perturbation_biology
perturb function
mechanical function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
http://en.wikipedia.org/wiki/Mechanical_work
mechanical function
transfer function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
A transfer function is a function to displace a material from one location to another.
transfer function
cool function
Daniel Schober
Frank Gibson
Melanie Courtot
A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
cool function
information processor function
Frank Gibson
An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process.
data processor function
information processor function
image acquisition function
Frank Gibson
An image acquisition function is a function to acquire an image of a material
image acquisition function
image acquisition device
Frank Gibson
sep:00096
An image acquisition device is a device which captures a digitized image of an object
image acquisition device
solid support function
Daniel Schober
Frank Gibson
Melanie Courtot
Taped, glued, pinned, dried or molecularly bonded to a solid support
solid support function
A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
environment control function
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
environment control function
PCR product
GROUP: OBI BIomaterial Branch
GROUP: OBI BIomaterial Branch
PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
PCR product
We are using PCR and not the written out words, as this is the most common used.
is double stranded DNA that is the specified output of a polymerase chain reaction
nucleic acid template role
a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy.
nucleic acid template role
cloning vector role
PERSON: Helen Parkinson
cloning vector role
pBluescript plays the role of a cloning vector
a vector role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
polymerase chain reaction
OBI Plan
adapted from wikipedai
polymerase chain reaction
Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
PCR
PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
cloning insert role
Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process"
GROUP: Role branch
OBII and Wikipedia
cloning insert role
cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process.
reverse transcriptase
group:OBI
person:Melanie Courtot
enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase
activity)
reverse transcriptase
syringe
OBI Instrument adapted from Wikipedia
Philippe Rocca-Serra
syringe
Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832
a processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw
extract
GROUP: OBI Biomatrial Branch
PERSON: Philippe Rocca-Serra
Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
an extract is a material entity which results from an extraction process
extract
extracted material
transcription profiling assay
OBI
Philippe Rocca-Serra
transcription profiling assay
An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot
Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
gene expression profiling
averaging objective
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
James Malone
averaging objective
injection
OBI Biomaterial
Philippe Rocca-Serra
injection
Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712
injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue.
enzyme
GROUP:OBI
MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything
that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
person: Melanie Courtot
(protein or rna) or has_part (protein or rna) and
has_function some GO:0003824 (catalytic activity)
enzyme
intraperitoneal administration
Person:Bjoern Peters
Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h
The administration of a substance into the peritoneum of an organism
intraperitoneal administration
plasmid
group:OBI
person:Melanie Courtot
plasmid
plasmid = DNA and has_quality circular and has_function
(is_realized_as some gene expression) GO:0010467
adding material objective
BP
adding material objective
creating a mouse infected with LCM virus
is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
genotyping assay
OBI Biomaterial
Philippe Rocca-Serra
genotyping assay
High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923
an assay which generates data about a genotype from a specimen of genomic DNA. A variety of
techniques and instruments can be used to produce information about sequence variation at particular genomic positions.
genotype profiling, SNP genotyping
analyte measurement objective
PERSON: Bjoern Peters
PPPB branch
The objective to measure the concentration of glucose in a blood sample
analyte measurement objective
is an assay objective to determine the presence or concentration of an analyte in the evaluant
assay objective
PPPB branch
PPPB branch
assay objective
the objective to determine the weight of a mouse.
is the specification of an objective to determine a specified type of information about an evaluated entity (independent continuant bearing evaluant role)
analyte assay
PERSON:Bjoern Peters
PERSON:Helen Parkinson
PERSON:Philippe Rocca-Serra
PERSON:Alan Ruttenberg
GROUP:OBI Planned process branch
PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
analyte assay
logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum
and
('has measurement unit label' some 'measurement unit label') and
('is quality measurement of' some 'molecular concentration'))
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
target of material addition role
From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
GROUP: Role Branch
OBI
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
target of material addition role
target of material addition role is a role realized by an entity into which a material is added in a material addition process
normalized data set
PERSON: James Malone
PERSON: Melanie Courtot
normalized data set
A data set that is produced as the output of a normalization data transformation.
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
PERSON: Daniel Schober
PERSON: Helen Parkinson
PERSON: Melanie Courtot
PERSON:Frank Gibson
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
measure function
consume data function
PERSON: Daniel Schober
PERSON: Frank Gibson
PERSON: Melanie Courtot
Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data.
consume data function
material transformation objective
GROUP: OBI PlanAndPlannedProcess Branch
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
material transformation objective
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
manufacturing
GROUP: OBI PlanAndPlannedProcess Branch
Manufacturing implies reproducibility and responsibility AR
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
manufacturing
Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
This includes a single scientist making a processed material for personal use.
manufacturing objective
GROUP: OBI PlanAndPlannedProcess Branch
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
manufacturing objective
is the objective to manufacture a material of a certain function (device)
study design execution
6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
a planned process that realizes the concretization of a study design
branch derived
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
study design execution
reverse transcribed polymerase chain reaction
3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation
Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group.
Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW.
Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094
Philippe Rocca-Serra
RT-PCR
reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity.
reverse transcribed polymerase chain reaction
reverse transcription polymerase chain reaction
manufacturer role
GROUP: Role Branch
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
OBI
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
manufacturer role
scattered molecular aggregate
scattered molecular aggregate
the sodium and chloride ions in a glass of salt water
A scattered molecular aggregate is a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
Collective
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
PERSON: Alan Ruttenberg
DNA sequencing
DNA sequencing
DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.
Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858
OBI Branch derived
Philippe Rocca-Serra
DNA methylation profiling assay
DNA methylation profiling assay
Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J.
Genome Res. 2008 Mar;18(3):469-76. Epub 2008 Jan 24. PMID: 18218979
OBI branch derived
Philippe Rocca-Serra
an assay which aims to provide information about state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion.
material separation objective
PPPB branch
PPPB branch
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is an objective to transform a material entity into spatially separated components.
material separation objective
clustered data set
A clustered data set is the output of a K means clustering data transformation
AR thinks could be a data item instead
PERSON: James Malone
PERSON: Monnie McGee
clustered data set
data set with assigned discovered class labels
A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
differential expression analysis data transformation
A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of
James Malone
Melanie Courtot
Monnie McGee
WEB:
differential expression analysis data transformation
urine specimen
4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active
a portion of urine collected from an organism
are we happy calling collection of urine a material separation?
urine specimen
material combination
Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
bp
bp
created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
material combination
specimen collection
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
6/9/09: used at workshop
Bjoern Peters
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
a planned process with the objective of obtaining specimen.
specimen creation
error correction data transformation
EDITORS
Monnie McGee
An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation.
James Malone
error correction data transformation
sample from organism
5/29: This is a helper class for now
a material obtained from an organism in order to be a representative of the whole
sample from organism
we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
center value
PERSON: James Malone
PERSON: Monnie McGee
center value
median
A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
portioning objective
The objective to obtain multiple aliquots of an enzyme preparation.
is the objective to separate material into multiple portions, each of which contains a similar composition of the input material.
portioning objective
average value
PERSON: James Malone
PERSON: Monnie McGee
arithmetic mean
average value
A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
whole organism preparation
A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained
does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged.
putting a mouse in the blender. Not: putting a mouse on a scale
whole organism preparation
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
is the objective to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities)
separation into different composition objective
specimen creation objective
A specimen creation objective is to obtain a material entity for potential use as an input during an investigation
Bjoern Peters
Bjoern Peters
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
specimen creation objective
material combination objective
PPPB branch
bp
is an objective to obtain an output material that contains several input materials.
material combination objective
454 Genome Sequence 20
454 Genome Sequence 20
GS 20
PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults.
Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20.
Philippe Rocca-Serra
is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are
controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
immunoprecipitation
OBI plan and planned process branch
PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8.
Philippe Rocca-Serra
immunoprecipitation
is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity
ABI 377 automated sequencer
ABI 377 automated sequencer
Applied Biosystems
Philippe Rocca-Serra
is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers.
MeDIP-SEQ assay
MeDIP-SEQ assay
Methylated DNA immunoprecipitation sequencing assay
PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85.
Philippe Rocca-Serra
adapted from wikipedia
is an assay which aims at identifying methylated sites in genomic DNA and determining methylation pattern that affect gene transcription by relying on immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
animal feeding
Bjoern Peters
In an investigation, this will typically be part of an animal care process
animal feeding
animal feeding is a process in which animals are provided with food
branch derived
giving crickets to a snake.
chain termination sequencing
PMID: 271968. DNA sequencing with chain-terminating inhibitors.
Sanger F, Nicklen S, Coulson AR. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7.
Philippe Rocca-Serra
Sanger sequencing
adapted from wikipedia
chain termination sequencing
dye terminator sequencing
is a DNA sequencing which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position
AB SOLiD System
AB SOLiD System
Applied Biosystems
PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57.
Philippe Rocca-Serra
is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation
Helicos sequencing
Helicos sequencing
PMID: 18388294. Single-molecule DNA sequencing of a viral genome.
Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Science. 2008 Apr 4;320(5872):106-9.
Philippe Rocca-Serra
adapted from wikipedia
is a DNA sequencing which allows sequence identification of billions of DNA molecules immobilized to a surface by using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not requires amplification step and is typically able to produce reads of 25 base pair length.
true single molecule sequencing
454 Genome Sequencer FLX
454 GS FLX
454 Genome Sequencer FLX
GS-FLX
PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B.
J Biotechnol. 2008 Aug 31;136(1-2):3-10.
Philippe Rocca-Serra
adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay
is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are
controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
Illumina Genome Analyzer II
Illumina Corporation
Illumina Genome Analyzer II
PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57.
Philippe Rocca-Serra
is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology
Edman degradation
Edman degradation
PMID 4773306. Niall HD (1973). "Automated Edman degradation: the protein sequenator". Meth. Enzymol. 27: 942-1010
adapted from Wikipedia (http://en.wikipedia.org/wiki/Edman_degradation)
is a process which produces a sequence from an input peptide or protein. In this process, the amino-terminal (N-terminal) residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues.
SOLiD sequencing
PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108.
Philippe Rocca-Serra
SOLiD sequencing
adapted from Wikipedia and Applied Biosystems web site
is a DNA sequencing which allows sequence identification by relying on the following steps:
1. Primers hybridize to the P1 adapter sequence within the library template.
2. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction.
3. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length.
4. Following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles
Li-Cor 4300 DNA Analysis System
Li-Cor 4300 DNA Analysis System
OBI and Li-Cor
Philippe Rocca-Serra
is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing
library preparation
PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120.
Philippe Rocca-Serra
is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors.
library construction
library preparation
ChIP-seq assay
ChIP-seq assay
PMID: 19275939
ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions.
Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT.
Methods. 2009 Jul;48(3):240-8. Epub 2009 Mar 9.
Philippe Rocca-Serra
adapted from Wikipedia
an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
chromatin immunoprecipitation sequencing assay
made some modification based on the discussion on 2011/4/4 obi dev call, using DNA sequencing instead of union of some specific DNA sequencing processes
HeliScope Single Molecule Sequencer
HeliScope Single Molecule Sequencer
Philippe Rocca-Serra
is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
paired-end library
PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y.
Philippe Rocca-Serra
adapted from information provided by Solid web site
is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
mate-paired library
paired-end library
paired-end tag (PET) library
DNA sequencing by ligation
DNA sequencing by ligation
PERSON: Philippe Rocca-Serra
PMID: 19546169. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding.
McKernan KJ, Peckham HE, Costa G, McLaughlin S, Tsung E, Fu Y,
Clouser C, Dunkan C, Ichikawa J, Lee C, Zhang Z, Sheridan A, Fu H, Ranade S, Dimilanta E, Sokolsky T, Zhang L, Hendrickson C, Li B, Kotler L, Stuart J, Malek J, Manning J, Antipova A, Perez D, Moore M, Hayashibara K, Lyons M, Beaudoin R, Coleman B, Laptewicz M, Sanicandro A, Rhodes M, De La Vega F, Gottimukkala RK, Hyland F, Reese M, Yang S, Bafna V, Bashir A, Macbride A, Aklan C, Kidd JM, Eichler EE, Blanchard AP. Genome Res. 2009 Jun 22.
is a DNA sequencing which relies on DNA ligase activity to perform chain extension during the sequencing reaction step.
Solexa sequencing
PMID: 18987734
Accurate whole human genome sequencing using reversible terminator chemistry. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ. Nature. 2008 Nov 6;456(7218):53-9.
Philippe Rocca-Serra
Solexa sequencing
adapted from Wikipedia and Illumina / Solexa web site (SS_DNAsequencing.pdf document available on july 2009)
is a DNA sequencing which allows sequence identification by relying on use of DNA polymerase and reversible terminator. The methods requires immobilization of genomic DNA fragment onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on reversible terminator allow cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing.
reversible terminator sequencing
host role
30 Mar09 submitted by vaccine community
30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition
GROUP: Role Branch
In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
OBI
host role
host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role
http://en.wikipedia.org/wiki/Host_(biology)
pyrosequencing
Philippe Rocca-Serra
Pyrosequencing sheds light on DNA sequencing.
PMID: 1115661. Ronaghi M. Genome Res. 2001 Jan;11(1):3-11. Review.
Wikipedia (http://en.wikipedia.org/wiki/Pyrosequencing) and Roche 454 life science web site
is a DNA sequencing which allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template.
ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin.
pyrosequencing
recombinant vector
A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector.
recombinant vector
DNA sequencing by synthesis
DNA sequencing by synthesis
PERSON: Philippe Rocca-Serra
PMID: 18263613. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Turcatti G, Romieu A, Fedurco M, Tairi AP. Nucleic Acids Res. 2008 Mar;36(4):e25.
is a DNA sequencing which relies on DNA polymerase activity to perform chain extension during the sequencing reaction step.
single fragment library
Philippe Rocca-Serra
fragment library
is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
single fragment library
cloning vector
A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site.
cloning vector
material sample role
7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
material sample role
material sample
A material entity that has the material sample role
OBI: workshop
blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
material sample
sample population
bisulfite sequencing
8/19/09: Chris says that there may used to be a way of doing bisulfite sequencing comparing lengths of restriction fragments, which implies that it is possible to do without DNA sequencing.
PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J.
Genome Res. 2009 Jul 6.
Philippe Rocca-Serra
adapted from Wikipedia
bisulfite sequencing
is a DNA sequencing which allows to determine the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location.
independent variable specification
2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Chris Stoeckert
Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
independent variable specification
2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
multiple testing correction objective
A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously
Application of the Bonferroni correction
http://en.wikipedia.org/wiki/Multiple_Testing_Correction
multiple comparison correction objective
multiple testing correction objective
transcription factor binding site
PLace_holder for sequence ontology term
SO:0000235
transcription factor binding site
purification objective
10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality
BP
PERSON:Bjoern Peters
The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest
isolation objective
purification objective
the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides.
material maintenance objective
PERSON: Bjoern Peters
is the objective to maintain some or all of the qualities of a material over time.
material maintenance objective
amplified DNA
Alan Ruttenberg
Amplied DNA created by PCR
DNA that has been produced in an enzymatic amplification process
PERSON: Alan Ruttenberg
amplified DNA
primary structure of DNA macromolecule
BP et al
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
placeholder for SO
primary structure of DNA macromolecule
DNA residue methylation
DNA residue methylation
a quality of a DNA residue that has a methyl group attached to it
measurement device
A ruler, a microarray scanner, a Geiger counter.
GROUP:OBI Philly workshop
OBI
a processed material created to have the function to measure
measurement device
high molecular weight DNA extract
Extraction of chromosomal DNA from mammalian cells by first isolating nucei
OBI
PERSON:Chris Stoeckert
The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
high molecular weight DNA extract
material maintenance
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
material maintenance
primary structure of RNA molecule
Person:Bjoern Peters
The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together
primary structure of RNA molecule
polyA RNA extraction
A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.
Person: Chris Stoeckert
Person: Jie Zheng
UPenn Group
polyA RNA extraction
organellar RNA extraction
A RNA extraction process in which the desired output material is RNA in the organelle(s).
Person: Chris Stoeckert
Person: Jie Zheng
UPenn Group
organellar RNA extraction
record of missing knowledge
A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
Bjoern Peters
This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.
a information content entity created to indicate that information about something is not available to the person recording it.
record of missing knowledge
total RNA extraction
A RNA extraction process in which total cellular and organelle RNA are extracted.
Person: Chris Stoeckert
Person: Jie Zheng
UPenn Group
total RNA extraction
record of unknown sex
A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record.
Bjoern Peters
I think the statement is still about the instance of the biological sex quality of an organism. It is also about information available to the person making the statement.
a record indicating that the biological sex of an organism is not known.
record of unknown sex
cytoplasmic RNA extraction
A RNA extraction process in which the desired output material is RNA in the cytoplasm.
Person: Chris Stoeckert
Person: Jie Zheng
UPenn Group
cytoplasmic RNA extraction
nuclear RNA extract
A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted.
Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30)
PERSON: Chris Stoeckert
PERSON: Jie Zheng
UPenn Group
nuclear RNA extract
polyA RNA extract
A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3’ end are purified.
PERSON: Chris Stoeckert
PERSON: Jie Zheng
Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.)
UPenn Group
polyA RNA extract
pre-mortem specimen
Bjoern Peters
a specimen that was taken from a live organism
material obtained through a liver biopsy from a human patient
pre-mortem specimen
MO_705 premortem
cytoplasmic RNA extract
A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted.
Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.)
PERSON: Chris Stoeckert
PERSON: Jie Zheng
UPenn Group
cytoplasmic RNA extract
cell line immortalization
Bjoern Peters
OBI
Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs
cell line immortalization
is the planned process of experimentally creating a cell line which is capable of dividing indefinitely in vitro. Has specified output cell line
RNA extract
Group: UPenn Group
PERSON: Chris Stoeckert
PERSON: Jie Zheng
RNA extract
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
nuclear RNA extraction
A RNA extraction process in which the desired output material is RNA in the nucleus.
Person: Chris Stoeckert
Person: Jie Zheng
UPenn Group
nuclear RNA extraction
real time polymerase chain reaction assay
A laboratory technique based on the PCR, which is used to
amplify and simultaneously quantify a specific DNA
molecule based on the use of complementary probes/primers. It enables
both detection and quantification (as absolute number of copies or relative
amount when normalized to DNA input or additional normalizing genes) of one
or more specific sequences in a DNA sample.
Q-PCR
WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
kinetic polymerase chain reaction
person: Bjoern Peters
person: Melanie Courtot
qPCR
quantitative real time polymerase chain reaction
real time polymerase chain reaction assay
protein extract
OBI & wikipedia
PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE.
J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23.
Person: Philippe Rocca-Serra
a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation,
protein extract
total RNA extract
A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
Extraction of total RNA from cells with Qiagen mini RNeasy kit.
PERSON: Chris Stoeckert
PERSON: Jie Zheng
UPenn Group
total RNA extract
organellar RNA extract
A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted.
Extraction of organellar RNA from plant cells using organellar RNA binding protein.
PERSON: Chris Stoeckert
PERSON: Jie Zheng
UPenn Group
organellar RNA extract
post mortem specimen
Bjoern Peters
a specimen that was taken from a dead organism
post mortem specimen
the spleen taken from a dead mouse
MO_416 postmortem
sequence feature annotation
Bjoern Peters
Bjoern Peters
Information about a sequence region
place holder for sequence ontology term
sequence feature annotation
labeled DNA extract
Group: OBI group
Group: OBI group
Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group.
Added duirng Mar 1, 2010 dev call
a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments.
labeled DNA extract
freezing storage
2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance"
A process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities
Freezing a pellet for later assay
OBI
Person: Alan Ruttenberg
freezing storage
MO_481 frozen_storage
animal euthanization
A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject
Helen Parkinson and Melissa Haendel
Melissa Haendel
Rats were euthanized with CO2
animal euthanization
animal sacrifice
may later be refined with more specific list of organisms
labeled RNA extract
Group: OBI group
Group: OBI group
Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group.
Added duirng Mar 1, 2010 dev call
a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments.
labeled RNA extract
frozen specimen
A specimen that has been frozen in order to store it.
Frozen blood plasma
MO_610 frozen_sample
Person:Alan Ruttenberg
frozen specimen
labeled specimen
A specimen that has been modified in order to be able to detect it in future experiments
OBI group
added during call 3/1/2010
labeled specimen
lyophilization storage
PERSON: Chris Stoeckert
PERSON: Jie Zheng
a storage process with input material entity and output freeze dried material for long time storage
can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed
lyophilization storage
study intervention
GROUP: OBI
PERSON: Bjoern Peters
study intervention
the part of the execution of an intervention design study which is varied between two or more subjects in the study
material separation device
A device with a separation function realized in a planed process
flow cytometer
material separation device
intramuscular injection
intramuscular injection
is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe
service provider role
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
PERSON:Helen Parkinson
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
service provider role
paraffin specimen
MO_990 paraffin_sample
PERSON: Chris Stoeckert
PERSON: Jie Zheng
a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
liver tissue embedded in paraffin
paraffin specimen
compound treatment design
MO_555 compound_treatment_design
PERSON: Bjoern Peters
This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc.
an intervention design in which the treatment is the administration of a compound
compound treatment design
processed specimen
A specimen that has been intentionally physically modified.
Bjoern Peters
Bjoern Peters
processed specimen
subcutaneous injection
PERSON: Melanie Courtot
is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe
subcutaneous injection
lyophilized specimen
MO_589 freeze_dried_sample
PERSON: Chris Stoeckert
PERSON: Jie Zheng
a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
freezing dried DNA
lyophilized specimen
container
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
A device that can be used to restrict the location of material entities over time
PERSON: Bjoern Peters
container
device
A device is a processed material which is designed to perform some function or functions
A voltmeter is a measurement device which is intended to perform some measure function.
OBI Vancouver workshop 2010
PERSON: Helen Parkinson
device
food should not classify as a device - counter example for using manufacturer and not device. macroscopic only
if we keep this exploratory term we could reinstate the old device class which is obsolete_device. didn't work before as we had manufacturing as part of the definition. device was needed, but couldn't define in Philadelphia. If we decide that in addition to function there are also capabilities for which a device is created we will include these in the definition.
instrument
would include reagents
dose specification
a directive information entity that describes the dose that will be administered to a target
a protocol specifying to administer 1 ml of vaccine to a mouse
dose specification
fresh specimen
MO_730 fresh_sample
PERSON: Chris Stoeckert
PERSON: Jie Zheng
a liver freshly removed from a rat
a specimen that is output of a specimen creation process used for an investigation without storage.
fresh specimen
sequence data
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
GROUP: OBI
Person:Chris Stoeckert
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
sequence data
paraffin storage
PERSON: Chris Stoeckert
PERSON: Jie Zheng
UPenn Group
a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
need to specify paraffin or wax is one of specified input of the process
paraffin storage
agar stab specimen
MO_971 agar_stab
PERSON: Chris Stoeckert
PERSON: Jie Zheng
a specimen that is output of a process that cell culture inoculated into agar for long term storage.
agar stab specimen
growth condition intervention design
A study design in which the independent variable is the environmental condition in which the specimen is growing
MO_588 growth_condition_design
PERSON: Bjoern Peters
growth condition intervention design
intravenous injection
PERSON: Melanie Courtot
intravenous injection
is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe
administration of material to specimen
Bjoern Peters
Bjoern Peters
Staining cells in a tissue slice with a dye.
The directed combination of a material entity with a specimen.
administration of material to specimen
growth environment
OBI group
PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters
Right now this may be incomplete. Should also cover e.g. sound, light as well.
The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth.
growth environment
agar stab storage
PERSON: Chris Stoeckert
PERSON: Jie Zheng
UPenn Group
a storage process with input cell culture and agar and output agar stab for long time storage
agar stab storage
need to specify that agar is one of input for this process
image acquisition
A planned process that captures an image of an object.
PERSON: Jie Zheng
Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
image acquisition
nucleic acid extract
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
PERSON: Jie Zheng
UPenn Group
nucleic acid extract
feature extraction
A planed process with objective of obtaining quantified values from an image.
MO_928: feature_extraction
PERSON: Jie Zheng
feature extraction
array image acquisition
An image acquisition process that generate an image from the array.
MO_929: image_acquisition
PERSON: Jie Zheng
array image acquisition
light emission device
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)
OBI
Person:Helen Parkinson
a device which has a function to emit light.
light emission device
perturbation device
A homogenizer is a perturbation device.
A perturbation device is a device which is designed to perform a perturb function
Helen Parkinson
OBI Vancouver workshop 2010
PERSON: Helen Parkinson
perturbation device
environmental control device
A growth chamber is an environmental control device.
An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
Helen Parkinson
OBI
environmental control device
DNA extract
DNA extract
Group: UPenn group
Person: Jie Zheng
The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
array manufacturer role
a manufacturer role which is played by the person or organization that manufactured the array
MO_695 array_manufacturer
PERSON: Chris Stoeckert, Jie Zheng
array manufacturer role
spike-in quality control role
MO_937 spike_quality_control
PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter
a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes
spike-in quality control role
individual organism identifier
PERSON: Chris Stoeckert, Jie Zheng
MO_169 Individual
a CRID symbol used to distinguish one individual organism from another.
individual organism identifier
dye swap quality control role
MO_524 dye_swap_quality_control
PERSON: Chris Stoeckert, Jie Zheng
a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes
dye swap quality control role
labeled nucleic acid extract
MO_221 labeledExtract
Person: Jie Zheng
a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
labeled extract
labeled nucleic acid extract
cell culture expansion
BP:
add it as subclass of 'cell culturing'
JZ:
No 'cell culturing' in OBI
Has term 'cell co-culturing' and 'maintaining cell culture'. Don't think either of it fit. So leave the term under process.
MO_758 grow
PERSON: Chris Stoeckert, Jie Zheng
a processual entity that results in the increase of cell numbers
cell culture expansion
including grow of yeast and bacteria
gene knock out
MO_771 gene_knock_out
PERSON: Chris Stoeckert, Jie Zheng
a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.
gene knock out
gene knock in
PERSON: Chris Stoeckert, Jie Zheng
MO_437 gene_knock_in
WEB: http://en.wikipedia.org/wiki/Gene_Knock-in
a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion.
gene knock in
chromosomal substitution
A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'.
MO_995 chromosomal_substitution
PERSON: Chris Stoeckert, Jie Zheng
chromosomal substitution
genetically modified material
GROUP: OBI
PERSON: Jie Zheng
a material entity, organism or cell, that is the output of a genetic transformation process.
genetically modified material
term is proposed by BP on Oct 25, 2010 dev call
transfection
MO_366 transfection
transfection
PERSON: Chris Stoeckert, Jie Zheng
a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell
genetic transformation objective
suggested to be added by BP and AR during Oct 25, 2010 dev call
Person: Jie Zheng
Person: Jie Zheng
a material transformation objective aims to create genetically modified organism or cell
genetic transformation objective
induced mutation
MO_564 induced_mutation
PERSON: Chris Stoeckert, Jie Zheng
a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation.
induced mutation
age since planting measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing.
Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call.
Term proposed by Bjoern on Nov 8, 2010 dev call
Supported by Alan on Nov 15, 2010 dev call
MO_495 planting
PERSON:Chris Stoeckert, Jie Zheng
age since planting measurement datum
age since hatching measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg.
MO_745 hatching
PERSON:Chris Stoeckert, Jie Zheng
age since hatching measurement datum
age measurement assay
An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted.
OBI group
PERSON: Alan Ruttenberg
This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature.
age measurement assay
age since egg laying measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism.
MO_767 egg laying
PERSON:Chris Stoeckert, Jie Zheng
age since egg laying measurement datum
assay validation objective
GROUP: Penn Group
PERSON: Chris Stoeckert, Jie Zheng
an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results
assay validation objective
age since germination measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth.
Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance.
MO_590 germination
PERSON:Chris Stoeckert, Jie Zheng
age since germination measurement datum
validation by reverse transcription PCR design
MO_986 reverse_transcription_PCR_quality_control
PERSON: Chris Stoeckert, Jie Zheng
a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results
validation by reverse transcription PCR design
age since eclosion measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon.
MO_876 eclosion
PERSON:Chris Stoeckert, Jie Zheng
age since eclosion measurement datum
age since sowing measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination.
MO_748 sowing
PERSON:Chris Stoeckert, Jie Zheng
age since sowing measurement datum
age since coitus measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction.
MO_783 coitus
PERSON:Chris Stoeckert, Jie Zheng
age since coitus measurement datum
validation by real time PCR design
MO_434 real_time_PCR_quality_control
PERSON: Chris Stoeckert, Jie Zheng
a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results
validation by real time PCR design
age measurement datum
A time measurement datum that is the result of measurement of age of an organism
In MageTab file, we use
initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.)
Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class
MO_178 Age
PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
discussed on Nov 15, dev call
All subtype will be defined by textual definition now.
note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet.
life of bearer doesn't imply organism
this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature
age as a quality is dubious; we plan to revisit
stages in development are currently handled with controlled vocabulary, such as 2-somite stage
age measurement datum
age since fertilization measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote.
Definition of fertilization comes from GO.
MO_701 fertilization
PERSON:Chris Stoeckert, Jie Zheng
age since fertilization measurement datum
age since birth measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
MO_710 birth
PERSON:Chris Stoeckert, Jie Zheng
age since birth measurement datum
reverse transcription polymerase chain reaction assay
GROUP: Penn Group
PERSON: Chris Stoeckert, Jie Zheng
an assay that evaluates the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR.
reverse transcription polymerase chain reaction assay
selective organism creation objective
PERSON: Chris Stoeckert, Jie Zheng
WEB: wikipedia
http://en.wikipedia.org/wiki/Cultivar
http://en.wikipedia.org/wiki/Ecotype
http://en.wikipedia.org/wiki/Strain_%28biology%29
an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms.
selective organism creation objective
RNA sequencing
BP 12/21:Created based on a request from Melanie
Bjoern Peters
Bjoern Peters
RNA sequencing
RNA sequencing is a sequencing process which uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact
selectively maintained organism
An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms
Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert
MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar
cultivar
ecotype
strain
selectively maintained organism
operator variation design
Person: Chris Stoeckert, Jie Zheng
A study design that assesses the operator performance and relation to data consistency and quality.
MO_519 operator_variation_design
operator variation design
comparative genome hybridization by array design
Person: Chris Stoeckert, Jie Zheng
A study design that detects genomic copy number variations using microarray technology.
MO_856 comparative_genome_hybridization_design
comparative genome hybridization by array design
in vivo design
Person: Chris Stoeckert, Jie Zheng
A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
MO_454 in_vivo_design
in vivo design
cell component comparison design
A study design that compares samples from different cell components.
Person: Chris Stoeckert, Jie Zheng
MO_1019 cell_component_comparison_design
cell component comparison design
ex vivo design
Person: Chris Stoeckert, Jie Zheng
A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment.
MO_808 ex_vivo_design
ex vivo design
normalization testing design
Person: Chris Stoeckert, Jie Zheng
A study design that tests different normalization procedures.
MO_729 normalization_testing_design
normalization testing design
genetic population background information
Group: OBI group
Group: OBI group
a genetic characteristics information which is a part of genotype information that identifies the population of organisms
genetic population background information
genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
proposed and discussed on San Diego OBI workshop, March 2011
environmental history design
MO_698 environmental_history_design
Person: Chris Stoeckert, Jie Zheng
A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.
environmental history design
epigenetic modification identification objective
A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications.
Chris Stoeckert, Jie Zheng
Person: Chris Stoeckert
epigenetic modification identification objective
transcription profiling by tiling array assay
Person: James Malone
An assay in which the transcriptome of a biological sample is analysed using a tiling path array.
EFO_0002769 transcription profiling by tiling array
transcription profiling by tiling array assay
genotyping by high throughput sequencing assay
Person: James Malone
An assay in which high througput sequencer is used to detect polymorphisms in DNA samples
EFO_0002771: genotyping by high throughput sequencing
genotyping by high throughput sequencing assay
array platform variation design
Person: Chris Stoeckert, Jie Zheng
A study design in which the array platform is compared, e.g. Agilent versus Affymetrix.
MO_899 array_platform_variation_design
array platform variation design
translational bias design
Person: Chris Stoeckert, Jie Zheng
A study design that characterizes the association of transcripts and translation machinery.
MO_939 translational_bias_design
translational bias design
DNA methylation profiling by high throughput sequencing assay
EFO_0002761 methylation profiling by high throughput sequencing
Group: ArrayExpress production team, James Malone, Helen Parkinson
Philippe Rocca-Serra
An assay in which the methylation state of DNA is determined and is compared between samples using sequencing based technology
DNA methylation profiling by high throughput sequencing assay
RNA-seq assay
An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance
EFO_0002770 transcription profiling by high throughput sequencing
PERSON: James Malone
RNA-seq assay
an assay that uses high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content. RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions.
WEB: http://en.wikipedia.org/wiki/RNA-Seq
transcription profiling by high throughput sequencing
in vitro design
Person: Chris Stoeckert, Jie Zheng
A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.
MO_347 in_vitro_design
in vitro design
transcription profiling by array design
MO_533 transcript_identification_design
Person: Chris Stoeckert, Jie Zheng
A study design that identifies forms and abundance of transcripts in the genome using microarray technology.
transcription profiling by array design
disease state design
Person: Chris Stoeckert, Jie Zheng
A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress.
MO_902 disease_state_design
disease state design
wild type organism genotype information
C57BL/6J wild type
Group: OBI group
Group: OBI group
a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms.
proposed and discussed on San Diego OBI workshop, March 2011
wild type organism genotype information
genotype information
Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
Group: OBI group
Group: OBI group
a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
discussed on San Diego OBI workshop, March 2011
genotype information
RNA stability design
Person: Chris Stoeckert, Jie Zheng
A study design that examines the stability and/or decay of RNA transcripts.
MO_553 RNA_stability_design
RNA stability design
tiling microarray
EFO_0002704: tiling array
Person: Helen Parkinson
a DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions.
genome tiling array
tiling microarray
species comparison design
A study design that assays differences between distinct species.
Person: Chris Stoeckert, Jie Zheng
MO_675 species_design
species comparison design
organism development design
Person: Chris Stoeckert, Jie Zheng
A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state.
MO_892 development_or_differentiation_design
organism development design
family history design
Person: Chris Stoeckert, Jie Zheng
A study design in which the family history such as traits, characteristics, susceptibility to disease is studied.
MO_544 family_history_design
family history design
transcription profiling identification objective
A molecular feature identification objective that aims to characterize the abundance of transcripts
Group: Penn Group
Person: Chris Stoeckert, Jie Zheng
transcription profiling identification objective
quality control testing design
Person: Chris Stoeckert, Jie Zheng
A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance.
MO_981 quality_control_testing_design
quality control testing design
clinical history design
Person: Chris Stoeckert, Jie Zheng
A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
MO_832 clinical_history_design
clinical history design
allele information
MO_58 Allele
Person: Chris Stoeckert, Jie Zheng
a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
allele information
discussed on San Diego OBI workshop, March 2011
genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
post-transcriptional modification design
Person: Chris Stoeckert, Jie Zheng
A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
MO_392 cellular_modification_design
post transcription modification design?
or more clear RNAi design / antibody targeting design?
need to check the use cases
post-transcriptional modification design
genetic alteration information
Group: OBI group
Group: OBI group
a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
genetic alteration information
proposed and discussed on San Diego OBI workshop, March 2011
cellular process design
Person: Chris Stoeckert, Jie Zheng
A study design that aims to study the processes 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.
MO_810 cellular_process_design
cellular process design
wild type allele information
MO_605 genotype
Person: Chris Stoeckert, Jie Zheng
an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism.
discussed on San Diego OBI workshop, March 2011
wild type allele information
injury design
Person: Chris Stoeckert, Jie Zheng
A study design in which the response of an organism(s) to injury or damage is studied.
MO_726 injury_design
injury design
organism status comparison design
Person: Chris Stoeckert, Jie Zheng
A study design that compares samples from live and dead organisms.
MO_841 organism_status_design
organism status comparison design
comparative genomic hybridization by array assay
Philippe Rocca-Serra
An assay in which changes in DNA sequence copy number are analysed using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria.
EFO_0000749: comparative genomic hybridization by array
Person: James Malone
array CGH
comparative genomic hybridization by array assay
stimulus or stress design
Person: Chris Stoeckert, Jie Zheng
A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc.
MO_568 stimulus_or_stress_design
stimulus or stress design
protein and DNA interaction identification objective
A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites.
MO_933 binding_site_identification_design
Person: Chris Stoeckert, Jie Zheng
protein and DNA interaction identification objective
protocol optimization design
Person: Chris Stoeckert, Jie Zheng
A study design where different protocols or protocol parameters are compared aims to find an optimized protocol
MO_934 optimization_design
protocol optimization design
genetic characteristics information
MO definition:
The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.
examples in ArrayExpress
wild_type
MutaMouse (CD2F1 mice with lambda-gt10LacZ integration)
AlfpCre; SNF5 flox/knockout
p53 knock out
C57Bl/6 gp130lox/lox MLC2vCRE/+
fer-15; fem-1
df/df
pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)
MO_66 IndividualGeneticCharacteristics
Person: Chris Stoeckert, Jie Zheng
a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
genetic characteristics information
imprinting design
Person: Chris Stoeckert, Jie Zheng
A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared.
MO_914 imprinting_design
imprinting design
cell cycle design
Person: Chris Stoeckert, Jie Zheng
A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells.
MO_822 cell_cycle_design
cell cycle design
cell type comparison design
Person: Chris Stoeckert, Jie Zheng
A study design that compares cells of different type, for example different cell lines.
MO_764 cell_type_comparison_design
cell type comparison design
dose response design
Person: Chris Stoeckert, Jie Zheng
A study design that examines the relationship between the size of the administered dose and the extent of the response.
MO_485 dose_response_design
dose response design
organism part comparison design
A study design that compares tissues, regions, organs within or between organisms
Person: Chris Stoeckert, Jie Zheng
MO_953 organism_part_comparison_design
organism part comparison design
protein binding site identification design
A study design that investigates protein binding sites on nucleic acids.
MO_933 binding_site_identification_design
Person: Chris Stoeckert, Jie Zheng
protein binding site identification design
sex comparison design
A study design that assays differences associated with an organism's sex, gender or mating type.
Person: Chris Stoeckert, Jie Zheng
MO_575 sex_design
sex comparison design
transcription profiling by tiling array design
MO_507 tiling_path_design
Person: Chris Stoeckert, Jie Zheng
A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals.
transcription profiling by tiling array design
cell differentiation design
Person: Chris Stoeckert, Jie Zheng
A study design that assays events associated with cell development or differentiation.
MO_892 development_or_differentiation_design
cell differentiation design
transcription profiling design
A study design that identifies forms and abundance of transcripts in the genome.
MO_533 transcript_identification_design
Person: Chris Stoeckert, Jie Zheng
transcription profiling design
operon identification design
Person: Chris Stoeckert, Jie Zheng
A study design that identifies locations and members of operons in a genome.
MO_772 operon_identification_design
operon identification design
all pairs design
Person: Chris Stoeckert, Jie Zheng
A study design in which all specimens are compared to every other specimen.
MO_565 all_pairs
all pairs design
genotyping design
Person: Chris Stoeckert, Jie Zheng
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
MO_560 genotyping_design
genotyping design
individual genetic characteristics comparison design
Person: Chris Stoeckert, Jie Zheng
A study design where genotype, haplotype, or other individual genetic characteristics are compared.
MO_527 individual_genetic_characteristics_design
individual genetic characteristics comparison design
pathogenicity design
Person: Chris Stoeckert, Jie Zheng
A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
MO_807 pathogenicity_design
pathogenicity design
genetic modification design
Person: Chris Stoeckert, Jie Zheng
A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out.
MO_447 genetic_modification_design
genetic modification design
transcription profiling by array assay
An assay in which the transcriptome of a biological sample is analysed using array technology.
Person: James Malone
EFO_0002768: transcription profiling by array
transcription profiling by array assay
strain comparison design
Person: Chris Stoeckert, Jie Zheng
A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
MO_462 strain_or_line_design
strain comparison design
cell specimen
A specimen primarily composed of cells collected from a multicellular organism or a cell culture
MO_612 cell
PERSON: Chris Stoeckert, Jie Zheng
cell specimen
specimen with known storage state
A specimen for which it is known whether it has been subjected to storage of a specified type.
MO_95 BiosourceType
PERSON: Chris Stoeckert, Jie Zheng
specimen with known storage state
lowess group transformation
A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed.
MO_861 lowess_group_normalization
Person: Elisabetta Manduchi
lowess group transformation
lowess transformation
A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria.
MO_720 lowess_normalization
Person: Elisabetta Manduchi
lowess transformation
tissue specimen
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
MO_954 organism_part
PERSON: Chris Stoeckert, Jie Zheng
tissue specimen
lowess global transformation
A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample.
MO_692 lowess_global_normalization
Person: Elisabetta Manduchi
lowess global transformation
cell collecting
A planned process that collects cells from culture.
MO_982 harvest
PERSON: Chris Stoeckert, Jie Zheng
cell collecting
linear amplification
An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template.
An example is the use of the T7 promoter for amplification by transcribing many RNA copies.
MO_997 linear_amplification
PERSON: Chris Stoeckert, Jie Zheng
linear amplification
atmosphere
A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism.
MO_219 atmosphere
PERSON: Chris Stoeckert, Jie Zheng
atmosphere
dissection
A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures.
EFO_0003856 dissection
MO_374 dissect
PERSON: Chris Stoeckert, Jie Zheng
dissection
purification
A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest
MO_406 purify
PERSON: Chris Stoeckert, Jie Zheng
purification
specimen with pre- or post-mortem status
A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
MO_84 OrganismStatus
PERSON: Chris Stoeckert, Jie Zheng
organizational term, used in description of specimen that is created from known pre- or post-mortem status
specimen with pre- or post-mortem status
sampling time measurement datum
A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
MO_738 timepoint
Person: Chris Stoeckert
sampling time measurement datum
time point
DNA sequence data
8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
A sequence data item that is about the primary structure of DNA
DNA sequence data
OBI call; Bjoern Peters
OBI call; Melanie Courtout
The part of a FASTA file that contains the letters ACTGGGAA
binding
9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point.
A peptide binding to an MHC molecule to form a complex.
IEDB
PERSON: Bjoern Peters, Randi Vita
The process of material entities forming complexes.
binding
immunoprecipitation assay
An assay with the objective to determine presence of an analyte by mixing a solution of antigen and antibody and separating out bound antigen:antibody complexes using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies.
Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum.
IEDB
PERSON:Bjoern Peters, Randi Vita
immunoprecipitation assay
organism
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009:
OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.
This issue is outside the scope of OBI.
GROUP: OBI Biomaterial Branch
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
WEB: http://en.wikipedia.org/wiki/Organism
animal
fungus
organism
plant
virus
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
PERSON: James Malone
PERSON: Philippe Rocca-Serra
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch
specimen
immortalized cell line culture
GROUP: OBI Biomaterial Branch
immortalized cell line
immortalized cell line culture
An immortalized cell line is a cell line that is able to replicate indefinitely as a result of an in vitro cell line immortalization process
GROUP: OBI Biomaterial Branch
Isolation and characterization of an immortalized oral keratinocyte cell line of mouse origin.
Arch Oral Biol. 2008 Nov;53(11):1091-100. Epub 2008 Aug 21. PMID: 1872191
cell culture
GROUP: OBI Biomaterial Branch
Jurkat cell line in RPMI w/ 10% FCS. PBMCs were purified from blood sample and put into tissue culture media.
Purification of recombinant human growth hormone from CHO cell culture supernatant by Gradiflow preparative electrophoresis technology.
Protein Expr Purif. 2003 Nov;32(1):126-34.
PMID: 14680949
PERSON: Bjoern Peters
a cell culture is a material entity consisting of a population of cells that is maintained in vitro
cell culture
cell line culture
GROUP: OBI Biomaterial Branch
PERSON: Susanna Sansone
HeLa cells
Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line. Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592
a cell line culture is a cell culture where the cells grown are from a cell line, long term culture of cells that are replicating continuously. The cell population is homogenous but not clonal
cell line culture
organ section
GROUP: OBI Biomaterial Branch
PERSON: Philippe Rocca-Serra
A liver slice used in a perfusion experiment.
Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521
A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ)
GROUP: CEBS
PERSON: Helen Parkinson
organ section
data transformation
Philippe Rocca-Serra
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A data transformation is a process which produces output data from input data
Branch editors
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
data transformation
feature extraction objective
Elisabetta Manduchi
A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image.
James Malone
TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction
feature extraction objective
linlog transformation
Philippe Rocca-Serra
A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm.
Elisabetta Manduchi
PMID: 16646782
This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782.
linlog transformation
loess global transformation
Philippe Rocca-Serra
A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation.
Elisabetta Manduchi
James Malone
Melanie Courtot
OTHER: Editor's generalization based on MGED Ontology term
loess global transformation
loess group transformation
Philippe Rocca-Serra
A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs.
Elisabetta Manduchi
James Malone
Melanie Courtot
OTHER: Editor's generalization based on MGED Ontology term
loess group transformation
loess scale group transformation
A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling.
Elisabetta Manduchi
James Malone
Melanie Courtot
OTHER: Editor's generalization based on MGED Ontology term
loess scale group transformation
total intensity transformation single
Philippe Rocca-Serra
A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice.
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent.
OTHER: Adjusted from MGED Ontology
This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)).
total intensity transformation single
total intensity transformation paired
Philippe Rocca-Serra
A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors).
Elisabetta Manduchi
Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent.
OTHER: Adjusted from MGED Ontology
This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays.
total intensity transformation paired
quantile transformation
A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles.
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
This can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
quantile transformation
differential expression analysis objective
A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
differential expression analysis objective
dye swap merge
A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met.
Elisabetta Manduchi
James Malone
PERSON: Elisabetta Manduchi
PERSON: James Malone
dye swap merge
moving average
Philippe Rocca-Serra
A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set.
Elisabetta Manduchi
Helen Parkinson
PERSON: Elisabetta Manduchi
PERSON: Helen Parkinson
The moving average is often used to handle data from tiling arrays.
moving average
replicate analysis
A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc.
Elisabetta Manduchi
Helen Parkinson
PERSON: Helen Parkinson
PERSON:Elisabetta Manduchi
Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data.
replicate analysis
loess transformation
Philippe Rocca-Serra
A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves.
Elisabetta Manduchi
James Malone
Melanie Courtot
OTHER: Editor's generalization based on MGED Ontology term
loess transformation
multiple testing correction method
A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate
Monnie McGee
PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10.
multiple testing correction method
multiple testing procedure
data transformation objective
A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed.
James Malone
PERSON: James Malone
data transformation objective
normalize objective
data normalization objective
Elisabetta Manduchi
Helen Parkinson
PERSON: Elisabetta Manduchi
PERSON: Helen Parkinson
A normalization objective is a data transformation objective where the aim is to remove
systematic sources of variation to put the data on equal footing in order
to create a common base for comparisons.
James Malone
PERSON: James Malone
Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
data normalization objective
correction objective
PERSON: James Malone
PERSON: Melanie Courtot
A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself
James Malone
Type I error correction
correction objective
normalization data transformation
James Malone
A normalization data transformation is a data transformation that has objective normalization.
PERSON: James Malone
normalization data transformation
averaging data transformation
James Malone
An averaging data transformation is a data transformation that has objective averaging.
PERSON: James Malone
averaging data transformation
class discovery data transformation
James Malone
clustering data transformation
unsupervised classification data transformation
A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
PERSON: James Malone
class discovery data transformation
center calculation objective
PERSON: James Malone
A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
James Malone
center calculation objective
class discovery objective
PERSON: Elisabetta Manduchi
PERSON: James Malone
clustering objective
A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
James Malone
class discovery objective
discriminant analysis objective
unsupervised classification objective
center calculation data transformation
James Malone
A center calculation data transformation is a data transformation that has objective of center calculation.
PERSON: James Malone
center calculation data transformation
scaling objective
Person:Helen Parkinson
Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13
is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum
Awaiting English definition from Monnie McGee
James Malone
scaling objective
scaling data transformation
A scaling data transformation is a data transformation that has objective scaling.
James Malone
PERSON: James Malone
scaling data transformation
error correction objective
Application of a multiple testing correction method
PERSON: James Malone
An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself.
James Malone, Helen Parkinson
error correction objective
observation design
OBI branch derived
PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
Philippe Rocca-Serra
observation design
observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
pool of specimens
GROUP: CEBS
PERSON: Jennifer Fostel
A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish
pool of specimens
genetically modified organism
PERSON: Philippe Rocca-Serra
genetically modified organism
A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis.
Nat Protoc. 2008;3(10):1550-8. PMID: 18802436
OBI Biomaterial
an organism that is the output of a genetic transformation process
extraction
A material separation in which a desired component of an input material is separated from the remainder
Person:Bjoern Peters
Philippe Rocca-Serra
extraction
nucleic acid extraction using phenol chloroform
Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity.
'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
centrifugation
Philippe Rocca-Serra
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
centrifugation
PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
staining
Philippe Rocca-Serra
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
staining
PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
washing
OBI-Branch
Philippe Rocca-Serra
washing
PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4.
washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow.
irradiation
Philippe Rocca-Serra
adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation)
irradiation
PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370.
irradiation is a process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays or X-rays) or not such as UV light or microwaves
storage
OBI-Branch
Philippe Rocca-Serra
storage
A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
cell lysis
BP, JG, RV: There is also a need for the unplanned cell lysis, which is probably not in the scope of OBI, but should be linked to from this process.
Philippe Rocca-Serra
adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis]
cell lysis
PMID: 18484276.Cell lysis with dimethyl sulphoxide produces stable homogeneous solutions in the dichlorofluorescein oxidative stress assay. Free Radic Res. 2008 May;42(5):435-41.
cell lysis is a process by which cell membrane integrity of live cells is compromised and leads to cell death. Cell lysis may be achieved by means of viral action or osmotic shock.
immobilization
OBI-Branch
Philippe Rocca-Serra
immobilization
PMID: 18562258. The immobilization of proteins on biodegradable fibers via biotin-streptavidin bridges.Acta Biomater. 2008 May 23.
immbolization is a process by which material entity become (possibly covalently but not necessarily) attached to the surface of another material entity used a substratum.
nucleic acid hybridization
Philippe Rocca-Serra
adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]
nucleic acid hybridization
PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.
a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity.
light source
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
Elizabeth M. Goralczyk
John Quinn
Olga Tchuvatkina
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
light source
DNA sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
DNA sequencer
MO
Trish Whetzel
array scanner
GROUP: MGED Ontology
An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip
GenePix 4200A, GenePix4000B
Trish Whetzel
array scanner
arrayer
BioRobotics Microgrid II TAS, Affymetrix GMS 417
MO_697 arrayer
Trish Whetzel
a device which deposits biological material onto a substrate in a defined pattern.
arrayer
centrifuge
A device with a rapidly rotating container that applies centrifugal force to its contents
Person: Jennifer Fostel
Melanie Courtot
Trish Whetzel
centrifuge
http://en.wikipedia.org/wiki/Centrifuge
computer
A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions.
Apple PowerBook, Dell OptiPlex
Melanie Courtot
Trish Whetzel
computer
http://en.wikipedia.org/wiki/Computer
heating block
A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay
An instrument used to heat and/or maintain material at a set temperature.
Daniel Schober
MO
heating block
homogenizer
A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
Melanie Courtot
Trish Whetzel
homogenizer
http://en.wikipedia.org/wiki/Homogenizer
mortar, blender
hybridization chamber
A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide.
Glass Array Hybridization Cassette
MO_563 hybridization_chamber
Trish Whetzel
hybridization chamber
hybridization station
A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature.
Labnet Problot12
MO_497 hybridization station
Trish Whetzel
hybridization station
liquid handler
Beckman BioMek 2000
DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses.
TW: This is required by MO.
FG & DS: Capture as function.
All: Needs to be reviewed, according to query use case. If we keep it its kept as unnamed owl class.
The liquid handling class remains but as an undefined class with are unlikely to have children. It is expected that the reasoner would classifiy appropriate classes under this class that meet the have the liquid_handling function relation.
DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses.
TW: This is required by MO.
FG: Or as function.
MO_868 liquid_handler
a device that is used for automated liquid transfer and handling.
liquid handler
liquid_handling_instrument
oligonucleotide synthesizer
An instrument used to chemically synthesize oligonucleotides.
Automated Multiplex Oligonucleotide Synthesizer
MO
Trish Whetzel
oligonucleotide synthesizer
sonicator
An instrument that converts a variable electrical current to mechanical vibration of a metallic probe. The instrument is used for the lysis of cells, the mixing of compounds or solutions, or to create emulsions.
MO
Sonicator 3000
Trish Whetzel
sonicator
spectrophotometer
A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance.
Helios Gamma Spectrophotometer
MO
Melanie Courtot
Trish Whetzel
spectrophotometer
thermal cycler
An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time.
DNA_amplifier
MO
Melanie Courtot
PCR_machine
Piko(tm) 96-well Thermal Cycler
Polymerase_Chain_Reaction_ machine
Trish Whetzel
thermal cycler
thermocycler
vortexer
A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created.
Melanie Courtot
Trish Whetzel
VWR Genie 2
http://en.wikipedia.org/wiki/Vortex_mixer
vortex_mixer
vortexer
microarray wash station
ArrayIt(r) Microarray Wash Station
MO_626 wash_station
Trish Whetzel
a device that is used to wash Affymetrix-type arrays.
microarray wash station
temperature control bath
Alan Ruttenburg
Daniel Schober
Frank Gibson
OBI Instrument branch
A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well.
DS: This was heated_bath. It was renamed to reflect the possability that the same bath can be used for cooling. We can now define the temperature variables and based on that infer if it is a cooling device or a heating device (also quite relative to surrounding temperature).
VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C.
temperature control bath
microarray
An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays.
PERSON: Chris Stoeckert
A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position.
Daniel Schober
microarray
DNA microarray
PERSON: Frank Gibson
Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03
A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample.
DNA Chip
DNA microarray
DNA-array
Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115
PERSON: Daniel Schober
water bath
Daniel Schober
PERSON: Daniel Schober
A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure).
A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours.
water bath
microtome
PERSON: Daniel Schober
PERSON: Phillippe Rocca-Serra
A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand.
PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7.
microtome
study design
A study design is a plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
PERSON: Chris Stoeckert
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
study design
loop design
A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design
MO_912
PMID: 12933549
Philippe Rocca-Serra on behalf of MO
loop design
reference design
A reference experiment design type is where all samples are compared to a common reference.
MO_699
PMID: 12933549
Philippe Rocca-Serra on behalf of MO
reference design
dye swap design
An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip
MO_858
PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
Philippe Rocca-Serra on behalf of MO
dye swap design
replicate design
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
MO_885
Philippe Rocca-Serra on behalf of MO
replicate design
self vs self design
A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared.
MO_490
PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
Philippe Rocca-Serra on behalf of MO
self vs self design
time series design
Groups of assays that are related as part of a time series.
MO_887
PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources.
Philippe Rocca-Serra on behalf of MO
time series design
tumor grading
Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney
Determination of the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus.
OBI branch derived; submitted by MO
grading of tumor
tumor grading
collecting specimen from organism
IEDB
PERSON:Bjoern Peters
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
collecting specimen from organism
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
killing
Philippe Rocca-Serra
A protocol application in which an organism is intentionally put to death
CEBS, Biomaterial_branch
Jennifer Fostel
Terminal sacrifice of animals by cervical dislocation at the end of an investigation.
death status type
difficult to place this properly - JG. Death process (e.g. unscheduled death) is out of scope but should be added somewhere. All killings have death process as a part, but not all death processes are part of a killing.
euthanisia
killing
life termination
sacrifice
administering substance in vivo
1
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178
A process by which a substance is intentionally given to an organism
Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
Person:Bjoern Peters
Bjoern Peters
Different routes and means of administration should go as children underneath this
IEDB
administering substance in vivo
injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor.
exposure of material to environment
Alan says there will be problmes, e.g. with selection by survival
Bjoern Peters
IEDB
Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber.
a planned process in which an input material is exposed to a defined set of conditions in a controlled environment. The environment is a specified input.
exposure of material to environment
acclimatization
A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment.
CEBS, Biomaterial_branch
Jennifer Fostel
acclimatization
placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress
material component separation
Bjoern Peters
IEDB
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
material component separation
pooling specimens
2
pooling specimens
OBI branch derived
PlanAndPlannedProcess Branch
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points
like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class.
physical combination of several instances of like material
sample pooling
material portioning
OBI branch derived
PERSON:Bjoern Peters
a material processing in which the input substance is partitioned into a number of portions that are similar in composition.
aliquoting
apportioning
material portioning
pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock
histology
PRS:20090901: addition of alternative term = histopathology
histopathology
OBI branch derived
PERSON:Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney
histology
need to incorporate parts\n---\nThis is a very vague term, it should be in the same place as transcriptomics, proteomics metaboloimcs. It is the 'study' of tissues, not the process of studying tissues\n
the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated
the visual examination of cells or tissue (or images of them) with an assessment regarding a quality of the cells or tissue. Parts are: staining, imaging, judgement
excision
Alan Ruttenberg, Kevin Clancy
Cutting out the portion of a gel which contains a DNA fragment
excision
the use physical means to remove a portion of a substance from the rest
www.crohnsresource.com/glossary.jsp (via google define:resection)
artificially induced reverse transcription
It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process.
OBI branch derived
PERSON:Kevin Clancy
The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA
We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope
a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA)
artificially induced reverse transcription
cell permeabilization
A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application
Electroporation of HeLa cells to allow transfection with pUC19.
OBI branch derived
PERSON:Bjoern Peters
cell permeabilization
definition blessed by Jay, Alan, Randi
need to add output cell has_quality permeable
establishing cell culture
Effects of establishing cell cultures and cell culture conditions on the proliferative life span of human fibroblasts isolated from different tissues and donors of different ages.
Exp Cell Res. 2002 Apr 1;274(2):275-87. PMID: 11900488
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the establishing_cell_culture step comprises preparing the cells at a certain dilution and plating them in a container with growth medium.
OBI branch derived
PlanAndPlannedProcess Branch
establishing a cell culture is a process which results in creating an in vitro environment in which cells are sustained from input material containing cells. input: cell-containing material, output cell culture, part of cell culturing. Cells are originally plated at a certain concentration referred to as seeding density.
establishing cell culture
labeling
OBI branch derived
PERSON:Kevin Clancy
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
definition blessed by Allyson, Bjoern, Jay & Randi
labeling
the addition of a labeling reagent to an input biomaterial in order to detect the labeled material in the future
concentrate
Evaporation of the solution containing DNA to increase the concentration of the DNA molecules
OBI branch derived
PERSON:Kevin Clancy
a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material
concentrate
genetic transformation
OBI branch derived
PERSON:Kevin Clancy
The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35
genetic modification
genetic transformation
the introduction. alteration or integration of genetic material into a cell or organism
sequencing assay
OBI branch derived
PlanAndPlannedProcess Branch
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
has_output should be sequence of input; we don't have sequence well defined yet
sequencing assay
the use of a chemical or biochemical means to infer the sequence of a biomaterial
vector mediated amplification
vector mediated amplification
E coli expressing the gene for M avium p35 were cultured in order to produce p35.
OBI branch derived
PERSON:Kevin Clancy
The process of creating a copy of some biological entity in cell culture
enzymatic amplification
OBI branch derived
PERSON:Kevin Clancy
enzymatic amplification
the use of a polymerase chain reaction to amplify a fragment of DNA
the use of enzymes to increase the number of molecules of a biomaterial
recombinant vector cloning
molecular cloning
OBI branch derived
a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material
pa_branch (Alan, Randi, Kevin, Jay, Bjoern)
recombinant vector cloning
RNA extraction
A RNA extraction is a nucleic acid extraction where the desired output material is RNA
OBI branch derived
PlanAndPlannedProcess Branch
RNA extraction
requested by Helen Parkinson for MO
nucleic acid extraction
OBI branch derived
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
PlanAndPlannedProcess Branch
a material separation to recover the nucleic acid fraction of an input material
nucleic acid extraction
requested by Helen Parkinson for MO. Could be defined class
phage display library
PERSON: Bjoern Peters
PERSON: Philippe Rocca-Serra
PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides]
PRS: 22022008. class moved under population,
modification of definition and replacement of biomaterials in previous definition with 'material'
addition of has_role restriction
WEB: http://www.immuneepitope.org/home.do
a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified.
display library
phage display library
cell lysate
The effect of vaccination with the lysate of heat-shocked tumor cells on nitric oxide production in BALB/c mice with fibrosarcoma tumor. Cell Biol Int. 2008 Jul;32(7):835-40. PMID: 18455932
lysed material
GROUP: PSI
PERSON: Susanna Sansone
PRS:22-02-2008: is a material which has output_role during lysis protocol-application.
old defintion: A mixture (collection) of cell components created by rupturing of the cell wall resulting from a lysis process
a cell lysate is a material entity which is output of a cell lysis process
cell lysate
lysate
infection
infection
IEDB
IEDB
the detrimental process in which an infectious agent colonizes or replicates in a host environment
adaptive immune receptor
adaptive immune receptor
IEDB
IEDB
is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes.
disease
disease
IEDB
IEDB
placeholder to be imported from disease ontology
disposition to infect an organism
disposition to infect an organism
IEDB
IEDB
Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease
material to be added
10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export
2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes
A mixture of peptides that is being added into a cell culture.
IEDB
a material that is added to another one in a material combination process
material to be added
pathologic process
pathologic process
IEDB
IEDB
abnormal, harmful processes caused by or associated with a disease
clinical history
A series of statements representing health-relevant qualities of a patient and of a patient's family.
clinical history
phenotype
phenotype
A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
disease course
disease course
The totality of all processes through which a given disease instance is realized.
treatment
treatment
A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
quality
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.
PATO:0000001
PATO:0000072
quality
trait
age
A time quality inhering in a bearer by virtue of how long the bearer has existed.
PATO:0000011
quality
composition
A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts.
For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood).
PATO:0000025
PATO:0002015
compositionality
content
quality
structure, composition
biological sex
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
PATO:0000047
quality
morphology
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
PATO:0000051
quality
shape
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).
PATO:0000052
PATO:0001647
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.
quality
relational shape quality
qualitative
PATO:0000068
TODO: define this or obsolete it and move children somewhere else.
quality
deviation(from_normal)
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
PATO:0000069
quality
size
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
PATO:0000117
quality
structure
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
PATO:0000141
PATO:0001452
quality
relational structural quality
temperature
A physical quality of the thermal energy of a system.
PATO:0000146
quality
time
A quality in which events occur in sequence.
PATO:0000165
quality
viability
An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
PATO:0000169
quality
maturity
A quality of a single physical entity which is held by a bearer when the latter exhibits complete growth, differentiation, or development.
PATO:0000261
quality
female
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
PATO:0000383
quality
male
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
PATO:0000384
quality
circular
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.
PATO:0000411
quality
round
rounded
normal
A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
PATO:0000461
average
quality
increased size
A size quality which is relatively high.
PATO:0000586
PATO:0001202
big
enlarged
expanded
great
large
quality
elliptic
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.
PATO:0000947
ellipse-shaped
ellipsoid
elliptical
oval
ovoid
quality
physical quality
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
PATO:0001018
PATO:0002079
Wikipedia:Physical_property
quality
relational physical quality
physical object quality
A quality which inheres in a continuant.
PATO:0001237
PATO:0001238
PATO:0001241
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.
monadic quality of a continuant
monadic quality of an object
monadic quality of continuant
multiply inhering quality of a physical entity
quality
quality of a continuant
quality of a single physical entity
quality of an object
quality of continuant
snap:Quality
bacterial mating type
A mating type that indicates whether the F plasmid has integrated into the chromosome.
PATO:0001335
quality
yeast mating type
A yeast mating type.
PATO:0001337
quality
mixed sex
A biological sex quality inhering in a population of multiple sexes.
For example a mixture of females and male or males and hermaphrodites.
PATO:0001338
quality
biomaterial purity
A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial.
PATO:0001339
quality
hermaphrodite
A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual.
PATO:0001340
intersex
quality
a mating type (yeast)
A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating.
PATO:0001341
a
quality
Saccharomyces cerevisiae mating type
A S. cerevisiae mating type.
PATO:0001342
quality
Schizosaccharomyces pombe mating type
A S. pombe mating type determined by the gene configuration on the mat1 locus.
PATO:0001343
quality
alpha mating type (yeast)
A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids.
PATO:0001344
alpha
quality
h minus
A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus.
M
PATO:0001345
h -
quality
h plus
A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus.
P
PATO:0001346
h+
quality
F mating type
A bacterial mating type indicating the presence of F plasmid in a bacterial cell.
PATO:0001347
quality
F minus mating type
A bacterial mating type indicating the absence of F plasmid in a bacterial cell.
F-
PATO:0001348
quality
ploidy
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.
PATO:0001374
quality
haploid
A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes.
PATO:0001375
quality
polyploid
A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes.
PATO:0001377
quality
aneuploid
A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes.
PATO:0001385
quality
euploid
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.
PATO:0001393
quality
diploid
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.
PATO:0001394
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.
quality
cellular quality
A monadic quality of continuant that exists at the cellular level of organisation.
PATO:0001396
quality
cellular potency
A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types.
PATO:0001397
quality
unipotent
A cellular potency that is the capacity to produce only one differentiated cell type.
PATO:0001400
Unipotent cells have the quality of self-renewal which distinguishes them from non-stem cells.
quality
oligopotent
A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity.
Less potent than multipotent, often thought of as precursor or progenitor cell status.
PATO:0001401
quality
multipotent
A cellular potency that is the capacity to form multiple differentiated cell types.
PATO:0001402
quality
nucleate quality
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
PATO:0001404
quality
anucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus.
PATO:0001405
quality
mononucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
PATO:0001407
quality
alive
A viability quality inhering in a bearer by virtue of the bearer's condition before death.
PATO:0001421
quality
dead
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
PATO:0001422
quality
immature
A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development.
PATO:0001501
quality
underdeveloped
mature
A quality inhering in a bearer by virtue of the bearer's exhibiting complete growth, differentiation, or development.
PATO:0001701
quality
concave
A shape quality in a bearer by virtue of the bearer's curving inward.
PATO:0001857
quality
cylindrical
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
PATO:0001203
PATO:0001873
quality
rod-like
rod-shaped
tubulate
discoid
A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter.
PATO:0001874
disc-shaped
disk-shaped
quality
phenotypic sex
PATO:0001894
quality
mating type
A biological sex quality inhering in an individual or a population that undergo sexual reproduction.
PATO:0001895
quality
frozen
A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
PATO:0001985
quality
organismal quality
A quality that inheres in an entire organism or part of an organism.
PATO:0001995
quality
population quality
A quality that inheres in an entire population or part of a population.
PATO:0002003
quality
concavity
PATO:0002005
Surface shape that refers to the inward or outward curvature of the surface.
quality
2-D shape
2-D projection
A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.
PATO:0002006
cross-sectional
quality
convex 3-D shape
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.
Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png
PATO:0002007
Use this term or an is_a child of this term when the entire shape of the object is known.
quality
biconcave
A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces.
PATO:0002039
quality
affinity
2009-09-18T01:16:16Z
A molecular quality that arises from the molecular attraction exerted between two atoms or compounds.
George Gkoutos
PATO:0002070
quality
basophilic
2009-10-05T12:05:23Z
An affinity inhering in a tissue constituent by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific ph conditions.
PATO:0002094
george
quality
molecular quality
2010-03-10T03:18:15Z
A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.
George Gkoutos
PATO:0002061
PATO:0002182
quality
relational molecular quality
3-D shape
2010-10-05T12:31:16Z
A shape that inheres in a 3 dimensional entity.
PATO:0002266
george
quality
increased quality
2011-06-16T06:39:43Z
A quality that has a value that is increased compared to normal or average.
George Gkoutos
PATO:0002300
quality
increased object quality
2011-06-16T06:54:01Z
A quality of an object that has a value that is increased compared to normal or average.
George Gkoutos
PATO:0002305
quality
superelliptic
2011-10-12T12:45:16Z
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
George Gkoutos
Lamé curve
PATO:0002318
quality
protein
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
protein
CD19 molecule
A protein that is a translation product of the human 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.
CD19 molecule
CD34 molecule
A protein that is a translation product of the human 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.
CD34 molecule
CD4 molecule
A protein that is a translation product of the human 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.
CD4 molecule
receptor-type tyrosine-protein phosphatase C
A protein that is a translation product of the human 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.
receptor-type tyrosine-protein phosphatase C
integrin alpha-M
An integrin alpha with A domain that is a translation product of the human 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.
integrin alpha-M
receptor-type tyrosine-protein phosphatase C isoform CD45RA
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).
receptor-type tyrosine-protein phosphatase C isoform CD45RA
CD3 epsilon
A CD3 subunit that is a translation product of the human CD3E gene or a 1:1 ortholog thereof.
CD3 epsilon
neural cell adhesion molecule 1
A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof.
neural cell adhesion molecule 1
CD2 molecule
A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof.
CD2 molecule
T-cell surface glycoprotein CD8 alpha chain
A protein that is a translation product of the human 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.
T-cell surface glycoprotein CD8 alpha chain
chemokine receptor CCR1/3/1L
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).
chemokine receptor CCR1/3/1L
chemokine receptor CCR1
A chemokine receptor CCR1/3/1L that is a translation product of the human CCR1 gene or a 1:1 ortholog thereof.
chemokine receptor CCR1
chemokine receptor CCR3
A chemokine receptor CCR1/3/1L that is a translation product of the human CCR3 gene or a 1:1 ortholog thereof.
chemokine receptor CCR3
membrane-spanning 4-domains subfamily A member 1
A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof.
membrane-spanning 4-domains subfamily A member 1
CD44 molecule
A protein that is a translation product of the human CD44 gene or a 1:1 ortholog thereof.
CD44 molecule
carcinoembryonic antigen-related cell adhesion molecule 8
A protein that is a translation product of the human CEACAM8 gene or a 1:1 ortholog thereof.
carcinoembryonic antigen-related cell adhesion molecule 8
CD69 molecule
A protein that is a translation product of the human 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.
CD69 molecule
ectonucleotide pyrophosphatase/phosphodiesterase family member 3
A protein that is a translation product of the human ENPP3 gene or a 1:1 ortholog thereof.
ectonucleotide pyrophosphatase/phosphodiesterase family member 3
endoglin
A protein that is a translation product of the human ENG gene or a 1:1 ortholog thereof.
endoglin
immunoglobulin gamma Fc receptor II/III/IV
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.
immunoglobulin gamma Fc receptor II/III/IV
interleukin-2 receptor subunit beta
A protein that is a translation product of the human IL2RB gene or a 1:1 ortholog thereof.
interleukin-2 receptor subunit beta
cadherin-5
A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof.
cadherin-5
alpha-(1,3)-fucosyltransferase FUT4
A fucosyltransferase that is a translation product of the human FUT4 gene or a 1:1 ortholog thereof.
alpha-(1,3)-fucosyltransferase FUT4
low affinity immunoglobulin gamma Fc region receptor II
An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr2 gene or a 1:1 ortholog thereof.
low affinity immunoglobulin gamma Fc region receptor II
low affinity immunoglobulin gamma Fc region receptor III
An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr3 gene or a 1:1 ortholog thereof.
low affinity immunoglobulin gamma Fc region receptor III
tumor-associated calcium signal transducer 1
A tumor-associated calcium signal transducer that is a translation product of the human TACSTD1 gene or a 1:1 ortholog thereof.
tumor-associated calcium signal transducer 1
5'-nucleotidase
5'-nucleotidase
A protein that is a translation product of the human NT5E gene or a 1:1 ortholog thereof.
T-cell surface glycoprotein CD5
A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof.
T-cell surface glycoprotein CD5
Thy-1 membrane glycoprotein
A protein that is a translation product of the human THY1 gene or a 1:1 ortholog thereof.
Thy-1 membrane glycoprotein
interleukin-3 receptor class 2 alpha chain
A protein that is a translation product of the human IL3RA gene or a 1:1 ortholog thereof.
interleukin-3 receptor class 2 alpha chain
interleukin-7 receptor subunit alpha
A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof.
interleukin-7 receptor subunit alpha
KLRB1-like protein
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.
KLRB1-like protein
leukosialin
A protein that is a translation product of the human SPN gene or a 1:1 ortholog thereof.
leukosialin
CD14 molecule
A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof.
CD14 molecule
CD33 molecule
A protein that is a translation product of the human CD33 gene or a 1:1 ortholog thereof.
CD33 molecule
neprilysin
A protein that is a translation product of the human MME gene or a 1:1 ortholog thereof.
neprilysin
paired box protein PAX-5
A protein that is a translation product of the human PAX5 gene or a 1:1 ortholog thereof.
paired box protein PAX-5
signal transducer CD24
A protein that is a translation product of the human CD24 gene or a 1:1 ortholog thereof.
signal transducer CD24
transcription factor PU.1
A protein that is a translation product of the human SPI1 gene or a 1:1 ortholog thereof.
transcription factor PU.1
transferrin receptor protein 1
A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof.
transferrin receptor protein 1
tumor necrosis factor ligand superfamily member 5
A protein that is a translation product of the human CD40LG gene or a 1:1 ortholog thereof.
tumor necrosis factor ligand superfamily member 5
urokinase plasminogen activator surface receptor
A protein that is a translation product of the human PLAUR gene or a 1:1 ortholog thereof.
urokinase plasminogen activator surface receptor
mast/stem cell growth factor receptor
A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human KIT gene or a 1:1 ortholog thereof.
mast/stem cell growth factor receptor
vascular endothelial growth factor receptor 2
A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof.
vascular endothelial growth factor receptor 2
lymphocyte antigen 6G
A ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof.
lymphocyte antigen 6G
lymphocyte antigen 76
A protein that is a translation product of the mouse Ly76 gene or a 1:1 ortholog thereof.
lymphocyte antigen 76
CD9 molecule
A tetraspanin that is a translation product of the human CD9 gene or a 1:1 ortholog thereof.
CD9 molecule
CCAAT/enhancer-binding protein alpha
A protein that is a translation product of the human CEBPA gene or a 1:1 ortholog thereof.
CCAAT/enhancer-binding protein alpha
DNA nucleotidylexotransferase
A protein that is a translation product of the human DNTT gene or a 1:1 ortholog thereof.
DNA nucleotidylexotransferase
high affinity immunoglobulin epsilon receptor subunit alpha
An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCER1A gene or a 1:1 ortholog thereof.
high affinity immunoglobulin epsilon receptor subunit alpha
erythroid transcription factor
A protein that is a translation product of the human GATA1 gene or a 1:1 ortholog thereof.
erythroid transcription factor
endothelial transcription factor GATA-2
A protein that is a translation product of the human GATA2 gene or a 1:1 ortholog thereof.
endothelial transcription factor GATA-2
glucagon
A protein that is a translation product of the human GCG gene or a 1:1 ortholog thereof.
glucagon
insulin
A protein that is a translation product of the human INS gene or a 1:1 ortholog thereof.
insulin
insulinoma-associated protein 1
A protein that is a translation product of the human INSM1 gene or a 1:1 ortholog thereof.
insulinoma-associated protein 1
insulin gene enhancer protein ISL-1
A protein that is a translation product of the human ISL1 gene or a 1:1 ortholog thereof.
insulin gene enhancer protein ISL-1
transcription factor MafA
A protein that is a translation product of the human MAFA gene or a 1:1 ortholog thereof.
transcription factor MafA
neurogenin-3
A protein that is a translation product of the human NEUROG3 gene or a 1:1 ortholog thereof.
neurogenin-3
pancreas/duodenum homeobox protein 1
A protein that is a translation product of the human PDX1 gene or a 1:1 ortholog thereof.
pancreas/duodenum homeobox protein 1
pancreas transcription factor 1 subunit alpha
A protein that is a translation product of the human PTF1A gene or a 1:1 ortholog thereof.
pancreas transcription factor 1 subunit alpha
transcription factor SOX-17
A protein that is a translation product of the human SOX17 gene or a 1:1 ortholog thereof.
transcription factor SOX-17
T-cell acute lymphocytic leukemia protein 1
A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof.
T-cell acute lymphocytic leukemia protein 1
DNA ligase
A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof.
DNA ligase
ICR
region
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
region
sequence
polypeptide
A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
polypeptide
protein
sequence_feature
An extent of biological sequence.
located sequence feature
located_sequence_feature
sequence feature
sequence_feature
read
A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.
read
pseudogene
A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog).
pseudogene
polymer_attribute
An attribute to describe the kind of biological sequence.
polymer_attribute
pseudogenic_region
A non-functional descendent of a functional entity.
pseudogenic region
pseudogenic_region
SRP_RNA
7S RNA
SRP RNA
SRP_RNA
The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding.
signal recognition particle RNA
transcript
An RNA synthesized on a DNA or RNA template by an RNA polymerase.
transcript
gene
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
gene
QTL
A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.
QTL
quantitative trait locus
transgene
A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another.
transgene
circular
A quality of a nucleotide polymer that has no terminal nucleotide residues.
circular
BAC_end
A region of sequence from the end of a BAC clone that may provide a highly specific marker.
BAC end
BAC end sequence
BAC_end
BES
protein_coding_gene
protein coding gene
protein_coding_gene
ncRNA_gene
ncRNA gen
ncRNA gene
ncRNA_gene
non-coding RNA gene
miRNA_gene
miRNA gene
miRNA_gene
scRNA_gene
scRNA gene
scRNA_gene
snoRNA_gene
snoRNA gene
snoRNA_gene
snRNA_gene
snRNA gene
snRNA_gene
tRNA_gene
tRNA gene
tRNA_gene
biological_region
A region defined by its disposition to be involved in a biological process.
biological region
biological_region
YAC_end
A region of sequence from the end of a YAC clone that may provide a highly specific marker.
YAC end
YAC_end
heritable_phenotypic_marker
A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.
heritable phenotypic marker
heritable_phenotypic_marker
phenotypic marker
rRNA_gene
A gene that encodes for ribosomal RNA.
rRNA gene
rRNA_gene
RNase_P_RNA_gene
A gene that encodes an RNase P RNA.
RNase P RNA gene
RNase_P_RNA_gene
RNase_MRP_RNA_gene
A gene that encodes a RNase_MRP_RNA.
RNase MRP RNA gene
RNase_MRP_RNA_gene
lincRNA_gene
A gene that encodes large intervening non-coding RNA.
lincRNA gene
lincRNA_gene
telomerase_RNA_gene
A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase.
TERC
Telomerase RNA component
telomerase RNA gene
telomerase_RNA_gene
pseudogenic_gene_segment
A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product.
pseudogenic_gene_segment
gene_segment
A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination.
gene segment
gene_segment
uterine cervix
BTO:0001421
BTO:0002249
EFO:0000979
EMAPA:29927
EV:0100114
FMA:17740
GAID:376
Lower, narrow portion of the uterus where it joins with the top end of the vagina.
MA:0000392
MAT:0000292
MESH:A05.360.319.679.256
OpenCyc:Mx4rvVipEJwpEbGdrcN5Y29ycA
SCTID:245494008
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]
The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]
UBERON:0000002
UMLS:C0007874
VHOG:0001359
canalis cervicis uteri
caudal segment of uterus
cervical
cervical canal
cervical canal of uterus
cervix
cervix uteri
galen:CervixUteri
ncithesaurus:Cervix
neck of uterus
uberon
uterine cervix
olfactory apparatus
BTO:0000840
EFO:0000828
EHDAA2:0001274
EHDAA:1502
EMAPA:16542
EV:0100037
EV:0100370
FMA:46472
GAID:77
MA:0000281
MAT:0000139
MESH:A01.456.505.733
MIAA:0000139
Nasus
OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA
SCTID:181195007
TAO:0000047
TODO - distinguish generic olfactory apparatus from nose; we have olfactory organ for the generic organ - add new class 'olfactory structure'?
UBERON:0000004
UMLS:C0028429
ZFA:0000047
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).
galen:Nose
http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg
nasal sac
ncithesaurus:Nose
nose
peripheral olfactory organ
proboscis
uberon
islet of Langerhans
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]
AAO:0010406
Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO]
BTO:0000991
EFO:0000856
EMAPA:19246
EMAPA:19247
EMAPA:19248
EV:0100130
FMA:16016
GAID:324
MA:0000127
MAT:0000076
MESH:A03.734.414
MIAA:0000076
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]
Regions of the pancreas that contain its endocrine (i.e., hormone-producing) cells.
UBERON:0000006
UMLS:C0022131
VHOG:0000646
XAO:0000159
http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png
island of Langerhans
island of pancreas
islets of langerhans
ncithesaurus:Islet_of_Langerhans
pancreatic insula
pancreatic islet
uberon
pituitary gland
AAO:0010536
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]
An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO]
BM:Die-Hy-HY
BTO:0001073
EFO:0000857
EHDAA2:0001471
EHDAA:2183
EHDAA:4477
EMAPA:16647
EMAPA:16898
EV:0100132
FMA:13889
GAID:457
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]
MA:0000176
MAT:0000077
MESH:A06.407.747
MIAA:0000077
NIF_GrossAnatomy:birnlex_1353
OpenCyc:Mx4rv6NQYJwpEbGdrcN5Y29ycA
SCTID:181125003
TAO:0000118
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]
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].
UBERON:0000007
UMLS:C0032005
VHOG:0000143
XAO:0000017
ZFA:0000118
glandula pituitaria
http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png
http://upload.wikimedia.org/wikipedia/commons/thumb/9/97/Gray1180.png/200px-Gray1180.png
hypophysis
hypophysis cerebri
hypophysis, glandula pituitaria
ncithesaurus:Pituitary_Gland
pituitary
pituitary body
uberon
submucosa
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].
BTO:0002107
FMA:85391
FMA:85392
SCTID:68439008
UBERON:0000009
UMLS:C0225344
http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png
http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png
ncithesaurus:Submucosa
organ submucosa
region of submucosa
submucosa of organ
submucosa of region of organ
submucosal
submucous layer
tela submucosa
tunica submucosa
uberon
peripheral nervous system
(...) 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]
AAO:0000429
BILA:0000081
BTO:0001028
EFO:0000891
EHDAA2:0001445
EHDAA:2893
EMAPA:16665
EMAPA:18370
EV:0100335
FBbt:00005098
FMA:9903
GAID:715
MA:0000218
MAT:0000338
MESH:A08.800
MIAA:0000338
NIF_GrossAnatomy:birnlex_1111
Nervous structures including ganglia outside of the central nervous system. Divided into somatic nervous system and autonomic nervous system
Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
PNS
Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
SCTID:362292005
TAO:0000142
UBERON:0000010
UMLS:C0206417
VHOG:0000399
XAO:0000178
ZFA:0000142
http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png
http://upload.wikimedia.org/wikipedia/commons/thumb/b/ba/Nervous_system_diagram.png/200px-Nervous_system_diagram.png
ncithesaurus:Peripheral_Nervous_System
pars peripherica; systema nervosum periphericum
uberon
parasympathetic nervous system
AAO:0010488
BTO:0001833
Development notes: has developmental contribution from NC in verteberates (UBERONREF:0000002)
EFO:0000894
EHDA:10096
EHDAA2:0001402
EHDAA:4655
EMAPA:17270
FMA:9907
GAID:708
In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG]
MA:0000223
MAT:0000101
MESH:A08.800.050.600
MIAA:0000101
NIF_GrossAnatomy:birnlex_2517
PNS - parasympathetic
Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO]
SCTID:362496006
TAO:0001575
The parasympathetic nervous system (PSNS) is a division of the autonomic nervous system (ANS), along with the sympathetic nervous system (SNS) and enteric nervous system (ENS). The ANS is a subdivision of the peripheral nervous system (PNS). ANS sends fibers to three tissues: cardiac muscle, smooth muscle, or glandular tissue. This stimulation, sympathetic or parasympathetic, is to control smooth muscle contraction, regulate cardiac muscle, or stimulate or inhibit glandular secretion [Wikipedia]. The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia [GO].
UBERON:0000011
UMLS:C0030510
VHOG:0000755
ZFA:0001575
http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png
http://upload.wikimedia.org/wikipedia/commons/thumb/f/f7/Gray839.png/200px-Gray839.png
ncithesaurus:Parasympathetic_Nervous_System
parasympathetic part of autonomic division of nervous system
pars parasympathica divisionis autonomici systematis nervosi
pars parasympathica divisionis autonomici systematis nervosi
uberon
sympathetic nervous system
AAO:0010487
BTO:0001832
Development notes: has developmental contribution from NC in verteberates (UBERONREF:0000002)
EFO:0000893
EHDAA2:0001971
EHDAA:3769
EMAPA:16985
FMA:9906
GAID:710
MA:0000225
MESH:A08.800.050.800
MIAA:0000100
NIF_GrossAnatomy:birnlex_2516
Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO]
SCTID:362484004
TAO:0001576
The Sympathetic Nervous System (SNS) is a branch of the autonomic nervous system along with the enteric nervous system and parasympathetic nervous system. It is always active at a basal level (called sympathetic tone) and becomes more active during times of stress. Its actions during the stress response comprise the fight-or-flight response [Wikipedia]. The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO].
The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG]
The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
UBERON:0000013
UMLS:C0039044
VHOG:0000384
ZFA:0001576
http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png
http://upload.wikimedia.org/wikipedia/commons/thumb/7/77/Gray838.png/200px-Gray838.png
ncithesaurus:Sympathetic_Nervous_System
pars sympathica divisionis autonomici systematis nervosi
pars sympathica divisionis autonomici systematis nervosi
sympathetic nervous system
sympathetic part of autonomic division of nervous system
uberon
zone of skin
(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
A sub-region of the skin. Note the distinct between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
EHDAA2:0001844
EHDAA:6530
EV:0100152
FMA:86166
GAID:933
MA:0000151
MAT:0000284
MESH:A17.815
MIAA:0000284
OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA
SCTID:20795001
UBERON:0000014
VHOG:0000860
http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Skin.svg/200px-Skin.svg.png
portion of skin
region of skin
skin
skin region
skin zone
uberon
we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
anatomical boundary
AEO:0000192
FMA:50705
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.
UBERON:0000015
anatomical boundary entity
uberon
endocrine pancreas
BTO:0000650
EV:0100129
Editor notes - endocrine and exocrine pancrease are not co-associated in hagfishes or lampreys [PMID:20959416] - create a separate class for these?
FMA:16018
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]
MA:0001582
SCTID:361339003
TAO:0001260
The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin[GO].
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]
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]
UBERON:0000016
VHOG:0000049
ZFA:0001260
endocrine pancreas
endocrine part of pancreas
islets of Langerhans part of pancreas
ncithesaurus:Endocrine_Pancreas
pars endocrina pancreatis
uberon
camera-type eye
A cavitated compound organ that transduces light waves into neural signals.[TAO]
AAO:0010340
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
BTO:0004688
EHDAA2:0000484
EHDAA:936
EMAPA:16198
FMA:54448
MA:0000261
NIF_GrossAnatomy:birnlex_1169
OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvVil5pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycA
SCTID:181143004
TAO:0000107
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.
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]
UBERON:0000019
UMLS:C0015392
VHOG:0000275
XAO:0000179
ZFA:0000107
camera-type eye plus associated structures
eye
eyes
ncithesaurus:Eye
orbital part of face
orbital region
regio orbitalis
uberon
vertebrate eye
sense organ
AEO:0000094
An organ that is capable of detection of chemical stimulus involved in sensory perception of smell.
BTO:0000202
EHDAA2:0001824
EHDAA:500
EMAPA:16192
FBbt:00005155
GAID:63
HAO:0000930
MA:0000017
MESH:A09
SCTID:244485009
Sinnesorgan
UBERON:0000020
UMLS:C0935626
VHOG:0001407
WBbt:0006929
http://upload.wikimedia.org/wikipedia/commons/thumb/c/c0/Gray722.png/200px-Gray722.png
ncithesaurus:Organ_of_the_Special_Sense
organ of sense organ system
organ of sensory organ system
organ of sensory system
sense organ system organ
sensillum
sensor
sensory organ
sensory organ system organ
sensory system organ
uberon
tube
UBERON:0000025
epithelial or endothelial lined tube
galen:Tube
tubular
uberon
appendage
AEO:0000193
BILA:0000018
BTO:0001492
CARO:0010003
EFO:0000799
EHDAA2:0003193
EV:0100155
Extremitaet
FBbt:00007000
GO includes tree trunks, but excludes antennae. We modify trunk to body in our definition. Note this is currently a subtype of organism subdivision - which would exclude feathers
HAO:0000144
MAT:0000023
MESH:A01.378
MIAA:0000023
Major subdivision of an organism that protrudes from the body[DOS]. Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified]. An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA].
OpenCyc:Mx4rvViC-JwpEbGdrcN5Y29ycA
UBERON:0000026
UMLS:C0598782
VSAO:0000075
XAO:0000218
appendicular
extremity
limbs/digits/tail
ncithesaurus:Appendage
uberon
lymph node
BTO:0000784
EFO:0000872
EV:0100050
FMA:5034
GAID:947
Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG]
MA:0000139
MAT:0000442
MESH:A15.382.520.604.412
OpenCyc:Mx4rwLPqLpwpEbGdrcN5Y29ycA
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].
SCTID:181756000
TAO:0005318
UBERON:0000029
UMLS:C0024204
VHOG:0001273
ZFA:0005318
galen:Lymphnode
http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png
lymph gland
ncithesaurus:Lymph_Node
nodus lymphaticus
uberon
head
AAO:0010335
AEO:0000106
BILA:0000115
BTO:0000282
EFO:0000964
EHDAA2:0003106
FBbt:00000004
FMA:7154
GAID:61
HAO:0000397
MA:0000023
MAT:0000294
MESH:A01.456
MIAA:0000294
NIF_GrossAnatomy:birnlex_1230
OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg
OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA
Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
SCTID:302548004
SPD:0000016
TAO:0001114
TGMA:0000002
The head is the anterior-most division of the body [GO].
UBERON:0000033
UMLS:C0018670
VHOG:0001644
Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
WBbt:0005739
XAO:0003024
ZFA:0001114
adult head
cephalic area
galen:Head
head (volume)
ncithesaurus:Head
uberon
serous membrane
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
FMA:9581
GAID:19
MESH:A10.615.789
SCTID:362878009
TAO:0005425
UBERON:0000042
UMLS:C0036760
ZFA:0005425
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]
http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png
http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png
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.
multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
ncithesaurus:Serosa
serosa
tunica serosa
uberon
wall of serous sac
tendon
AEO:0000091
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
BTO:0001356
Dense regular connective tissue that connects muscle to bone.[VSAO]
Dense regular connective tissue that connects muscle to bone[VSAO].
EHDAA2:0003091
EV:0100149
FMA:9721
GAID:276
MA:0000115
MESH:A02.880
OpenCyc:Mx4rvVjefJwpEbGdrcN5Y29ycA
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]
SCTID:256667004
UBERON:0000043
UMLS:C0039508
VHOG:0001286
VSAO:0000073
XAO:0000173
ZFA:0005647
galen:Tendon
http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/3/3c/Achilles-tendon.jpg/200px-Achilles-tendon.jpg
ncithesaurus:Tendon
sinew
tendo
uberon
dorsal root ganglion
AAO:0011032
BTO:0001264
DRG
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)
EFO:0000900
EHDAA2:0000418
EHDAA2:0001897
EHDAA:2899
EMAPA:16668
EMAPA:18372
EV:0100373
FMA:5888
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]
MA:0000231
MA:0000232
MAT:0000162
MIAA:0000162
NIF_GrossAnatomy:birnlex_2596
SCTID:244455004
TAO:0000200
Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves.[TAO]
UBERON:0000044
UMLS:C0017070
VHOG:0000222
XAO:0000210
ZFA:0000200
dorsal root ganglia
dorsal root ganglion
ganglion of dorsal root
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].
ganglion sensorium nervi spinalis
ganglion spinale
ganglion spinalis
http://upload.wikimedia.org/wikipedia/commons/7/71/DRG_Chicken_e7.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/7/71/DRG_Chicken_e7.jpg/200px-DRG_Chicken_e7.jpg
ncithesaurus:Dorsal_Root_Ganglion
spinal ganglion
uberon
ganglion
A biological tissue mass, most commonly a mass of nerve cell bodies.
AAO:0010426
AEO:0000135
BTO:0000497
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]
EFO:0000899
EHDAA2:0003135
EHDAA:2897
EHDAA:4662
EHDAA:5621
EHDAA:918
EV:0100372
FBbt:00005137
FMA:5884
MA:0002406
MAT:0000207
MAT:0000343
MESH:A08.340
MIAA:0000207
MIAA:0000343
NIF_GrossAnatomy:nlx_anat_100302
Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO]
Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO]
TAO:0000190
TGMA:0001016
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).
UBERON:0000045
UMLS:C0017067
VHOG:0000156
WBbt:0005189
XAO:0000209
ZFA:0000190
ganglia
ganglionic
ncithesaurus:Ganglion
neural ganglion
uberon
simple eye
An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity.
TGMA:0000729
UBERON:0000047
uberon
vessel
A tubular structure that contains, conveys body fluid, such as blood or lymph.
UBERON:0000055
compare with UBERON:0008782
uberon
urethra
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.
BTO:0001426
EFO:0000931
EMAPA:30901
EV:0100099
FMA:19667
GAID:390
MA:0000379
MAT:0000121
MESH:A05.360.444.492.726
MIAA:0000121
OpenCyc:Mx4rvVjkypwpEbGdrcN5Y29ycA
SCTID:302513006
UBERON:0000057
UMLS:C0041967
VHOG:0001264
XAO:0000153
galen:Urethra
http://upload.wikimedia.org/wikipedia/commons/thumb/c/cb/Female_anatomy.png/200px-Female_anatomy.png
ncithesaurus:Urethra
uberon
urethral
duct
A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA].
AAO:0011123
FBbt:00100314
FMA:30320
SCTID:91726008
TAO:0005171
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
UBERON:0000058
UMLS:C0687028
XAO:0004000
ZFA:0005171
anatomical duct
exocrine duct
exocrine gland duct
galen:Duct
ncithesaurus:Duct
uberon
large intestine
A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
AAO:0010396
BTO:0000706
EFO:0000840
EMAPA:19252
EV:0100077
FMA:7201
GAID:306
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]
MA:0000333
MESH:A03.492.411.495
MIAA:0000046
OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA
SCTID:181254001
UBERON:0000059
UMLS:C0021851
VHOG:0000054
XAO:0000131
galen:LargeIntestine
intestinum crassum
ncithesaurus:Large_Intestine
uberon
anatomical wall
AO notes: in FMA, serosa is a wall
EMAPA:25036
FMA:82482
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
UBERON:0000060
UBERON:0009915
galen:Wall
organ wall
uberon
wall
wall of organ
anatomical structure
AAO:0010825
AEO:0000003
BILA:0000003
CARO:0000003
EHDAA2:0003003
FBbt:00007001
FMA:67135
GAID:781
HAO:0000003
MA:0003000
MESH:A13
Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.
SCTID:362889002
TAO:0000037
TGMA:0001823
UBERON:0000061
VHOG:0001759
XAO:0003000
ZFA:0000037
biological structure
uberon
organ
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].
EFO:0000634
FMA:67498
MA:0003001
NIF_GrossAnatomy:birnlex_4
OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA
OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA
SCTID:272625005
UBERON:0000062
UMLS:C0178784
body organ
element
ncithesaurus:Organ
note that CARO does not include a generic 'organ' class, only simple and compound organ
uberon
organ segment
FMA:86140
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].
UBERON:0000063
organ region with fixed fiat boundary
segment of organ
uberon
organ part
AAO:0011124
EFO:0000635
FMA:82472
SCTID:113343008
SCTID:91717005
UBERON:0000064
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].
cardinal organ part
uberon
respiratory tract
EHDAA2:0001606
EHDAA:1568
EHDAA:2219
EMAPA:16737
OpenCyc:Mx4rvvM--pwpEbGdrcN5Y29ycA
SCTID:361110005
UBERON:0000065
VHOG:0000393
anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts
uberon
fully formed stage
BTO:0001043
BilaDO:0000004
EFO:0001272
FBdv:00005369
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both juvenile stage, and adult stage.
UBERON:0000066
WBls:0000041
XtroDO:0000084
adult stage
fully formed animal stage
juvenile-adult stage
uberon
embryo stage part
A stage that is part of the embryo stage.
UBERON:0000067
embryonic stage part
uberon
embryo stage
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
BilaDO:0000002
EV:0300001
FBdv:00005289
HsapDv:0000002
MmusDv:0000002
OGES:000000
OGES:000022
SCTID:296280003
UBERON:0000068
XAO:1000012
embryogenesis
embryonic stage
uberon
segment of respiratory tract
An organ segment that is part of a respiratory tract [Automatically generated definition].
MA:0000434
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
UBERON:0000072
respiratory tract
uberon
regional part of nervous system
2009-06-18T09:00:04Z
An anatomical structure that is part of a nervous system [Automatically generated definition].
Melissa Haendel
NIF_GrossAnatomy:birnlex_1157
SCTID:25087005
UBERON:0000073
UMLS:C1518256
ncithesaurus:Nervous_System_Part
part of nervous system
uberon
subdivision of skeletal system
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
FMA:85544
SCTID:118966000
UBERON:0000075
UBERON:0010322
UMLS:C1519343
galen:ComplexSkeletalStructure
ncithesaurus:Skeletal_System_Part
skeletal system part
skeletal system subdivision
uberon
external ectoderm
EHDAA2:0001968
EHDAA:1494
EHDAA:350
EHDAA:4784
EHDAA:4790
EHDAA:4796
EHDAA:7860
EMAPA:16096
EMAPA:16539
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).
FMA:87656
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].
UBERON:0000076
UMLS:C1515087
http://upload.wikimedia.org/wikipedia/commons/thumb/1/1d/Ectoderm.png/200px-Ectoderm.png
ncithesaurus:Surface_Ectoderm
surface ectoderm
uberon
mixed endoderm/mesoderm-derived structure
An anatomical structure that develops from the endoderm and the mesoderm.
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
UBERON:0000077
uberon
mixed ectoderm/mesoderm/endoderm-derived structure
An anatomical structure that develops from the ectoderm, mesoderm and endoderm.
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
UBERON:0000078
uberon
male reproductive system
BTO:0000082
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]
EFO:0000970
EHDAA2:0001054
EHDAA:8136
EMAPA:17968
EV:0100101
FBbt:00004927
FMA:45664
GAID:386
HAO:0000505
MA:0000396
MESH:A05.360.444
OpenCyc:Mx4rvViCepwpEbGdrcN5Y29ycA
SCTID:361340001
TGMA:0000634
UBERON:0000079
UMLS:C0017422
UMLS:C1963704
VHOG:0000725
WBbt:0008423
XAO:0000155
genitalia of male organism
male genital organ
male genital system
male genitalia
male genitals
male organism genitalia
male organism reproductive system
male reproductive tract
ncithesaurus:Male_Genitalia
ncithesaurus:Male_Reproductive_System
reproductive system of male organism
systema genitale masculinum
the organs associated with producing offspring in the gender that produces spermatozoa.
uberon
mesonephros
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]
AAO:0010384
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]
BTO:0001542
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]
EFO:0000928
EHDAA2:0001130
EHDAA:1581
EHDAA:5903
EMAPA:16744
EMAPA:17369
EMAPA:27644
FMA:72171
GAID:1308
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.
MESH:A16.254.500
Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]
SCTID:308799002
TAO:0000529
UBERON:0000080
UMLS:C0025492
VHOG:0000038
Wolffian body
XAO:0000141
ZFA:0000529
http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png
http://upload.wikimedia.org/wikipedia/commons/thumb/a/ad/Gray986.png/200px-Gray986.png
mesonephric
mesonephric kidney
mesonephroi
ncithesaurus:Mesonephros
opisthonephros
opisto nephros
opistonephros
uberon
mesonephric tubule
A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP].
AAO:0010389
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]
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]
EHDAA2:0001134
EMAPA:27588
EMAPA:27659
TODO check
UBERON:0000083
VHOG:0000500
XAO:0000148
renal tubules
tubuli mesonephrici
uberon
morula
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.
BTO:0001508
EHDAA2 has embryo starting later
EHDAA2:0000005
GAID:1295
MESH:A16.254.270.550
SCTID:361474003
UBERON:0000085
UMLS:C0026573
XAO:1000029
http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png
http://upload.wikimedia.org/wikipedia/commons/thumb/c/c6/Blastulation.png/200px-Blastulation.png
morula (2-16 cells)
ncithesaurus:Morula
uberon
zona pellucida
A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes.
BTO:0003135
EHDAA2:0002220
EHDAA:31
EHDAA:62
EMAPA:16035
EMAPA:16049
FMA:18674
GAID:410
MA:0001715
MESH:A05.360.490.690.950
Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG]
TAO:0001111
UBERON:0000086
UMLS:C0043519
VHOG:0000720
ZFA:0001111
http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png
http://upload.wikimedia.org/wikipedia/commons/thumb/8/81/Gray3.png/200px-Gray3.png
ncithesaurus:Zona_Pellucida
oolemma
pellucid zone
striated membrane
uberon
vitelline envelope
vitelline membrane
zona pellucida - vitelline membrane
zona radiata
zona striata
inner cell mass
A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG]
A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG]
EFO:0000547
EHDAA2:0000830
EHDAA:40
EMAPA:16041
FMA:86557
ICM
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.
SCTID:361456007
UBERON:0000087
UMLS:C1283994
VHOG:0000742
embryoblast
embryoblastus; massa cellularis interna; pluriblastus senior
http://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/7/72/Blastocyst_English.svg/200px-Blastocyst_English.svg.png
ncithesaurus:Inner_Cell_Mass
pluriblast
uberon
trophoblast
Aggregate of cells forming the outer layer of a blastocyst, which provide nutrients to the embryo and develop into a large part of the placenta. They are formed during the first stage of pregnancy and are the first cells to differentiate from the fertilized egg.
BTO:0001079
Development notes: The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta[PMID:19829370]
EV:0100120
FMA:83029
GAID:1152
MESH:A11.936
SCTID:362839005
UBERON:0000088
UMLS:C0041178
http://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/7/72/Blastocyst_English.svg/200px-Blastocyst_English.svg.png
massa cellularis externa
ncithesaurus:Trophoblast
the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP]
trophoblast layer
trophoblastic
trophoblastus
trophoderm
uberon
bilaminar disc
UBERON:0000091
UMLS:C1283997
bilaminar disk
bilaminary embryonic disc
bilaminary germ disc
http://upload.wikimedia.org/wikipedia/commons/thumb/e/e3/Gray21.png/200px-Gray21.png
ncithesaurus:Bilaminar_Embryonic_Disc
the epiblast and the hypoblast, evolved from the embryoblast
uberon
post-embryonic stage
BilaDO:0000003
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
MmusDv:0000030
OGES:000010
OGES:000014
OGES:000024
UBERON:0000092
WBls:0000022
post-hatching stage
postembryonic
postembryonic stage
stage succeeding embryo, including mature structure
uberon
sulcus
2009-04-09T06:23:22Z
UBERON:0000093
a depression or fissure in the surface of an organ.
cjm
uberon
membrane organ
2009-07-30T05:19:13Z
FMA:7145
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]
UBERON:0000094
cjm
membrane of organ
uberon
life cycle stage boundary
Instant starting or ending a life cycle stage. These can be arbitrary/fiat.
UBERON:0000103
life cycle stage transition event
life cycle stage transition instant
span:ProcessBoundary
uberon
life cycle
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
FBdv_root:00000000
HsapDv:0000000
MmusDv:0000000
OGES:000011
UBERON:0000104
life
lifespan
ncithesaurus:Life
uberon
life cycle stage
A spatiotemporal region encompassing some part of the life cycle of an organism.
BILS:0000105
EFO:0000399
Editor notes: we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
MmusDv:0000001
OlatDv:0000010
UBERON:0000105
WBls:0000002
XAO:1000000
ZFS:0000000
ZFS:0100000
developmental stage
ncithesaurus:Developmental_Stage
stage
uberon
zygote stage
1-cell stage
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
BILS:0000106
BilaDO:0000005
EFO:0001322
EHDAA:27
EMAPA:16033
FBdv:00005288
UBERON:0000106
VHOG:0000745
XAO:1000001
ZFS:0000001
fertilized egg stage
fertilized egg stage
one cell stage
one-cell stage
uberon
zygote
zygotum
cleavage stage
BILS:0000107
BilaDO:0000006
EFO:0001290
MESH:A16.254.270
MmusDv:0000004
OGES:000015
OGES:000020
The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
UBERON:0000107
XAO:1000004
ZFS:0000046
uberon
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.
BILS:0000108
BilaDO:0000007
EFO:0001282
HsapDv:0000006
MmusDv:0000007
OGES:000003
OGES:000016
OGES:000021
OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg
UBERON:0000108
XAO:1000003
ZFS:0000045
http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png
http://upload.wikimedia.org/wikipedia/commons/thumb/c/c6/Blastulation.png/200px-Blastulation.png
uberon
gastrula stage
A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
BILS:0000109
BilaDO:0000008
EFO:0001296
FBdv:00005317
HsapDv:0000010
MmusDv:0000013
OGES:000004
OGES:000019
UBERON:0000109
XAO:1000005
ZFS:0000047
blastocystis trilaminaris stage
trilaminar blastocyst stage
trilaminar blastoderm stage
trilaminar disk stage
trilaminar germ stage
trilaminar stage
uberon
neurula stage
BILS:0000110
BilaDO:0000009
HsapDv:0000012
MmusDv:0000016
Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
UBERON:0000110
XAO:1000006
uberon
organogenesis stage
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
BILS:0000111
BilaDO:0000010
HsapDv:0000015
MmusDv:0000018
OGES:000005
OGES:000032
UBERON:0000111
segmentation stage
uberon
juvenile stage
BILS:0000112
BTO:0002168
Consider renaming this to '(sexually) immature stage'; in mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)
EFO:0001300
EV:0300051
OGES:000009
TS28
The stage of being a sexually immature adult animal[XAO:1000010].
UBERON:0000112
XAO:1000010
XtroDO:0000083
ZFS:0000051
immature stage
uberon
post-juvenile adult stage
BILS:0000113
EFO:0001272
EV:0300064
EV:0300070
MIAA:0000403
MmusDv:0000039
MmusDv:0000040
OGES:000026
OGES:000027
The stage of being a sexually mature adult animal.
UBERON:0000113
XAO:1000009
ZFS:0000044
adult stage
uberon
lung epithelium
BTO:0001653
MA:0001783
UBERON:0000115
epithelial tissue of lung
epithelium of lung
lung epithelial tissue
pulmonary epithelium
the epithelial layer of the lung.
uberon
respiratory tube
A tube in the respiratory tract.
Consider merging into respiratory tract
FMA:12224
UBERON:0000117
segment of tracheobronchial tree
tracheobronchial tree segment
uberon
lung bud
BTO:0001643
EHDAA2:0004089
Editors note: clarify successors - include bronchi?
SCTID:361427007
Structure derived from foregut that becomes a lung[GO].
UBERON:0000118
UMLS:C1514420
UMLS:C1514897
gemma pulmonalis
gemma respiratoria
http://upload.wikimedia.org/wikipedia/commons/thumb/7/71/Gray948.png/200px-Gray948.png
lung bud
ncithesaurus:Primary_Bronchial_Bud
ncithesaurus:Respiratory_Diverticulum
primary lung bud
respiratory diverticulum
uberon
cell layer
Portion of tissue, that consists of one or more layers of cells connected to each other by cell junctions
UBERON:0000119
cell sheath
layer of cells
uberon
neuron projection bundle
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
CARO:0001001
FBbt:00005099
UBERON:0000122
UBERON:0005163
funiculus
nerve fiber bundle
neural fiber bundle
uberon
neural nucleus
AEO:0000136
Anatomical structure consisting of a discrete aggregate of neuronal soma[GO].
FMA:83686
UBERON:0000125
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.
neuraxis nucleus
neuronal nucleus
nucleus
nucleus of neuraxis
uberon
cranial nerve nucleus
FMA:54501
SCTID:280160003
UBERON:0000126
collection of neurons (gray matter) in the brain stem that is associated with one or more cranial nerves.
cranial neural nucleus
http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png
http://upload.wikimedia.org/wikipedia/commons/thumb/3/30/Gray696.png/200px-Gray696.png
nucleus nervi cranialis
nucleus of cranial nerve
uberon
anterior region of body
UBERON:0000153
uberon
posterior region of body
UBERON:0000154
uberon
membranous layer
FMA:82500
UBERON:0000158
membranous organ component
uberon
intestine
AAO:0000246
ANISEED:1235303
BTO:0000648
EFO:0000834
EV:0100071
FMA:7199
GAID:295
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.
MA:0000328
MA:0001524
MESH:A03.492.411
MIAA:0000043
Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
SCTID:256876008
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.
TAO:0001338
The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
UBERON:0000160
UMLS:C0021853
VHOG:0000056
WBbt:0005772
XAO:0000129
ZFA:0001338
bowel
galen:Intestine
intestinal
ncithesaurus:Intestine
uberon
orifice
Anatomical conduit that connects two adjacent body spaces, surrounded by two or more subdivisions of two or more organs. Examples: right atrioventricular orifice, orifice of artery, hilum of kidney, porta hepatis[FMA,modified].
FMA:3724
SCTID:91837002
UBERON:0000161
anatomical orifice
anatomical ostium
hilum
in FMA, this is an anatomical conduit *space*, rather than anatomical conduit
uberon
cloaca
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]
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]
AAO:0000095
Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]
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
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
GAID:1206
MESH:A13.223
SCTID:362857006
UBERON:0000162
UMLS:C0008987
VHOG:0001186
XAO:0000244
cloacal
cloacal chamber
ncithesaurus:Cloaca
uberon
vent
embryonic cloaca
EHDAA2:0000256
EHDAA:4895
EMAPA:27573
EMAPA:27638
UBERON:0000163
cloaca
compare UBERON:0000162 cloaca
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].
uberon
primitive urogenital sinus
EHDAA2:0004060
EHDAA:5029
EHDAA:5919
EMAPA:17211
EMAPA:17379
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]
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]
SCTID:50961009
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]
UBERON:0000164
UGS
UMLS:C0231057
VHOG:0000414
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].
fetal UGS
http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png
http://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Gray1109.png/200px-Gray1109.png
ncithesaurus:Urogenital_Sinus
sinus urogenitalis
uberon
urogenital sinus
mouth
AAO:0010355
AO notes: in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face.
BTO:0001090
BTO:0004698
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
EFO:0000825
EHDAA2:0001326
EHDAA:542
EMAPA:16262
FBbt:00003126
FMA:49184
GAID:75
MA:0000341
MA:0002474
MAT:0000038
MESH:A01.456.505.631
MIAA:0000038
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]
OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA
SCTID:21082005
TADS:0000040
TAO:0000547
TAO:0000590
TGMA:0000131
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.
UBERON:0000165
VHOG:0000280
VHOG:0000812
XAO:0003029
ZFA:0000547
ZFA:0000590
adult mouth
cavital oralis
cavitas oris
cavum oris
galen:Mouth
http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/0/06/Mouth_illustration-Otis_Archives.jpg/180px-Mouth_illustration-Otis_Archives.jpg
mouth cavity
oral
oral region
oral vestibule
regio oralis
rima oris
stoma
stomatodaeum
uberon
vestibule of mouth
vestibulum oris
oral opening
(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]
FMA:59806
The orifice that connects the mouth to the exterio of the body.
UBERON:0000166
mouth
oral fissure
oral orifice
oral part of face
subdivision of mouth
uberon
oral cavity
AAO:0000053
AAO:0000960
Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present)
Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]
EFO:0001975
EHDAA2:0001324
EHDAA:6970
EMAPA:17411
EMAPA:18399
EV:0100057
Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]
FMA:20292
HAO:0000669
SCTID:181220002
TAO:0001027
TGMA:0000102
The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]
UBERON:0000167
UMLS:C0226896
VHOG:0000188
WBbt:0005255
XAO:0000126
ZFA:0001027
bucca
buccal cavity
cavity of mouth
ncithesaurus:Oral_Cavity
uberon
segment of colon
An organ segment that is part of a colon [Automatically generated definition].
FMA:222905
UBERON:0000168
uberon
pair of lungs
FMA:68877
OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA
UBERON:0000170
lungs
lungs pair
pulmones
set of lungs
uberon
respiration organ
EMAPA:17607
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.
SCTID:272626006
SPD:0000428
TGMA:0001247
UBERON:0000171
apparatus respiratorius organ
breathing organ
gas exchange organ
organ of apparatus respiratorius
organ of respiratory system
respiratory organ
respiratory system organ
uberon
excreta
AEO:0000184
BTO:0000491
EHDAA2:0003184
ENVO:02000022
Excreta are bodily fluids consisting of waste matter, such as sweat or feces, discharged from the body.
FMA:9674
UBERON:0000174
UBERON:0000324
UBERON:0007550
excreted substance
excretion
galen:Excretion
uberon
waste substance
blood
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]
AAO:0000046
BTO:0000089
Circulating body substance which consists of blood plasma and hemoglobin-carrying red blood cells. Excludes blood analogues (see UBERON:0000179 haemolymphatic fluid).
EFO:0000296
EHDAA2:0000176
EHDAA:418
EMAPA:16332
ENVO:02000027
EV:0100047
FMA:9670
GAID:965
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
MA:0000059
MESH:A12.207.152
MIAA:0000315
OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA
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]
TAO:0000007
UBERON:0000178
UMLS:C0005767
VHOG:0000224
XAO:0000124
ZFA:0000007
galen:Blood
ncithesaurus:Blood
portion of blood
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
uberon
vertebrate blood
whole blood
haemolymphatic fluid
2009-04-08T04:38:19Z
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
UBERON:0000179
blood or blood analog
cjm
uberon
gyrus
A ridge, generally surrounded by one or more sulci.
BTO:0002495
FMA:83874
SCTID:279165009
UBERON:0000200
UMLS:C0458308
cerebral gyrus
gyri
gyri of cerebrum
gyrus of cerebrum
gyrus of neuraxis
ncithesaurus:Cerebral_Gyrus
neuraxis gyrus
uberon
pallium
2009-04-18T12:03:09Z
Dorsal part (roof region) of the telencephalon[GO].
EFO:0003534
SCTID:369224000
TAO:0000505
TAO:0007007
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]
The mantle of gray matter forming the cerebral cortex. http://www.thefreedictionary.com/pallium[TAO]
UBERON:0000203
ZFA:0000505
area dorsalis telencephali
cjm
dorsal part of telencephalon
dorsal telencephalic area
dorsal telencephalon
uberon
ventral part of telencephalon
2009-04-18T12:12:27Z
AO notes: BTO term refers specifically to the avian structure
BTO:0003401
Dorsal part (base region) of the telencephalon.
EFO:0003522
TAO:0000304
UBERON:0000204
ZFA:0000304
area ventralis telencephali
cjm
subpallium
subpallium
uberon
ventral telencephalon
ligament
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]
EFO:0001966
FMA:21496
MA:0000113
MESH:A02.513
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].
Note this groups both skeletal and non-skeletal ligaments. What is called a "ligament" in many AOs is actually a skeletal ligament
OpenCyc:Mx4rvVjqpZwpEbGdrcN5Y29ycA
Portion of connective tissue that connects bone or cartilage.[TAO]
SCTID:182358004
TAO:0001682
UBERON:0000211
UMLS:C0023685
VHOG:0001272
XAO:0004031
ZFA:0001675
galen:Ligament
http://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg
ligament organ
ncithesaurus:Ligament
uberon
blastula
BILA:0000059
BTO:0000128
GAID:1294
MESH:A16.254.270.274
OGEM:000006
OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg
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.
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
UBERON:0000307
UBERON:0007011
blastosphere
blastula embryo
http://upload.wikimedia.org/wikipedia/commons/thumb/c/c6/Blastulation.png/200px-Blastulation.png
uberon
gastric gland
BTO:0000503
FMA:14919
UBERON:0000325
any of the branched tubules in the inner lining of the stomach that secrete gastric juice and protective mucus.
uberon
mucosa
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]
AEO:0000199
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
BTO:0000886
EHDAA2:0003234
EV:0100382
FMA:85355
FMA:85358
GAID:297
MESH:A10.615.550
OpenCyc:Mx4rvmKNOpwpEbGdrcN5Y29ycA
SCTID:361693009
UBERON:0000344
UMLS:C0026724
galen:Mucosa
http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png
http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png
mucosa of organ
mucosa of organ part
mucosal
mucosal region
mucous membrane
ncithesaurus:Mucosa
organ mucosa
region of mucosa
tunica mucosa
uberon
limbic system
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].
BTO:0000928
FMA:242000
GAID:615
MESH:A08.186.211.577
OpenCyc:Mx4rwAeba5wpEbGdrcN5Y29ycA
SCTID:361342009
UBERON:0000349
UMLS:C0023715
http://upload.wikimedia.org/wikipedia/commons/5/5c/Brain_limbicsystem.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/5/5c/Brain_limbicsystem.jpg/200px-Brain_limbicsystem.jpg
ncithesaurus:Limbic_System
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.
uberon
pharyngeal mucosa
A mucosa that is part of a pharynx [Automatically generated definition].
BTO:0001047
EMAPA:26957
EMAPA:26965
FMA:55031
Mucous membrane of pharynx
SCTID:362121003
UBERON:0000355
UBERON:0003344
mucosa of organ of pharynx
mucosa of pharynx
mucous membrane of pharynx
mucous membrane of the pharynx
organ mucosa of pharynx
pharynx mucosa
pharynx mucosa of organ
pharynx mucous membrane
pharynx organ mucosa
tunica mucosa pharyngea
tunica mucosa pharyngis
uberon
blastocyst
BTO:0001099
EFO:0000295
EV:0100394
Editor's note: Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm)
FMA:83041
GAID:1153
MESH:A16.254.085
SCTID:308837009
The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO].
UBERON:0000358
UMLS:C1281743
blastocystis
blastula
http://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/7/72/Blastocyst_English.svg/200px-Blastocyst_English.svg.png
ncithesaurus:Blastocyst
uberon
preputial gland
An exocrine gland that are located in front of the genitals of some mammals (including mice) and produce pheromones[WP].
FMA:71652
SCTID:278916008
There is debate about whether humans have functional homologues to preputial glands.
UBERON:0000359
UMLS:C1947929
glandulae preputiales
ncithesaurus:Prepucial_Gland_MMHCC
preputial glands
preputial glands set
set of preputial glands
the paired, lobulated, modified sebaceous glands of the corona, the neck of the glans penis, and the inner surface of the prepuce with pheromonal functions in male rodents; male preputial secretions strongly attract females, may accelerate estrus, and have been implicated in intermale aggression; homologous to the clitoral glands (aka female preputial glands) in female rodents; there is no true anatomical equivalent in humans.
uberon
flexor muscle
A muscle that decreases the angle of a joint.[TAO]
A muscle that when contracted acts to bend a joint or limb in the body.
BTO:0001257
FMA:74559
FMA:74999
TAO:0005271
UBERON:0000366
ZFA:0005271
flexor
uberon
corpus striatum
BTO:0001311
CALOHA:TS-0183
EFO:0000381
EMAPA:17549
EV:0100184
FMA:77616
GAID:667
MESH:A08.186.211.730.885.105.487
SCTID:279318005
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].
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
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]
UBERON:0000369
UMLS:C0010097
VHOG:0001175
http://upload.wikimedia.org/wikipedia/commons/thumb/b/b3/Gray656.png/200px-Gray656.png
ncithesaurus:Corpus_Striatum
striate body
striated body
uberon
hindlimb stylopod
AAO:0000887
BTO:0001376
EFO:0001943
EHDAA2:0002130
EHDAA:5171
EHDAA:6200
EMAPA:17499
FMA:24967
GAID:50
In humans the thigh is the area between the pelvis and the knee. Anatomically, it is part of the lower limb. The single bone in the thigh is called the femur. This bone is very thick and strong (due to the high proportion of cortical bone), and forms a ball and socket joint at the hip, and a condylar joint at the knee. [WP,unvetted].
MA:0000052
MESH:A01.378.610.750
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here
OpenCyc:Mx4rvVjN7JwpEbGdrcN5Y29ycA
SCTID:302544002
Segment of the forearm corresponding to the humerus.[AAO]
UBERON:0000376
UMLS:C0039866
VHOG:0000349
femur
galen:Thigh
hind limb stylopod
hind limb stylopodium
hind propodium
hindlimb propodium
hindlimb stylopod
hindlimb stylopodium
http://upload.wikimedia.org/wikipedia/commons/4/4b/Gray1238.png
http://upload.wikimedia.org/wikipedia/commons/thumb/4/4b/Gray1238.png/200px-Gray1238.png
inferior member stylopod
lower extremity stylopod
ncithesaurus:Thigh
proximal segment of free lower limb
stylopod of hind limb
stylopod of hindlimb
stylopod of inferior member
stylopod of lower extremity
stylopod of lower limb
thigh
uberon
upper leg
musculature of body
AAO:0000307
AO notes: we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
Anatomical system that consists of all the muscles of the body[VSAO, modified].
Anatomical system that consists of the muscles of the body.[VSAO]
BILA:0000088
BTO:0001369
BTO:0001485
EFO:0000801
FBbt:00005069
FMA:72954
MA:0002888
MAT:0000025
MIAA:0000025
UBERON:0000383
VSAO:0000033
XAO:0004042
muscle system
muscle system of body
muscular system
musculature system
muskelsystem
set of all muscles
set of muscles of body
uberon
vertebrate muscular system
prefrontal cortex
BTO:0002807
EFO:0001384
FMA:224850
GAID:676
MA:0000906
MESH:A08.186.211.730.885.213.270.700
NIF_GrossAnatomy:nlx_anat_090801
TODO - check MA
The prefrontal cortex (PFC) is the anterior part of the frontal lobes of the brain, lying in front of the motor and premotor areas. This brain region has been implicated in planning complex cognitive behaviors, personality expression, decision making and moderating correct social behavior. The basic activity of this brain region is considered to be orchestration of thoughts and actions in accordance with internal goals. The most typical psychological term for functions carried out by the pre-frontal cortex area is executive function. Executive function relates to abilities to differentiate among conflicting thoughts, determine good and bad, better and best, same and different, future consequences of current activities, working toward a defined goal, prediction of outcomes, expectation based on actions, and social 'control' (the ability to suppress urges that, if not suppressed, could lead to socially-unacceptable outcomes). Many authors have indicated an integral link between a person's personality and the functions of the prefrontal cortex. [WP,unvetted].
UBERON:0000451
frontal association cortex
http://upload.wikimedia.org/wikipedia/commons/5/59/Gray726-Brodman-prefrontal.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/5/59/Gray726-Brodman-prefrontal.svg/200px-Gray726-Brodman-prefrontal.svg.png
prefrontal association complex
prefrontal association cortex
uberon
cerebral subcortex
BTO:0002858
Cerebral medulla
FMA:242188
UBERON:0000454
ncithesaurus:Cerebral_Subcortex
subcortex
uberon
bodily secretion
AEO:0001005
AO notes: BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
BTO:0002977
BTO:0002979
Body substance in a liquid or semisolid state produced by an exocrine gland. Example: saliva, sebum, blood, plasma, semen, urine.
FMA:9675
MA:0002504
MESH:A12.200
UBERON:0000456
UBERON:0006540
UMLS:C1516992
exocrine gland fluid
exocrine gland fluid or secretion
exocrine gland fluid/secretion
exocrine gland secretion
external secretion
galen:Secretion
ncithesaurus:Exocrine_Gland_Fluid_or_Secretion
secreted substance
secretion
uberon
uterine wall
An anatomical wall that is part of a uterus [Automatically generated definition].
BTO:0003083
FMA:17560
SCTID:245485002
UBERON:0000459
anatomical wall of uterus
uberon
uterus anatomical wall
uterus wall
wall of uterus
portion of organism substance
AAO:0010839
AEO:0000004
BILA:0000004
CARO:0000004
EHDAA2:0003004
FBbt:00007019
FMA:9669
HAO:0000004
MA:0002450
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.
SPD:0000008
TAO:0001487
TGMA:0001824
UBERON:0000463
VHOG:0001726
XAO:0004001
ZFA:0001487
body fluid or substance
body substance
galen:BodySubstance
ncithesaurus:Body_Fluid_or_Substance
organism substance
portion of body substance
uberon
anatomical space
AAO:0010110
AEO:0000005
BILA:0000005
CARO:0000005
EHDAA2:0003005
FBbt:00007017
FMA:5897
HAO:0000005
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.
TAO:0001668
TGMA:0001825
UBERON:0000464
UMLS:C0524461
VHOG:0001728
XAO:0003190
ZFA:0001643
lumen
lumen space
ncithesaurus:Lumen_Space
space
uberon
material anatomical entity
AAO:0010264
AEO:0000006
Anatomical entity that has mass.
BILA:0000006
CARO:0000006
EHDAA2:0003006
FBbt:00007016
FMA:67165
HAO:0000006
TAO:0001836
TGMA:0001826
UBERON:0000465
VHOG:0001721
uberon
immaterial anatomical entity
AAO:0010265
AEO:0000007
Anatomical entity that has no mass.
BILA:0000007
CARO:0000007
EHDAA2:0003007
FBbt:00007015
FMA:67112
HAO:0000007
TAO:0001835
TGMA:0001827
UBERON:0000466
VHOG:0001727
immaterial physical anatomical entity
uberon
anatomical system
AAO:0000007
AEO:0000011
Anatomical group that has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[TAO]
Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[AAO]
Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[CARO]
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].
BILA:0000011
CARO:0000011
EHDAA2:0001330
EHDAA2:0003011
EHDAA:392
EMAPA:16103
EV:0100000
FBbt:00004856
FMA:7149
HAO:0000011
MA:0000003
NIF_GrossAnatomy:birnlex_14
OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ
SCTID:278195005
TAO:0001439
TGMA:0001831
UBERON:0000467
UMLS:C0460002
VHOG:0001725
WBbt:0005746
XAO:0003002
ZFA:0001439
body system
galen:AnatomicalSystem
ncithesaurus:Organ_System
organ system
system
uberon
multi-cellular organism
AAO:0010026
AEO:0000103
AEO:0000191
Anatomical structure that is an individual member of a species and consists of more than one cell.
Anatomical structure that is an individual member of a species.[TAO]
BILA:0000012
BTO:0001489
CARO:0000012
EFO:0002906
EHDAA2:0003103
EHDAA2:0003191
EHDAA:1
EHDAA:9178
EMAPA:25765
EV:0100016
FBbt:00000001
FMA:256135
HAO:0000012
Koerper
MA:0002405
NIF_GrossAnatomy:birnlex_18
SCTID:243928005
TADS:0000001
TAO:0001094
TGMA:0001832
TODO - split body and mc organism? body continues after death stage
TS28
UBERON:0000468
VHOG:0000671
WBbt:0007833
XAO:0003004
ZFA:0001094
adult mouse
body
galen:Organism
ncithesaurus:Whole_Organism
organism
organismal
uberon
whole body
whole organism
cell part
AAO:0010271
Anatomical structure that is a direct part of the cell.
BILA:0000014
CARO:0000014
FBbt:00007012
FMA:86454
GO:0044464
HAO:0000014
NIF_Subcellular:sao-1337158144
OpenCyc:Mx4rwQwkcZwpEbGdrcN5Y29ycA
TGMA:0001834
UBERON:0000470
UMLS:C1178969
cell component
ncithesaurus:Cell_Part
todo - move metadata to GO and obsolete this class. Note the inconsistency between the usage of the label 'cell component' in GO and CARO
uberon
testis
(...) 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]
AAO:0000606
BILA:0000124
BTO:0001363
EFO:0000984
EHDAA2:0002007
EHDAA:8146
EMAPA:17972
EV:0100102
Either of paired male reproductive organs which are involved in the production of sperm and male sex hormones.[AAO]
FBbt:00004928
FMA:7210
GAID:396
HAO:0001007
MA:0000411
MAT:0000132
MESH:A05.360.444.849
MIAA:0000132
Male reproductive organ.[TAO]
OpenCyc:Mx4rvVjM25wpEbGdrcN5Y29ycA
SCTID:181431007
TAO:0000598
UBERON:0000473
UBERON:0002117
UMLS:C0039597
VHOG:0000252
WBbt:0006794
XAO:0000157
ZFA:0000598
galen:Testis
genitalia of male organism gonad
genitalia of male organism gonada
gonad of a male animal, produces and releases sperm.
gonad of genitalia of male organism
gonad of male genitalia
gonad of male genitals
gonad of male organism genitalia
gonad of male organism reproductive system
gonad of male reproductive system
gonad of reproductive system of male organism
gonada of genitalia of male organism
gonada of male genitalia
gonada of male genitals
gonada of male organism genitalia
gonada of male organism reproductive system
gonada of male reproductive system
gonada of reproductive system of male organism
http://upload.wikimedia.org/wikipedia/commons/thumb/c/c3/Gray1144.png/200px-Gray1144.png
male genitalia gonad
male genitalia gonada
male genitals gonad
male gonad
male organism genitalia gonad
male organism genitalia gonada
male organism reproductive system gonad
male organism reproductive system gonada
male reproductive system gonad
male reproductive system gonada
ncithesaurus:Testis
orchis
reproductive system of male organism gonad
reproductive system of male organism gonada
testes
testicle
testicular
testiculus
uberon
female reproductive system
BTO:0000083
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]
EFO:0000969
EHDAA2:0000506
EHDAA:8116
EMAPA:17959
EV:0100110
FBbt:00004864
FMA:45663
GAID:364
HAO:0000324
MA:0000381
MESH:A05.360.319
MIAA:0000028
OpenCyc:Mx4rvVipTZwpEbGdrcN5Y29ycA
SCTID:361386004
TGMA:0000635
The organs of the female reproductive system.
UBERON:0000474
UMLS:C0700038
VHOG:0000726
WBbt:0006748
WikipediaCategory:Female_reproductive_system
XAO:0000156
female genital system
female genitalia
female organism genitalia
female organism reproductive system
female reproductive tract
genitalia of female organism
gynaecological tissue
http://upload.wikimedia.org/wikipedia/commons/thumb/6/68/Scheme_female_reproductive_system-en.svg/200px-Scheme_female_reproductive_system-en.svg.png
ncithesaurus:Female_Reproductive_System
reproductive system of female organism
systema genitale femininum
uberon
organism subdivision
AAO:0010053
AEO:0000032
Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism.
BILA:0000032
CARO:0000032
EFO:0000808
EHDAA2:0003032
Editor note: revise after CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
FBbt:00007009
FMA:7153
HAO:0000032
MA:0002433
MAT:0000293
MESH:A01
MIAA:0000293
OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA
TAO:0001308
TGMA:0001840
UBERON:0000475
UMLS:C0229962
VHOG:0001758
XAO:0003013
ZFA:0001308
anatomic region
body part
body region
cardinal body part
galen:BodyPart
ncithesaurus:Body_Part
uberon
acellular anatomical structure
AAO:0010268
AEO:0000040
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or tissue.[AAO]
BILA:0000040
CARO:0000040
EHDAA2:0003040
FBbt:00007013
FMA:63863
HAO:0000040
TAO:0000382
TGMA:0001841
UBERON:0000476
XAO:0003162
ZFA:0000382
uberon
anatomical cluster
AAO:0010009
AEO:0000041
Anatomical group that has its parts adjacent to one another.
BILA:0000041
CARO:0000041
EHDAA2:0003041
FBbt:00007277
FMA:49443
HAO:0000041
TADS:0000605
TAO:0001478
TGMA:0001842
UBERON:0000477
VHOG:0001737
XAO:0003160
ZFA:0001478
uberon
extraembryonic structure
AAO:0010020
AEO:0000042
Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo.
BILA:0000042
CARO:0000042
EHDAA2:0003042
EHDAA:46
EMAPA:16042
FMA:85537
HAO:0000042
SCTID:314908006
TAO:0000020
TGMA:0001843
UBERON:0000478
UMLS:C1282438
VHOG:0000292
XAO:0004005
ZFA:0000020
extra-embryonic structure
extraembryonic component
extraembryonic tissue
ncithesaurus:Extraembryonic_Structure
see also conceptus extraembryonic component in EHDAA2. Note that the FBbt class is *not* placed here until the tracker issue is resolved.
uberon
tissue
AAO:0000607
AAO:0010054
AEO:0000043
Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships.
BILA:0000043
CARO:0000043
EHDAA2:0003043
FBbt:00007003
FMA:9637
HAO:0000043
MA:0003002
MESH:A10
NIF_GrossAnatomy:birnlex_19
TAO:0001477
TGMA:0001844
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'
UBERON:0000479
UMLS:C0040300
VHOG:0001757
WBbt:0005729
XAO:0003040
ZFA:0001477
galen:Tissue
ncithesaurus:Tissue
portion of tissue
simple tissue
tissue portion
uberon
anatomical group
AAO:0010008
AEO:0000054
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.
BILA:0000054
CARO:0000054
EHDAA2:0003054
HAO:0000054
TAO:0001512
TGMA:0001846
UBERON:0000480
VHOG:0001724
XAO:0003001
ZFA:0001512
uberon
multi-tissue structure
AAO:0010048
AEO:0000055
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.
BILA:0000055
CARO:0000055
EHDAA2:0003055
FBbt:00007010
HAO:0000055
TAO:0001488
TGMA:0001847
UBERON:0000481
VHOG:0001762
XAO:0003037
ZFA:0001488
uberon
epithelium
AAO:0000144
AAO:0010055
AEO:0000066
BILA:0000066
BTO:0000416
CARO:0000066
EHDAA2:0003066
FBbt:00007005
FMA:9639
GAID:402
HAO:0000066
MESH:A10.272
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].
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]
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]
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]
SCTID:31610004
TAO:0001486
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]
UBERON:0000483
UMLS:C0014609
VHOG:0000387
XAO:0003045
ZFA:0001486
epithelial
epithelial tissue
http://upload.wikimedia.org/wikipedia/commons/c/c3/Tkanka_nablonkowa.png
ncithesaurus:Epithelium
portion of epithelium
uberon
simple columnar epithelium
AAO:0010063
AEO:0000068
BILA:0000068
CARO:0000068
EHDAA2_RETIRED:0003068
FBbt:00007027
FMA:45567
HAO:0000068
SCTID:32210007
TAO:0001496
UBERON:0000485
UMLS:C0836135
Unilaminar epithelium that consists of a single layer of columnar cells.[AAO]
Unilaminar epithelium that consists of a single layer of columnar cells.[CARO]
Unilaminar epithelium that consists of a single layer of columnar cells.[TAO]
Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]
XAO:0004008
ZFA:0001496
columnar epithelium
columnar epithlium
epithelium simplex columnare
http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png
http://upload.wikimedia.org/wikipedia/commons/thumb/8/8b/Gray1059.png/200px-Gray1059.png
ncithesaurus:Simple_Columnar_Epithelium
simple columnar epithelium
uberon
multilaminar epithelium
AAO:0010059
AEO:0000069
BILA:0000069
BTO:0002074
CARO:0000069
EHDAA2:0003069
Epithelium that consists of more than one layer of epithelial cells.[AAO]
Epithelium that consists of more than one layer of epithelial cells.[CARO]
Epithelium that consists of more than one layer of epithelial cells.[TAO]
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]
FMA:45562
HAO:0000069
SCTID:309044005
TAO:0001494
UBERON:0000486
UMLS:C0682575
XAO:0004006
ZFA:0001494
laminated epithelium
ncithesaurus:Stratified_Epithelium
stratified epithelium
uberon
simple squamous epithelium
AAO:0010066
AEO:0000070
BILA:0000070
BTO:0002073
CARO:0000070
EHDAA2:0003070
FMA:45565
HAO:0000070
TAO:0001498
UBERON:0000487
UMLS:C0836133
Unilaminar epithelium that consists of a single layer of squamous cells.[AAO]
Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
Unilaminar epithelium that consists of a single layer of squamous cells.[TAO]
Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]
XAO:0004010
ZFA:0001498
epithelium simplex squamosum
http://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg
ncithesaurus:Simple_Squamous_Epithelium
uberon
atypical epithelium
AAO:0010057
AEO:0000071
BILA:0000071
CARO:0000071
EHDAA2:0003071
Epithelium that consists of epithelial cells not arranged in one or more layers.[TAO]
Epithelium that consists of epithelial cells not arranged in one ore more layers.
FMA:61741
HAO:0000071
TAO:0001493
UBERON:0000488
XAO:0004004
ZFA:0001493
heterogenous epithelium
uberon
cavitated compound organ
AAO:0010016
AEO:0000072
BILA:0000072
CARO:0000072
Compound organ that contains one or more macroscopic anatomical spaces.
EHDAA2:0003072
FMA:55671
HAO:0000072
TAO:0001490
TGMA:0001857
UBERON:0000489
VHOG:0001730
XAO:0003165
ZFA:0001490
cavitated organ
uberon
unilaminar epithelium
AAO:0010062
AEO:0000073
AO/editor notes: consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable
BILA:0000073
BTO:0002073
CARO:0000073
EHDAA2:0003073
Epithelium that consists of a single layer of epithelial cells.[AAO]
Epithelium that consists of a single layer of epithelial cells.[CARO]
Epithelium that consists of a single layer of epithelial cells.[TAO]
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]
FMA:45561
HAO:0000073
SCTID:309043004
TAO:0001495
UBERON:0000490
UMLS:C0682574
XAO:0004007
ZFA:0001495
ncithesaurus:Simple_Epithelium
simple epithelium
uberon
interstitial fluid
ENVO:02000042
FMA:9673
Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid.
UBERON:0000913
intercellular fluid
tissue fluid
uberon
thoracic segment of trunk
FMA:259209
MA:0000022
Organismal subdivision of body that lies between the head and the abdomen [Wikipedia].
SCTID:302551006
UBERON:0000915
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
thorax
uberon
upper body
abdomen
BTO:0000020
EFO:0000968
EV:0100011
FMA:9577
GAID:16
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.
MA:0000029
MAT:0000298
MESH:A01.047
MIAA:0000298
OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA
SCTID:302553009
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
UBERON:0000916
abdominal
abdominopelvic region
abdominopelvis
adult abdomen
belly
celiac region
galen:Abdomen
uberon
embryo
AAO:0011035
AEO:0000169
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.
BILA:0000056
BTO:0000379
EFO:0001367
EHDAA2:0000002
EHDAA2_RETIRED:0003236
EHDAA:38
EMAPA:16039
FBbt:00000052
FMA:69068
GAID:963
MAT:0000226
MESH:A16.254
MIAA:0000019
OGEM:000001
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA
SCTID:57991002
UBERON:0000922
UMLS:C0013935
VHOG:0001766
XAO:0000113
ZFA:0000103
developing organism
developmental tissue
embryonic
embryonic organism
http://neurolex.org/wiki/Category:Embryonic_organism
http://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg
ncithesaurus:Embryo
uberon
germ layer
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.
AAO:0000480
BILA:0000035
BTO:0000556
Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[UBERONREF:0000002]
FBbt:00000110
FMA:69069
GAID:1303
MESH:A16.254.425
TAO:0001122
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
UBERON:0000923
UMLS:C0920502
UMLS:C1708239
VHOG:0001223
XAO:0003011
ZFA:0001122
embryonic germ layer
embryonic germ layers
embryonic tissue
germinal layer
ncithesaurus:Embryonic_Tissue
ncithesaurus:Germinal_Layer
primary germ layer
uberon
ectoderm
AAO:0000137
BILA:0000036
BTO:0000315
EFO:0000414
EHDAA2:0000428
EMAPA:16069
EV:0100003
FBbt:00000111
FMA:69070
GAID:1304
MAT:0000155
MAT:0000173
MESH:A16.254.425.273
MIAA:0000173
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
SCTID:362851007
TAO:0000016
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
UBERON:0000924
UMLS:C0013574
VHOG:0000153
XAO:0000001
ZFA:0000016
ectodermal
embryonic ectoderm
http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png
ncithesaurus:Ectoderm
uberon
endoderm
AAO:0000139
BILA:0000038
BTO:0000800
EFO:0002545
EHDAA2:0000436
EV:0100005
FBbt:00000125
FMA:69071
GAID:1305
MAT:0000175
MESH:A16.254.425.407
MIAA:0000175
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
SCTID:362855003
TAO:0000017
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
This class was created automatically from a combination of ontologies
UBERON:0000925
UMLS:C0014144
VHOG:0000154
XAO:0000090
ZFA:0000017
endodermal
entoderm
http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png
http://upload.wikimedia.org/wikipedia/commons/thumb/d/df/Gray10.png/200px-Gray10.png
ncithesaurus:Endoderm
uberon
mesoderm
AAO:0000304
BILA:0000037
BTO:0000839
EFO:0001981
EHDAA2:0001128
EHDAA:124
EHDAA:160
EHDAA:168
EHDAA:183
EMAPA:16083
EV:0100006
FBbt:00000126
FMA:69072
GAID:522
MAT:0000174
MESH:A16.254.425.660
MIAA:0000174
Primary germ layer that is the middle of the embryonic germ layers.[AAO]
SCTID:362854004
TAO:0000041
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]
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
The middle germ layer of the embryo, between the endoderm and ectoderm.
UBERON:0000926
UBERON:0003263
UMLS:C0025485
VHOG:0000152
XAO:0000050
ZFA:0000041
embryonic mesoderm
entire mesoderm
http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png
http://upload.wikimedia.org/wikipedia/commons/thumb/e/e8/Mesoderm.png/200px-Mesoderm.png
mesodermal
mesodermal mantle
ncithesaurus:Mesoderm
uberon
stomodeum
Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
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].
BTO:0004224
EHDAA2:0001929
EMAPA:16263
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.
FBbt:00000439
TAO:0001290
TGMA:0000135
UBERON:0000930
UMLS:C1514977
XAO:0000269
ZFA:0001290
http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png
http://upload.wikimedia.org/wikipedia/commons/thumb/9/93/Gray977.png/200px-Gray977.png
mouth primordium
ncithesaurus:Stomodeum
primitive oral cavity
stomatodeum
stomodaeum
stomodeal
uberon
proctodeum
AAO:0011087
An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]
EHDAA2:0000121
FBbt:00000440
Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]
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].
TAO:0000066
UBERON:0000931
UMLS:C0231054
VHOG:0000139
XAO:0001019
ZFA:0000066
anal pit
embryonic proctodaeum
ncithesaurus:Proctodeum
proctodaeum
proctodeal
removed WBbt:0006795 - junction between the alimentary and genital tracts in the male.
uberon
stomach
AAO:0000579
ANISEED:1235297
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.
BTO:0001307
EFO:0000837
EHDAA2:0001915
EHDAA:2993
EMAPA:17021
EMAPA:18889
EV:0100070
FMA:7148
GAID:293
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]
MA:0000353
MAT:0000051
MESH:A03.492.766
MIAA:0000051
OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA
Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
SCTID:181246003
TAO:0002121
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
UBERON:0000945
UMLS:C0038351
VHOG:0000408
Ventricular
XAO:0000128
anterior intestine
galen:Stomach
gaster
http://upload.wikimedia.org/wikipedia/commons/e/e0/Stomach_diagram.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/e/e0/Stomach_diagram.svg/200px-Stomach_diagram.svg.png
mesenteron
ncithesaurus:Stomach
stomach
uberon
ventriculus
aorta
AAO:0010213
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
BTO:0000135
EFO:0000265
EMAPA:18601
EV:0100027
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].
FMA:3734
GAID:469
MA:0000062
MAT:0000035
MESH:A07.231.114.056
MIAA:0000035
OpenCyc:Mx4rvVjvTpwpEbGdrcN5Y29ycA
SCTID:181298001
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]
UBERON:0000947
UMLS:C0003483
VHOG:0001523
When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]
XAO:0003010
aorta, arteria maxima
aortic
dorsal aorta
galen:Aorta
http://upload.wikimedia.org/wikipedia/commons/9/91/Aorta_scheme.jpg
ncithesaurus:Aorta
trunk of aortic tree
trunk of systemic arterial tree
uberon
heart
AAO:0010210
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]
BILA:0000020
BTO:0000562
Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
EFO:0000815
EHDAA2:0000738
EHDAA:420
EMAPA:16105
EV:0100018
FMA:7088
GAID:174
Herz
MA:0000072
MAT:0000036
MESH:A07.541
MIAA:0000036
OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA
Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
SCTID:302509004
TAO:0000114
UBERON:0000948
UMLS:C0018787
VHOG:0000276
XAO:0000064
ZFA:0000114
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].
branchial heart
cardiac
chambered heart
galen:Heart
ncithesaurus:Heart
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
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
uberon
vertebrate heart
endocrine system
AAO:0010279
Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]
Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
EFO:0002969
EHDAA2:0002224
EV:0100128
FBbt:00005068
FMA:9668
GAID:439
MA:0000012
MESH:A06
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]
SCTID:278876000
TAO:0001158
UBERON:0000949
UMLS:C0014136
VHOG:0000098
XAO:0000158
ZFA:0001158
endocrine
endocrine glandular system
endocrine system
ncithesaurus:Endocrine_System
systema endocrinum
uberon
brain
(...) 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]
AAO:0010478
ABA:Brain
BILA:0000135
BTO:0000142
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
EFO:0000302
EHDAA2:0000183
EHDAA:2641
EHDAA:6485
EMAPA:16894
EV:0100164
FBbt:00005095
FMA:50801
GAID:571
MA:0000168
MAT:0000098
MESH:A08.186.211
MIAA:0000098
NIF_GrossAnatomy:birnlex_796
OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
SCTID:258335003
TAO:0000008
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].
UBERON:0000955
UMLS:C0006104
VHOG:0000157
XAO:0000010
ZFA:0000008
encephalon
galen:Brain
include synganglion?
ncithesaurus:Brain
synganglion
uberon
cerebral cortex
ABA:CTX
BM:Tel-Cx
BTO:0000233
EFO:0000328
EHDAA2:0000234
EHDAA:5464
EMAPA:17544
EV:0100166
FMA:61830
GAID:629
MA:0000185
MAT:0000108
MESH:A08.186.211.730.885.213
MIAA:0000108
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]
NIF_GrossAnatomy:birnlex_1494
SCTID:362880003
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].
This class was created automatically from a combination of ontologies
UBERON:0000956
UMLS:C0007776
VHOG:0000722
brain cortex
cortex cerebri
cortex of cerebral hemisphere
http://upload.wikimedia.org/wikipedia/commons/9/9a/Brainmaps-macaque-hippocampus.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/7/7b/Cerebral_Cortex_location.jpg/200px-Cerebral_Cortex_location.jpg
ncithesaurus:Cortex
pallium of the brain
uberon
lens of camera-type eye
AAO:0010348
BTO:0000723
EHDAA:9057
EMAPA:17838
EV:0100343
FMA:58241
MA:0000275
MAT:0000141
MESH:A09.371.509
MIAA:0000141
OpenCyc:Mx4rvVj0fZwpEbGdrcN5Y29ycA
RETIRED_EHDAA2:0000975
SCTID:181169005
TAO:0000035
Taxon notes: This class excludes compound eye corneal lenses.
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]
Transparent part of camera-type eye that helps to refract light to be focused on the retina.
UBERON:0000965
UMLS:C0023317
VHOG:0000169
XAO:0000008
ZFA:0000035
camera-type eye lens
crystalline lens
eye lens
lens
lens crystallina
ncithesaurus:Crystalline_Lens
ocular lens
uberon
retina
AAO:0010352
BTO:0001175
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
EFO:0000832
EHDAA2:0001627
EHDAA:4757
EMAPA:17168
EV:0100348
FMA:58301
GAID:755
MA:0000276
MAT:0000142
MESH:A09.371.729
MIAA:0000142
NIF_GrossAnatomy:birnlex_1153
NIF_GrossAnatomy:birnlex_1156
Netzhaut
OpenCyc:Mx4rvViTfpwpEbGdrcN5Y29ycA
SCTID:181171005
TAO:0000152
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]
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]
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.
UBERON:0000966
UMLS:C0035298
VHOG:0000229
XAO:0000009
ZFA:0000152
http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png
http://upload.wikimedia.org/wikipedia/commons/thumb/e/ed/Human_eye_cross-sectional_view_grayscale.png/200px-Human_eye_cross-sectional_view_grayscale.png
inner layer of eyeball
ncithesaurus:Retina
retina of camera-type eye
retinal
tunica interna of eyeball
uberon
eye
An organ that detects light.
BILA:0000017
BTO:0000439
EFO:0000827
EV:0100336
FBbt:00005162
GAID:69
MAT:0000140
MESH:A01.456.505.420
MIAA:0000140
OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA
UBERON:0000970
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,
light-detecting organ
optic
photoreceptor
uberon
visual apparatus
neck
AEO:0000108
BTO:0000420
EFO:0000967
EHDAA2:0003108
FMA:7155
GAID:86
MA:0000024
MAT:0000297
MESH:A01.598
MIAA:0000297
OpenCyc:Mx4rvVjLF5wpEbGdrcN5Y29ycA
SCTID:302550007
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].
UBERON:0000974
UMLS:C0027530
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.
cervical
collum
galen:Neck
http://upload.wikimedia.org/wikipedia/commons/thumb/9/99/Female_neck.jpg/200px-Female_neck.jpg
ncithesaurus:Neck
neck (volume)
uberon
leg
BTO:0000721
EFO:0001411
EHDAA2:0000972
EHDAA:5151
EHDAA:6176
EHDAA:8289
EMAPA:17489
GAID:49
MA:0000047
MESH:A01.378.610
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
OpenCyc:Mx4rvViYzZwpEbGdrcN5Y29ycA
The portion of the hindlimb that contains both the stylopod and zeugopod.
The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For [3] we use the less open to misinterpretation 'hindlimb zeugopod'. Editor note: currently declared as overlapping foot, as AOs disagree over whether some ankle parts are in the leg or foot
UBERON:0000978
VHOG:0000345
lower extremity
tetrapod leg
uberon
tibia
AAO:0000890
BTO:0001252
EFO:0003054
EMAPA:19142
FMA:24476
GAID:204
MA:0001361
MESH:A02.835.232.500.883
One of the two long bones of endochondral origin of the hind-epipodium; it is a straight, simple bone whose section is more or less rectangular at the ends and circular at its central portion.[AAO]
OpenCyc:Mx4rvtq3-ZwpEbGdrcN5Y29ycA
SCTID:182061009
The major preaxial endochondral bone in the posterior zeugopod[Phenoscape].
UBERON:0000979
UMLS:C0040184
galen:Tibia
http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray260.png
http://upload.wikimedia.org/wikipedia/commons/thumb/2/2a/Gray260.png/200px-Gray260.png
ncithesaurus:Tibia
shankbone
shinbone
uberon
femur
AAO:0000889
BTO:0001284
EFO:0001396
EMAPA:18514
EMAPA:19143
Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified].
Endochondral longbone connecting the pelvic girdle with posterior zeugopodium.[VSAO]
FMA:9611
GAID:199
MA:0001359
MESH:A02.835.232.500.247
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
OpenCyc:Mx4rvVjOJJwpEbGdrcN5Y29ycA
Paired, elongate, cylindrical bones of endochondral origin that form the thighs, extending from the pelvic girdles to the knees.[AAO]
SCTID:182046008
UBERON:0000981
UMLS:C0015811
VHOG:0001159
VSAO:0000186
XAO:0003214
femoral
femoral bone
galen:Femur
homologous to proximal metapterygial mesomere of pelvic appendage [Hall 2007].
http://upload.wikimedia.org/wikipedia/commons/7/73/Gray252.png
http://upload.wikimedia.org/wikipedia/commons/thumb/7/73/Gray252.png/200px-Gray252.png
ncithesaurus:Femur
os femorale
os femoris
os femoris, os longissimum
thigh bone
uberon
skeletal joint
AEO:0000182
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
BTO:0001686
EFO:0000948
FMA:7490
GAID:102
MA:0000319
MAT:0000188
MESH:A02.835.583
MIAA:0000188
OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA
RETIRED_EHDAA2:0003182
SCTID:302536002
TAO:0000367
UBERON:0000982
UMLS:C0022417
VHOG:0001276
VSAO:0000101
XAO:0000171
ZFA:0001596
articular joint
articulation
galen:Joint
joint
ncithesaurus:Joint
uberon
metatarsus region
A metapodium region that is part of a pes.
FMA:24997
MA:0000049
Note that mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton
SCTID:280711000
UBERON:0000983
hind metapodium
metatarsal part of foot
metatarsal region
metatarsus
regio metatarsalis
uberon
pons
ABA:P
BM:Pons
BTO:0001101
Brainstrem structure that has as its parts the pontine tegmentum and basal part of pons[FMA].
During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG]
EFO:0001394
EHDAA2:0004394
EMAPA:17563
EV:0100253
FMA:67943
GAID:578
MA:0000204
MAT:0000115
MESH:A08.186.211.132.810.428.600
MIAA:0000115
NIF_GrossAnatomy:birnlex_733
SCTID:279103004
The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG]
The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved
UBERON:0000988
UMLS:C0032639
VHOG:0001176
http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png
http://upload.wikimedia.org/wikipedia/commons/thumb/3/36/Gray768.png/200px-Gray768.png
ncithesaurus:Pons_Varolii
pons Varolii
pons of Varolius
uberon
penis
BTO:0000405
EFO:0000987
EHDAA2:0001433
EHDAA:9380
EMAPA:18682
EMAPA:18996
EV:0100107
FMA:9707
GAID:389
MA:0000408
MAT:0000186
MESH:A05.360.444.492
MIAA:0000186
Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca[WP]
OpenCyc:Mx4rvVjkCZwpEbGdrcN5Y29ycA
SCTID:265793009
The penis (plural penises, penes) is an external sexual organ of certain biologically male organisms, in both vertebrates and invertebrates. The penis is a reproductive organ, technically an intromittent organ, and for placental mammals, additionally serves as the external organ of urination. The penis is generally found on mammals and reptiles. [WP,unvetted].
UBERON:0000989
UMLS:C0030851
VHOG:0000727
galen:Penis
http://upload.wikimedia.org/wikipedia/commons/thumb/8/87/Labelled_flaccid_penis.jpg/200px-Labelled_flaccid_penis.jpg
ncithesaurus:Penis
penile
phallic
phallus
uberon
reproductive system
AAO:0010258
Anatomical system that has as its parts the organs concerned with reproduction.
Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]
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]
BILA:0000103
BTO:0000081
EFO:0000809
EHDAA2:0001603
EHDAA:5923
EMAPA:17381
EV:0100100
Editor notes: consider splitting genitalia from reproductive system
FBbt:00004857
FMA:7160
GAID:363
Geschlechtsorgan
HAO:0000374
HAO:0000895
MA:0000326
MIAA:0000305
OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA
SCTID:278875001
TAO:0000632
UBERON:0000990
UMLS:C1261210
VHOG:0000182
WBbt:0005747
XAO:0000142
ZFA:0000632
animal reproductive system
genital system
genitalia
http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/5/52/Penis.svg/200px-Penis.svg.png
ncithesaurus:Reproductive_System
organa genitalia
reproductive tissue
systemata genitalia
uberon
gonad
AAO:0000213
Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]
BILA:0000123
BTO:0000534
EMAPA:16857
EMAPA:17383
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]
FBbt:00004858
FMA xref is a 'general anatomical term'
FMA:18250
GAID:368
HAO:0000379
MA:0002420
MESH:A05.360.576
OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
SCTID:304623008
TAO:0000413
The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]
UBERON:0000991
UMLS:C0018067
VHOG:0000397
WBbt:0005175
XAO:0003146
ZFA:0000413
gonada
gonadal
ncithesaurus:Gonad
uberon
female gonad
(...) 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]
AAO:0000371
BILA:0000125
BTO:0000975
EFO:0000973
EHDAA2:0001360
EHDAA:8124
EMAPA:17962
EV:0100111
Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]
FBbt:00004865
FMA:7209
Female reproductive organ.[TAO]
GAID:367
MA:0000384
MESH:A05.360.319.114.630
MIAA:0000125
OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA
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].
Ovum-producing female reproductive organ.
SCTID:181464007
TAO:0000403
UBERON:0000992
UMLS:C0029939
VHOG:0000251
XAO:0000258
ZFA:0000403
female organism genitalia gonad
female organism genitalia gonada
female organism reproductive system gonad
female organism reproductive system gonada
female reproductive system gonad
female reproductive system gonada
genitalia of female organism gonad
genitalia of female organism gonada
gonad of female organism genitalia
gonad of female organism reproductive system
gonad of female reproductive system
gonad of genitalia of female organism
gonad of reproductive system of female organism
gonada of female organism genitalia
gonada of female organism reproductive system
gonada of female reproductive system
gonada of genitalia of female organism
gonada of reproductive system of female organism
http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png
http://upload.wikimedia.org/wikipedia/commons/thumb/c/cb/Female_anatomy.png/200px-Female_anatomy.png
ncithesaurus:Ovary
ovarian
ovaries
ovarium
ovary
ovum-producing ovary
relationship type change: subclass gonad (TAO:0000413) CHANGED TO: develops_from gonad (UBERON:0000991)[TAO]
reproductive system of female organism gonad
reproductive system of female organism gonada
uberon
oviduct
A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG]
AAO:0010533
BTO:0000980
EFO:0000974
EMAPA:18984
GAID:366
In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG]
MAT:0000126
MESH:A13.706
MIAA:0000126
TAO:0000560
UBERON:0000993
UMLS:C0029954
Usage notes: sometimes oviduct is used interchangeably with follaopian tube. Here they are different - the oviduct connects the gonad to the outside in a variety of animals. The mammal-class fallopian tube is derived from the mullerian duct and connects the gonads to the uterus. Taxon notes: in birds divided into infundibulum, magnum, isthmus, uterus, and vagina
VHOG:0001136
XAO:0003052
ZFA:0000560
ncithesaurus:Oviduct
passage from the ovaries to the outside of the body[Wikipedia:Oviduct].
salpinx
tuba uterina
tuba uterinae
uberon
uterine tube
uterus
An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]
BTO:0001424
EFO:0000975
EMAPA:29915
EV:0100113
FMA:17558
GAID:172
MA:0000389
MAT:0000127
MESH:A05.360.319.679
MIAA:0000127
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.
OpenCyc:Mx4rvViojJwpEbGdrcN5Y29ycA
SCTID:181452004
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]
UBERON:0000995
UMLS:C0042149
VHOG:0001137
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].
galen:Uterus
http://upload.wikimedia.org/wikipedia/commons/6/6a/Female_reproductive_system_lateral_nolabel.png
http://upload.wikimedia.org/wikipedia/commons/thumb/c/cb/Female_anatomy.png/200px-Female_anatomy.png
ncithesaurus:Uterus
uberon
uterine
vagina
BTO:0000243
EFO:0000976
EMAPA:18986
EV:0100117
FMA:19949
GAID:381
MA:0000394
MAT:0000128
MESH:A05.360.319.779
MIAA:0000128
OpenCyc:Mx4rvVj1B5wpEbGdrcN5Y29ycA
Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA]
SCTID:181441005
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
The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG]
The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG]
UBERON:0000996
UMLS:C0042232
VHOG:0001138
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].
distal oviductal region
distal portion of oviduct
galen:Vagina
http://upload.wikimedia.org/wikipedia/commons/1/1b/Illu_repdt_female.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/a/a4/Vaginal_opening_-_english_description.jpg/200px-Vaginal_opening_-_english_description.jpg
ncithesaurus:Vagina
uberon
vaginae
vaginal
mammalian vulva
BTO:0003101
EFO:0000978
EV:0100118
FMA:20462
GAID:383
MA:0000395
MAT:0000169
MESH:A05.360.319.887
MIAA:0000169
OpenCyc:Mx4rvgAWeJwpEbGdrcN5Y29ycA
SCTID:265796001
The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG]
UBERON:0000997
UMLS:C0042993
VHOG:0001458
editor note: todo - add pudendum
external genital organs of the female mammal[WP].
female pudendum
galen:Vulva
http://upload.wikimedia.org/wikipedia/commons/d/da/Female_unshaved_genitalia.jpg
mammalian vulva
ncithesaurus:Vulva
puboperineal region
pudendum femininum
pudendum femininum
skin of female pudendum
skin of vulva
uberon
vulva
vulval
seminal vesicle
(In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra.[well established][VHOG]
AAO:0010788
BTO:0001234
EFO:0000986
EMAPA:19180
EV:0100106
Either of a pair of glandular pouches that lie one on either side of the male reproductive tract and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct.
Either of a pair of pouchlike glands situated on each side of the male urinary bladder that secrete seminal fluid and nourish and promote the movement of spermatozoa through the urethra. [TFD][VHOG]
FMA:19386
Function notes: The seminal vesicles secrete a significant proportion of the fluid that ultimately becomes semen. Lipofuscin granules from dead epithelial cells give the secretion its yellowish color. About 50-70%[2] of the seminal fluid in humans originates from the seminal vesicles, but is not expelled in the first ejaculate fractions which are dominated by spermatozoa and zinc-rich prostatic fluid.
GAID:394
MA:0000410
MAT:0000171
MESH:A05.360.444.713
MIAA:0000171
OpenCyc:Mx4rwTtRpJwpEbGdrcN5Y29ycA
SCTID:181434004
UBERON:0000998
UMLS:C0036628
VHOG:0001379
glandula seminalis
glandula vesiculosa
gon_male_sves
http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/d/d1/Male_anatomy_en.svg/200px-Male_anatomy_en.svg.png
ncithesaurus:Seminal_Vesicle
seminal gland
uberon
vas efferens
vesicul%c3%a6 seminales
vesicula seminalis
vesiculae seminales
vesicular gland
vesicular glands
vesicular seminalis
vesiculæ seminales
ejaculatory duct
BTO:0001580
EFO:0000985
EMAPA:19088
FMA:19325
GAID:388
MAT:0000170
MESH:A05.360.444.251
MIAA:0000170
OpenCyc:Mx4rwOt7MJwpEbGdrcN5Y29ycA
SCTID:279665005
The Ejaculatory ducts (ductus ejaculatorii) are paired structures in male anatomy, about 2 cm in length. Each ejaculatory duct is formed by the union of the vas deferens with the duct of the seminal vesicle. They pass through the prostate, and empty into the urethra at the Colliculus seminalis. During ejaculation, semen passes through the ducts and exits the body via the penis[WP,unvetted].
UBERON:0000999
UMLS:C0013747
ductus ejaculatorii
ductus ejaculatorii
ductus ejaculatorius
http://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png
http://upload.wikimedia.org/wikipedia/commons/thumb/3/35/Male_anatomy.png/200px-Male_anatomy.png
ncithesaurus:Ejaculatory_Duct
uberon
vas deferens
BTO:0001427
EFO:0000981
EMAPA:18681
EV:0100105
FMA:19234
GAID:404
MA:0000413
MESH:A05.360.444.930
MIAA:0000129
OpenCyc:Mx4rvjv7bpwpEbGdrcN5Y29ycA
SCTID:245467009
Taxon notes (from WP): Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall.
The continuation of the archinephric duct, now called the deferent duct, extends caudally to the cloaca or to the part of the mammalian urethra that is derived from the cloaca.[well established][VHOG]
UBERON:0001000
UMLS:C0042360
VHOG:0001135
deferent duct
duct that transports sperm from the testis. In mammals this is from the epididymis.
ductus deferens
galen:VasDeferens
http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/d/d1/Male_anatomy_en.svg/200px-Male_anatomy_en.svg.png
ncithesaurus:Vas_Deferens
sperm duct
uberon
vas deferen
vasa deferentia
epidermis
(...) 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]
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]
AAO:0000143
BTO:0000404
EFO:0000954
EV:0100153
FMA:70596
GAID:932
MA:0000153
MAT:0000154
MESH:A10.272.497
MIAA:0000154
SCTID:361694003
TAO:0000105
The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]
The outer layer of the skin[WP]. cellular, multilayered epithelium derived from the ectoderm[ZFA].
UBERON:0001003
UMLS:C0014520
VHOG:0000077
XAO:0000028
ZFA:0000105
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).
adult epidermis
epidermal
ncithesaurus:Epidermis
relationship loss: subclass external integument structures (AAO:0000961)[AAO]
skin
uberon
vertebrate epidermis
respiratory system
AAO:0000541
Atmungssystem
BTO:0000203
EFO:0000804
EHDAA2:0001604
EHDAA:2203
EMAPA:16727
EV:0100036
FMA:7158
Functional system which consists of structures involved in respiration.
GAID:78
MA:0000327
MAT:0000030
MESH:A04
MIAA:0000030
OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA
SCTID:278197002
TAO:0000272
The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
UBERON:0001004
UMLS:C0035237
VHOG:0000202
XAO:0000117
ZFA:0000272
apparatus respiratorius
apparatus respiratorius
http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/5/5e/Respiratory_system_complete_en.svg/200px-Respiratory_system_complete_en.svg.png
ncithesaurus:Respiratory_System
respiratory system
systema respiratorium
uberon
respiratory airway
An airway through which respiratory air passes in organisms.
SCTID:361380005
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)
UBERON:0001005
uberon
digestive system
AAO:0000129
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
BILA:0000082
BTO:0000058
EFO:0000793
EV:0100056
FBbt:00005055
FMA:7152
GAID:278
MA:0002431
MAT:0000018
MESH:A03
MIAA:0000018
SCTID:278859004
TADS:0000170
TAO:0000339
UBERON:0001007
WBbt:0005748
XAO:0000125
ZFA:0000339
alimentary system
alimentary tract
digestive
galen:DigestiveSystem
gastrointestinal system
gut
ncithesaurus:Digestive_System
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
uberon
excretory system
AAO:0010257
An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]
BILA:0000015
BTO:0001244
BTO:0003092
EFO:0000803
EHDAA2:0001601
EHDAA:5901
EMAPA:17366
EV:0100095
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]
FBbt:00005056
FMA:7159
GAID:391
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
MA:0000325
MAT:0000027
MESH:A05.810
MIAA:0000027
SCTID:362204003
TADS:0000162
TAO:0000163
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.
UBERON:0001008
UMLS:C1508753
VHOG:0000723
WBbt:0005736
XAO:0000143
ZFA:0000163
galen:UrinaryTract
ncithesaurus:Urinary_System
renal or urinary system
renal system
renal/urinary system
systema urinaria
systema urinarium
uberon
urinary system
urinary tract
circulatory system
AAO:0000959
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]
FBbt:00005057
OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA
UBERON:0001009
VHOG:0001248
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]
http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/2/29/Circulatory_System_en.svg/200px-Circulatory_System_en.svg.png
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].
systema cardiovasculare
the cardiovascular system and the lymphatic system are parts of the circulatory system
uberon
adipose tissue
AAO:0000001
AEO:000020
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]
BTO:0001487
Connective tissue composed of adipocytes.
Connective tissue in which fat is stored.[TAO]
EFO:0000234
EFO:0000790
EHDAA2:0003120
EV:0100381
FMA:20110
GAID:920
MA:0000009
MAT:0000015
MESH:A10.165.114
MIAA:0000015
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.
OpenCyc:Mx4rvVjc_ZwpEbGdrcN5Y29ycA
SCTID:55603005
TAO:0002134
Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
UBERON:0001013
UMLS:C0001527
VHOG:0001284
XAO:0003049
ZFA:0005345
adipose
bodyfat
fat
fat tissue
fatty depot
fatty tissue
galen:FattyTissue
ncithesaurus:Adipose_Tissue
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
uberon
musculature
A subdivision of the muscular system.
AAO:0011066
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.
BTO:0000887
EFO:0001949
FMA:32558
MA:0000165
OpenCyc:Mx4rvVjmr5wpEbGdrcN5Y29ycA
TAO:0000548
UBERON:0001015
UMLS:C0026845
VSAO:0005038
WBbt:0005737
ZFA:0000548
http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png
muscle group
muscle system
muscles
muscles set
musculature
musculature system
musculi
ncithesaurus:Muscle
set of muscles
set of skeletal muscles
uberon
nervous system
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]
AAO:0000324
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
BILA:0000079
BTO:0001484
EFO:0000802
EHDAA2:0001246
EHDAA:826
EMAPA:16469
EV:0100162
FBbt:00005093
FMA:7157
GAID:466
MA:0000016
MAT:0000026
MESH:A08
MIAA:0000026
NIF_GrossAnatomy:birnlex_844
Nervensystem
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA
SCTID:278196006
TAO:0000396
This class was created automatically from a combination of ontologies
UBERON:0001016
UMLS:C0027763
VHOG:0000402
WBbt:0005735
XAO:0000177
ZFA:0000396
a network of specialized cells that communicate information about an organism's surroundings and itself[Wikipedia].
http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/b/ba/Nervous_system_diagram.png/200px-Nervous_system_diagram.png
ncithesaurus:Nervous_System
nerve net
nervous
neural
relationship type change: differentiates_from ectoderm (AAO:0000137) CHANGED TO: develops_from ectoderm (UBERON:0000924)[AAO]
systema nervosum
uberon
central nervous system
(...) 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]
AAO:0000090
BILA:0000080
BTO:0000227
CNS
EFO:0000908
EHDAA2:0000225
EHDAA:828
EMAPA:16470
EMAPA:16754
EV:0100163
FBbt:00005094
FMA:55675
GAID:570
MA:0000167
MAT:0000457
MESH:A08.186
NIF_GrossAnatomy:birnlex_1099
OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA
Part of the nervous system which includes the brain and spinal cord.[AAO]
SCTID:278199004
TAO:0000012
The brain and spinal cord. Kimmel et al, 1995.[TAO]
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].
UBERON:0001017
UMLS:C0927232
VHOG:0000293
XAO:0000215
ZFA:0000012
cerebrospinal axis
ncithesaurus:Central_Nervous_System
neuraxis
systema nervosum centrale
uberon
axon tract
A group of axons linking two or more neuropils and having a common origin, termination[FBbt].
EV:0100304
FBbt:00005100
FMA:83847
UBERON:0001018
WP says this is the analog of peripheral nerves in CNS
axonal tract
neuraxis tract
tract
tract of neuraxis
uberon
fascicle
A slender neuron projection bundle[FBbt].
BTO:0004101
FBbt:00005101
FMA:12235
NIF_GrossAnatomy:birnlex_872
TGMA:0000088
TODO - invert specific? note FBbt class not disjoint from tract. Consider merging with 'neuron projection bundle'
UBERON:0001019
UMLS:C1185741
fasciculus
ncithesaurus:Fascicle
nerve bundle
nerve fasciculus
neural fasciculus
uberon
commissure
*not* the same as FMA:76741 Commissure
FBbt:00005103
FMA:83906
NIF_GrossAnatomy:nlx_anat_20090513
OpenCyc:Mx4rdBrmE6gOEdudWQACs5b6Bw
TADS:0000201
UBERON:0001020
UMLS:C1185742
White matter fiber bundle that crosses the midline of the brain or spinal cord[NIF]. In the context of Drosophila refers to a broad band of axons connecting the same neuropils each side of the brain[FBbt].
commissural
commissure of neuraxis
ncithesaurus:Commissure
neuraxis commissure
uberon
nerve
A portion of tissue which is a fasiculated group of axons.[TAO]
AAO:0011070
AEO:0000137
BTO:0000925
EHDAA2:0003137
EHDAA:2851
EHDAA:3776
EHDAA:4657
EV:0100162
FBbt:00005105
FMA:65132
GAID:758
MA:0000217
OpenCyc:Mx4rwP3lkpwpEbGdrcN5Y29ycA
SCTID:256864008
TAO:0007009
UBERON:0001021
UMLS:C0027740
XAO:0003047
ZFA:0007009
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].
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
galen:Nerve
ncithesaurus:Nerve
nerves
nervous
neural subtree
uberon
sensory system
AAO:0000555
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]
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
BILA:0000099
EFO:0000805
EHDAA2:0003094
FBbt:00005827
FMA:75259
MA:0002442
MAT:0000031
MIAA:0000031
NIF_GrossAnatomy:nlx_anat_090816
TAO:0000282
UBERON:0001032
VHOG:0001674
XAO:0003194
ZFA:0000282
http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png
http://upload.wikimedia.org/wikipedia/commons/thumb/c/c0/Gray722.png/200px-Gray722.png
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
organa sensuum
organa sensuum
sense organ subsystem
sense organs
sense organs set
sensory organ system
sensory subsystem
sensory systems
set of sense organs
uberon
gustatory system
A subset of the sensory system for the sensing of taste.
AAO:0010577
BILA:0000143
EFO:0000830
FMA:7194
MA:0002446
MAT:0000275
MIAA:0000275
NIF_GrossAnatomy:nlx_anat_090803
SCTID:423940004
TAO:0001101
The sensory system used for the sense of taste.[AAO]
UBERON:0001033
XAO:0003197
ZFA:0001101
gustatory
gustatory organ system
in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes
taste system
uberon
yolk sac
BTO:0001471
EFO:0003078
EHDAA2:0002212
EHDAA:164
EMAPA:16085
FMA:87180
GAID:1301
MESH:A16.254.403.981
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.
One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG]
SCTID:362845002
Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]
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"]
UBERON:0001040
UMLS:C0043425
VHOG:0000830
http://upload.wikimedia.org/wikipedia/commons/1/17/Gray22.png
http://upload.wikimedia.org/wikipedia/commons/thumb/1/17/Gray22.png/200px-Gray22.png
ncithesaurus:Yolk_Sac
saccus vitellinus
uberon
vesicula umbilicalis
foregut
AAO:0011042
Anterior subdivision of a digestive tract[CJM]. An anterior part of the alimentary canal derived from the ectoderm[WP].
BILA:0000085
BTO:0000507
EHDAA2:0000557
EHDAA:520
EMAPA:16548
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)
FBbt:00005379
FMA:45616
MA:0001526
SCTID:361409009
TGMA:0001014
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]
UBERON:0001041
UMLS:C0231051
VHOG:0000285
XAO:0000232
http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png
ncithesaurus:Foregut
praeenteron
proenteron
uberon
chordate pharynx
(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]
AAO:0000967
Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]
BTO:0001049
EFO:0000836
EHDAA2:0001458
EHDAA:2947
EMAPA:16706
EMAPA:18838
EV:0100065
FMA:46688
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].
GAID:155
MA:0000432
MESH:A03.867
Note that MA/FMA pharynx not part of digestive/alimentary system, we follow their lead here
OpenCyc:Mx4rvViv7ZwpEbGdrcN5Y29ycA
SCTID:181211006
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]
TAO:0000056
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]
UBERON:0001042
UMLS:C0031354
VHOG:0000462
XAO:0003227
ZFA:0000056
galen:Pharynx
ncithesaurus:Pharynx
pharynx
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]
uberon
esophagus
AAO:0000145
ANISEED:1235301
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)
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]
BTO:0000959
EFO:0000835
EHDAA2:0001285
EHDAA:2937
EMAPA:16833
EMAPA:18860
EV:0100069
FMA:7131
GAID:291
MA:0000352
MAT:0000048
MESH:A03.365
MIAA:0000048
OpenCyc:Mx4rvVj9Q5wpEbGdrcN5Y29ycA
SCTID:181245004
TAO:0000204
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]
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).
UBERON:0001043
UMLS:C0014876
VHOG:0000450
XAO:0000127
ZFA:0000204
esophageal
galen:Esophagus
gullet
http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg
ncithesaurus:Esophagus
oesophagus
uberon
Åsophagus
salivary gland
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]
BTO:0001203
EFO:0000859
EHDAA2:0001775
EHDAA:7987
EMAPA:17751
EV:0100059
FBbt:00005382
FMA:9597
GAID:937
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]
MA:0000346
MAT:0000079
MESH:A10.336.779
MIAA:0000079
OpenCyc:Mx4rvVjl5ZwpEbGdrcN5Y29ycA
SCTID:181236000
UBERON:0001044
UMLS:C0036098
VHOG:0000376
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
galen:SalivaryGland
glandulae salivariae
http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/5/51/Illu_quiz_hn_02.jpg/200px-Illu_quiz_hn_02.jpg
ncithesaurus:Salivary_Gland
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].
uberon
midgut
BILA:0000086
BTO:0000863
EFO:0001950
EHDAA2:0001185
EHDAA:983
EMAPA:16255
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.
FBbt:00005383
FMA:45617
MA:0001564
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.
SCTID:361410004
TGMA:0001036
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]
UBERON:0001045
UMLS:C0231052
VHOG:0000290
XAO:0000103
http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg
mesenteron
ncithesaurus:Midgut
uberon
hindgut
AAO:0011052
BILA:0000087
BTO:0000510
EHDAA2:0000779
EHDAA:975
EMAPA:16715
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.
FBbt:00005384
FMA:45618
MA:0001527
Posterior subdivision of a digestive tract[CJM].
SCTID:362856002
TGMA:0001020
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]
UBERON:0001046
UMLS:C0231053
VHOG:0000459
XAO:0000104
http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png
metenteron
ncithesaurus:Hindgut
uberon
primordium
AEO:0000171
BTO:0001886
EFO:0001652
EHDAA2:0003171
FBbt:00005495
FMA:86589
MAT:0000482
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.
This class was created automatically from a combination of ontologies
UBERON:0001048
UMLS:C0678727
XAO:0003043
bud
ncithesaurus:Primordium
placode
rudiment
uberon
neural tube
(...) 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]
AAO:0010617
BTO:0001057
EHDAA2:0001254
EHDAA:2869
EHDAA:908
EMAPA:16164
EMAPA:16530
EMAPA:16757
Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
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].
MAT:0000069
MIAA:0000069
SCTID:362852000
TAO:0001135
The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]
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]
UBERON:0001049
UMLS:C0231024
VHOG:0000307
XAO:0003204
ZFA:0001135
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Gray19_with_color.png/200px-Gray19_with_color.png
ncithesaurus:Neural_Tube
presumptive central nervous system
tubus neuralis
uberon
rectum
AAO:0010401
BTO:0001158
EFO:0000848
EHDAA2:0001592
EHDAA:5836
EMAPA:17896
EMAPA:18925
EV:0100081
FMA:14544
GAID:311
MA:0000336
MAT:0000050
MESH:A03.492.411.495.767
MIAA:0000050
OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA
SCTID:181261002
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
The terminal portion of the intestine.
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]
UBERON:0001052
UMLS:C0034896
VHOG:0000427
VHOG:0001751
XAO:0000238
galen:Rectum
http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif
http://upload.wikimedia.org/wikipedia/commons/thumb/7/75/Anorectum.gif/200px-Anorectum.gif
intestinum rectum
ncithesaurus:Rectum
rectal
rectal sac
terminal portion of intestine
terminal portion of large intestine
uberon
anatomical entity
AAO:0010841
AEO:0000000
BILA:0000000
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:0000000
EHDAA2:0002229
FBbt:10000000
FBbt_root:00000000
FMA:62955
HAO:0000000
MA:0000001
NIF_GrossAnatomy:birnlex_6
TAO:0100000
TGMA:0001822
UBERON:0001062
UMLS:C1515976
ZFA:0100000
ncithesaurus:Anatomic_Structure_System_or_Substance
uberon
pericardial cavity
Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO]
Cavity of serous sac surrounded by serous pericardium.[FMA]
EHDAA2:0001434
EMAPA:18447
EMAPA:18448
FMA:11350
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]
MA:0000053
SCTID:362027001
TAO:0002220
UBERON:0001074
UMLS:C0225972
VHOG:0000556
ZFA:0001655
cavitas pericardiaca
cavity of pericardial sac
galen:PericardialSpace
http://upload.wikimedia.org/wikipedia/commons/1/16/Gray968.png
http://upload.wikimedia.org/wikipedia/commons/thumb/1/16/Gray968.png/200px-Gray968.png
ncithesaurus:Pericardial_Cavity
pericardial space
uberon
skin of head
A zone of skin that is part of a head [Automatically generated definition].
FMA:12166
FMA:24756
MA:0000582
SCTID:181484006
UBERON:0001084
UMLS:C0205029
adult head zone of skin
head skin
head zone of skin
ncithesaurus:Head_Skin
todo - distinguish between entire skin of region and arbitrary zone of skin on region
uberon
zone of skin of adult head
zone of skin of head
urine
BTO:0001419
EFO:0001939
ENVO:00002047
Excretion in liquid state processed by the kidney.[FMA]
FMA:12274
GAID:1189
MA:0002545
MAT:0000058
MESH:A12.207.927
MIAA:0000058
OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA
This class was created automatically from a combination of ontologies
UBERON:0001088
UMLS:C0042036
galen:Urine
ncithesaurus:Urine
uberon
calcareous tooth
AEO:0000220
BTO:0000397
EFO:0000839
EHDAA2:0004605
EV:0100063
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
FMA:12516
GAID:1260
MA:0000348
MAT:0000041
MESH:A14.254.860
MIAA:0000041
OpenCyc:Mx4rvVjUEZwpEbGdrcN5Y29ycA
Organ with a cavity which consist of dentine surrounded by enamel. Examples: incisor, molar.
SCTID:302214001
TAO:0001625
The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG]
UBERON:0001091
UMLS:C0040426
VHOG:0000127
VHOG:0001733
XAO:0000431
ZFA:0000694
dental
dentine containing tooth
http://upload.wikimedia.org/wikipedia/commons/thumb/1/14/Teeth_by_David_Shankbone.jpg/200px-Teeth_by_David_Shankbone.jpg
ncithesaurus:Tooth
tooth
uberon
vertebrate tooth
wall of esophagus
An anatomical wall that is part of a esophagus [Automatically generated definition].
FMA:12611
MA:0002691
This class was created automatically from a combination of ontologies
UBERON:0001096
anatomical wall of esophagus
anatomical wall of gullet
anatomical wall of oesophagus
esophageal wall
esophagus anatomical wall
esophagus wall
gullet anatomical wall
gullet wall
oesophagus anatomical wall
oesophagus wall
uberon
wall of gullet
wall of oesophagus
diaphragm
A musculomembranous partition separating the abdominal and thoraic cavities and functioning in respiration. [TFD][VHOG]
BTO:0000341
EFO:0000937
EHDAA2:0003495
EMAPA:17701
EV:0100376
FMA:13295
GAID:158
MA:0001904
MAT:0000502
MESH:A02.633.567.900.300
OpenCyc:Mx4rvVivz5wpEbGdrcN5Y29ycA
SCTID:181614006
The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO].
The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3] The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution)
The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG]
UBERON:0001103
UMLS:C0011980
VHOG:0000713
diaphragm muscle
midriff
ncithesaurus:Diaphragm
phren
phrenic
thoracic diaphragm
uberon
parathyroid gland
AAO:0010545
Any one of several small structures, usually four, attached to the dorsal surfaces of the lateral lobes of the thyroid gland. [TFD][VHOG]
BTO:0000997
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]
EFO:0000862
EV:0100134
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]
FMA:13890
GAID:452
MA:0000128
MAT:0000082
MESH:A06.407.560
MIAA:0000082
SCTID:181121007
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]
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].
UBERON:0001132
UMLS:C0030518
VHOG:0001188
XAO:0000167
ncithesaurus:Parathyroid_Gland
parathyroid
parathyroid secreting cell
uberon
cardiac muscle tissue
AAO:0010245
AEO:0000142
BILA:0000134
BTO:0000199
EHDAA2:0003142
FMA:14068
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].
TAO:0005280
UBERON:0001133
UBERON:0007096
ZFA:0005280
cardiac muscle
cardiac muscle muscle tissue
cardiac muscle textus muscularis
cardiac musculature
check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit
galen:CardiacMuscle
galen:CardiacMuscleTissue
heart muscle muscle tissue
heart muscle textus muscularis
heart myocardium muscle tissue
heart myocardium textus muscularis
muscle of heart muscle tissue
muscle of heart textus muscularis
muscle tissue of cardiac muscle
muscle tissue of heart muscle
muscle tissue of heart myocardium
muscle tissue of muscle of heart
muscle tissue of myocardium
myocardium muscle tissue
myocardium textus muscularis
ncithesaurus:Heart_Muscle
textus muscularis of cardiac muscle
textus muscularis of heart muscle
textus muscularis of heart myocardium
textus muscularis of muscle of heart
textus muscularis of myocardium
uberon
skeletal muscle tissue
AAO:0011099
BTO:0001103
EFO:0000888
EHDAA2:0001842
EHDAA:2923
EHDAA:5035
EHDAA:5043
EHDAA:5978
EHDAA:5984
EHDAA:8277
EHDAA:8291
EHDAA:8326
EHDAA:9146
EV:0100377
FMA:14069
GAID:141
MA:0002439
MAT:0000302
MESH:A02.633.567
MIAA:0000302
Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]
OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA
SCTID:426215008
TAO:0005277
TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.
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]
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].
UBERON:0001134
UMLS:C0242692
VHOG:0000319
XAO:0000174
ZFA:0005277
http://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg
ncithesaurus:Skeletal_Muscle_Tissue
skeletal muscle
skeletal muscle organ
skeletal muscle system
somatic muscle
uberon
smooth muscle tissue
(...) 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]
A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]
AAO:0010244
AEO:0000141
BTO:0001260
EFO:0000889
EHDAA2:0003141
EV:0100378
FBbt:00003525
FMA:14070
GAID:167
Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]
MA:0000166
MAT:0000303
MESH:A02.633.570
MIAA:0000303
OpenCyc:Mx4rvvSS3pwpEbGdrcN5Y29ycA
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.
TAO:0005274
UBERON:0001135
UMLS:C1267092
VHOG:0001246
WBbt:0005781
XAO:0000175
ZFA:0005274
galen:SmoothMuscle
galen:SmoothMuscleTissue
http://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg
involuntary muscle
ncithesaurus:Smooth_Muscle_Tissue
non-striated muscle
smooth muscle
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.
textus muscularis levis; textus muscularis nonstriatus
textus muscularis nonstriatus
uberon
visceral muscle
visceral muscle tissue
mesothelium
AEO:0000111
BTO:0002422
EHDAA2_RETIRED:0003111
EHDAA:2331
EHDAA:2349
EHDAA:295
EHDAA:6073
EHDAA:640
EHDAA:646
FMA:14074
MA:0000565
SCTID:361918002
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).
This class was created automatically from a combination of ontologies
UBERON:0001136
UMLS:C0086610
http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg
ncithesaurus:Mesothelium
uberon
dorsum
BTO:0001713
EFO:0001405
FMA:14181
GAID:30
MESH:A01.176
OpenCyc:Mx4rvVkEU5wpEbGdrcN5Y29ycA
SCTID:123961009
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
The dorsal part of an animal, which in vertebrares includes the vertebral column. [cjm].
UBERON:0001137
UMLS:C0004600
back
back of body proper
dorsal
dorsal part of organism
galen:Back
http://upload.wikimedia.org/wikipedia/commons/thumb/e/ee/432px-Gray-back.PNG/200px-432px-Gray-back.PNG
ncithesaurus:Back
uberon
caecum
BTO:0000166
EFO:0000850
EHDAA2:0000206
EHDAA:3913
EV:0100397
FMA:14541
GAID:307
MA:0000334
MESH:A03.492.411.495.209
MIAA:0000288
OpenCyc:Mx4rve6u4JwpEbGdrcN5Y29ycA
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.
SCTID:181256004
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
UBERON:0001153
UMLS:C0007531
VHOG:0001559
blind intestine
blindgut
caeca
caecal
ceca
cecum
galen:Cecum
http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/8/82/Stomach_colon_rectum_diagram.svg/200px-Stomach_colon_rectum_diagram.svg.png
intestinum caecum
intestinum crassum caecum
intestinum crassum cecum
ncithesaurus:Cecum
uberon
vermiform appendix
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]
BTO:0000084
EFO:0000849
EHDAA2:0000588
EV:0100076
EV:0100080
FMA:14542
GAID:308
MA:0001540
MAT:0000287
MESH:A03.492.411.495.209.290
MIAA:0000287
OpenCyc:Mx4rvVjGgJwpEbGdrcN5Y29ycA
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].
SCTID:181255000
UBERON:0001154
UMLS:C0003617
VHOG:0001306
a blind-ended tube connected to the cecum, from which it develops embryologically[WP].
apex of cecum
appendiceal
appendix
appendix vermiformis
appendix vermiformis
caecal appendix
cecal appendix
galen:AppendixVermiformis
http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png
http://upload.wikimedia.org/wikipedia/commons/thumb/a/ad/Gray536.png/200px-Gray536.png
ncithesaurus:Vermiform_Appendix
uberon
vermix
colon
AAO:0010400
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]
BTO:0000269
EFO:0000361
EMAPA:18939
EV:0100079
FMA:14543
GAID:309
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. <a href='http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-PUB-050120-6'>Wallace et al, 2005.</a>
MA:0000335
MAP:0000001
MAT:0000526
MESH:A03.492.411.495.356
OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA
SCTID:302508007
TAO:0000706
TODO: abstract this such that it legitimately covers all vertebrates
The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
UBERON:0001155
UMLS:C0009368
VHOG:0000648
XAO:0000243
ZFA:0000706
colonic
galen:Colon
hindgut
large bowel
ncithesaurus:Colon
posterior intestine
posterior intestine - zebrafish
uberon
ascending colon
BTO:0000270
EFO:0000843
FMA:14545
MA:0001541
MAT:0000311
MIAA:0000311
Note that in MA, this is a subclass of colon
OpenCyc:Mx4rv3H0FZwpEbGdrcN5Y29ycA
Organ part which is continuous with the cecum proximally and the transverse colon distally.[FMA]
SCTID:362162009
UBERON:0001156
UMLS:C0227375
colon ascendens
galen:AscendingColon
http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/3/3b/Dickdarm-Schema.svg/200px-Dickdarm-Schema.svg.png
ncithesaurus:Ascending_Colon
spiral colon
uberon
transverse colon
BTO:0000272
EFO:0000844
FMA:14546
MA:0001543
MAT:0000312
MIAA:0000312
OpenCyc:Mx4rvg7qyJwpEbGdrcN5Y29ycA
SCTID:362163004
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].
This class was created automatically from a combination of ontologies
UBERON:0001157
UMLS:C0227386
colon transversum
galen:TransverseColon
http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/3/3b/Dickdarm-Schema.svg/200px-Dickdarm-Schema.svg.png
ncithesaurus:Transverse_Colon
uberon
descending colon
BTO:0000641
EFO:0000845
FMA:14547
MA:0001542
MAT:0000313
MIAA:0000313
OpenCyc:Mx4rwHsNhpwpEbGdrcN5Y29ycA
SCTID:362165006
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].
This class was created automatically from a combination of ontologies
UBERON:0001158
UMLS:C0227389
colon descendens
galen:DescendingColon
http://upload.wikimedia.org/wikipedia/commons/c/ca/Gray1223.png
http://upload.wikimedia.org/wikipedia/commons/thumb/c/ca/Gray1223.png/200px-Gray1223.png
ncithesaurus:Descending_Colon
uberon
sigmoid colon
BTO:0000645
EFO:0000846
FMA:14548
MAT:0000314
MESH:A03.492.411.495.356.668
MIAA:0000314
OpenCyc:Mx4rwHX_-5wpEbGdrcN5Y29ycA
SCTID:362166007
This class was created automatically from a combination of ontologies
UBERON:0001159
UMLS:C0227391
UMLS:C0682612
colon sigmoideum
galen:SigmoidColon
http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/3/3b/Dickdarm-Schema.svg/200px-Dickdarm-Schema.svg.png
ncithesaurus:Sigmoid_Colon
ncithesaurus:Sigmoid_Flexure
pelvic colon
sigmoid colon
sigmoid flexure
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.
uberon
body of stomach
BTO:0000505
FMA:14560
MA:0002559
Note that we include this as zone of stomach even though it is not distinguished by gland type
SCTID:362140009
The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO].
UBERON:0001161
UMLS:C0227230
corpus gastricum
corpus gastricum (ventriculare)
corpus ventriculare
corpus ventriculi
galen:GastricCorpus
gastric body
gastric corpus
http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/3/31/Gray1046.svg/200px-Gray1046.svg.png
ncithesaurus:Body_of_Stomach
stomach body
uberon
pyloric antrum
BTO:0001732
EFO:0002555
EMAPA:17891
EMAPA:18919
FMA:14579
GAID:332
MA:0001624
MESH:A03.492.766.716
Pyloric antrum (antrum, lesser cul-de-sac) is the initial portion of the pyloric part of the stomach. It is near the bottom of the stomach on the left side of the pyloric sphincter, which separates the stomach and the duodenum. It may temporarily become partially or completely shut off from the remainder of the stomach during digestion by peristaltic contraction of the prepyloric sphincter; it is demarcated, sometimes, from the second part of the pyloric part of the stomach by a slight groove. [WP,unvetted].
SCTID:362142001
UBERON:0001165
UMLS:C0034193
antrum
antrum of Willis
antrum of stomach
antrum pylori
antrum pyloricum
galen:PyloricAntrum
gastric antrum
http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/3/31/Gray1046.svg/200px-Gray1046.svg.png
ncithesaurus:Antrum_Pylori
stomach antrum
stomach pyloric antrum
uberon
pylorus
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]
BTO:0001146
EHDAA2:0001580
EHDAA:4860
EMAPA:17631
EMAPA:18915
Editor notes: We follow Kardong in defining stomach regions by glands
FMA:14581
GAID:333
MA:0002560
MESH:A03.492.766.799
SCTID:362143006
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]
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].
UBERON:0001166
UMLS:C0034196
VHOG:0000420
galen:Pylorus
http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/3/31/Gray1046.svg/200px-Gray1046.svg.png
ncithesaurus:Pylorus
pars pylorica
pars pylorica gastricae
pyloric
pyloric part of stomach
pyloric region
stomach pyloric region
uberon
valvula pylori
wall of stomach
An anatomical wall that is part of a stomach [Automatically generated definition].
FMA:14582
MA:0002692
SCTID:279995000
This class was created automatically from a combination of ontologies
UBERON:0001167
anatomical wall of stomach
anatomical wall of ventriculus
galen:WallOfStomach
gastric wall
stomach anatomical wall
stomach wall
uberon
ventriculus anatomical wall
ventriculus wall
wall of ventriculus
biliary tree
AAO:0011020
FMA:14665
GAID:279
Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO]
Hollow tree organ, the organ parts of which consists of the bile ducts[FMA].
MA:0001273
MESH:A03.159
SCTID:181267003
UBERON:0001173
UMLS:C0005423
XAO:0000455
biliary tract
ncithesaurus:Biliary_Tract
uberon
peritoneal cavity
BTO:0001782
Cavity of serous sac surrounded by the peritoneum.[FMA]
EHDAA2:0001446
EMAPA:18452
EMAPA:18454
EMAPA:18461
FMA:14704
GAID:24
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]
MA:0000054
MESH:A01.047.025.600.678
SCTID:181616008
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]
This class was created automatically from a combination of ontologies
UBERON:0001179
UMLS:C1704247
VHOG:0000852
cavitas peritonealis
cavitas peritonealis; saccus serosus peritonei
ncithesaurus:Peritoneal_Cavity
uberon
mucosa of stomach
BTO:0001308
FMA:14907
GAID:321
MA:0002683
MESH:A03.492.766.440
Magenschleimhaut
OpenCyc:Mx8NhB4rvcD6KJwpEbGdrcN5Y29ycB4rvmKNOpwpEbGdrcN5Y29ycB4rvVj5FpwpEbGdrcN5Y29ycB4rvVjlqpwpEbGdrcN5Y29ycA
SCTID:362131005
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].
This class was created automatically from a combination of ontologies
UBERON:0001199
UMLS:C0017136
galen:GastricMucosa
gastric mucosa
gastric mucous membrane
http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_stomach2.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Illu_stomach2.jpg/200px-Illu_stomach2.jpg
mucosa of organ of stomach
mucosa of organ of ventriculus
mucosa of ventriculus
mucous membrane of stomach
mucous membrane of ventriculus
ncithesaurus:Gastric_Mucosa
organ mucosa of stomach
organ mucosa of ventriculus
stomach mucosa
stomach mucosa of organ
stomach mucous membrane
stomach organ mucosa
tunica mucosa (gaster)
tunica mucosa gastricae
tunica mucosa gastris
uberon
ventriculus mucosa
ventriculus mucosa of organ
ventriculus mucous membrane
ventriculus organ mucosa
pyloric sphincter
(...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG]
A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP].
AAO:0011093
EMAPA:19251
FMA:14916
MA:0002952
OpenCyc:Mx4rvly2ZZwpEbGdrcN5Y29ycA
SCTID:268073008
UBERON:0001202
UMLS:C0227238
VHOG:0001466
XAO:0000457
ncithesaurus:Pyloric_Sphincter
pyloric valve
uberon
adrenal cortex
AAO:0011009
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]
BTO:0000045
EFO:0000237
EMAPA:18427
EV:0100136
FMA:15632
GAID:447
MA:0000118
MAT:0000494
MESH:A06.407.071.140
SCTID:362584002
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].
Taxon notes: Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO
UBERON:0001235
UMLS:C0001613
VHOG:0001481
XAO:0000165
adrenal gland cortex
cortex (glandula suprarenalis)
cortex glandulae suprarenalis
cortex of adrenal gland
cortex of suprarenal gland
http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png
http://upload.wikimedia.org/wikipedia/commons/thumb/5/5c/Gray1185.png/200px-Gray1185.png
ncithesaurus:Adrenal_Cortex
suprarenal
suprarenal cortex
uberon
anus
BTO:0001680
EV:0100082
FBbt:00001893
FBbt:00003148
FMA:15711
GAID:312
MA:0000331
MESH:A03.492.411.495.767.288
OpenCyc:Mx4rvVjaEZwpEbGdrcN5Y29ycA
Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts.
SCTID:181262009
TADS:0000066
TGMA:0001279
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
UBERON:0001245
UMLS:C0003461
WBbt:0005364
anal
anal opening
anal orifice
galen:Anus
http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/7/75/Anorectum.gif/200px-Anorectum.gif
ncithesaurus:Anus
opening of terminal part of digestive tract
proctodeum
uberon
urinary bladder
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]
AAO:0000623
Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]
BTO:0001418
EFO:0000290
EHDAA2:0000174
EHDAA:9328
EMAPA:18321
EV:0100098
FMA:15900
GAID:0000004
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]
MA:0000380
MAT:0000122
MESH:A05.810.161
MIAA:0000122
OpenCyc:Mx4rvVjMmZwpEbGdrcN5Y29ycA
SCTID:302512001
UBERON:0001255
UMLS:C0005682
VHOG:0000740
XAO:0000154
bladder
distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
galen:UrinaryBladder
http://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/3/30/Urinary_system.svg/200px-Urinary_system.svg.png
ncithesaurus:Bladder
uberon
urocyst
vesica urinaria
pancreas
AAO:0010112
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].
BTO:0000988
EFO:0000855
EHDAA2:0001367
EHDAA:6893
EMAPA:17503
EMAPA:18816
EV:0100092
FMA:7198
GAID:334
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]
MA:0000120
MAT:0000075
MESH:A03.734
MIAA:0000075
OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA
Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]
SCTID:181277001
TAO:0000140
UBERON:0001264
UMLS:C0030274
VHOG:0000050
XAO:0000136
ZFA:0000140
galen:Pancreas
http://upload.wikimedia.org/wikipedia/commons/3/3f/Illu_pancrease.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/3/3f/Illu_pancrease.svg/200px-Illu_pancrease.svg.png
ncithesaurus:Pancreas
pancreatic
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
uberon
pelvic girdle region
FMA:16581
Note that this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list
SCTID:360010001
Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. Examples: There are only two instances, right and left pelvic girdle regions.
Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]
UBERON:0001271
UMLS:C0684083
VSAO:0000304
girdle - pelvic
ncithesaurus:Pelvic_Girdle
pelvic girdle
uberon
epithelium of stomach
BTO:0000500
EHDAA2:0001918
FMA:17091
MA:0001610
SCTID:64977002
UBERON:0001276
VHOG:0001433
epithelial tissue of stomach
epithelial tissue of ventriculus
epithelium of ventriculus
gastric epithelium
in FMA this is classified as simple columnar, MA divides this into squamous and glandular
stomach epithelial tissue
stomach epithelium
the epithelial layer of the stomach .
uberon
ventriculus epithelial tissue
ventriculus epithelium
endometrium
BTO:0001422
EFO:0000980
EMAPA:29917
EV:0100115
FMA:17742
GAID:377
MA:0000390
MAT:0000319
MESH:A05.360.319.679.490
MIAA:0000319
SCTID:278867007
Taxon notes: nimals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead. AO notes: in FMA this is subdivided into basal and outer. In MA there is a single child term, endometrium epithelium
The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG]
The mucous membrane lining the uterus. [TFD][VHOG]
UBERON:0001295
UMLS:C0014180
VHOG:0001285
endometrial
http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/6/66/Illu_cervix.jpg/200px-Illu_cervix.jpg
inner mucous membrane of the mammalian uterus.
ncithesaurus:Endometrium
tunica mucosa (endometrium)
tunica mucosa uteri
uberon
uterine endometrium
myometrium
BTO:0000907
EFO:0001970
EMAPA:29923
EV:0100116
FMA:17743
GAID:171
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]
MA:0000391
MESH:A02.633.570.500
MeSH:D009215
SCTID:279879004
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.
The muscular wall of the uterus. [TFD][VHOG]
UBERON:0001296
UMLS:C0027088
VHOG:0001281
http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/6/66/Illu_cervix.jpg/200px-Illu_cervix.jpg
middle layer of the uterine wall consisting of smooth muscle cells and supporting stromal and vascular tissue.
myometrial
ncithesaurus:Myometrium
tunica muscularis
tunica muscularis (myometrium)
uberon
uterine smooth muscle
serosa of uterus
FMA:17744
MA:0001729
Outer serosa layer of the uterus.
SCTID:253705006
TODO - check for parallel structure with peritoneum
UBERON:0001297
UMLS:C0227824
http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/6/66/Illu_cervix.jpg/200px-Illu_cervix.jpg
ncithesaurus:Perimetrium
perimetrium
serous coat of uterus
serous membrane of uterus
tunica serosa (perimetrium)
tunica serosa uteri
uberon
uterine serosa
uterus serosa
uterus serous membrane
visceral peritoneum of uterus
glans penis
BTO:0003118
EMAPA:18988
EV:0100108
FMA:18247
GAID:0000012
MA:0002726
OpenCyc:Mx4rvdCpE5wpEbGdrcN5Y29ycA
SCTID:263378009
The glans penis (or simply glans) is the sensitive bulbous structure at the distal end of the penis. It is also commonly referred to as the 'head' of the penis. The glans penis is anatomically homologous to the clitoral glans of the female. [WP,unvetted].
UBERON:0001299
UMLS:C0227948
VHOG:0001475
balanus
glans
http://upload.wikimedia.org/wikipedia/commons/1/13/Anteriorglanspenis.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/3/35/Male_anatomy.png/200px-Male_anatomy.png
ncithesaurus:Glans_Penis
uberon
epididymis
A narrow, tightly-coiled tube connecting the efferent ducts from the rear of each testicle to its vas deferens.
BTO:0000408
EFO:0000982
EMAPA:19290
EV:0100103
FMA:18255
GAID:397
MA:0000397
MAT:0000130
MESH:A05.360.444.849.286
MIAA:0000130
SCTID:181432000
Taxon notes: A similar, but probably non-homologous, structure is found in cartilaginous fishes[WP]. Kardong has epididymis in elasmobranch.Structures notes: Typically divided into three main regions. In reptiles, there is an additional canal between the testis and the head of the epididymis, which receives the various efferent ducts. This is, however, absent in all birds and mammals. The epididymis is covered by a two layered pseudostratified epithelium. The epithelium is separated by a basement membrane from the connective tissue wall which has smooth muscle cells.
UBERON:0001301
UMLS:C0014533
VHOG:0001265
epididymal
epididymus
galen:Epididymis
http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_testis_surface.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/c/c3/Illu_testis_surface.jpg/200px-Illu_testis_surface.jpg
ncithesaurus:Epididymis
uberon
tibial nerve
FMA:19035
GAID:854
MA:0001173
MESH:A08.800.800.720.450.760.820
OpenCyc:Mx4rwNya8JwpEbGdrcN5Y29ycA
SCTID:181078002
The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted].
This class was created automatically from a combination of ontologies
UBERON:0001323
UMLS:C0040186
http://upload.wikimedia.org/wikipedia/commons/1/1a/Gray828.png
http://upload.wikimedia.org/wikipedia/commons/thumb/1/1a/Gray828.png/200px-Gray828.png
medial popliteal nerve
n. tibialis
ncithesaurus:Tibial_Nerve
uberon
prepuce of penis
BTO:0001113
EFO:0001664
EMAPA:18989
EV:0100109
FMA:19639
In male human anatomy, the foreskin is a retractable double-layered fold of skin and mucous membrane that covers the glans penis and protects the urinary meatus when the penis is not erect. It is also described as the prepuce, a technically broader term that also includes the clitoral hood in women, to which the foreskin is embryonically homologous. [WP,unvetted].
MA:0000407
OpenCyc:Mx4rvVjlTZwpEbGdrcN5Y29ycA
SCTID:181426005
UBERON:0001332
UMLS:C0227952
foreskin
http://upload.wikimedia.org/wikipedia/commons/e/e6/Foreskin_CloseupV2.jpg
http://upload.wikimedia.org/wikipedia/en/thumb/c/cc/Foreskin2.jpg/200px-Foreskin2.jpg
ncithesaurus:Male_Prepuce
penile prepuce
prepuce
prepuce of male
prepucium, præputium
preputium
uberon
seminiferous tubule of testis
AAO:0010399
Any of the coiled tubules located in the testes in which spermatozoa are produced.[AAO]
BTO:0001235
EFO:0001404
EMAPA:18685
EMAPA:31476
EV:0100380
FMA:19825
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]
GAID:400
MA:0000412
MAT:0000503
MESH:A05.360.444.849.700
One of two or three twisted curved tubules in each lobule of the testis in which spermatogenesis occurs. [TFD][VHOG]
SCTID:279614002
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].
UBERON:0001343
UMLS:C0036630
UMLS:C1519236
VHOG:0001363
XAO:0003088
http://upload.wikimedia.org/wikipedia/commons/4/49/Seminiferous_tubule_and_sperm_low_mag.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/6/6a/Gray1145.png/200px-Gray1145.png
ncithesaurus:Seminiferous_Cord
ncithesaurus:Seminiferous_Tubule
seminiferous cord
seminiferous tubule
testis - seminiferous tubule
tubuli seminiferi
tubuli seminiferi
uberon
white adipose tissue
Adipose tissue, cells of which contain a single large lipid droplet.[FMA]
BTO:0001456
EFO:0000813
FMA:20117
MA:0000058
MAT:0000199
MIAA:0000199
This class was created automatically from a combination of ontologies
UBERON:0001347
UMLS:C1704223
adipocytus unigutturalis
ncithesaurus:White_Adipose_Tissue
textus adiposus albus
textus adiposus albus
uberon
unilocular adipose tissue
white fat
brown adipose tissue
Adipose tissue, cells of which contain multiple small lipid droplets.[FMA]
BTO:0000156
EFO:0000812
EMAPA:19209
FMA:20118
GAID:921
MA:0000057
MAT:0000198
MESH:A10.165.114.322
MIAA:0000198
SCTID:15965003
This class was created automatically from a combination of ontologies
UBERON:0001348
UMLS:C0006298
adipocytus multigutturalis
brown fat
http://upload.wikimedia.org/wikipedia/commons/6/69/Brownfat_PETCT.jpg
multilocular adipose tissue
ncithesaurus:Brown_Adipose_Tissue
textus adiposus fuscus
textus adiposus fuscus
uberon
anal region
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]
EFO:0000847
EHDAA2:0000122
EHDAA:2931
EMAPA:16831
MA:0000329
MAT:0000042
MIAA:0000042
SCTID:362680001
The anus and surrounding regions. Encompasses both internal and external regions, where present
UBERON:0001353
UMLS:C0230120
VHOG:0000395
WBbt:0006919
http://upload.wikimedia.org/wikipedia/commons/thumb/f/fb/Gray408.png/200px-Gray408.png
ncithesaurus:Anal_Region
uberon
muscle of leg
A muscle that is part of the region of the hindlimb between the pelvis and ankle.
BTO:0000722
MA:0000672
Terminology notes: see notes on UBERON:0000978 for possible confusion over the term 'leg'.
UBERON:0001383
leg muscle
leg muscle organ
muscle of hindlimb zeugopod or stylopod
muscle of thigh or crus
muscle of upper or lower hindlimb segment
muscle of upper/lower leg
muscle organ of leg
uberon
tibialis anterior
BTO:0001382
EFO:0001385
FMA:22532
In human anatomy, the tibialis anterior is a muscle that originates in the upper two-thirds of the lateral surface of the tibia and inserts into the medial cuneiform and first metatarsal bones of the foot. Its acts to invert the foot. It is situated on the lateral side of the tibia; it is thick and fleshy above, tendinous below. This muscle overlaps the anterior tibial vessels and deep peroneal nerve in the upper part of the leg. [WP,unvetted]. The M. tibialis cranialis is a muscle that flexes the tarsometatarsus. It originates on the craniodistal aspect of the femur and proximal tibiotarsus and inserts on the cranial surface of the tarsometarsus[EvoWiki].
MA:0002395
SCTID:181696007
This class was created automatically from a combination of ontologies
UBERON:0001385
UMLS:C1710423
anterior tibialis
galen:TibialisAnterior
http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray1240.png
http://upload.wikimedia.org/wikipedia/commons/thumb/9/9c/Gray1240.png/200px-Gray1240.png
ibialis anticus
musculus tibialis anterior
ncithesaurus:Tibialis_Cranialis
tibialis anterior muscle
tibialis cranialis
tibilais cranialis
uberon
gastrocnemius
A muscle of the shank. In mammals it has two heads[Kardong]. It runs from its two heads just above the knee to the heel, and is involved in standing, walking, running and jumping. Along with the soleus muscle it forms the calf muscle. [WP].
BTO:0000506
EFO:0001413
EHDAA2:0000701
EHDAA:8293
FMA:22541
MA:0002306
SCTID:181700004
The most prominent ventral muscle of the shank is the gastrocnemius, the 'calf' muscle. In mammals, it has two heads, resulting from the fusion of two different phylogenetic predecessors.[well established][VHOG]
The most superficial calf muscle in the posterior part of the leg. [TFD][VHOG]
UBERON:0001388
UMLS:C0242691
VHOG:0001193
galen:Gastrocnemius
gastrocnemius muscle
http://upload.wikimedia.org/wikipedia/commons/8/8e/Gastrocnemius.png
http://upload.wikimedia.org/wikipedia/commons/thumb/8/8e/Gastrocnemius.png/200px-Gastrocnemius.png
m. gastrocnemius
m.gastrocnemius
musculus gastrocnemius
ncithesaurus:Gastrocnemius_Muscle
uberon
soleus muscle
BTO:0001265
EFO:0001946
FMA:22542
MA:0002424
SCTID:181702007
This class was created automatically from a combination of ontologies
UBERON:0001389
UMLS:C0242694
a powerful muscle in the back part of the lower leg (the calf). It runs from just below the knee to the heel, and is involved in standing and walking. It is closely connected to the gastrocnemius muscle and some anatomists consider them to be a single muscle, the triceps surae. Its name is derived from the solefish whose shape it resembles. The soleus is located in the superficial posterior compartment of the leg. Not all mammals have a soleus muscle; one familiar species that lacks the soleus is the dog.
galen:Soleus
http://upload.wikimedia.org/wikipedia/commons/5/57/Illu_lower_extremity_muscles.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/5/57/Illu_lower_extremity_muscles.jpg/200px-Illu_lower_extremity_muscles.jpg
ncithesaurus:Soleus
soleal
soleus
uberon
skeletal system
AAO:0000566
Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]
BTO:0001486
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]
EFO:0000806
EHDAA2:0003168
FMA:23881
MA:0000018
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
OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA
Organ system subdivision which consists of the skeleton and the articular system.[FMA]
Skelettsystem
System that provides physical support to the organism.[AAO]
TAO:0000434
UBERON:0001434
UMLS:C0037253
VHOG:0001254
VSAO:0000027
XAO:0003060
ZFA:0000434
http://purl.obolibrary.org/obo/uberon/references/reference_0000025
ncithesaurus:Skeletal_System
set of all bones and joints
skeletal
skeleton system
uberon
epiphysis
AAO:0000742
BTO:0000413
Cartilaginous expansion at the distal end of an anterior rib or transverse process that serves for the attachment of muscles suspending the pectoral girdle to the vertebral column.[AAO]
FMA:24012
MA:0001362
MESH:A02.835.232.251
SCTID:244701002
Subdivision of long bone which forms its expanded proximal or distal articular end; together with other the subdivisions of long bone, it constitutes the long bone. Examples: proximal epiphysis of humerus, distal epiphysis of femur.[FMA]
UBERON:0001437
UMLS:C1708734
end of long bone
epiphyseal
epiphyses
epiphysial
http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/9/94/Illu_long_bone.jpg/200px-Illu_long_bone.jpg
long bone epiphysis
ncithesaurus:Long_Bone_Epiphysis
see also: annular epiphysis
uberon
metaphysis
FMA:24014
MA:0001363
SCTID:304581004
Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA]
UBERON:0001438
UMLS:C0222671
adjacent to or containing epiphyseal plate? Note in FMA the metaphysis is part of the diaphysis, but not in MA. In the diagram in WP, it appears to be adjacent, not part_of.
diaphyseal end of long bone
long bone metaphysis
metaphyses
ncithesaurus:Metaphysis
uberon
hindlimb skeleton
AAO:0000217
EHDAA2:0002226
FMA:24144
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
OpenCyc:Mx4rvZcKkZwpEbGdrcN5Y29ycA
Skeletal structure of the paired, posterior appendages.[AAO]
Subdivision of skeleton consisting of all skeletal elements in an hindlimb region.
TOOD - find a home for: FMA:24140
UBERON:0001441
VHOG:0001255
VSAO:0000152
XAO:0003062
bones of lower limb
free lower limb skeleton
hind limb skeleton
hind-limb skeleton
hindlimb skeleton
lower limb skeleton
ossa membri inferioris
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
set of bones of lower limb
skeleton of free lower limb
skeleton of lower limb
uberon
chest
BTO:0001368
EFO:0000965
EV:0100010
FMA:9576
GAID:91
MA:0000031
MAT:0000295
MESH:A01.911
MIAA:0000295
OpenCyc:Mx4rvVikFZwpEbGdrcN5Y29ycA
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].
UBERON:0001443
UMLS:C0817096
UMLS:C1527391
anterior chest
anterior thoracic region
anterolateral part of thorax
editor note - FMA:24216 present in FMA1, but gone in subsequent versions
front of chest
front of thorax
galen:Chest
galen:Thorax
http://upload.wikimedia.org/wikipedia/commons/d/db/Chest.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Chest.jpg/200px-Chest.jpg
ncithesaurus:Chest
ncithesaurus:Thorax
pectus
thoracic body wall
thorax
uberon
ventral part of thoracic region
subdivision of head
FMA:24218
SCTID:123852005
This class was created automatically from a combination of ontologies
UBERON:0001444
XAO:0000040
head region
head subdivision
region of head
uberon
skeleton of pes
EHDAA2:0002228
FMA:24222
Subdivision of skeleton that is the collection of all skeletal elements in a pes, which is the distal section of the posterior hindlimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the ankle, sole, and toes)[Phenoscape].
UBERON:0001445
VSAO:0005021
foot region skeleton
foot skeleton
here 'pes' includes both the ankle region and foot proper
http://purl.obolibrary.org/obo/uberon/references/reference_0000015
pedal skeleton
pes
pes skeleton
posterior autopodium
posterior autopodium skeleton
set of bones of foot
skeleton of foot
uberon
fibula
AAO:0000891
BTO:0002346
EFO:0003052
EMAPA:18512
EMAPA:19141
FMA:24479
GAID:202
MA:0001360
MESH:A02.835.232.500.321
One of the two long bones of endochondral origin of the hind-epipodium; it is a rather more slender bone than the tibia but of about the same length.[AAO]
SCTID:302529003
The major postaxial endochondral bone in the posterior zeugopod[Phenoscape].
UBERON:0001446
UMLS:C0016068
fibular
galen:Fibula
http://upload.wikimedia.org/wikipedia/commons/1/16/Illu_lower_extremity.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/1/16/Illu_lower_extremity.jpg/200px-Illu_lower_extremity.jpg
ncithesaurus:Fibula
uberon
tarsal bone
A bone that is part of the tarsal skeleton. Examples: calcaneus, talus, centralia.
BTO:0002343
FMA:24491
GAID:194
In primitive tetrapods, such as Trematops, the tarsus consists of three rows of bones. There are three proximal tarsals, the tibiale, intermedium, and fibulare, named for their points of articulation with the bones of the lower limb. These are followed by a second row of four bones, referred to as the centralia (singular: centrale), and then a row of five distal tarsals, each articulating with a single metatarsal. In the great majority of tetrapods, including all of those alive today, this simple pattern is modified by the loss and fusion of various of the bones.[3] In reptiles and mammals, there are normally just two proximal tarsals, the calcaneus (equivalent to the amphibian fibulare) and the talus (probably derived from a fusion of multiple bones). In mammals, including humans, the talus forms a hinge joint with the tibia, a feature especially well developed in the artiodactyls. The calcaneus is also modified, forming a heel for the attachment of the Achilles tendon. Neither of these adaptations is found in reptiles, which have a relatively simple structure to both bones.[3] The fifth distal tarsal disappears relatively early in evolution, with the remainder becoming the cuneiform and cuboid bones. Reptiles usually retain two centralia, while mammals typically have only one (the navicular).[3] In birds, the tarsus has disappeared, with the proximal tarsals having fused with the tibia, the centralia having disappeared, and the distal bones having fused with the metatarsals to form a single tarsometatarsus bone, effectively giving the leg a third segment[Wikipedia:Tarsus_(skeleton)]
MA:0000297
MESH:A02.835.232.300.710
SCTID:108372004
UBERON:0001447
UMLS:C0039316
ankle bone
bone of ankle
bone of tarsus
bony tarsus
galen:TarsalBone
hind mesopodium
http://upload.wikimedia.org/wikipedia/commons/thumb/b/bf/Ankle_en.svg/200px-Ankle_en.svg.png
ncithesaurus:Tarsal_Bone
ossa tarsalia
ossa tarsi
tarsal
tarsus osseus
uberon
metatarsal bone
BTO:0002347
FMA:24492
GAID:193
MA:0000303
MESH:A02.835.232.300.492
SCTID:302532000
The metatarsus or metatarsal bones are a group of five long bones in the pes located between the tarsal bones of the hind- and mid-pes and the phalanges of the toes. Lacking individual names, the metatarsal bones are numbered from the medial side (side of big toe): the first, second, third, fourth, and fifth metatarsal. The metatarsals are analogous to the metacarpal bones of the manus. [WP,unvetted].
UBERON:0001448
UMLS:C0025584
galen:Metatarsal
http://upload.wikimedia.org/wikipedia/commons/thumb/5/52/Gray291.png/200px-Gray291.png
metatarsal
ncithesaurus:Metatarsal_Bone
ossa metatarsalia
ossa metatarsi
uberon
phalanx of pes
A phalanx that is part of a hindlimb autopod[Automatically generated definition].
AAO:0000930
Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the five digits of the pes. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the pes, in a medial to lateral sequence, is 2(1)-2-3-4(3)-3(2).[AAO]
FMA:24493
MA:0000305
SCTID:302533005
UBERON:0001449
UBERON:0004272
UMLS:C0584876
digital bone of pes
digitus pedis phalanx
foot digit phalanx
foot phalanx
ncithesaurus:Foot_Phalanx
ncithesaurus:Phalanx_of_the_Foot
pedal phalanx
phalanges of hind digit
phalanx of digit of foot
phalanx of digitus pedis
phalanx of foot digit
phalanx of hind digit
phalanx of pes
phalanx of toe
toe phalanx
uberon
calcaneus
BTO:0002355
EMAPA:18501
EMAPA:19134
FMA:24496
MA:0001348
MESH:A02.835.232.300.710.300
SCTID:182099002
The postaxial bone of the proximal tarsals series[Phenoscape].
UBERON:0001450
UMLS:C0006655
VSAO:0005016
calcaneal
calcaneal bone
calcaneum
fibulare
galen:Calcaneum
http://upload.wikimedia.org/wikipedia/commons/a/a9/Subtalar_Joint.PNG
http://upload.wikimedia.org/wikipedia/commons/thumb/a/a9/Subtalar_Joint.PNG/200px-Subtalar_Joint.PNG
ncithesaurus:Calcaneum
os calcis
os tarsi fibulare
synonymous with the fibulare of basal tetrapods.
uberon
navicular bone of pes
AAO:0000924
BTO:0002356
FMA:24499
MA:0001349
OpenCyc:Mx4rv67esJwpEbGdrcN5Y29ycA
Oval tarsal element that is located on the center of the mesopodium. It articulates with all other elements of the tarsus except tarsal 5.[AAO]
SCTID:182100005
The navicular bone is one of the tarsal bones, found in the pes. It is located on the medial side of the pes, and articulates proximally with the talus, distally with the three cuneiform bones, and occasionally laterally with the cuboid[WP].
UBERON:0001451
UMLS:C0223947
central tarsal bone
centrale
centrale (hind)
galen:Navicular
http://upload.wikimedia.org/wikipedia/commons/8/81/Gray276.png
http://upload.wikimedia.org/wikipedia/commons/thumb/8/81/Gray276.png/200px-Gray276.png
navicular
navicular bone of foot
navicular of foot
navicular of pes
ncithesaurus:Navicular_Bone
os naviculare
os naviculare
os naviculare pedis
taxon notes: connections vary depending on species. AAO: Oval tarsal element that is located on the center of the mesopodium. It articulates with all other elements of the tarsus except tarsal 5. In humans: there is a cuboid instead of distal tarsal 4 and 5 - may articulate laterally with the cuboid[WP]. TODO - add correct VSAO xref (currently broken)
uberon
distal tarsal bone 1
AAO:0000918
BTO:0002360
Endochondral tarsal bone articulating with centralia and metatarsal 1.
FMA:24518
MA:0001352
OpenCyc:Mx4rvYtfH5wpEbGdrcN5Y29ycA
SCTID:182116007
Small element that articulates with the prehallux, metatarsal I and element Y. It may be fused to tarsal 2.[AAO]
UBERON:0001452
UMLS:C1512869
VSAO:0005052
cuneiforme 1
distal tarsal 1
entocuneiforme
first cuneiform
first cuneiform bone
foot distal carpal bone 1
galen:MedialCuneiform
http://palaeos.com/vertebrates/glossary/images/450x218xEctocuneiform.gif.pagespeed.ic.kaiuLYQELL.png
http://upload.wikimedia.org/wikipedia/commons/8/81/Gray290.png
http://upload.wikimedia.org/wikipedia/commons/thumb/8/81/Gray290.png/200px-Gray290.png
medial cuneiform
medial cuneiform bone
ncithesaurus:Internal_Cuneiform_Bone_of_the_Foot
os cuneiform primum
os cuneiforme mediale
os cuneiforme mediale
os cuneiforme primum
ossa cuneiforme mediale
tarsal 1
uberon
face
BTO:0003369
FMA:24728
GAID:64
HAO:0000316
MA:0002473
MESH:A01.456.505
OpenCyc:Mx4rvVi5GZwpEbGdrcN5Y29ycA
SCTID:302549007
Subdivision of head which consists of the facial skeleton and all layers superficial to it[FMA,modified].
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]
UBERON:0001456
UMLS:C0015450
facia/facies
facial
galen:Face
http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/5/55/Mona_Lisa_headcrop.jpg/200px-Mona_Lisa_headcrop.jpg
ncithesaurus:Face
uberon
visage
skin of lip
A zone of skin that is part of a lip [Automatically generated definition].
FMA:24764
MA:0001579
SCTID:244092005
UBERON:0001458
UMLS:C0222101
lip skin
lip zone of skin
ncithesaurus:Skin_of_the_Lip
skin of lips
uberon
zone of skin of lip
hip
AO notes. See notes for shoulder. in BTO this is part of the abdomen - this creates an inconsistency if limb and abdomen are spatially disjoint
BTO:0001457
EFO:0001929
EHDAA2:0000783
EHDAA:5153
EHDAA:6178
EMAPA:17490
FMA:24964
GAID:47
MA:0000045
MESH:A01.378.610.400
OpenCyc:Mx4rvVjhy5wpEbGdrcN5Y29ycA
SCTID:302543008
The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,modified].
The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]
UBERON:0001464
UMLS:C0019552
VHOG:0000346
coxa
coxal
galen:Hip
hip region
http://upload.wikimedia.org/wikipedia/commons/9/9f/Hip.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/9/9f/Hip.jpg/200px-Hip.jpg
ncithesaurus:Hip
regio coxae
uberon
knee
A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod.
BTO:0003595
EFO:0001957
EHDAA2:0000895
EHDAA:5159
EHDAA:6184
EMAPA:17493
FMA:24974
GAID:48
MA:0000046
MESH:A01.378.610.450
OpenCyc:Mx4rvVjPKZwpEbGdrcN5Y29ycA
SCTID:361291001
UBERON:0001465
VHOG:0000347
galen:Knee
http://upload.wikimedia.org/wikipedia/commons/thumb/8/8d/Male_Knee_by_David_Shankbone.jpg/200px-Male_Knee_by_David_Shankbone.jpg
knee region
uberon
pedal digit
A digit that is part of a pes (foot).
AAO:0000888
BTO:0002348
FMA:25046
GAID:44
MA:0000048
One of the toes of the pes.[AAO]
OpenCyc:Mx4rvVjCHZwpEbGdrcN5Y29ycA
SCTID:116667001
UBERON:0000027
UBERON:0001466
UMLS:C0040357
XAO:0003035
digit of foot
digit of terminal segment of lower limb
digiti pedis
digiti pedis
digitipedis
digitus pedis
foot digit
galen:Toe
hind digit
hind_digit
hindlimb digit
http://upload.wikimedia.org/wikipedia/commons/5/5e/Toes.jpg
ncithesaurus:Toe
toe
uberon
lymphatic vessel
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]
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].
A vessel that contains or conveys lymph.[AAO]
AAO:0011005
BTO:0000752
EFO:0000873
FMA:30315
MA:0000138
MAT:0000443
OpenCyc:Mx4rwA1fYZwpEbGdrcN5Y29ycA
SCTID:279089004
TAO:0005105
Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG]
UBERON:0001473
UMLS:C0229889
VHOG:0001249
XAO:0000375
http://upload.wikimedia.org/wikipedia/commons/4/44/Illu_lymph_capillary.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/4/44/Illu_lymph_capillary.jpg/200px-Illu_lymph_capillary.jpg
lymph vessel
ncithesaurus:Lymphatic_Vessel
uberon
vas lymphaticum
bone
AAO:0000047
AEO:0000082
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]
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]
BTO:0000140
EFO:0000298
EHDAA2:0003082
ENVO:00002039
EV:0100140
FMA:30317
FMA:5018
GAID:92
MA:0001459
MAT:0000299
MIAA:0000299
OpenCyc:Mx4rvViDlpwpEbGdrcN5Y29ycA
OpenCyc:Mx4rvVkCG5wpEbGdrcN5Y29ycA
Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
SCTID:90780006
Skeletal element that is composed of bone tissue.[VSAO]
Skeletal element that is composed of bone tissue[VSAO].
TAO:0001514
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]
UBERON:0001474
UMLS:C0262950
VHOG:0001190
VSAO:0000057
XAO:0000169
ZFA:0001514
bone element
bone organ
galen:Bone
ncithesaurus:Bone
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
uberon
sesamoid bone
AEO:0000086
EHDAA2:0003086
FMA:32672
GAID:210
MA:0001375
MESH:A02.835.232.730
Ossicle that develops within bands of dense, regular connective tissue (e.g., tendons and ligaments). Sesamoids are generally located proximate to a bony prominence, over which the dense regular connective tissue wraps, and/or a joint or articulation.
SCTID:362914002
Sesamoids are often endochondral replacement elements and in addition to bone tissue, may also be composed of articular cartilage, fibrocartilage, hyaline cartilage, and calcified cartilage.[VSAO]
UBERON:0001479
UMLS:C0036846
VSAO:0000137
galen:SessamoidBone
http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray350.png
http://upload.wikimedia.org/wikipedia/commons/thumb/b/b3/Gray350.png/200px-Gray350.png
ncithesaurus:Sesamoid_Bone
ossa sesamoidea
sesamoid
uberon
knee joint
EFO:0001957
EMAPA:19137
FMA:35175
GAID:114
MA:0000471
MESH:A02.835.583.475
OpenCyc:Mx4rwCuaYZwpEbGdrcN5Y29ycA
SCTID:182204005
The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation. Since in humans the knee supports nearly the whole weight of the body, it is the joint most vulnerable both to acute injury and the development of osteoarthritis. [WP,unvetted].
UBERON:0001485
UMLS:C0022745
VHOG:0001003
articulatio genus
galen:KneeJoint
http://upload.wikimedia.org/wikipedia/commons/c/ca/Knee.agr.jpg
joint of knee
ncithesaurus:Knee_Joint
uberon
descending aorta
Development notes: results from fusion of left and right dorsal aortae
EMAPA:18605
FMA:3784
MA:0002571
OpenCyc:Mx4rv4EE35wpEbGdrcN5Y29ycA
SCTID:261399002
The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted].
UBERON:0001514
UMLS:C0011666
aorta descendens
http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/e/e6/Gray506.svg/200px-Gray506.svg.png
ncithesaurus:Descending_Aorta
pars descendens aortae
pars descendens aortae, aorta descendens
uberon
thoracic aorta
BTO:0000157
EFO:0002525
EMAPA:18603
FMA:3786
GAID:471
MA:0002569
MESH:A07.231.114.056.372
OpenCyc:Mx4rveb9TpwpEbGdrcN5Y29ycA
SCTID:302510009
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].
UBERON:0001515
UMLS:C1522460
aorta thoracalis
galen:ThoracicAorta
http://upload.wikimedia.org/wikipedia/commons/7/75/Gray530.png
http://upload.wikimedia.org/wikipedia/commons/thumb/7/75/Gray530.png/200px-Gray530.png
ncithesaurus:Thoracic_Aorta
pars thoracica aortae
thoracic part of aorta
uberon
abdominal aorta
Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted].
BTO:0002976
EFO:0002524
EMAPA:17856
EMAPA:18607
Editors note: Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates
FMA:3789
GAID:470
MA:0000474
MESH:A07.231.114.056.205
OpenCyc:Mx4rvYhWCZwpEbGdrcN5Y29ycA
SCTID:244231007
UBERON:0001516
UMLS:C0003484
abdominal part of aorta
abdominal part of aorta
aorta abdominalis
descending abdominal aorta
galen:AbdominalAorta
http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png
http://upload.wikimedia.org/wikipedia/commons/thumb/a/af/Gray531.png/200px-Gray531.png
ncithesaurus:Abdominal_Aorta
pars abdominalis aortae
pars abdominalis aortae
pars abdominalis aortae, aorta abdominalis
uberon
digestive tract
AAO:0010023
BILA:0000083
BTO:0000511
BTO:0000545
EHDAA2:0000726
EHDAA:518
EMAPA:16247
FBbt:00003125
FMA:45615
OpenCyc:Mx4rvVi0GpwpEbGdrcN5Y29ycA
TAO:0000112
TGMA:0001819
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.
The alimentary or digestive tract, and associated organs.[TAO]
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]
Tube extending from the mouth to the anus.
UBERON:0001555
UMLS:C0017189
VHOG:0000309
WBbt:0005743
ZFA:0000112
alimentary canal
digestive tube
enteric tract
galen:AlimentaryTract
gut
gut tube
ncithesaurus:Gastrointestinal_Tract
uberon
lower urinary tract
FMA:45659
MA:0002636
SCTID:181420004
Subdivision of urinary system which consists of the urinary bladder and the urethra.
UBERON:0001556
galen:LowerUrinaryTract
uberon
upper respiratory tract
EHDAA2:0002136
EMAPA:17669
FMA:45661
MA:0000442
OpenCyc:Mx4rtT2HwgJMEdyAAADggVbxzQ
SCTID:361381009
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]
Subdivision of respiratory system which consists of the nose, nasopharynx, oropharynx and larynx[FMA]
UBERON:0001557
VHOG:0000406
http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/c/c3/Illu_conducting_passages.jpg/200px-Illu_conducting_passages.jpg
uberon
lower respiratory tract
EHDAA2:0001036
EMAPA:16738
FMA:45662
MA:0000435
OpenCyc:Mx4rQRqjUgAKEdyHxgDggVfs8g
SCTID:281488008
The segment of respiratory tract from the trachea to the lungs[WP,modified]
UBERON:0001558
VHOG:0000382
http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/c/c3/Illu_conducting_passages.jpg/200px-Illu_conducting_passages.jpg
uberon
neck of organ
FMA:45733
UBERON:0001560
organ neck
uberon
cheek
BTO:0001754
Cheeks constitute the area of the face below the eyes and between the nose and the left or right ear. It is fleshy in humans and other mammals, the skin being suspended by the chin and the jaws, and forming the lateral wall of the human mouth, visibly touching the cheekbone below the eye. In vertebrates, markings on the cheek area (malar stripes/spots/... ), particularly immediately beneath the eye, often serve as important distinguishing features between species or individuals. 'Buccal' means relating to the cheek. In humans, the region is innervated by the buccal nerve. The inside of the cheek (forming part of the mouth cavity) is lined with a mucous membrane. It is the most common location from which a DNA sample can be taken (during a cheek swab). The cheeks are covered externally by hairy skin, and internally by stratified squamous epithelium. This is mostly smooth, but may have aborally directed papillae . The mucosa is supplied with secretions from the Buccal glands, which are arranged in superior and inferior groups. In carnivores, the superior buccal gland is large and discrete: the Zygomatic gland. During mastication (chewing), the cheeks and tongue between them serve to keep the food between the teeth. [WP,unvetted].
FMA:46476
GAID:65
MA:0002475
MESH:A01.456.505.173
OpenCyc:Mx4rvVi5WZwpEbGdrcN5Y29ycA
SCTID:182325008
Surface structure that includes the scales, skin, and muscles that are located ventral and posterior to the eye.[TAO]
TAO:0002113
UBERON:0001567
UMLS:C0007966
buccae
buccal
galen:Cheek
http://upload.wikimedia.org/wikipedia/commons/thumb/a/a9/Chica_cachetona.jpg/200px-Chica_cachetona.jpg
jowl
ncithesaurus:Cheek
uberon
muscle organ
AAO:0011066
EV:0100146
FMA:5022
GAID:131
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]
MA:0000015
OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA
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].
Portion of tissue composed of contractile fibers.[TAO]
SCTID:71616004
TAO:0005145
UBERON:0001630
VHOG:0001245
XAO:0000172
ZFA:0005145
galen:Muscle
muscle
muscular
uberon
artery
AAO:0010211
AEO:0000208
An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
BTO:0000573
EFO:0000814
EHDAA2:0000143
EHDAA2:0003253
EV:0100026
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.
FMA:50720
GAID:468
MA:0000064
MAT:0000034
MESH:A07.231.114
MIAA:0000034
OpenCyc:Mx4rvVjknZwpEbGdrcN5Y29ycA
Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]
SCTID:362877004
TAO:0000005
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]
UBERON:0001637
UMLS:C0003842
VHOG:0001251
XAO:0000114
ZFA:0000005
arterial
arterial subtree
arterial system
arterial tree organ part
arterial vessel
arteries
galen:Artery
ncithesaurus:Artery
uberon
vein
AAO:0010212
AEO:0000209
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
BTO:0000234
EFO:0000816
EHDAA2:0003254
EV:0100031
FMA:50723
GAID:492
MA:0000067
MAT:0000037
MESH:A07.231.908
MIAA:0000037
OpenCyc:Mx4rvVjkWpwpEbGdrcN5Y29ycA
Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]
SCTID:181367001
TAO:0000082
TODO - check with MA - vein vs venous blood vessel
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]
UBERON:0001638
UMLS:C0042449
VHOG:0001252
VHOG:0001743
XAO:0000115
ZFA:0000082
galen:Vein
http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/c/c2/Venous_system_en.svg/200px-Venous_system_en.svg.png
ncithesaurus:Vein
uberon
vena
venae
venous subtree
venous tree organ part
venous vessel
trochlear nerve
AAO:0010469
BM:IVN
CN-IV
Cranial nerve that runs to the eye muscles.
EHDAA2:0002090
EMAPA:18218
FMA:50865
GAID:838
MA:0001105
MESH:A08.800.800.120.800
NIF_GrossAnatomy:birnlex_1654
OpenCyc:Mx4rvyeBQ5wpEbGdrcN5Y29ycA
SCTID:180939009
Somatic efferent nerve which supplies a single eye muscle, the m. obliquus superior.[AAO]
TAO:0000600
This class was created automatically from a combination of ontologies
Trochlear nerve [IV]
UBERON:0001644
UMLS:C0041159
VHOG:0000705
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]
XAO:0003091
ZFA:0000600
cranial nerve IV
fourth cranial nerve
http://upload.wikimedia.org/wikipedia/commons/3/33/Trochlear_nerve.png
http://upload.wikimedia.org/wikipedia/commons/thumb/3/33/Trochlear_nerve.png/200px-Trochlear_nerve.png
ncithesaurus:Trochlear_Nerve
nervus trochlearis
nervus trochlearis [iv]
pathetic nerve
superior oblique nerve
trochlear
trochlear IV nerve
trochlear nerve tree
uberon
triceps surae
A set of muscles in FMA, a single organ in MA
FMA:51062
MA:0002400
The triceps surae is a pair of muscles located at the calf - the gastrocnemius and the soleus. These muscles both insert into the calcaneus, the bone of the heel of the human foot, and form the major part of the muscle of the back part of the lower leg, commonly known as the calf muscle. The triceps surae is connected to the foot through the Achilles tendon, and has 3 heads deriving from the 2 major masses of muscle. The superficial portion (the gastrocnemius) gives off 2 heads attaching to the base of the femur directly above the knee. The deep (profundis) mass of muscle (the soleus) forms the remaining head which attaches to the superior posterior area of the tibia. The triceps surae is innervated by the tibial nerve, specifically, nerve roots L5–S2. [WP,unvetted].
UBERON:0001665
UMLS:C0224458
calf muscle
gastrosoleus
gastrosoleus complex
http://upload.wikimedia.org/wikipedia/commons/5/57/Illu_lower_extremity_muscles.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/5/57/Illu_lower_extremity_muscles.jpg/200px-Illu_lower_extremity_muscles.jpg
musculus triceps surae
ncithesaurus:Triceps_Surae
sural triceps
uberon
tibialis posterior
BTO:0000867
FMA:51099
MA:0002394
SCTID:361824007
The Tibialis posterior is the most central of all the leg muscles, and is located in the posterior compartment of the leg. It is the key stabilizing muscle of the lower leg. [WP,unvetted].
This class was created automatically from a combination of ontologies
UBERON:0001667
UMLS:C1711425
http://upload.wikimedia.org/wikipedia/commons/9/92/Gray442.png
http://upload.wikimedia.org/wikipedia/commons/thumb/9/92/Gray442.png/200px-Gray442.png
ibialis posticus
musculus tibialis posterior
ncithesaurus:Tibialis_Caudalis
posterior tibialis
tibialis caudalis
tibialis posterior muscle
uberon
mandible
A dentary bone that is the only bone in one of the lateral halves of the lower jaw skeleton.
BTO:0001748
EFO:0001965
EHDAA2:0001059
EHDAA:8007
EMAPA:18290
Editor notes: consider merging with dentary - for now we make it a mammal-specific subclass. Terminology notes: 'mandible' also refers to either the upper OR lower part of the beak in birds. AO notes: Note in ZFA 'mandible' is a syn for the ventral mandibular arch, which is a portion of the 1st pharyngeal arch; however the term 'mandibular symphysis' refers to the dentary
FMA:52748
GAID:68
MA:0001487
MESH:A02.835.232.781.324.502.632
SCTID:181812008
UBERON:0001684
UMLS:C0024687
galen:Mandible
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png
http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Gray176.png/200px-Gray176.png
inferior maxillary bone
lower jaw
lower jaw bone
lower mandibula
mammaliam mandible
mandibula
mandibular
mandibular series
mandibulla
ncithesaurus:Mandible
uberon
nasal cavity
AAO:0000314
BTO:0002096
Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.[well established][VHOG]
EHDAA2:0001226
EHDAA:6801
EMAPA:17604
FMA:54378
GAID:350
MA:0000284
MESH:A04.531.449
SCTID:263481003
Saclike space internal to the nasal capsule lined by respiratory and sensory epithelium and glandular tissue.[AAO]
TAO:0000130
UBERON:0001707
UMLS:C0027423
VHOG:0000271
ZFA:0000130
a large air filled space above and behind the nose in the middle of the face[WP].
cavitas nasalis
cavitas nasi
cavity of nose
cavum nasi; cavitas nasi
http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/d/d4/Illu01_head_neck.jpg/200px-Illu01_head_neck.jpg
nasal canal
nasal fossa
nasal pit
ncithesaurus:Nasal_Cavity
olfactory cavity
olfactory pit
the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures[HP]
uberon
jaw skeleton
AAO:0000988
BTO:0001749
FMA:54396
GAID:214
MA:0001905
MESH:A02.835.232.781.324.502
OpenCyc:Mx4rvVjjEZwpEbGdrcN5Y29ycA
SCTID:181811001
Skeletal and cartilaginous elements of the first pharyngeal arch.[TAO]
Subdivision of skeleton which includes upper and lower jaw skeletons.
TAO:0001227
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).
UBERON:0001708
UMLS:C0022359
ZFA:0001227
anterior splanchnocranium
galen:Jaw
jaw
jaw cartilage
jaws
mandibular arch
mandibular arch skeleton
ncithesaurus:Jaw
oral jaw skeleton
pharyngeal arch 1 skeleton
uberon
visceral arch 1
lower jaw region
AAO:0000272
AO notes: Note isa/partof difference MA/FMA. See notes for jaw w.r.t skeletal element vs subdivision of head
EFO:0003660
EHDAA2:0001018
EHDAA:7995
EMAPA:17906
FMA:59398
Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO]
MESH:A02.835.232.781.324.502.632
SCTID:362637005
Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].
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]
UBERON:0001710
VHOG:0000453
http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Gray176.png/200px-Gray176.png
mandibular part of mouth
mandibular series
ncithesaurus:Lower_Jaw
uberon
oculomotor nuclear complex
ABA:III
BM:MB-III
EFO:0002468
EHDAA2:0004211
EV:0100250
FMA:54510
MA:0001073
NIF_GrossAnatomy:birnlex_1240
SCTID:362457000
TAO:0000553
The fibers of the oculomotor nerve arise from a nucleus in the midbrain, which lies in the gray substance of the floor of the cerebral aqueduct and extends in front of the aqueduct for a short distance into the floor of the third ventricle. From this nucleus the fibers pass forward through the tegmentum, the red nucleus, and the medial part of the substantia nigra, forming a series of curves with a lateral convexity, and emerge from the oculomotor sulcus on the medial side of the cerebral peduncle. The nucleus of the oculomotor nerve does not consist of a continuous column of cells, but is broken up into a number of smaller nuclei, which are arranged in two groups, anterior and posterior. Those of the posterior group are six in number, five of which are symmetrical on the two sides of the middle line, while the sixth is centrally placed and is common to the nerves of both sides. The anterior group consists of two nuclei, an antero-medial and an antero-lateral . The nucleus of the oculomotor nerve, considered from a physiological standpoint, can be subdivided into several smaller groups of cells, each group controlling a particular muscle. A nearby nucleus, the Edinger-Westphal nucleus, is responsible for the autonomic functions of the oculomotor nerve, including pupillary constriction and lens accommodation. [WP,unvetted].
This class was created automatically from a combination of ontologies
UBERON:0001715
UMLS:C0228686
VHOG:0001389
ZFA:0000553
http://upload.wikimedia.org/wikipedia/commons/thumb/d/da/Cn3nucleus.png/200px-Cn3nucleus.png
motor nucleus III
nIII
ncithesaurus:Oculomotor_Nucleus
nucleus nervi oculomotorii
nucleus of oculomotor nerve
nucleus of third cranial nerve
oculomotor III nucleus
oculomotor nucleus
third cranial nerve nucleus
uberon
tongue
A mobile mass of muscular tissue that is covered with mucous membrane, occupies much of the cavity of the mouth, forms part of its floor, bears the organ of taste, and assists in chewing and swallowing. [TFD][VHOG]
AAO:0010360
BTO:0001385
EFO:0000833
EHDAA2:0002062
EHDAA:9144
EMAPA:17185
EMAPA:18870
EV:0100058
FMA:54640
GAID:816
MA:0000347
MAT:0000040
MESH:A14.549.885
MIAA:0000040
Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]
Muscular organ in the floor of the mouth.[FEED]
OpenCyc:Mx4rvVjmJ5wpEbGdrcN5Y29ycA_53KXLq9EdqAAAACs6hnmQ
SCTID:181226008
TAO:0005333
The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech[GO].
UBERON:0001723
UMLS:C0040408
VHOG:0000419
XAO:0000446
ZFA:0005333
editor notes - in MA the tongue is part of the oral region, which in uberon is treated as the oral opening. consider revising oral opening - oral region equivalence. Taxon notes: Many species of fish have small folds at the base of their mouths that might informally be called tongues, but they lack a muscular structure like the true tongues found in most tetrapods. Development notes: The tongue has contributions from all pharyngeal arches which changes with time. The tongue initially begins as swelling rostral to foramen cecum, the median tongue bud.. tongue muscles derive from the somites - http://php.med.unsw.edu.au/embryology/index.php?title=Tongue_Development#Pharyngeal_Arch_Contributions
glossal
glossus
http://upload.wikimedia.org/wikipedia/commons/a/a6/Tongue.agr.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/a/a6/Tongue.agr.jpg/200px-Tongue.agr.jpg
lingual
ncithesaurus:Tongue
uberon
tonsillar ring
FMA:55070
MA:0000752
SCTID:56411004
UBERON:0001735
UMLS:C0459892
Waldeyer's ring
Waldeyer's tonsillar ring
anulus lymphoideus pharyngis
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].
ncithesaurus:Waldeyers_Tonsillar_Ring
oropharyngeal lymphoid tissue
pharyngeal lymphatic ring
pharyngeal lymphoid ring
see also FMA:79771 naso-pharyngeal lymphoid tissue
uberon
submandibular gland
BTO:0001316
EFO:0001387
EMAPA:18812
EV:0100061
Either of two major salivary glands situated in the neck near the lower edge of each side of the mandible and emptying into the submandibular duct. [TFD][VHOG]
FMA:55093
GAID:942
MA:0001589
MESH:A10.336.779.812
SCTID:181235001
The most common oral glands in mammals are the salivary glands. There are usually three primary pairs of salivary glands, named for their approximate positions: mandibular (submandibular or submaxillary), sublingual, and parotid.[well established][VHOG]
The paired submandibular glands (submaxillary glands) are salivary glands located beneath the floor of the mouth. In humans, they account for 70% of the salivary volume and weigh about 15 grams. [WP,unvetted].
UBERON:0001736
UMLS:C0038556
VHOG:0000364
glandula submandibularis
http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/5/51/Illu_quiz_hn_02.jpg/200px-Illu_quiz_hn_02.jpg
lobular, sexually dimorphic in mouse
ncithesaurus:Submandibular_Gland
submandibular salivary gland
submaxillary gland
uberon
lymphoid tissue
BTO:0000753
FMA:55220
GAID:342
MA:0002436
MESH:A10.549
Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP].
SCTID:181768009
This class was created automatically from a combination of ontologies
UBERON:0001744
UMLS:C0024296
galen:LymphoidTissue
lymphatic tissue
lymphocytic tissue
ncithesaurus:Lymphoid_Tissue
uberon
lacrimal apparatus
FMA:55605
GAID:901
MA:0000274
MESH:A09.371.463
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].
UBERON:0001750
UMLS:C0022903
apparatus lacrimalis
http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png
nasolacrimal drainage system
ncithesaurus:Lacrimal_Apparatus
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
uberon
dentine
BTO:0003453
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].
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]
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
FMA:55628
GAID:1272
MA:0002542
MESH:A14.254.900.280
Mineralized collagen containing substance that forms the tooth structure.[TAO]
SCTID:362112004
TAO:0005143
UBERON:0001751
UMLS:C0011429
VHOG:0001589
VSAO:0000069
XAO:0004051
ZFA:0005143
dentin
dentinal
dentine of tooth
ncithesaurus:Dentin
predentin
uberon
odontogenic papilla
BTO:0001839
Cell condensation that is a well-defined population of densely organized mesenchymal cells that aggregates adjacent to an epithelium.[VSAO]
FMA:57662
GAID:1277
MA:0001598
MESH:A14.254.900.720.250
TAO:0005140
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]
Tissue of the developing tooth. It is composed of pre-odontoblast and undiffentiated mesnchyme cells and connects to the basal lamina.[TAO]
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.
UBERON:0001763
VHOG:0001465
VSAO:0000025
XAO:0004045
ZFA:0005140
dental papilla
dentinal papilla
dermal papilla
http://upload.wikimedia.org/wikipedia/commons/2/22/Gray1011.png
http://upload.wikimedia.org/wikipedia/commons/thumb/2/22/Gray1011.png/200px-Gray1011.png
odontogenic condensation
papilla dentis
pharyngeal tooth mesenchyme
tooth mesenchyme
uberon
muscle of trunk
AAO:0000611
EFO:0003531
FMA:58274
MA:0000514
Muscle organ which is a part of the trunk. Examples: external intercostal muscle, external oblique, levator ani.
TAO:0000473
TODO - check muscle organ vs musculature
UBERON:0001774
XAO:0003230
ZFA:0000473
body musculature
muscle organ of torso
muscle organ of trunk
torso muscle organ
trunk muscle
trunk muscle organ
trunk musculature
uberon
spinal nerve
AAO:0011101
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]
BTO:0000870
EHDAA2:0001898
EMAPA:16989
FMA:5858
GAID:841
MA:0000233
MESH:A08.800.800.720
Neural tree (organ) which is directly continuous with the spinal cord. Examples: Fifth cervical spinal nerve, third lumbar spinal nerve.
OpenCyc:Mx4rwK_iFJwpEbGdrcN5Y29ycA
SCTID:361099009
This class was created automatically from a combination of ontologies
UBERON:0001780
UMLS:C0037941
VHOG:0000824
XAO:0003101
backbone nerve
http://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg
ncithesaurus:Spinal_Nerve
nerve of backbone
nerve of spinal column
nerve of spine
nerve of vertebral column
nervi spinales
spinal column nerve
spinal nerve tree
spine nerve
uberon
vertebral column nerve
layer of retina
AAO:0010353
FMA:58617
MA:0001319
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
SCTID:280657006
UBERON:0001781
UMLS:C0459649
XAO:0000266
any of the layers that make up the retina[MP].
ncithesaurus:Retina_Layer
retina layer
retina neuronal layer
retinal layer
retinal neuronal layer
uberon
cranial nerve
AAO:0000108
BTO:0001104
Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. In humans, there are traditionally twelve pairs of cranial nerves. Only the first and the second pair emerge from the cerebrum; the remaining ten pairs emerge from the brainstem[WP].
EHDAA2:0000323
EMAPA:17263
EMAPA:17264
Editors note: classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN. Note EMAPA subdivides nerve into CNS nerve and PNS nerve, with *all* cranial nerves classified as CNS nerves.
FMA:5865
GAID:802
MA:0000215
MESH:A08.800.800.120
NIF_GrossAnatomy:birnlex_1623
OpenCyc:Mx4rvWvJVpwpEbGdrcN5Y29ycA
SCTID:244447006
TAO:0000641
Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO]
UBERON:0001785
UMLS:C0010268
VHOG:0000279
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG]
XAO:0000429
XAO:0003089
ZFA:0000641
cranial nerves
cranial neural tree organ
http://upload.wikimedia.org/wikipedia/commons/1/18/Brain_human_normal_inferior_view_with_labels_en-2.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/8/84/Brain_human_normal_inferior_view_with_labels_en.svg/200px-Brain_human_normal_inferior_view_with_labels_en.svg.png
ncithesaurus:Cranial_Nerve
nervus cranialis
uberon
sensory ganglion
AEO:0001000
FMA:5885
MA:0002566
MESH:A08.340.390
This class was created automatically from a combination of ontologies
UBERON:0001800
UMLS:C0206429
ganglion sensorium
ncithesaurus:Sensory_Ganglion
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.
uberon
anterior segment of eyeball
FMA:58865
MA:0002484
MESH:A09.371.060
SCTID:280658001
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.
UBERON:0001801
UMLS:C0003153
ZFA:0005566
anterior segment of eye
anterior segment of the eye
eye anterior segment
http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png
ncithesaurus:Anterior_Eye_Segment
segmentum anterius (bulbus oculi)
segmentum anterius bulbi oculi
uberon
posterior segment of eyeball
FMA:58868
MA:0002485
SCTID:280659009
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.
UBERON:0001802
UMLS:C0278450
ZFA:0005567
eye posterior segment
http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg
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
ncithesaurus:Posterior_Eye_Segment
posterior segment of eye
posterior segment of the eye
segmentum posterius (bulbus oculi)
segmentum posterius bulbi oculi
uberon
autonomic ganglion
AEO:0001001
EMAPA:17157
EMAPA:18221
FMA:5889
MA:0000220
This class was created automatically from a combination of ontologies
UBERON:0001805
UMLS:C0017068
autonomic nervous system ganglion
ganglion autonomicum
ganglion of autonomic nervous system
ganglion of visceral nervous system
ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion.
http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png
ncithesaurus:Autonomic_Ganglion
uberon
visceral nervous system ganglion
sympathetic ganglion
AAO:0010773
BTO:0001333
EHDAA2:0001969
EMAPA:17157
FMA:5890
MA:0000226
SCTID:362485003
Sympathetic ganglia are the ganglia of the sympathetic nervous system. They deliver information to the body about stress and impending danger, and are responsible for the familiar fight-or-flight response. They contain approximately 20000–30000 nerve cell bodies and are located close to and on either side of the spinal cord in long chains. [WP,unvetted].
UBERON:0001806
UMLS:C0017071
ganglion of sympathetic nervous system
ganglion of sympathetic part of autonomic division of nervous system
ganglion sympatheticum
ganglion sympathicum
http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png
http://upload.wikimedia.org/wikipedia/commons/thumb/f/f7/Gray839.png/200px-Gray839.png
ncithesaurus:Sympathetic_Ganglion
sympathetic nervous system ganglion
sympathetic part of autonomic division of nervous system ganglion
uberon
paravertebral ganglion
FMA:5891
TAO:0001556
This class was created automatically from a combination of ontologies
Trunk ganglion which is part of a bilaterally paired set of sympathetic ganglia located anterior and lateral to the spinal cord.
UBERON:0001807
ZFA:0001556
ganglion of sympathetic trunk
ganglion trunci sympathetici
ganglion trunci sympathici
http://upload.wikimedia.org/wikipedia/commons/thumb/2/2d/Gray847.png/200px-Gray847.png
sympathetic chain ganglion
uberon
parasympathetic ganglion
BTO:0001256
EHDAA2:0001400
FMA:5894
MA:0002469
NIF_GrossAnatomy:nlx_anat_100303
Parasympathetic ganglia are the autonomic ganglia of the parasympathetic nervous system. Most are small terminal ganglia or intramural ganglia, so named because they lie near or within (respectively) the organs they innervate. The exceptions are the four paired parasympathetic ganglia of the head and neck. [WP,unvetted].
SCTID:279284004
This class was created automatically from a combination of ontologies
UBERON:0001808
UMLS:C0017069
ganglion parasympathicum
http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png
http://upload.wikimedia.org/wikipedia/commons/thumb/f/f7/Gray839.png/200px-Gray839.png
ncithesaurus:Parasympathetic_Ganglion
uberon
lacrimal gland
BTO:0000044
EFO:0001389
EV:0100339
FMA:59101
Lobular organ the parenchyma of which consists of glandular acini which communicate the lacrimal sac. Examples: There only two instances, right lacrimal and left lacrimal glands[FMA]. The lacrimal glands are paired almond-shaped glands, one for each eye, that secrete the aqueous layer of the tear film. They are situated in the upper, outer portion of each orbit. Inflammation of the lacrimal glands is called dacryoadenitis[WP].
MA:0001296
SCTID:181147003
The preorbital gland is a paired exocrine gland found in many species of hoofed animals, which is homologous to the lacrimal gland found in humans. These glands are trenchlike slits of dark blue to black, nearly bare skin extending from the medial canthus of each eye. They are lined by a combination of sebaceous and sudoriferous glands, and they produce secretions which contain pheromones and other semiochemical compounds. Ungulates frequently deposit these secretions on twigs and grass as a means of communication with other animals. The preorbital gland serves different roles in different species. Pheromone-containing secretions from the preorbital gland may serve to establish an animal's dominance (especially in preparation for breeding), mark its territory, or simply to produce a pleasurable sensation to the animal. Because of its critical role in scent marking, the preorbital gland is usually considered as a type of scent gland. A further function of these glands may be to produce antimicrobial compounds against skin pathogens. Antimicrobial compounds found in these glands may be biosynthesized by the animal itself, or by microorganisms that live in these glands[Wikipedia:Preorbital_gland].
UBERON:0001817
UMLS:C0022907
VHOG:0001476
glandula lacrimalis
http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png
http://upload.wikimedia.org/wikipedia/commons/thumb/c/cf/Gray896.png/200px-Gray896.png
ncithesaurus:Lacrimal_Gland
preorbital gland
tear gland
uberon
sebaceous gland
A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP].
Any of the numerous holocrine glands in the dermis that empty into a hair follicle and produce and secrete sebum. [TFD][VHOG]
BTO:0001980
EV:0100161
FMA:59160
GAID:900
MA:0002565
MESH:A10.336.827
SCTID:361697005
Sebaceous glands are also limited to mammals.[well established][VHOG]
UBERON:0001821
UMLS:C0036505
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.
VHOG:0001468
glandula sebacea
glandula sebaceae
http://upload.wikimedia.org/wikipedia/commons/4/49/HairFollicle.png
http://upload.wikimedia.org/wikipedia/commons/thumb/4/49/HairFollicle.png/200px-HairFollicle.png
ncithesaurus:Sebaceous_Gland
sebaceous follicle
uberon
nasal cavity mucosa
BTO:0000912
FMA:59684
GAID:302
SCTID:310211009
TODO - check lining vs part of. split olfactory and nasal mucosa?
UBERON:0001826
mucosa of nose
mucous membrane of nose
nasal mucosa
the mucous membrane that lines the nasal cavity[MP].
tunica mucosa nasalis
tunica mucosa nasi
uberon
major salivary gland
FMA:59788
MA:0002478
SCTID:303049006
There are 3 pairs of major salivary glands in human and mouse[ISBN10:0123813611]
UBERON:0001829
UMLS:C0930553
galen:MajorSalivaryGland
ncithesaurus:Major_Salivary_Gland
the three largest glands of the oral cavity that secrete most of the saliva, including the parotid, submandibular, and sublingual glands.
uberon
parotid gland
A mammalian salivary gland located caudal to the ear. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-22, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
AAO:0010095
BTO:0001004
EFO:0002558
EMAPA:18537
EV:0100060
FMA:59790
GAID:938
MA:0001585
MESH:A10.336.779.464
OpenCyc:Mx4rvqwyg5wpEbGdrcN5Y29ycA
SCTID:181234002
The most common oral glands in mammals are the salivary glands. There are usually three primary pairs of salivary glands, named for their approximate positions: mandibular (submandibular or submaxillary), sublingual, and parotid.[well established][VHOG]
The mouse parotid, exorbital lacrimal gland and exocrine pancreas have similar histological appearances[ISBN10:0123813611]
The parotid gland is the largest of the salivary glands. It is found wrapped around the mandibular ramus, and it secretes saliva through Stensen's duct into the oral cavity, to facilitate mastication and swallowing. [WP,unvetted].
UBERON:0001831
UMLS:C0030580
VHOG:0000308
galen:ParotidGland
glandula parotidea
http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/5/51/Illu_quiz_hn_02.jpg/200px-Illu_quiz_hn_02.jpg
ncithesaurus:Parotid_Gland
parotid
uberon
lip
BTO:0001647
FMA:59816
GAID:76
MA:0000343
MESH:A01.456.505.631.515
One of the two fleshy folds which surround the opening of the mouth.
OpenCyc:Mx4rvVi4U5wpEbGdrcN5Y29ycA
SCTID:181221003
Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO]
TAO:0007006
UBERON:0001833
UMLS:C0023759
VHOG:0000677
ZFA:0007006
galen:Lip
http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG
http://upload.wikimedia.org/wikipedia/commons/thumb/9/99/Mouth.jpg/200px-Mouth.jpg
labia oris
labial
lips
ncithesaurus:Lip
uberon
saliva
BTO:0001202
ENVO:02000036
FMA:59862
GAID:1167
In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin[GO].
MA:0002507
MAT:0000444
MESH:A12.200.666
OpenCyc:Mx4rvVjJ95wpEbGdrcN5Y29ycA
This class was created automatically from a combination of ontologies
UBERON:0001836
UMLS:C0036087
galen:Saliva
ncithesaurus:Saliva
sailva normalis
saliva atomaris
saliva molecularis
salivary
salivary gland secretion
uberon
cortex
EFO:0000383
EHDAA:9344
FMA:61109
Note that this class is used more generically than in FMA, and includes e.g. cortex of hair
Outermost layer of an organ[WP].
UBERON:0001851
cortex
cortex of organ
cortical
galen:Cortex
uberon
sebum
BTO:0001981
ENVO:02000037
FMA:61304
Fatty lubricant matter secreted by sebaceous glands, and made of made of triglyceride oils, wax, squalene, and metabolytes of fat-producing cells[BTO,WP].
GAID:1168
MA:0002538
MESH:A12.200.702
The composition of sebum varies across species. In humans, the lipid content is as follows: 25% wax monoesters, 41% triglycerides, 16% free fatty acids, 12% squalene; Sapienic acid is a sebum fatty acid that is unique to humans.
UBERON:0001866
UMLS:C0036511
ncithesaurus:Sebum
uberon
cerebral hemisphere
AAO:0010480
BTO:0000231
EFO:0002521
FMA:61817
MA:0000133
NIF_GrossAnatomy:birnlex_1042
One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA]
OpenCyc:Mx4rvigx5ZwpEbGdrcN5Y29ycA
Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO]
SCTID:278251007
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]
UBERON:0001869
UMLS:C0228174
VHOG:0001639
galen:CerebralHemisphere
hemisphere
hemispherium cerebri
http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png
ncithesaurus:Cerebral_Hemisphere
telencephalic vesicle
uberon
frontal cortex
BM:Tel-Cx-FR
BTO:0000484
EFO:0000913
EV:0100167
Editor note: Many species don't have lobes but they do have frontal cortex. Lobe isn't a really well defined term though [MM]
FMA:61824
Frontal lobe is the anterior-most of five lobes of the cerebral hemisphere. It is bounded by the central sulcus on its posterior border and by the longitudinal cerebral fissure on its medial border.
GAID:674
MA:0000905
MAT:0000505
MESH:A08.186.211.730.885.213.270
NIF_GrossAnatomy:birnlex_928
NIF_GrossAnatomy:nlx_anat_20090601
OpenCyc:Mx4rv3OJ8JwpEbGdrcN5Y29ycA
SCTID:180920004
UBERON:0001870
UMLS:C0016733
frontal lobe
frontal region
http://upload.wikimedia.org/wikipedia/commons/b/b4/Gray729.png
http://upload.wikimedia.org/wikipedia/commons/thumb/b/b4/Gray729.png/200px-Gray729.png
lobus frontalis
ncithesaurus:Frontal_Lobe
regio frontalis
uberon
temporal lobe
BM:Tel-Cx-Te
BTO:0001355
EFO:0000917
EMAPA:18797
EV:0100169
FMA:61825
GAID:635
MA:0000941
MAT:0000508
MESH:A08.186.211.730.885.213.863
NIF_GrossAnatomy:birnlex_1160
OpenCyc:Mx4rwQLi-ZwpEbGdrcN5Y29ycA
SCTID:180921000
Temporal lobe is the ventrolateral lobe of five lobes comprising each cerebral hemisphere. It is bounded dorsally by the lateral fissure and posteriorly by an arbitrary border shared with the occipital lobe.
UBERON:0001871
UMLS:C0039485
http://upload.wikimedia.org/wikipedia/commons/9/91/Gray730.png
http://upload.wikimedia.org/wikipedia/commons/thumb/9/91/Gray730.png/200px-Gray730.png
lobus temporalis
ncithesaurus:Temporal_Lobe
temporal cortex
temporal neocortex
uberon
parietal lobe
BTO:0001001
EFO:0000914
EV:0100168
FMA:61826
GAID:680
MA:0000916
MAT:0000506
MESH:A08.186.211.730.885.213.670
NIF_GrossAnatomy:birnlex_1148
OpenCyc:Mx4rvg-typwpEbGdrcN5Y29ycA
Parietal lobe is the one of five lobes of the cerebral hemisphere which occupies the dorsal-posterior portion of the hemisphere. It is bounded by the central sulcus on its anterior border and and by the longitudinal cerebral fissure on its medial border. Posteriorly it shares an arbitrary border with the occipital lobe.
SCTID:180922007
This class was created automatically from a combination of ontologies
UBERON:0001872
UMLS:C0030560
http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray726_parietal_lobe.png
http://upload.wikimedia.org/wikipedia/commons/thumb/b/b2/Gray726_parietal_lobe.png/200px-Gray726_parietal_lobe.png
lobus parietalis
ncithesaurus:Parietal_Lobe_of_the_Brain
parietal cortex
parietal neocortex
parietal region
regio parietalis
uberon
caudate nucleus
BM:Tel-CA
BTO:0000211
CHECK - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM)
EFO:0000907
EMAPA:18207
EV:0100185
FMA:61833
GAID:670
MA:0000894
MAT:0000513
MESH:A08.186.211.730.885.105.487.550.184
NIF_GrossAnatomy:birnlex_1373
Nucleus of brain which is an elongated crescent-shaped mass lying parallel and adjacent to the lateral ventricle throughout its extent.
OpenCyc:Mx4rvvyAjJwpEbGdrcN5Y29ycA
SCTID:279297002
UBERON:0001873
UMLS:C0007461
caudatus
http://upload.wikimedia.org/wikipedia/commons/9/91/Telencephalon-Horiconatal.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/9/91/Telencephalon-Horiconatal.jpg/200px-Telencephalon-Horiconatal.jpg
ncithesaurus:Caudate_Nucleus
nucleus caudatus
uberon
putamen
All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates.[well established][VHOG]
BM:Tel-Pu
CHECK - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM)
EV:0100187
FMA:61834
GAID:671
MA:0000895
MESH:A08.186.211.730.885.105.487.550.784
NIF_GrossAnatomy:birnlex_809
Nucleus of brain which lies ventral to the caudate nucleus and internal capsule and medial to the external capsule. The putamen and caudate nucleus together form the dorsal striatum. It is also one of the structures that comprises the basal ganglia. Through various pathways, the putamen is connected to the substantia nigra and globus pallidus. The main function of the putamen is to regulate movements and influence various types of learning. It employs dopamine to perform its functions. The putamen also plays a role in degenerative neurological disorders, such as Parkinson's disease.
SCTID:281512002
UBERON:0001874
UMLS:C0034169
VHOG:0001456
http://upload.wikimedia.org/wikipedia/commons/3/33/BrainCaudatePutamen.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/3/33/BrainCaudatePutamen.svg/200px-BrainCaudatePutamen.svg.png
ncithesaurus:Putamen
nucleus putamen
uberon
globus pallidus
BTO and MA are inconsistent w.r.t striatum and pallidum being non-overlapping as in ABA. Note that we have pallidum as part_of basal gangion, so we can make the direct link to basal ganglion. ISBN10:1588900649 says: ... a derivative of the diencephalon, seperates as a result of growing fibers of theinternal capsule and is finally displaced into telencephalon. only a small medial remnannt remains, the entopeduncular nucleus. The globus pallidus should be regarded as part of the subthalamus
BTO:0002246
EFO:0000905
EV:0100188
FMA:61835
GAID:668
MA:0000890
MAT:0000510
MESH:A08.186.211.730.885.105.487.397
NIF_GrossAnatomy:birnlex_1234
SCTID:362361005
Subcortical nucleus, functionally part of the basal ganglia, which consists of two segments the external (or lateral) and internal (or medial) separated by the medial medullary lamina in primates. In rodents, The globus pallidus lateral is separated from the medial segment by the fibers of the internal capsule/cerebral peduncle[NIF]. Nucleus of brain which is located medially to the putamen and laterally to the internal capsule[FMA].
UBERON:0001875
UMLS:C0017651
http://upload.wikimedia.org/wikipedia/commons/e/ee/Brain_structure.gif
http://upload.wikimedia.org/wikipedia/commons/thumb/e/ee/Brain_structure.gif/200px-Brain_structure.gif
ncithesaurus:Globus_Pallidus
pale body
paleostriatum
pallidal
pallidium
pallidum
uberon
amygdala
AO notes: MA and FMA differ on relationship to basal ganglion. The FMA text def suggests a subdivision, but it is classified as a subtype
BM:Tel-Am
BTO:0001042
EFO:0000252
EV:0100189
EV:0100190
FMA:61841
GAID:616
MA:0000887
MAT:0000289
MESH:A08.186.211.577.090
MIAA:0000289
NIF_GrossAnatomy:birnlex_1241
One part of the striatum is called the archistriatum. (...) The archistriatum of fishes consists of several indistinctly segregated nuclei called the amygdaloid (...) complex. Tetrapods retain the structure, and in mammals the corresponding amygdala is a globular mass that tends to be ventral to the other basal nuclei.[well established][VHOG]
OpenCyc:Mx4rwJC_2ZwpEbGdrcN5Y29ycA
SCTID:279404004
Subdivision of basal ganglion of telencephalon which is an almond-shaped gray mass in the dorsomedial part of the temporal lobe[FMA]
UBERON:0001876
UMLS:C0002708
VHOG:0001277
amygdalar
amygdaloid area
amygdaloid body
amygdaloid complex
amygdaloid nuclear complex
amygdaloid nuclear group
amygdaloid nuclear groups
amygdaloid nucleus
archistriatum
corpus amygdaloideum
http://upload.wikimedia.org/wikipedia/commons/8/8b/Amyg.png
http://upload.wikimedia.org/wikipedia/commons/thumb/8/8b/Amyg.png/200px-Amyg.png
ncithesaurus:Amygdala
nucleus amygdalae
uberon
dentate gyrus of hippocampal formation
ABA:DG
BM:Tel-DG
BTO says dentate gyrus = fascia dentata + hilus. Note that GO classifies dentate gyrus development under hippocampus development
BTO:0002496
BTO:0002615
EFO:0001366
EMAPA:19037
FMA:61922
GAID:624
MA:0000190
MESH:A08.186.211.577.405.200
NIF_GrossAnatomy:birnlex_1178
SCTID:279211002
The dentate gyrus is one of two interlocking gyri of the hippocampus. It contains granule cells, which project to the pyramidal cells and interneurons of the CA3 region of the ammon gyrus[GO].
UBERON:0001885
UMLS:C0152314
area dentata
dentate gyrus
fascia dentata
gyrus dentatus
hippocampal dentate gyrus
http://upload.wikimedia.org/wikipedia/commons/a/ab/HippocampalRegions.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/a/ab/HippocampalRegions.jpg/200px-HippocampalRegions.jpg
ncithesaurus:Dentate_Gyrus
uberon
forebrain
AAO:0010147
BTO:0000478
EFO:0000909
EHDAA2:0000556
EHDAA:3470
EMAPA:16895
FMA:61992
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]
MA:0000170
MAT:0000105
MESH:A08.186.211.730
MIAA:0000105
Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO]
NIF_GrossAnatomy:birnlex_1509
SCTID:362291003
TAO:0000109
The most anterior region the brain including both the telencephalon and diencephalon.
The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO]
UBERON:0001890
UMLS:C0085140
VHOG:0000383
XAO:0000011
ZFA:0000109
http://upload.wikimedia.org/wikipedia/commons/thumb/5/54/EmbryonicBrain.svg/200px-EmbryonicBrain.svg.png
ncithesaurus:Fore-Brain
ncithesaurus:Prosencephalon
prosencephalic
prosencephalon
relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO]
uberon
midbrain
AAO:0010149
ABA:MB
BM:MB
BTO:0000138
EFO:0000919
EHDAA2:0001162
EHDAA:3694
EMAPA:16974
EV:0100242
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
FMA:61993
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]
MA:0000207
MAT:0000106
MESH:A08.186.211.132.659
MIAA:0000106
Middle part of the brain composed of the optic tectum and penducular region.[AAO]
NIF_GrossAnatomy:birnlex_1667
OpenCyc:Mx4rvsBUqpwpEbGdrcN5Y29ycA
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].
RETIRED_EHDAA2:0001104
SCTID:279099009
TAO:0000128
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]
UBERON:0001891
UMLS:C0025462
VHOG:0000069
XAO:0000014
ZFA:0000128
http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG
http://upload.wikimedia.org/wikipedia/commons/thumb/f/f9/Human_brain_inferior_view_description.JPG/200px-Human_brain_inferior_view_description.JPG
mesencephalic
mesencephalon
ncithesaurus:Mesencephalon
uberon
telencephalon
AAO:0010479
ABA:CH
BM:Tel
BTO:0000239
EFO:0000912
EHDAA2:0001982
EMAPA:16652
EMAPA:16910
EV:0100165
FMA:62000
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]
GAID:621
In mammals the cortex covers almost the whole of the cerebral hemispheres.
In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles.
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.
In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb.
MA:0000183
MAT:0000421
MESH:A08.186.211.730.885
MIAA:0000421
NIF_GrossAnatomy:birnlex_1115
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].
Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO]
SCTID:263353005
TAO:0000079
The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO]
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.
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).
UBERON:0001893
VHOG:0000283
XAO:0000012
ZFA:0000079
cerebral
cerebrum
dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight.
endbrain
relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO]
telenencephalic
uberon
diencephalon
AAO:0010481
ABA:IB
BM:Die
BTO:0000342
EFO:0000911
EHDAA2:0000385
EHDAA:1969
EHDAA:2645
EHDAA:3472
EMAPA:16641
EMAPA:16896
EV:0100194
FMA:62001
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]
GAID:618
MA:0000171
MAT:0000420
MESH:A08.186.211.730.385
MIAA:0000420
NIF_GrossAnatomy:birnlex_1503
Note that in ABA, this is part of the brain stem
OpenCyc:Mx4rwC-V0JwpEbGdrcN5Y29ycA
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). <a href='http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-PUB-961014-576'>Kimmel et al, 1995.</a>
SCTID:279328001
TAO:0000101
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]
UBERON:0001894
UMLS:C0012144
Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO]
VHOG:0000318
XAO:0000013
ZFA:0000101
between brain
betweenbrain
diencephalic
diencephalon
http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/5/54/EmbryonicBrain.svg/200px-EmbryonicBrain.svg.png
interbrain
mature diencephalon
ncithesaurus:Diencephalon
uberon
metencephalon
BTO:0000673
EHDAA2:0001149
EHDAA:5498
EMAPA:17071
FMA:62003
GAID:594
MA:0000197
MESH:A08.186.211.132.810.428
NIF_GrossAnatomy:birnlex_965
Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum.
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]
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]
UBERON:0001895
UMLS:C1516904
VHOG:0000741
epencephalon
epencephalon-2
http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/5/54/EmbryonicBrain.svg/200px-EmbryonicBrain.svg.png
ncithesaurus:Epencephalon
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].
uberon
medulla oblongata
AAO:0010486
ABA:MY
BTO:0000041
Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]
EFO:0000924
EHDAA2:0001088
EHDAA:7588
EMAPA:17550
EV:0100275
FMA:62004
GAID:590
MA:0000206
MAT:0000111
MAT:0000367
MESH:A08.186.211.132.810.406
MIAA:0000111
NIF_GrossAnatomy:birnlex_957
OpenCyc:Mx4rvVjxSJwpEbGdrcN5Y29ycA
OpenCyc:Mx4rwCqnXJwpEbGdrcN5Y29ycA
Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].
Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]
SCTID:279104005
TAO:0000545
The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
UBERON:0001896
UMLS:C0025148
VHOG:0000181
XAO:0003100
ZFA:0000545
bulb
bulbus
http://upload.wikimedia.org/wikipedia/commons/thumb/6/6b/Illu_pituitary_pineal_glands.jpg/200px-Illu_pituitary_pineal_glands.jpg
medulla
medulla oblonzata
metepencephalon
ncithesaurus:Medulla_Oblongata
uberon
thalamus
(...) the brain regions of tetrapods, the structures they contain, and their basic organizational features are the same as in fishes.[well established][VHOG]
A midline paired symmetrical structure within the brains of vertebrates, including humans. It is situated between the cerebral cortex and midbrain, both in terms of location and neurological connections. Its function includes relaying sensation, special sense and motor signals to the cerebral cortex, along with the regulation of consciousness, sleep and alertness. The thalamus surrounds the third ventricle. It is the main product of the embryonic diencephalon.
AAO:0010483
ABA:TH
AO notes: MA and ZFA think there is a distinct dorsal thalamus, but FMA says its an exact synonym. FMA has a distinct class for thalamic complex.
BTO:0001365
EFO:0000910
EMAPA:17540
EV:0100195
FMA:62007
GAID:656
MA:0000179
MAT:0000109
MESH:A08.186.211.730.385.826
MIAA:0000109
NIF_GrossAnatomy:birnlex_954
One of a pair of large oval nervous structures made of gray matter and forming most of the lateral walls of the third ventricle of the brain and part of the diencephalon. [TFD][VHOG]
OpenCyc:Mx4rwMPQ65wpEbGdrcN5Y29ycA
Part of the diencephalon consisting of a mass of connecting fibers which relay sensory information to the cerebral cortex.[AAO]
SCTID:244433007
TAO:0001215
UBERON:0001897
UMLS:C0039729
VHOG:0000657
ZFA:0001215
dorsal thalamus
dorsal thalamus (anthoney)
galen:Thalamus
http://upload.wikimedia.org/wikipedia/commons/c/ce/Brain_chrischan_thalamus.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/c/ce/Brain_chrischan_thalamus.jpg/200px-Brain_chrischan_thalamus.jpg
ncithesaurus:Thalamus
thalami
thalamic
thalamus dorsalis
uberon
hypothalamus
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]
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].
AAO:0010484
ABA:HY
BM:Die-Hy
BTO:0000614
EFO:0000107
EHDAA2:0000802
EHDAA:5446
EMAPA:17536
EV:0100225
FMA:62008
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]
GAID:460
MA:0000173
MAT:0000112
MESH:A08.186.211.577.482
MIAA:0000112
NIF_GrossAnatomy:birnlex_734
OpenCyc:Mx4rwEgr9JwpEbGdrcN5Y29ycA
Part of the diencephalon ventral to the thalamus consisting of connecting fibers and is a center for control of the autonomous nervous system.[AAO]
SCTID:264483005
TAO:0000032
Taxon notes: all vertebrates contain a hypothalamus[WP].
UBERON:0001898
UMLS:C0020663
VHOG:0000179
XAO:0004070
ZFA:0000032
galen:Hypothalamus
http://upload.wikimedia.org/wikipedia/commons/9/9f/LocationOfHypothalamus.jpg
hypothalamic
hypothalamus
ncithesaurus:Hypothalamus
preoptico-hypothalamic area
preoptico-hypothalamic region
uberon
subthalamus
Anterior part of the diencephalon that lies between the thalamus, hypothalamus, and tegmentum of the mesencephalon, including subthalamic nucleus, zona incerta, the fields of Forel, and the nucleus of ansa lenticularis[GO].
BM:Die-VTh
EHDAA2:0004470
EV:0100223
FMA:62010
GAID:653
MA:0000181
MESH:A08.186.211.730.385.800
NIF_GrossAnatomy:birnlex_708
SCTID:279332007
TAO:0000458
This class was created automatically from a combination of ontologies
UBERON:0001900
UMLS:C0152349
ZFA:0000458
ncithesaurus:Ventral_Thalamus
prethalamus
subthalamic
subthalamic region
thalamus ventralis
uberon
ventral thalamus
subthalamic nucleus
ABA:STN
BM:Die-Sb
BTO:0002252
EFO:0001392
EV:0100224
FMA:62035
GAID:655
Luys' body
MA:0000877
MESH:A08.186.211.730.385.800.800
NIF_GrossAnatomy:nlx_anat_1010002
The subthalamic nucleus is the lens-shaped nucleus located in the ventral part of the subthalamus on the inner aspect of the internal capsule that is concerned with the integration of somatic motor function[GO].
This class was created automatically from a combination of ontologies
UBERON:0001906
UMLS:C0152355
body of forel
body of luys
http://upload.wikimedia.org/wikipedia/commons/3/33/Basal-ganglia-coronal-sections-large.png
http://upload.wikimedia.org/wikipedia/commons/thumb/3/33/Basal-ganglia-coronal-sections-large.png/200px-Basal-ganglia-coronal-sections-large.png
ncithesaurus:Subthalamic_Nucleus
nucleus of corpus luysii
nucleus of luys
nucleus subthalamicus
subthalamic nucleus (of luys)
uberon
zona incerta
ABA:ZI
BM:Die-VTh-ZI
BTO:0003146
FMA:62038
MA:0000878
SCTID:369186007
The zona incerta is a horizontally elongated region of gray matter cells in the subthalamus below the thalamus. Its connections project extensively over the brain from the cerebral cortex down into the spinal cord. Its function is unknown though several have been proposed related to “limbic–motor integration” such as controlling visceral activity and pain; gating sensory input and synchronizing cortical and subcortical brain rhythms. Its dysfunction may play a role in central pain syndrome. It is also been identified as a promising deep brain stimulation therapy target for treating Parkinsons Disease. Its existence was first described by Auguste Forel in 1877 as a “region of which nothing certain can be said”. A hundred and thirty years later in 2007, Nadia Urbain and Martin Deschênes of Université Laval noted that the “zona incerta is among the least studied regions of the brain; its name does not even appear in the index of many textbooks. ” [WP,unvetted].
UBERON:0001907
uberon
mammary gland
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]
BTO:0000817
Brustdruese
EFO:0000854
EMAPA:17759
EV:0100125
MA:0000145
MAT:0000073
MESH:A10.336.482
MIAA:0000073
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
OpenCyc:Mx4rvVjVq5wpEbGdrcN5Y29ycA
SCTID:361720005
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]
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.
UBERON:0001911
UMLS:C0929301
VHOG:0000398
dug
glandula mammaria
glandula mammaria
http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Illu_breast_anatomy.jpg/200px-Illu_breast_anatomy.jpg
lactiferous gland
lobe of breast
lobe of mammary gland
mamma
mammary
ncithesaurus:Mammary_Gland
uberon
milk
AO notes: ncit:Milk refers specifically to cow milk
BTO:0000868
ENVO:02000031
EV:0100126
FMA:62100
GAID:1230
MA:0002552
MAT:0000056
MESH:A13.622
MIAA:0000056
OpenCyc:Mx4rvVjGZJwpEbGdrcN5Y29ycA
Secretion produced by the mammary gland.[FMA]
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]
UBERON:0001913
UMLS:C1511310
VHOG:0001263
galen:Milk
mammary gland milk
ncithesaurus:Breast_Fluid_or_Secretion
uberon
endothelium of artery
AAO:0011013
An endothelium that is part of an artery [Automatically generated definition].
BTO:0004757
FMA:62116
MA:0000707
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]
This class was created automatically from a combination of ontologies
UBERON:0001917
UMLS:C1179025
VHOG:0001215
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
XAO:0000357
arterial endothelium
artery endothelium
ncithesaurus:Artery_Endothelium
uberon
preoptic area
Area of the forebrain anterior to the posterior tuberculum and the hypothalamus and ventral to the ventral thalamus. See Figure 7, Atlas of Early Zebrafish Brain Development.[TAO]
Area of the forebrain anterior to the posterior tuberculum and the hypothalamus and ventral to the ventral thalamus[ZFA].
BM:Die-Hy-POA
BTO:0001796
EFO:0002523
FMA:62313
GAID:644
MESH:A08.186.211.730.385.357.342.450
NIF_GrossAnatomy:birnlex_1706
SCTID:362382004
TAO:0000470
This class was created automatically from a combination of ontologies
UBERON:0001928
ZFA:0000470
area hypothalamica rostralis
area praeoptica
area preoptica
http://upload.wikimedia.org/wikipedia/commons/8/8c/HypothalamicNuclei.PNG
http://upload.wikimedia.org/wikipedia/commons/thumb/8/8c/HypothalamicNuclei.PNG/200px-HypothalamicNuclei.PNG
preoptic hypothalamic area
preoptic hypothalamic region
preoptic nuclei
preoptic region
preoptic region of hypothalamus
regio hypothalamica anterior
uberon
lateral preoptic nucleus
ABA:LPO
BM:Die-Hy-LPO
FMA:62326
MA:0000835
NIF_GrossAnatomy:birnlex_1722
SCTID:369129002
The lateral preoptic nucleus is lateral to the medial preoptic nucleus. It also mediates non-REM sleep onset.[WP,unvetted].
This class was created automatically from a combination of ontologies
UBERON:0001931
http://upload.wikimedia.org/wikipedia/commons/thumb/8/8c/HypothalamicNuclei.PNG/200px-HypothalamicNuclei.PNG
lateral preoptic area
lateral preoptic hypothalamic nucleus
uberon
retrochiasmatic area
ABA:RCH
FMA:62330
MA:0000841
NIF_GrossAnatomy:birnlex_1569
This class was created automatically from a combination of ontologies
UBERON:0001933
retrochiasmatic region
uberon
midbrain tegmentum
'tegmentum' is used generically for the ventral part of the brainstem (ISBN10:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum
BTO:0003388
EFO:0000921
EHDAA2:0004475
EMAPA:18215
FMA:62393
MA:0000212
MAT:0000452
NIF_GrossAnatomy:birnlex_1200
SCTID:362392007
TAO:0000160
Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]
UBERON:0001943
VHOG:0001367
Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN10:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].
ZFA:0000160
http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png
http://upload.wikimedia.org/wikipedia/commons/thumb/b/b6/Gray712.png/200px-Gray712.png
mesencephalic tegmentum
tegmentum
tegmentum mesencephali
tegmentum of midbrain
uberon
pretectal region
ABA:PRT
BM:MB-Tec-PT
FMA:62402
MA:0001062
NIF_GrossAnatomy:birnlex_703
Region between dorsal thalamus and optic tectum[pub]. It receives binocular sensory input from retinal ganglion cells of the eyes, and is the region responsible for maintaining the pupillary light reflex. [WP,unvetted].
SCTID:416333003
TAO:0000418
UBERON:0001944
ZFA:0000418
area pretectalis
nuclei pretectales
part of diencephalon in ZFA - modify to adjacent here, supported by pub
pretectal area
pretectal nuclei
pretectum
uberon
red nucleus
ABA:RN
BM:MB-RN
EHDAA2:0004706
EV:0100248
FMA:62407
Function notes: in animals without a significant corticospinal tract, gait is mainly controlled by the red nucleus.
GAID:586
MA:0001063
MESH:A08.186.211.132.659.822.642
NIF_GrossAnatomy:birnlex_1478
SCTID:279287006
TAO:0000552
The red nucleus is a structure in the rostral midbrain involved in motor coordination. It comprises a caudal magnocellular and a rostral parvocellular part. [WP,unvetted].
UBERON:0001947
ZFA:0000552
http://upload.wikimedia.org/wikipedia/commons/d/da/Cn3nucleus.png
http://upload.wikimedia.org/wikipedia/commons/thumb/d/da/Cn3nucleus.png/200px-Cn3nucleus.png
nucleus ruber
nucleus ruber
uberon
neocortex
ABA:Isocortex
BTO:0000920
EHDAA2:0004662
FMA:62429
GAID:677
MA:0002754
MESH:A08.186.211.730.885.213.420
NIF_GrossAnatomy:birnlex_2547
The neocortex is a part of the brain of mammals. It is the outer layer of the cerebral hemispheres, and made up of six layers, labelled I to VI (with VI being the innermost and I being the outermost). The neocortex is part of the cerebral cortex (along with the archicortex and paleocortex, which are cortical parts of the limbic system). It is involved in higher functions such as sensory perception, generation of motor commands, spatial reasoning, conscious thought and, in humans, language. Other names for the neocortex include neopallium and isocortex ('equal rind'). [WP,unvetted].
UBERON:0001950
cerebral neocortex
homogenetic cortex
homotypical cortex
http://upload.wikimedia.org/wikipedia/commons/7/77/Neocortex.jpg
isocortex
isocortex (sensu lato)
neopallial cortex
neopallium
nonolfactory cortex
uberon
Ammon's horn
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].
ABA:CA
Ammon's horn
BM:Tel-CAM
BTO:0003705
EFO:0000530
EHDAA2:0004443
EMAPA:19039
EMAPA:19148
EV:0100180
FMA:62493
GAID:623
MA:0000191
MAT:0000114
MESH:A08.186.211.577.405
MIAA:0000114
NIF_GrossAnatomy:birnlex_721
OpenCyc:Mx4rv3piFJwpEbGdrcN5Y29ycA
SCTID:361561007
UBERON:0001954
UBERON:0003940
UBERON:0004165
UMLS:C0019564
VHOG:0001177
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.
ammon gyrus
ammon horn
cornu ammonis
hippocampal
hippocampus
hippocampus major
hippocampus proper
hippocampus proprius
http://scalablebrainatlas.incf.org/services/thumbnail.php?template=ABA07&size=L&dim=2d3d&format=png®ion=CA
http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray739-emphasizing-hippocampus.png
ncithesaurus:Cornu_Ammonis
ncithesaurus:Hippocampus
uberon
mucosa-associated lymphoid tissue
Editor notes: todo - add part relationships to specific layers
FMA:62819
MA:0000140
MALT
UBERON:0001961
UMLS:C0599921
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].
epithelio-lymphoid tissue
mucosa associated lymphatic tissue
mucosa associated lymphoid tissue
mucosa-associated lymphoid tissue
mucosal-associated lymphatic tissue
mucosal-associated lymphoid tissue
ncithesaurus:Mucosa-Associated_Lymphoid_Tissue
uberon
gut-associated lymphoid tissue
Editor notes: phylogenetic relationships to be added. Taxon notes: guts of jawless fish contains cells with lymphocyte-like morphology (Mayer 2002).
FMA:62820
GALT
MA:0000136
Mucosa-associated lymphoid tissue in digestive tract. includes Peyer's patches, appendix, and solitary lymph nodules[GO].
UBERON:0001962
UMLS:C0596638
gut associated lymphoid tissue
ncithesaurus:Gut_Associated_Lymphoid_Tissue
uberon
substantia nigra pars reticulata
ABA:SNr
BM:MB-SNr
BTO:0003750
FMA:62908
MA:0001066
NIF_GrossAnatomy:birnlex_968
Regional part of substantia nigra consisting of loosely packed cells, generally located ventral and lateral to the pars compacta. Many cells in this region use GABA as a neurotransmitter (MM)[NLex].
This class was created automatically from a combination of ontologies
UBERON:0001966
pars reticularis substantiae nigrae
pars reticulata
reticular part of substantia nigra
substantia nigra, reticular part
uberon
semen
BTO:0001230
Body substance which consists of spermatozoa and seminal plasma.[FMA]
FMA:62966
GAID:1169
MA:0002522
MESH:A12.200.732
OpenCyc:Mx4rvgC-zpwpEbGdrcN5Y29ycA
Taxon notes: Note that in this ontology, semen is defined as the sum of sperm and seminal fluid, where seminal fluid is defined a taxonomically generic way (see comments for UBERON:0006530).
UBERON:0001968
UMLS:C1518159
UMLS:C2756969
http://upload.wikimedia.org/wikipedia/commons/thumb/4/40/Human_semen_in_petri_dish2.jpg/180px-Human_semen_in_petri_dish2.jpg
ncithesaurus:Male_Genital_System_Fluid_or_Secretion
ncithesaurus:Semen
seminal
uberon
substance of tooth
Body substance in solid state produced by odontoblasts, amyloblasts or cementoblasts.[FMA]
FMA:63001
MA:0002540
UBERON:0001973
note the asserted dual parentage. This is deliberate, pending better definitions of the distinction between substance and tissue
portion of substance of tooth
tooth substance
uberon
serosa of esophagus
A serous membrane that is part of a esophagus [Automatically generated definition].
FMA:63057
MA:0001571
This class was created automatically from a combination of ontologies
UBERON:0001975
esophagus serosa
esophagus serous membrane
gullet serosa
gullet serous membrane
oesophagus serosa
oesophagus serous membrane
serosa of abdominal part of esophagus
serosa of gullet
serosa of oesophagus
serous coat of oesophagus
serous membrane of esophagus
serous membrane of gullet
serous membrane of oesophagus
tunica serosa oesophageae
uberon
venule
BTO:0002626
FMA:63130
MA:0000071
MESH:A07.231.432.952
Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]
SCTID:341687009
Subdivision of venous tree (organ) which is directly continuous with the capillary vessel.
TAO:0005315
This class was created automatically from a combination of ontologies
UBERON:0001979
UMLS:C0042520
VHOG:0001765
ZFA:0005315
http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/d/da/Illu_capillary.jpg/200px-Illu_capillary.jpg
ncithesaurus:Venule
uberon
venula
arteriole
AAO:0010253
BTO:0001997
FMA:63182
MA:0000063
MESH:A07.231.114.060
Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]
SCTID:337724002
Small, terminal branch of an artery which generally connects to capillaries.[AAO]
TAO:0002138
This class was created automatically from a combination of ontologies
UBERON:0001980
UMLS:C0003847
VHOG:0001763
ZFA:0005255
arteriola
http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/d/da/Illu_capillary.jpg/200px-Illu_capillary.jpg
ncithesaurus:Arteriole
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].
uberon
blood vessel
A vessel through which blood circulates in the body.
AAO:0011004
AEO:0000207
Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
Any of the vessels through which blood circulates in the body.[AAO]
BTO:0001102
EFO:0000817
EHDAA2:0003252
EHDAA:240
FMA:50722
FMA:63183
GAID:169
MA:0000060
MAT:0000393
MESH:A07.231
NIF_GrossAnatomy:nlx_anat_090901
OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA
SCTID:361097006
TAO:0002137
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]
UBERON:0001981
UMLS:C0005847
VHOG:0001250
XAO:0001011
ZFA:0005314
http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/2/29/Circulatory_System_en.svg/200px-Circulatory_System_en.svg.png
ncithesaurus:Blood_Vessel
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.
region of vascular tree organ
uberon
vas sanguineum
vascular tree organ region
capillary
AAO:0010252
Any of the smallest blood vessels connecting arterioles with venules.
Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]
BTO:0002045
EFO:0001906
EMAPA:28039
EMAPA:28075
EV:0100035
FMA:63194
MA:0000065
MESH:A07.231.432.410
NIF_GrossAnatomy:nlx_anat_090902
OpenCyc:Mx4rvWEU-5wpEbGdrcN5Y29ycA
Structure notes: capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs
TAO:0005250
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]
UBERON:0001982
UMLS:C0935624
VHOG:0001253
XAO:0000116
ZFA:0005250
blood capillary
capillary vessel
http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg
ncithesaurus:Capillary
uberon
endothelium
A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]
BTO:0000393
EFO:0002548
EMAPA:18578
EMAPA:19063
FMA:63916
GAID:520
MESH:A10.272.491
SCTID:27168002
The term ‘‘endothelium’’ has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980)
UBERON:0001986
UMLS:C0014257
UMLS:C0014261
endothelial
galen:Endothelium
ncithesaurus:Endothelium
ncithesaurus:Vascular_Endothelium
uberon
placenta
BTO:0001078
EFO:0001407
EV:0100119
FMA:63934
GAID:379
MA:0000386
MAT:0000279
MESH:A16.759
MIAA:0000279
OpenCyc:Mx4rvv4zZ5wpEbGdrcN5Y29ycA
Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG]
SCTID:181455002
Taxon notes: Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother's uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN10:0073040584 "Vertebrates, Kardong"]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: doi:10.1002/jmor.11011 // Marsupials possess only a rudimentary placenta, with reduced nutrient and oxygen exchanging capabilities.
UBERON:0001987
UMLS:C0032043
VHOG:0001266
allantoic placenta
eutherian placenta
http://upload.wikimedia.org/wikipedia/commons/f/f1/Placenta.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/6/66/Placenta.jpg/200px-Placenta.jpg
ncithesaurus:Placenta
organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
placental
uberon
superior cervical ganglion
BTO:0001325
EFO:0001945
EHDAA:8943
EMAPA:18441
FMA:6467
GAID:712
MA:0001156
MESH:A08.340.315.350.850
RETIRED_EHDAA2:0001946
SCTID:279278002
TAO:0001572
This class was created automatically from a combination of ontologies
Trunk ganglion which is bilaterally paired and located at the anterior end of the sympathetic ganglion chain.
UBERON:0001989
UMLS:C0206257
ZFA:0001572
ganglion cervicale superius
http://upload.wikimedia.org/wikipedia/commons/e/e1/Gray844.png
http://upload.wikimedia.org/wikipedia/commons/thumb/e/e1/Gray844.png/200px-Gray844.png
ncithesaurus:Superior_Cervical_Ganglion
superior cervical sympathetic ganglion
superior sympathetic cervical ganglion
uberon
cervical ganglion
BTO:0000113
EMAPA:18438
FMA:6470
MA:0001153
SCTID:181100007
The cervical ganglia are paravertebral ganglia of the sympathetic nervous system. They consist of three paravertebral ganglia: superior cervical ganglion middle cervical ganglion inferior cervical ganglion. The inferior ganglion may be fused with the first thoracic ganglion to form a single structure, the stellate ganglion. Nerves emerging from cervical sympathetic ganglia contribute to the cardiac plexus, among other things. [WP,unvetted].
This class was created automatically from a combination of ontologies
UBERON:0001991
cervical sympathetic ganglion
http://upload.wikimedia.org/wikipedia/commons/thumb/e/e1/Gray844.png/200px-Gray844.png
uberon
olfactory epithelium
AAO:0010158
BTO:0000108
EFO:0001972
EHDAA2:0001228
EHDAA:4774
EMAPA:17606
Epithelium inside the nasal cavity that is responsible for detecting odors[WP].
FMA:64803
Genes: V1Rs, Trpc2 present in lamprey // See also: FMA:77199
MA:0001325
MAT:0000445
NIF_GrossAnatomy:birnlex_2703
SCTID:37623003
Sensory lining of the medial wall, roof and anterior aspects of the main olfactory cavity (cavum principale).[AAO]
TAO:0000554
UBERON:0001997
UBERON:0004853
UMLS:C0599332
VHOG:0000985
ZFA:0000554
http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray857.png
http://upload.wikimedia.org/wikipedia/commons/thumb/4/4d/Gray857.png/200px-Gray857.png
nasal cavity olfactory epithelium
nasal epithelium
nasal sensory epithelium
ncithesaurus:Olfactory_Epithelium
olfactory membrane
olfactory mucosa
olfactory sensory epithelium
relationship loss: part_of principal cavity (AAO:0000992)[AAO]
sensory olfactory epithelium
uberon
peripheral nerve
BTO:0001027
EMAPA:25148
EV:0100371
FMA:65239
GAID:747
MA:0000228
MESH:A08.800.800
NIF_GrossAnatomy:birnlex_1615
Neural tree (organ) which is directly continuous with the neuraxis. Examples: phrenic nerve, radial nerve, ilioinguinal nerve, sciatic nerve[FMA]. The peripheral nerves include the 12 cranial nerves, the spinal nerves and roots, and what are called the autonomic nerves that are concerned specifically with the regulation of the heart muscle, the muscles in blood vessel walls, and glands[BTO]. The nerves outside of the brain and spinal cord, including the autonomic, cranial, and spinal nerves. Peripheral nerves contain non-neuronal cells and connective tissue as well as axons. The connective tissue layers include, from the outside to the inside, the epineurium, the perineurium, and the endoneurium[GAID]. A peripheral nerve, or simply nerve is an enclosed, cable-like bundle of peripheral axons (the long, slender projections of neurons). A nerve provides a common pathway for the electrochemical nerve impulses that are transmitted along each of the axons. Nerves are found only in the peripheral nervous system. In the central nervous system, the analogous structures are known as tracts[WP].
SCTID:244457007
TODO - check definition vs nerve. See notes for cranial nerve II (optic nerve)
UBERON:0002003
UBERON:0003377
UMLS:C0031119
VHOG:0000901
XAO:0000204
http://upload.wikimedia.org/wikipedia/commons/thumb/b/ba/Nervous_system_diagram.png/200px-Nervous_system_diagram.png
ncithesaurus:Peripheral_Nerve
nerve part of peripheral nervous system
peripheral nerve tree
uberon
gray matter of neuraxis
AEO:0001012
EHDAA2:0003136
EHDAA2_RETIRED:0004658
FMA:67242
Heterogeneous cluster of neural somas in the brain and the spinal cord.
MA:0001112
Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]
OpenCyc:Mx4rwDdKMpwpEbGdrcN5Y29ycA
TAO:0002197
UBERON:0002020
UMLS:C0018220
VHOG:0001768
ZFA:0001681
gray mater
gray matter
grey matter
grey substance
http://upload.wikimedia.org/wikipedia/commons/thumb/d/d2/Spinal_nerve.svg/200px-Spinal_nerve.svg.png
ncithesaurus:Gray_Matter
neuronal grey matter
substantia grisea
uberon
hindbrain
AAO:0010150
ABA:HB
BTO:0000672
EFO:0000923
EHDAA2:0000746
EHDAA:3514
EHDAA:6487
EMAPA:16916
FMA:67687
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]
MA:0000195
MAT:0000107
MESH:A08.186.211.132.810
MIAA:0000107
NIF_GrossAnatomy:birnlex_942
Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]
TAO:0000029
The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]
The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. 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 (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA].
UBERON:0002028
UMLS:C0035507
VHOG:0000070
XAO:0000015
ZFA:0000029
http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/5/54/EmbryonicBrain.svg/200px-EmbryonicBrain.svg.png
in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps
ncithesaurus:Hind-Brain
relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]
rhombencephalic
rhombencephalon
uberon
epithelium of bronchus
An epithelium that is part of a bronchus [Automatically generated definition].
BTO:0001845
EFO:0000307
FMA:67782
MA:0001839
This class was created automatically from a combination of ontologies
UBERON:0002031
UMLS:C0599333
bronchi epithelial tissue
bronchi epithelium
bronchial epithelium
bronchial trunk epithelial tissue
bronchial trunk epithelium
bronchus epithelial tissue
bronchus epithelium
epithelial tissue of bronchi
epithelial tissue of bronchial trunk
epithelial tissue of bronchus
epithelium of bronchi
epithelium of bronchial trunk
ncithesaurus:Bronchial_Epithelium
uberon
striated muscle tissue
AAO:0010762
AEO:0000140
EHDAA2:0003140
FMA:67905
MA:0002438
OpenCyc:Mx4rwAoze5wpEbGdrcN5Y29ycA
Tissue which consists of striated muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue, Cardiac muscle tissue[FMA].
UBERON:0002036
UMLS:C1331262
Voluntary muscle tissue arranged in bundles of fibers.[AAO]
WBbt:0005779
galen:StriatedMuscle
ncithesaurus:Striated_Muscle_Tissue
striated muscle
uberon
cerebellum
AAO:0010485
ABA:CB
BM:CB
BTO:0000232
Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO]
EFO:0000327
EHDAA2:0000232
EMAPA:17787
EV:0100293
FMA:67944
GAID:595
However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG]
MA:0000198
MAT:0000110
MESH:A08.186.211.132.810.428.200
MIAA:0000110
NIF_GrossAnatomy:birnlex_1489
OpenCyc:Mx4rvl1eipwpEbGdrcN5Y29ycA
Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA].
SCTID:180924008
Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO]
TAO:0000100
UBERON:0002037
UMLS:C0007765
VHOG:0000024
XAO:0003098
ZFA:0000100
cerebellar
epencephalon-1
http://upload.wikimedia.org/wikipedia/commons/thumb/a/a7/Cerebellum_NIH.png/200px-Cerebellum_NIH.png
ncithesaurus:Cerebellum
note that almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem
uberon
substantia nigra
(...) the substantia nigra first appears in reptiles and is best developed in primates.[well established][VHOG]
BTO:0000143
EFO:0000922
EHDAA2:0004711
EV:0100247
FMA:67947
GAID:581
MA:0000210
MAT:0000504
MESH:A08.186.211.132.659.687
NIF_GrossAnatomy:birnlex_789
SCTID:279286002
Soemmering's substance
Subdivision of the midbrain anterior to the midbrain tegmentum which contains darkly pigmented neurons[FMA].
TODO: In BTO and NIF, part of basal ganglion which is part of telencephalon - but this is inconsistent with being part of midbrain, if these are spatially disjoint, as in ABA
UBERON:0002038
UMLS:C0038590
VHOG:0001573
http://upload.wikimedia.org/wikipedia/commons/5/5f/Midbraincrosssection.png
http://upload.wikimedia.org/wikipedia/commons/thumb/5/5f/Midbraincrosssection.png/200px-Midbraincrosssection.png
ncithesaurus:Substantia_Nigra
nucleus of basis pedunculi
substancia nigra
uberon
thyroid gland
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG]
A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO].
AAO:0010544
BTO:0001379
EFO:0000861
EHDAA2:0002028
EHDAA:2148
EHDAA:2975
EMAPA:17068
EMAPA:18827
EV:0100133
Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO]
FMA:9603
GAID:465
In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes
In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine)
In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species
MA:0000129
MAT:0000081
MESH:A06.407.900
MIAA:0000081
OpenCyc:Mx4rvVjLT5wpEbGdrcN5Y29ycA
SCTID:181117000
UBERON:0002046
UMLS:C0040132
VHOG:0000418
XAO:0000162
galen:ThyroidGland
glandula thyroidea
http://upload.wikimedia.org/wikipedia/commons/a/a3/Illu_thyroid_parathyroid.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/c/c6/Illu_endocrine_system.jpg/200px-Illu_endocrine_system.jpg
ncithesaurus:Thyroid_Gland
thyroid
uberon
lung
AAO:0000275
AAO:0010567
BTO:0000763
EFO:0000934
EHDAA2:0001042
EHDAA:1554
EHDAA:2205
EMAPA:16728
EV:0100042
Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
FMA:7195
GAID:345
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]
MA:0000415
MAT:0000135
MESH:A04.411
MIAA:0000135
OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA
Respiration organ present in all air-breathing animals whose principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere[WP]. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax[GO].
SCTID:181216001
UBERON:0002048
UMLS:C0024109
VHOG:0000310
XAO:0000119
galen:Lung
ncithesaurus:Lung
pulmo
pulmonary
respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi // Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
uberon
vasculature
BTO:0003718
FMA:69050
TAO:0005249
UBERON:0002049
ZFA:0005249
an interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.
http://upload.wikimedia.org/wikipedia/commons/thumb/2/29/Circulatory_System_en.svg/200px-Circulatory_System_en.svg.png
see also: vascular system. Consider merging?
uberon
vascular network
embryonic structure
AAO:0000138
AEO:0000125
Anatomical structure that is part of an embryo.
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
BILA:0000034
BTO:0000174
EFO:0000461
FBbt:00004208
FMA:69067
GAID:407
MESH:A16
Note in FMA embryo is_a embryonic structure
RETIRED_EHDAA2:0003169
SCTID:667009
TAO:0001105
UBERON:0002050
UMLS:C0013948
VSAO:0000178
XAO:0003042
ZFA:0001105
developing embryonic structure
developing structure
embryonale Struktur
embryonic anatomical structure
ncithesaurus:Embryonic_Structure
uberon
ciliary ganglion
EFO:0002559
EHDAA2:0000251
EHDAA:5623
EMAPA:18222
FMA:6964
Little is known about the development of parasympathetic neurons apart from the ciliary ganglion in chicks. Although there are considerable gaps in our knowledge, some of the mechanisms controlling sympathetic and enteric neuron development appear to be conserved between mammals, avians and zebrafish.[uncertain][VHOG]
MA:0001136
NIF_GrossAnatomy:nlx_anat_100304
SCTID:279281007
The ciliary ganglion is a parasympathetic ganglion located in the posterior orbit. It measures 1–2 millimeters in diameter and contains approximately 2,500 neurons. Preganglionic axons from the Edinger-Westphal nucleus form synapses with these cells. The postganglionic axons run in the short ciliary nerves and innervate two eye muscles: the sphincter pupillae constricts the pupil, known as Miosis. The opposite, Mydriasis, is the dilation of the pupil. the ciliaris muscle contracts, releasing tension on the Zonular Fibers, making the lens more convex, also known as accommodation. Both of these muscles are involuntary – they are controlled by the autonomic nervous system. It is one of four parasympathetic ganglia of the head and neck.. [WP,unvetted].
This class was created automatically from a combination of ontologies
UBERON:0002058
VHOG:0000805
ganglion ciliare
http://upload.wikimedia.org/wikipedia/commons/3/30/Augennerven.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/3/30/Augennerven.jpg/200px-Augennerven.jpg
uberon
umbilical vein
BTO:0001509
EFO:0001940
EHDAA:1034
EHDAA:488
EMAPA:16243
EMAPA:16375
EV:0100392
Extraembryonic part of the vein passing through the umbilical cord to the fetus and returning the purified and nutrient blood from the placenta. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]
FMA:70317
GAID:542
MA:0002249
MESH:A07.231.908.670.874
OpenCyc:Mx4rdu17MmWaEd2AAABQjYGu0g
RETIRED_EHDAA2:0002107
SCTID:367567000
The umbilical vein is a blood vessel present during fetal development that carries oxygenated blood from the placenta to the growing fetus. [WP,unvetted].
UBERON:0002066
UMLS:C0041637
VHOG:0000015
http://upload.wikimedia.org/wikipedia/commons/e/ee/Gray502.png
http://upload.wikimedia.org/wikipedia/commons/thumb/e/ee/Gray502.png/200px-Gray502.png
ncithesaurus:Umbilical_Vein
uberon
vena umbilicalis
dermis
A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]
AAO:0000128
BTO:0000294
EFO:0000953
EV:0100154
Editor notes: Consider adding a layer-of-skin grouping class for all skin layers
FMA:70323
GAID:1321
MA:0000152
MAT:0000153
MESH:A17.815.180
MIAA:0000153
SCTID:361696001
TAO:0001119
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
UBERON:0002067
UMLS:C0011646
VHOG:0000108
When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]
XAO:0000217
ZFA:0001119
corium
cutis
dermal
http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg
ncithesaurus:Dermis
uberon
vertebrate dermis
hypodermis
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]
AO Notes: BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypoderis and superficial fascia, and including these as part of the non-skin intgeument.
BTO:0001314
FMA:70544
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA].
TAO:0001136
UBERON:0002072
UMLS:C0278403
ZFA:0001136
http://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Skin.svg/200px-Skin.svg.png
hypoderm
hypodermal
ncithesaurus:Subcutis
sub-tegumental tissue
subcutaneous tissue
subcutis
subtegumental tissue
superficial fascia
tela subcutanea
uberon
vertebrate hypodermis
viscus
AAO:0010386
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. // An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.
BTO:0001491
EHDAA:512
EMAPA:16245
FMA:7085
MA:0000019
MESH:A01.960
RETIRED_EHDAA2:0002201
SCTID:118760003
UBERON:0002075
UMLS:C0042779
XAO:0003034
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs
ncithesaurus:Viscera
uberon
viscera
visceral organ
visceral organ system
cardiac atrium
AAO:0010246
BTO:0000903
Cardiac atria
Cardiac chamber which consists of a wall that surrounds the cavity of an atrium.[FMA]
EFO:0000277
EFO:0000314
EHDAA2:0000154
EHDAA:1265
EMAPA:16688
EV:0100019
FMA:7099
GAID:555
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]
MA:0000073
MAT:0000496
MESH:A07.541.358
One of four heart chambers.[TAO]
One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]
SCTID:261405004
TAO:0000471
This class was created automatically from a combination of ontologies
UBERON:0002081
UMLS:C0018792
VHOG:0000175
ZFA:0000471
atria
atrial tissue
atrium
atrium of heart
cardiac atria
galen:Atrium
heart atrium
ncithesaurus:Cardiac_Atrium
uberon
cardiac ventricle
A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO]
AAO:0010249
BTO:0000862
Cardiac chamber which consists of a wall that surrounds the cavity of a ventricle.
EFO:0000317
EHDAA2:0004164
EHDAA:1912
EMAPA:17331
EV:0100020
FMA:7100
GAID:568
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG]
MA:0000091
MAT:0000497
MESH:A07.541.560
One of four heart chambers.[TAO]
OpenCyc:Mx4rvVjj1pwpEbGdrcN5Y29ycA
SCTID:277699000
TAO:0000009
UBERON:0002082
UMLS:C0018827
VHOG:0000435
XAO:0003193
ZFA:0000009
galen:Ventricle
heart ventricle
lower chamber of heart
ncithesaurus:Cardiac_Ventricle
uberon
ventricle
ventricle of heart
postcranial axial skeleton
AAO:0000034
EHDAA2:0000161
EHDAA:5049
EMAPA:17214
EMAPA:18043
FMA:71221
MA:0002986
MAT:0000148
MIAA:0000148
Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]
TAO:0000317
The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]
The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]
The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]
The post-cranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
UBERON:0002090
VHOG:0000317
VSAO:0000093
XAO:0003073
ZFA:0000317
axial skeleton
post-cranial axial skeleton
previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed.
uberon
entire appendicular skeleton
AAO:0000747
EFO:0000951
FMA:71222
MA:0000290
MAT:0000278
MIAA:0000278
Note that ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved.
SCTID:322050006
Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]
Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]
Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm].
The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]
UBERON:0002091
UMLS:C0222646
VHOG:0001666
VSAO:0000076
XAO:0003166
appendicular skeleton
http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg
ncithesaurus:Appendicular_Skeleton
paired fin skeleton
skeleton appendiculare
uberon
mesentery
AAO:0011061
Anatomical organ component composed of a double layer of serous membrane that suspends a viscus from the body wall or connects adjacent viscera and in doing so conveys blood vessels, lymphatics and nerves to and from the viscera. Examples: greater omentum, broad ligament of uterus, sigmoid mesocolon.
BTO:0001380
EV:0100083
FMA:7144
GAID:21
MESH:A01.047.025.600.451
Note that in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: "In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.". TODO - check. Consider FMA:259286 - Region of mesentery.
SCTID:362707009
UBERON:0002095
UMLS:C0025474
galen:Mesentery
generic mesentery
http://upload.wikimedia.org/wikipedia/commons/1/19/Gray1038.png
http://upload.wikimedia.org/wikipedia/commons/thumb/1/19/Gray1038.png/200px-Gray1038.png
mesenteric
mesentery (generic)
ncithesaurus:Mesentery
uberon
skin of body
BTO:0001253
EFO:0000962
EHDAA2:0001844
EMAPA:17525
FMA:7163
MESH:A17.815
Nonparenchymatous organ that consists of the dermis and epidermis. Subdivisions of the skin surround various body parts; as a whole, the skin constitutes the external layer of the body. Examples: There is only one skin[FMA]. Surface structure that consists of the external membranous integument of the animal.
Note that FMA uses 'skin' for the entire organ. XAO seems consistent. MA seems to use it analagously to zone of skin
OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA
SCTID:181469002
UBERON:0002097
UMLS:C1123023
XAO:0000023
entire skin
galen:Skin
http://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Skin.svg/200px-Skin.svg.png
integument
ncithesaurus:Skin
pelt
skin
uberon
trunk
AAO:0010339
BILA:0000116
BTO:0001493
EFO:0000966
FMA:7181
MA:0000004
MAT:0000296
MIAA:0000296
OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA
Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]
Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]
Rumpf
SCTID:262225004
TAO:0001115
UBERON:0002100
UMLS:C0460005
XAO:0000054
XAO:0003025
ZFA:0001115
editor note - check AAO
galen:Trunk
ncithesaurus:Trunk
thoracolumbar region
torso
trunk region
uberon
limb
A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts.
AAO:0010336
AEO:0000172
EFO:0000876
EHDAA2:0003172
EHDAA:1697
EHDAA:8273
EMAPA:16405
FMA:24875
GAID:36
MA:0000007
MAT:0000090
MIAA:0000090
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
OpenCyc:Mx4rvn1uSZwpEbGdrcN5Y29ycA
Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO]
SCTID:243996003
UBERON:0002101
UMLS:C0015385
VHOG:0000336
VSAO:0000121
XAO:0003027
extremities
extremity
flipper
free limb
galen:Extremity
limb sensu vertebrata
ncithesaurus:Limb
pentadactyl limb
tetrapod limb
uberon
hindlimb
A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts.
AAO:0000219
AO notes: note that this corresponds to FMA:'free lower limb' (a limb segment), NOT 'lower limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton
BTO:0002345
CALOHA:TS-2215
EFO:0000883
EHDAA2:0001033
EHDAA:6094
EMAPA:17458
EV:0100015
FMA:24879
GAID:1221
GAID:38
Lower limb, which connects the pes with the pelvic girdle.[AAO]
MA:0000026
MAT:0000395
MESH:A13.473
MIAA:0000395
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
SCTID:182281004
UBERON:0002103
UMLS:C0023216
UMLS:C1522391
VHOG:0000337
VSAO:0000150
XAO:0003031
crural
free lower limb
free part of lower limb
galen:LowerExtremity
hind limb
hind-limb
hindlimb
http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray1239.png
http://upload.wikimedia.org/wikipedia/commons/thumb/d/dc/Gray1239.png/200px-Gray1239.png
inferior member
lower extremity
lower limb
membrum inferius
membrum inferius
ncithesaurus:Hind_Limb
ncithesaurus:Lower_Extremity
pelvic appendage
uberon
visual system
.
AAO:0000632
FMA:7191
MA:0002444
NIF_GrossAnatomy:FMAID_7191
OpenCyc:Mx4rvViCtpwpEbGdrcN5Y29ycA
SCTID:281831001
TAO:0001127
The sensory system used for sight.[AAO]
This class was created automatically from a combination of ontologies
UBERON:0002104
UMLS:C0587900
XAO:0003198
ZFA:0001127
ncithesaurus:Visual_System
uberon
visual organ system
vestibulo-auditory system
A sensory system for the sense of hearing[WP].
AAO:0000631
Auditory system is general anatomical term in FMA
FMA:7192
FMA:78500
MA:0002443
NIF_GrossAnatomy:nlx_anat_090817
OpenCyc:Mx4rvViwtJwpEbGdrcN5Y29ycA
TAO:0001138
The sensory system used for balance and hearing.[AAO]
UBERON:0002105
UMLS:C0587901
XAO:0003195
ZFA:0001138
auditory organ system
auditory system
auditory/vestibular system
http://upload.wikimedia.org/wikipedia/commons/d/d2/Anatomy_of_the_Human_Ear.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/7/7c/HumanEar.jpg/200px-HumanEar.jpg
ncithesaurus:Auditory_System
uberon
vestibuloauditory system
vestibuloauditory system
spleen
AAO:0010395
An organ involved in red blood cell filtration and immune response.[AAO]
BTO:0001281
EFO:0000869
EMAPA:18767
EV:0100055
FMA:7196
GAID:1289
MA:0000141
MAT:0000085
MESH:A15.382.520.604.713
MIAA:0000085
OpenCyc:Mx4rvVjgw5wpEbGdrcN5Y29ycA
Organ found in virtually all vertebrate animals with important roles in regard to red blood cells and the immune system. In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron. It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells.
SCTID:181279003
TAO:0000436
Taxon notes: Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96) [PMID:20959416]
UBERON:0002106
UMLS:C0037993
VHOG:0000120
With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG]
XAO:0000328
ZFA:0000436
galen:Spleen
http://upload.wikimedia.org/wikipedia/commons/d/d6/Illu_spleen.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/d/d6/Illu_spleen.jpg/200px-Illu_spleen.jpg
lien
lienal
ncithesaurus:Spleen
splenic
uberon
liver
AAO:0010111
AO notes: Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function. Taxon notes: WP: The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.[7] An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. // The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]
An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
BTO:0000759
EFO:0000887
EHDAA2:0000997
EHDAA:2197
EMAPA:16846
EV:0100089
FMA:7197
GAID:288
MA:0000358
MAT:0000097
MESH:A03.620
MIAA:0000097
OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA
Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
SCTID:181268008
TAO:0000123
UBERON:0002107
UMLS:C0023884
VHOG:0000257
XAO:0000133
ZFA:0000123
galen:Liver
hepatic
http://upload.wikimedia.org/wikipedia/commons/6/64/Leber_Schaf.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Leber_Schaf.jpg/200px-Leber_Schaf.jpg
iecur
jecur
ncithesaurus:Liver
relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
uberon
small intestine
AAO:0010397
BTO:0000651
EFO:0000841
EV:0100072
FMA:7200
GAID:313
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]
MA:0000337
MAT:0000047
MESH:A03.492.411.620
MIAA:0000047
OpenCyc:Mx4rvVjlIJwpEbGdrcN5Y29ycA
SCTID:181250005
Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].
TAO:0001323
The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO]
UBERON:0002108
UMLS:C0021852
VHOG:0000055
XAO:0000130
ZFA:0001323
anterior intestine
galen:SmallIntestine
http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/8/82/Stomach_colon_rectum_diagram.svg/200px-Stomach_colon_rectum_diagram.svg.png
intestinum tenue
mid intestine
ncithesaurus:Small_Intestine
small bowel
small intestine
uberon
gallbladder
AAO:0010114
BTO:0000493
EFO:0000853
EHDAA2:0000699
EHDAA:8062
EMAPA:17202
EV:0100090
FMA:7202
MA:0000356
MAT:0000072
MESH:A03.159.439
MIAA:0000072
Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
OpenCyc:Mx4rvVkGr5wpEbGdrcN5Y29ycA
Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO]
Rats do not have a gallbladder, but produce bile. The bile flows directly from the liver through the (hepatic) bile duct into the small intestine (Hebel and Stromberg, 1988)
SCTID:181269000
TAO:0000208
The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG]
UBERON:0002110
UMLS:C0016976
VHOG:0000221
XAO:0000135
ZFA:0000208
a small organ that aids digestion and stores bile produced by the liver[WP]. Organ with organ cavity which is continuous proximally with the cystic duct and distally terminates in the fundus of the gallbladder[FMA].
galen:Gallbladder
gall bladder
http://upload.wikimedia.org/wikipedia/commons/3/3f/Illu_pancrease.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/f/f4/Abdomal_organs.svg/200px-Abdomal_organs.svg.png
ncithesaurus:Gallbladder
relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
uberon
vesica fellea; vesica biliaris
kidney
A paired organ which has the production of urine as its primary function.
AAO:0000250
BTO:0000671
EFO:0000929
EV:0100096
FMA:7203
GAID:423
MA:0000368
MAT:0000119
MESH:A05.810.453
MIAA:0000119
One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]
OpenCyc:Mx4rvVjlYpwpEbGdrcN5Y29ycA
SCTID:181414000
UBERON:0002113
UMLS:C0022646
XAO:0003267
galen:Kidney
ncithesaurus:Kidney
renal
reniculate kidney
uberon
duodenum
AAO:0010402
BTO:0000365
EFO:0000851
EMAPA:18852
EV:0100073
FMA:7206
GAID:284
In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum.
In humans, the duodenum is a hollow jointed tube about 10–15 inches (25–38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz.
MA:0000338
MAT:0000044
MESH:A03.492.411.620.270
MIAA:0000044
OpenCyc:Mx4rv4LJDpwpEbGdrcN5Y29ycA
SCTID:181247007
The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).
The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
UBERON:0002114
UMLS:C0013303
VHOG:0000052
XAO:0000236
duodenal
galen:Duodenum
http://upload.wikimedia.org/wikipedia/commons/b/b3/Tractus_intestinalis_duodenum.svg
ncithesaurus:Duodenum
proximal intestine
uberon
upper intestine
ileum
AAO:0010403
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]
BTO:0000620
EFO:0001334
EV:0100075
FMA:7208
GAID:315
MA:0000339
MAT:0000282
MESH:A03.492.411.620.484
MIAA:0000282
OpenCyc:Mx4rvdcLHZwpEbGdrcN5Y29ycA
SCTID:181249005
TODO consider ZFA:0000706 posterior intestine, see also colon
The ileum is the final section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms posterior intestine or distal intestine may be used instead of ileum. [WP,unvetted].
UBERON:0002116
UMLS:C0020885
VHOG:0000647
XAO:0000237
distal intestine
galen:Ileum
http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg
ileal
intestinum ileum
lower intestine
ncithesaurus:Ileum
uberon
pronephros
A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG]
AAO:0011089
BTO:0001541
EFO:0000927
EHDAA2:0001570
EHDAA:1017
EMAPA:16579
FMA:72170
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]
In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO].
MAT:0000117
MIAA:0000117
Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104
Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO]
SCTID:308804007
TAO:0000151
The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO]
UBERON:0002120
UBERON:0005794
UMLS:C0231048
VHOG:0000037
XAO:0002000
ZFA:0000151
archinephron
embryonic kidney
ncithesaurus:Pronephros
pronephric
pronephric kidney
pronephron
uberon
parvocellular oculomotor nucleus
ABA:EW
BM:EW
FMA:72424
MA:0001071
NIF_GrossAnatomy:birnlex_822
SCTID:62088007
TAO:0000244
The Edinger-Westphal nucleus (also known as the accessory oculomotor nucleus) is the accessory parasympathetic cranial nerve nucleus of the oculomotor nerve, supplying the constricting muscles of the iris. Alternatively, the Edinger-Westphal nucleus is a term often used to refer to the adjacent population of non-preganglionic neurons that do not project to the ciliary ganglion, but rather project to the spinal cord, dorsal raphe nucleus, and septal nuclei. Unlike the classical, preganglionic Edinger-Westphal neurons that contain choline acetyltransferase, neurons of the non-preganglionic Edinger-Westphal nucleus have been shown to contain various stress- and feeding-related neuropeptides, such as Urocortin and cocaine- and amphetamine-regulated transcript. Proper nomenclature for this distinct brain region has not yet been established. [WP,unvetted].
This class was created automatically from a combination of ontologies
UBERON:0002141
ZFA:0000244
accessory oculomotor nucleus
edinger-westphal nucleus
nucleus Edinger-Westphal
oculomotor nucleus, parvocellular part
uberon
right lung
EHDAA2:0001730
EHDAA:4969
EMAPA:17661
FMA:7309
Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
MA:0000426
OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA
SCTID:361967000
This class was created automatically from a combination of ontologies
UBERON:0002167
UMLS:C0225706
VHOG:0000301
http://upload.wikimedia.org/wikipedia/commons/thumb/3/32/Gray972.png/200px-Gray972.png
ncithesaurus:Right_Lung
uberon
left lung
EHDAA2:0000943
EHDAA:4947
EMAPA:17653
FMA:7310
Lung which consists of the left upper lobe and left lower lobe.[FMA]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
MA:0000425
OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA
SCTID:361982005
This class was created automatically from a combination of ontologies
UBERON:0002168
UMLS:C0225730
VHOG:0000618
http://upload.wikimedia.org/wikipedia/commons/thumb/d/dd/Gray973.png/200px-Gray973.png
ncithesaurus:Left_Lung
uberon
bronchus
A portion of the airway that connects to the lungs[GO].
BTO:0001340
EFO:0000932
EV:0100041
Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
FMA:7409
GAID:346
In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue
MA:0000436
MAT:0000133
MESH:A04.411.125
MIAA:0000133
SCTID:181215002
UBERON:0002185
UMLS:C0006255
VHOG:0000262
XAO:0000121
bronchi
bronchial
bronchial tissue
bronchial trunk
http://upload.wikimedia.org/wikipedia/commons/1/18/Respiratory_system_complete_numbered.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/1/18/Respiratory_system_complete_numbered.svg/200px-Respiratory_system_complete_numbered.svg.png
ncithesaurus:Bronchus
uberon
hemolymphoid system
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
EHDAA2:0004615
EMAPA:18534
EMAPA:18765
FMA:74562
MA:0000013
UBERON:0002193
haemolymphoid system
hematolymphoid system
lymphomyeloid complex
uberon
adenohypophysis
AAO:0010540
BM:AHy
BTO:0000040
BTO:0000496
EFO:0000230
EHDAA2:0000109
EMAPA:17514
FMA:74627
It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]
MA:0000177
MESH:A06.407.747.608
NIF_GrossAnatomy:birnlex_1581
Region of the pituitary gland derived from the buccal protrusion consisting of three regions.[AAO]
SCTID:245532007
TAO:0001282
The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin. In contrast to mamalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish. Herzog et al, 2004.[TAO]
The glandular, anterior lobe of the pituitary gland. The anterior pituitary regulates several physiological processes including stress, growth, and reproduction[WP]. The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin. In contrast to mammalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish[ZFA].
UBERON:0002196
UMLS:C0032008
VHOG:0000141
ZFA:0001282
anterior hypophysis
anterior lobe (hypophysis)
anterior lobe of hypophysis
anterior lobe of pituitary
anterior lobe of pituitary gland
anterior pituitary
anterior pituitary gland
http://upload.wikimedia.org/wikipedia/commons/thumb/f/fb/Gray1181.png/200px-Gray1181.png
lobus anterior (glandula pituitaria)
lobus anterior hypophysis
ncithesaurus:Anterior_Lobe_of_the_Pituitary_Gland
note that BTO may contain an error here. Also note we may need to introduce taxon-specific developmental relationships: "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"[NBK53175]
pituitary gland, anterior lobe
uberon
neurohypophysis
AAO:0010537
BM:NY
BTO:0000937
EHDAA2:0001271
EHDAA:7536
EMAPA:17519
Editor note - request magnocellular cell from CL. Request oxytocin secretion from GO. Notes: "The hypophysis or pituitary gland is derived, in part from an ectodermal outpocketing of the stomodeum (Rathke's Pouch) and in part from the floor of the diencephalon" [http://syllabus.med.unc.edu/courseware/embryo_images/]
FMA:74628
It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]
MA:0000178
MESH:A06.407.747.734
NIF_GrossAnatomy:birnlex_1586
SCTID:245527006
TAO:0001271
The infundibular part of the pituitary gland consisting of two regions.[AAO]
UBERON:0002198
UMLS:C0032009
VHOG:0000142
ZFA:0001271
comprises the posterior lobe of the pituitary gland and is part of the endocrine system[WP].
http://upload.wikimedia.org/wikipedia/commons/thumb/b/b9/Pituitary_gland_representation.PNG/200px-Pituitary_gland_representation.PNG
infundibular process
lobus nervosus neurohypophysis
lobus posterior (glandula pituitaria)
lobus posterior hypophysis
ncithesaurus:Posterior_Lobe_of_the_Pituitary_Gland
neural lobe
neural lobe of pituitary
neural lobe of pituitary gland
neurohypophysis
pituitary gland, posterior lobe
posterior lobe of pituitary
posterior lobe of pituitary gland
posterior pituitary
posterior pituitary gland
uberon
integument
AAO:0000239
Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]
BTO:0000634
EHDAA2:0001844
FMA:74657
Hautsystem
MESH:A17.815
Surface structure that is the outer protective covering of the body.[VSAO]
TAO:0000368
The dermis, epidermis and hypodermis.
The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]
UBERON:0002199
Usage notes: in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates. Note that the VSAO class appears to include adnexa by its definition.
VSAO:0000029
ZFA:0000368
dermal system
dermoid system
galen:Integument
integumental
integumentary
integumentum commune
skin
tegument
the integument
uberon
vasculature of head
EFO:0003656
FMA:74710
TAO:0001267
This class was created automatically from a combination of ontologies
UBERON:0002200
Vasculature that is part of a head [Automatically generated definition].
XAO:0004152
ZFA:0001267
adult head vascular network
adult head vasculature
cranial vasculature
head vascular network
head vasculature
uberon
vascular network of adult head
vascular network of head
vasculature of adult head
vasculature of trunk
A vasculature that is part of a trunk [Automatically generated definition].
FMA:74712
TAO:0005024
This class was created automatically from a combination of ontologies
UBERON:0002201
ZFA:0005024
torso vascular network
torso vasculature
trunk vascular network
trunk vasculature
uberon
vascular network of torso
vascular network of trunk
vasculature of torso
musculoskeletal system
AAO:0010546
Anatomical system that consists of the muscular and skeletal systems.
Anatomical system that provides locomotion and physical support to the organism.[AAO]
EV:0100139
FMA:7482
GAID:98
MA:0002418
MESH:A02
OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g
SCTID:278858007
There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]
UBERON:0002204
UMLS:C0026860
VHOG:0001275
VSAO:0000031
XAO:0000168
musculo-skeletal system
musculoskeletal
ncithesaurus:Musculoskeletal_System
uberon
nerve root
BTO:0000883
FMA:5981
SCTID:362295007
UBERON:0002211
UMLS:C0228084
ncithesaurus:Nerve_Root
uberon
we make nerve root continuous_with nerve to avoid inconsistencies with the spatial disjointness constraint between PNS and CNS, with nerves part_of CNS. FMA has segment of nerve with subtypes: segment of sympathetic trunk, nerve root, nerve rootlet, nerve root proper
synovial joint
AEO:0000183
EHDAA2:0003183
FMA:7501
Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]
MA:0000322
OpenCyc:Mx4rv2bBV5wpEbGdrcN5Y29ycA
SCTID:113234001
TAO:0005153
This class was created automatically from a combination of ontologies
UBERON:0002217
ZFA:0005153
articulatio synoviale
diarthrodial joints
diarthroses
diarthrosis
diarthrosis joint
galen:SynovialJoint
uberon
thoracic cavity
Body cavity subdivision which is enclosed by the thoracic wall and the diaphragm[FMA].
FMA:7565
GAID:93
MA:0000032
MESH:A01.911.800
OpenCyc:Mx4rmvyleLfEEduAAAACs6hRXg
OpenCyc:Mx4rvhU_TpwpEbGdrcN5Y29ycA
SCTID:243949006
This class was created automatically from a combination of ontologies
UBERON:0002224
UMLS:C0230139
cavitas thoracis
cavity of chest
cavity of thorax
chest cavity
http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png
http://upload.wikimedia.org/wikipedia/commons/thumb/e/ee/Scheme_body_cavities-en.svg/200px-Scheme_body_cavities-en.svg.png
ncithesaurus:Thoracic_Cavity
pectoral cavity
space of thoracic compartment
uberon
spinal cord
(...) 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]
AAO:0010151
BM:SpC
BTO:0001279
EFO:0000110
EHDAA2:0001255
EHDAA:2863
EMAPA:17577
EMAPA:17700
EV:0100316
Elongated, approximately cylindrical part of the central nervous system that lies in the vertebral canal and from which the spinal nerves emerge.
FMA:7647
GAID:695
MA:0000216
MAT:0000183
MESH:A08.186.854
MIAA:0000183
NIF_GrossAnatomy:birnlex_1709
OpenCyc:Mx4rvVjjk5wpEbGdrcN5Y29ycA
Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]
SCTID:180959008
TAO:0000075
TODO: add superclass to unify with VNC?
UBERON:0002240
UMLS:C0037925
VHOG:0000601
XAO:0000020
ZFA:0000075
http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg
medulla spinalis
ncithesaurus:Spinal_Cord
spinal cord structure
spinal medulla
uberon
vomeronasal organ
(...) the vomeronasal organ is known only in some tetrapods. It is absent in most turtles, crocodiles, birds, some bats, and aquatic mammals. In amphibians, it is in a recessed area off the main nasal cavity. (...) In mammals possesing this organ, it is an isolated area of olfactory membrane within the nasal cavity that is usually connected to the mouth via the nasopalatine duct (reference 1); The opinions concerning the presence and functioning of the vomeronasal organ in humans are controversial. The vomeronasal cavities appear early in human foetuses. (...) Historical examination of the nasal septum revealed the presence of vomeronasal cavities in approximately 70% of adults. In contrast to the situation in other mammals, the organ is not supported by a rigid tube of bone or cartilage (reference 2); (...) the best evidence for the homology of the human VNO to that of other primates (and of mammals in general) is ontogenetic in nature, based on a common embryonic origin from a thickening (vomeronasal primordium) on the medial aspect of each olfactory pit (reference 3); (...) suggesting that lungfish possess a region homologous to the accessory olfactory bulb of tetrapods. Based on these results, it seems appropriate to refer to the recess epithelium as a primordium of the vomeronasal organ (reference 4). [debated][VHOG]
AAO:0000997
An organ thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base. [TFD][VHOG]
BTO:0002608
EFO:0001934
EHDAA2:0002211
EHDAA:7865
EMAPA:17612
FMA:77280
GAID:354
Jacobson's organ
MA:0000289
MESH:A04.531.591.940
SCTID:361346007
Taxon notes: Generally formed only in tetrapods; lungfish have rudimentary VN organs; true VN organs are not normally found in recent fishes, birds, aquatic reptiles, aquatic mammals (Bertmar 1980). Humans: Its presence in many animals has been widely studied and the importance of the vomeronasal system to the role of reproduction and social behavior (through influence on anterior hypothalamus) has been shown in many studies. Its presence and functionality in humans was controversial, though most studies agree the organ regresses during fetal development. Many genes essential for VNO function in animals (such as TRPC2) are non-functional in humans (Liman ER. Use it or lose it: molecular evolution of sensory signaling in primates. Pflugers Arch. 2006;453(2):125-31.)
The vomeronasal organ (VNO), or Jacobson's organ, is an auxiliary olfactory sense organ that is found in many animals. It was discovered by Ludwig Jacobson in 1813. During embryological development, it forms from the nasal (olfactory) placode, at the anterior edge of the neural plate. It is a chemoreceptor organ which is completely separated from the nasal cavity the majority of the time, being enclosed in a separate bony or cartilaginous capsule which opens into the base of the nasal cavity. It is a tubular crescent shape and split into two pairs, separated by the nasal septum. It is the first processing stage of the accessory olfactory system, after which chemical stimuli go to the accessory olfactory bulb, then to targets in the amygdala and hypothalamus. The vomeronasal organ is mainly used to detect pheromones, chemical messengers that carry information between individuals of the same species, hence is sometimes referred to as the 'sixth sense. ' The VNO has two separate types of neuronal receptors, V1R and V2R, which are seven-transmembrane receptors that are coupled to G proteins. The receptors are distinct from each other and form the large family of receptors in the main olfactory system. Evidence shows that the VNO responds to nonvolatile cues which stimulate the receptor neurons. Information is then transferred to the accessory olfactory bulb as well as other centres of the brain such as the anterior part of the hypothalamus. Its presence in many animals has been widely studied and the importance of the vomeronasal system to the role of reproduction and social behavior (through influence on anterior hypothalamus) has been shown in many studies. Its presence and functionality in humans is widely controversial, though most studies agree the organ regresses during fetal development. [WP,unvetted].
UBERON:0002255
VHOG:0000665
VNO
XAO:0000272
http://upload.wikimedia.org/wikipedia/commons/8/84/Gray51.png
http://upload.wikimedia.org/wikipedia/commons/thumb/8/84/Gray51.png/200px-Gray51.png
organ of Jacobsen
organon vomeronasale
organum vomeronasale
organum vomeronasale
uberon
dorsal root of spinal cord
BTO:0000360
FMA xref is 'general anatomical term'. We xref both to ensure equivalence.
FMA:5980
In anatomy and neurology, the dorsal root (or posterior root) is the afferent sensory root of a spinal nerve. At the distal end of the dorsal root is the dorsal root ganglion, which contains the neuron cell bodies of the nerve fibres conveyed by the root. If the dorsal root of a spinal nerve were severed it would lead to numbness in certain areas of the body. The lateral division of the dorsal root contains lightly myelinated and unmyelinated axons of small diameter. These transmit pain and temperature sensation from the body. These fibers cross through the anterior white commissure to form the Anterior lateral system in the lateral funiculus. The medial division of the dorsal root contains myelinated axons of larger diameter. These transmit information of discriminative touch, pressure, vibration, and conscious proprioception originating from spinal levels C2 through S5. These fibers are pushed in towards the posterior medial sulcus to form the fasciculus gracilis and the fasciculus cuneatus. [WP,unvetted].
NIF_GrossAnatomy:nlx_anat_20090208
SCTID:362436008
TAO:0000652
UBERON:0002261
UMLS:C0205955
ZFA:0000652
dorsal root
dorsal root of spinal nerve
dorsal spinal nerve root
http://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/d/d2/Spinal_nerve.svg/200px-Spinal_nerve.svg.png
ncithesaurus:Dorsal_Root_of_the_Spinal_Nerve
posterior root of spinal nerve
radix dorsalis
radix posterior
radix posterior (nervus spinalis)
radix sensoria (nervus spinalis)
sensory root of spinal nerve
uberon
lentiform nucleus
AO notes: the EMAPA class is unclear. Editor notes: TODO - add parts
BTO:0002250
EMAPA:18208
EMAPA:19147
EV:0100186
FMA:77615
MA:0000896
OpenCyc:Mx4rvvyH2ZwpEbGdrcN5Y29ycA
SCTID:279319002
The lentiform nucleus or lenticular nucleus comprises the putamen and the globus pallidus within the basal ganglia. It is a large, cone-shaped mass of gray matter just lateral to the internal capsule. [WP,unvetted]. The part of the corpus striatum somewhat resembling a biconvex lens, divided into an external, larger, lateral part (putamen) and an internal, smaller, lighter colored medial part (globus pallidus), which is in turn subdivided into a smaller, medial, and a larger, lateral part by the medial medullary lamina[BTO].
UBERON:0002263
UMLS:C0162342
http://upload.wikimedia.org/wikipedia/commons/f/fc/Gray741.png
http://upload.wikimedia.org/wikipedia/commons/thumb/f/fc/Gray741.png/200px-Gray741.png
lenticular nucleus
ncithesaurus:Lenticular_Nucleus
nucleus lenticularis
nucleus lentiformis
nucleus lentiformis
uberon
olfactory bulb
A bulbous anterior projection of the olfactory lobe that is the place of termination of the olfactory nerves and is especially well developed in lower vertebrates (as fishes)[BTO]. Segment of neural tree organ which is continuous with a set of olfactory nerves and an olfactory tract. In most vertebrates, the olfactory bulb is the most rostral (forward) part of the brain. In humans, however, the olfactory bulb is on the inferior (bottom) side of the brain. The olfactory bulb is supported and protected by the cribriform plate which in mammals, separates it from the olfactory epithelium, and which is perforated by olfactory nerve axons. The bulb is divided into two distinct structures, the main olfactory bulb, and the accessory olfactory bulb[WP].
AAO:0010165
ABA:OLF
BM:Tel-OB
BTO:0000961
EHDAA2:0004705
EV:0100173
FMA:77624
GAID:633
MA:0000194
MESH:A08.186.211.577.699.573
NIF_GrossAnatomy:birnlex_1137
Note that in uberon 'main olfactory bulb' is a separate class, but some ontologies may treat this as partially synonymous. The distinction may only make sense in tetrapods with a vomeronasal organ (olfactory nerves terminate in OB in fishes and in main OB in tetrapods - Butler and Hodos). Development notes: the olfactory bulbs develop as bilateral evaginations from a region of the prosencephalic neural plate intercalated between the septal and the cortical anlagen (Cobos et al. 2001b, Rubenstein et al. 1998). Comparing the structure of the olfactory bulb among vertebrate species, such as the leopard frog and the lab mouse, reveals that they all share the same fundamental layout(WP).
Part of the rostral part of the cerebrum where axons of olfactory cells from the nasal mucosa terminate. Projects onto olfactory parts of pallium via olfactory tracts
Part of the telencephalon comprised of anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits.[AAO]
SCTID:279394006
Segment of neural tree organ which is continuous with a set of olfactory nerves and an olfactory tract[FMA:77624].
TAO:0000402
The part of the forebrain in which the olfactory nerves end and the olfactory tracts originate. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
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]
UBERON:0002264
UMLS:C0028936
VHOG:0000033
XAO:0004180
ZFA:0000402
bulbus olfactorius
bulbus olfactorius
http://upload.wikimedia.org/wikipedia/commons/f/f9/1543,Vesalius%27OlfactoryBulbs.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/d/d2/1543%2CVesalius%27OlfactoryBulbs.jpg/200px-1543%2CVesalius%27OlfactoryBulbs.jpg
ncithesaurus:Olfactory_Bulb
olfactory lobe
uberon
olfactory organ
AAO:0010180
BTO:0001772
FMA:77659
UBERON:0002268
VHOG:0000287
XAO:0000273
note - fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
olfactory neuroepithelium
organ olfactus
organum olfactorium
uberon
medial zone of hypothalamus
ABA:MEZ
FMA:77683
MA:0000837
This class was created automatically from a combination of ontologies
UBERON:0002272
hypothalamus medial zone
uberon
lateral zone of hypothalamus
ABA:LZ
FMA:77684
MA:0000833
This class was created automatically from a combination of ontologies
UBERON:0002273
hypothalamus lateral zone
uberon
telencephalic ventricle
A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere
BM:Tel-LV
BTO:0000879
EFO:0001961
EHDAA2:0001984
EHDAA:3502
EHDAA:6576
EV:0100307
FMA:78448
GAID:611
MA:0000192
MESH:A08.186.211.276.650
NIF_GrossAnatomy:birnlex_1263
OpenCyc:Mx4rvYsFdZwpEbGdrcN5Y29ycA
SCTID:180930008
TAO:0000696
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]
The lateral ventricles are part of the ventricular system of the brain. Classified as part of the telencephalon, they are the largest of the ventricles. The lateral ventricles connect to the central third ventricle through the interventricular foramina of Monro[WP].
The two lateral ventricles are a cavity in each of the cerebral hemispheres derived from the cavity of the embryonic neural tube. They are separated from each other by the septum pellucidum, and each communicates with the third ventricle by the foramen of Monro, through which also the choroid plexuses of the lateral ventricles become continuous with that of the third ventricle[GO].
UBERON:0002285
UMLS:C0152279
VHOG:0000643
ZFA:0000696
forebrain ventricle
http://upload.wikimedia.org/wikipedia/commons/thumb/7/7d/Gray734.png/200px-Gray734.png
lateral ventricle
lateral ventricle of brain
modeled as space in EHDAA2
ncithesaurus:Lateral_Ventricle
tectal ventricle
telencephalic ventricle
telencephalic vesicle
telencephalon lateral ventricle
uberon
biliary system
Anatomical system that consists of the organs and ducts (bile ducts, gallbladder, and associated structures) that are involved in the production and transportation of bile.
FMA:79646
SCTID:361354009
This class was created automatically from a combination of ontologies
UBERON:0002294
biliary apparatus
http://upload.wikimedia.org/wikipedia/commons/thumb/5/5d/Digestive_system_showing_bile_duct.png/200px-Digestive_system_showing_bile_duct.png
uberon
dorsal mesentery
EHDAA2:0004560
EHDAA:3019
EHDAA:3033
EHDAA:3921
EHDAA:3934
EHDAA:3957
EHDAA:3971
FMA:79795
SCTID:308823000
TAO:0005130
The mesentery that originates from the dorsal side of the peritoneal cavity.[TAO]
The mesentery that originates from the dorsal side of the peritoneal cavity[ZFA].
UBERON:0002296
ZFA:0005130
dorsal mesogastrium
http://upload.wikimedia.org/wikipedia/commons/8/85/Gray985.png
http://upload.wikimedia.org/wikipedia/commons/thumb/8/85/Gray985.png/200px-Gray985.png
mesenterium dorsale commune
uberon
brainstem
'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN10:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions).
ABA:BS
BTO:0000146
EFO:0001962
EV:0100241
FMA:79876
MA:0000169
MESH:A08.186.211.132
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted].
NIF_GrossAnatomy:birnlex_1565
SCTID:180925009
TAO:0002156
UBERON:0002298
UMLS:C0006121
VHOG:0001457
ZFA:0001707
brain stem
http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png
http://upload.wikimedia.org/wikipedia/commons/thumb/b/b7/Gray719.png/200px-Gray719.png
ncithesaurus:Brain_Stem
truncus encephali
truncus encephalicus
uberon
nucleus of brain
FMA:83840
MA:0000811
Nucleus of neuraxis which is located within the brain. Example: pontobulbar nucleus, globose nucleus[FMA]. brain structure consisting of a relatively compact cluster of neurons. It is one of the two most common forms of nerve cell organization, the other being layered structures such as the cerebral cortex or cerebellar cortex. In anatomical sections, a nucleus shows up as a region of gray matter, often bordered by white matter. The vertebrate brain contains hundreds of distinguishable nuclei, varying widely in shape and size. A nucleus may itself have a complex internal structure, with multiple types of neurons arranged in clumps (subnuclei) or layers.[Wikipedia]
SCTID:426465002
UBERON:0002308
UMLS:C1706993
We considered merging with 'neural nucleus'
ZFA:0005575
brain nucleus
ncithesaurus:Brain_Nucleus
uberon
midbrain tectum
BM:MB-Tec
BTO:0001793
Dorsal part of the midbrain, consisting of the superior and inferior colliculi and the pretectal nuclei [MM, NIF]. The tectum is a region of the brain, specifically the dorsal part of the mesencephalon (midbrain). This is contrasted with the tegmentum, which refers to the region ventral to the ventricular system. It is derived in embryonic development from the alar plate of the neural tube. [WP,unvetted].
EFO:0000920
EHDAA2:0004474
EMAPA:19051
FMA:83902
In adult humans it is present only in the mesencephalon as the inferior and the superior colliculi[WP].
MA:0000211
MAT:0000451
NIF_GrossAnatomy:birnlex_1032
SCTID:362394008
TAO:0001353
The tectum - a multisensory, topologically mapped structure in the roof of the midbrain presents a remarkable degree of conservation in all vertebrate radiations; although it varies in the extent of its development in different vertebrate classes, there is considerable evidence now to deem its layered structure, its cell types, and its hodological pattern as homologous in all vertebrates.[well established][VHOG]
UBERON:0002314
UMLS:C0039433
VHOG:0001388
http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray685.png
http://upload.wikimedia.org/wikipedia/commons/thumb/c/cf/Gray685.png/200px-Gray685.png
mesencephalic tectum
ncithesaurus:Tectum_Mesencephali
neuraxis tectum
t. mesencephali
tectum
tectum mesencephali
uberon
white matter
AEO:0000139
AEO:0001011
CNS tracts and commissures
CNS white matter
Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929].
FMA:83929
MA:0001135
Multi-tissue structure comprised largely of myelinated axons.[TAO]
NIF_GrossAnatomy:Class_2
Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system.
OpenCyc:Mx4rwOAsDZwpEbGdrcN5Y29ycA
TAO:0000145
TAO:0002142
TAO:0002143
The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG]
UBERON:0002316
UMLS:C0682708
VHOG:0001764
ZFA:0001682
http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/d/d2/Spinal_nerve.svg/200px-Spinal_nerve.svg.png
ncithesaurus:White_Matter
neuronal white matter
substantia alba
uberon
white mater
white matter of neuraxis
white substance
coelemic cavity lumen
AEO:0000186
Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA].
BTO:0001707
EHDAA2:0000267
FBbt:00005060
FMA:85006
MA:0002447
RETIRED_EHDAA2:0003186
SCTID:361348008
TAO:0001438
Taxon notes: In mammals it forms the peritoneal, pleural, and pericardial cavities. editor note: check the FMA placement here; ncit placement of body cavity here probably not correct
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO].
UBERON:0000169
UBERON:0002323
UMLS:C0333343
ZFA:0001438
celom
coelom
coelome
coelomic cavity
coelomic cavity lumen
galen:BodyCavity
hemocoel
ncithesaurus:Cavity
space of body compartment
uberon
ventral body cavity
notochord
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]
AAO:0000327
Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]
BTO:0001768
Development notes: In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. // The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]
EHDAA2:0001277
EHDAA:1241
EHDAA:6021
EMAPA:16191
EV:0100002
FMA:85521
GAID:1311
MAT:0000281
MESH:A16.254.610
Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]
SCTID:308820002
Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]
TAO:0000135
UBERON:0002328
UMLS:C0028439
VHOG:0000199
VSAO:0000032
XAO:0000055
ZFA:0000135
a flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube.
embryonic notocord
http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Gray19_with_color.png/200px-Gray19_with_color.png
ncithesaurus:Notochord
notochorda
notochordal
notocord
relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]
uberon
somite
(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]
AAO:0010569
AEO:0001015
BTO:0001558
EHDAA2:0003436
EHDAA:366
EHDAA:699
Editor notes: currently classified as an epithelial vesicle, consistent with EHDAA2 and UBERONREF:0000002. Consider making "somitic mesoderm" a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk // When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]
FMA:85522
GAID:1306
MAT:0000068
MESH:A16.254.425.660.750
MIAA:0000068
Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]
Somites are spheres of epithelial cells that form sequentially along the anterior–posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.
TAO:0000155
UBERON:0002329
UMLS:C0376449
Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]
VHOG:0000191
XAO:0000058
ZFA:0000155
epithelial somite
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Gray19_with_color.png/200px-Gray19_with_color.png
mesodermal cluster
ncithesaurus:Somite
relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]
relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]
relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]
somites
somitic
somitic mesoderm
somitus
uberon
exocrine system
Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
EHDAA2:0002225
FMA:85539
MA:0002411
UBERON:0002330
UMLS:C1516995
WikipediaCategory:Exocrine_system
exocrine glandular system
ncithesaurus:Exocrine_System
uberon
umbilical cord
BTO:0001415
EFO:0001415
EHDAA2:0000312
EHDAA:158
EMAPA:26115
EV:0100127
FMA:85541
GAID:517
MAT:0000280
MESH:A16.254.789
MIAA:0000280
OpenCyc:Mx4rvyewDJwpEbGdrcN5Y29ycA
SCTID:280644003
See notes for connecting stalk
The connecting cord from the developing embryo or fetus to the placenta. During prenatal development, the umbilical cord comes from the same zygote as the fetus and (in humans) normally contains two arteries (the umbilical arteries) and one vein (the umbilical vein), buried within Wharton's jelly. The umbilical vein supplies the fetus with oxygenated, nutrient-rich blood from the placenta. Conversely, the umbilical arteries return the deoxygenated, nutrient-depleted blood[WP].
UBERON:0002331
UMLS:C0041633
birth cord
connecting stalk
funiculus umbilicalis
http://upload.wikimedia.org/wikipedia/commons/f/f3/Umbilicalcord.jpg
ncithesaurus:Umbilical_Cord
uberon
umbilical
yolk stalk
corpus callosum
BM:Tel-CC
BTO:0000615
EFO:0001390
EV:0100305
FMA:86464
GAID:683
In addition to the anterior commissure, placental mammals have a phylogenetically new forebrain commissure, the corpus callosum, which primarily interconnects the neocortex of the cerebral hemispheres.[well established][VHOG]
MA:0000188
MAT:0000286
MESH:A08.186.211.730.885.362
MIAA:0000286
NIF_GrossAnatomy:birnlex_1087
OpenCyc:Mx4rvbNzdZwpEbGdrcN5Y29ycA
SCTID:362354006
The corpus callosum is a thick bundle of nerve fibers comprising a commissural plate connecting the two cerebral hemispheres. It consists of contralateral axon projections that provides communications between the right and left cerebral hemispheres[GO].
The corpus callosum is found only in placental mammals. other groups do have other brain structures that allow for communication between the two hemispheres, such as the anterior commissure, which serves as the primary mode of interhemispheric communication in marsupials.
The largest commissure of the brain connecting the cerebral hemispheres. [TFD][VHOG]
UBERON:0002336
UMLS:C0010090
VHOG:0001608
http://upload.wikimedia.org/wikipedia/commons/a/aa/Gray733.png
http://upload.wikimedia.org/wikipedia/commons/thumb/a/aa/Gray733.png/200px-Gray733.png
ncithesaurus:Corpus_Callosum
uberon
neural crest
A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]
AAO:0010578
BTO:0001764
EHDAA2:0004419
Editor note: consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). Taxon notes: A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]. Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells.
FMA:86666
GAID:1310
MAT:0000066
MESH:A16.254.600
MIAA:0000066
Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]
SCTID:361462002
TAO:0000045
The neural crest, a transient component of the ectoderm, is located in between the neural tube and the epidermis (or the free margins of the neural folds) of an embryo during neural tube formation. Neural crest cells quickly migrate during or shortly after neurulation, an embryological event marked by neural tube closure.
UBERON:0002342
UMLS:C0027789
VHOG:0000057
We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]
XAO:0000048
ZFA:0000045
crista neuralis
http://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png
http://upload.wikimedia.org/wikipedia/commons/thumb/5/5f/Gray644.png/200px-Gray644.png
ncithesaurus:Neural_Crest
neural crest material
relationship type change: differentiates_from ectoderm (AAO:0000137) CHANGED TO: develops_from ectoderm (UBERON:0000924)[AAO]
uberon
neurectoderm
(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]
AAO:0011074
BILA:0000039
EHDAA2:0001248
EHDAA:1498
EHDAA:255
EMAPA:16073
EV:0100004
Embryonic ectoderm that gives rise to nervous tissue.
FBbt:00001061
FMA:87657
MAT:0000176
MIAA:0000176
TAO:0001120
Terminology notes: we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here
UBERON:0002346
UMLS:C1518271
VHOG:0000150
XAO:0000042
ZFA:0001120
epithelium tubi neuralis; neuroectoderma
ncithesaurus:Neuroectoderm
neuaral ectoderm
neural ectoderm
neurectodermal
neuroectoderm
presumptive central nervous system
uberon
ventral neurogenic region
myocardium
AAO:0010410
BTO:0000901
EFO:0000819
EHDAA2:0004150
EV:0100022
FMA:9462
GAID:173
MA:0000164
MAT:0000453
MESH:A02.633.580
OpenCyc:Mx4ro36AFrCvEduAAAAOpmP6tw
RETIRED_EHDAA2:0001220
Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
SCTID:362012001
TAO:0001319
TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium
The middle layer of the heart, consisting of cardiac muscle.[AAO]
UBERON:0002349
UMLS:C0027061
VHOG:0000083
XAO:0000065
ZFA:0001319
cardiac muscle
galen:Myocardium
heart muscle
heart muscle
heart myocardium
http://upload.wikimedia.org/wikipedia/commons/thumb/6/6e/Glanzstreifen.jpg/200px-Glanzstreifen.jpg
middle muscular layer of the heart wall[M-W]. Muscle layer of organ which has as its parts the myocardium proper and the conducting system of the heart[FMA].
muscle of heart
myocardial
ncithesaurus:Myocardium
uberon
conducting system of heart
EFO:0003909
EHDAA2:0004185
EV:0100025
Editor notes: EHDAA2 divides the system from the tissue
FMA:9476
MA:0000094
MESH:A07.541.409
SCTID:281489000
TAO:0005063
The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO]
The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG]
UBERON:0002350
VHOG:0001271
ZFA:0005063
cardiac conducting system
cardiac conduction system
cardiac impulse conducting system
cardionector
central conduction system
heart conduction system
impulse conducting system
uberon
atrioventricular node
EFO:0000276
EHDAA2:0004183
FMA:9478
GAID:558
MA:0000095
MAT:0000498
MESH:A07.541.409.147
OpenCyc:Mx4rMfD91mMcEd2AAABQjYGu0g
SCTID:277688002
Subdivision of conducting system of heart which is located in the muscular part of the interatrial septum that is continuous with the atrioventricular bundle.[FMA]
TAO:0005070
This class was created automatically from a combination of ontologies
Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG]
UBERON:0002352
UMLS:C0004247
VHOG:0001474
ZFA:0005070
aschoff-tawara node
atrioventricular nodal muscle tissue
atriovetricular node
av nodal muscle tissue
av node
http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png
http://upload.wikimedia.org/wikipedia/commons/thumb/9/92/Gray501.png/200px-Gray501.png
ncithesaurus:Atrioventricular_Node
node of tawara
nodus atrioventricularis
uberon
pelvis
BTO:0001006
EFO:0002805
EV:0100012
FMA:9578
GAID:87
MA:0000030
MESH:A01.673
Note that MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs
OpenCyc:Mx4rvVjiTJwpEbGdrcN5Y29ycA
SCTID:229765004
Subdivision of abdomen, which is demarcated from the abdomen proper by the plane of the superior pelvic aperture, and from the perineum by the inferior surface of the pelvic diaphragm; together with the abdomen proper, it constitutes the abdomen[FMA].
UBERON:0002355
UMLS:C0030797
galen:Pelvis
http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png
http://upload.wikimedia.org/wikipedia/commons/thumb/f/fe/Gray242.png/200px-Gray242.png
lesser pelvis
ncithesaurus:Pelvis
pelvic
pelvic region
pelvis region
true pelvis
uberon
serous pericardium
FMA:9582
MA:0002739
SCTID:243954002
Serous membrane which has as its parts the epicardium and parietal serous pericardium that surrounds pericardial cavity.
This class was created automatically from a combination of ontologies
UBERON:0002357
http://upload.wikimedia.org/wikipedia/commons/1/16/Gray968.png
http://upload.wikimedia.org/wikipedia/commons/thumb/1/16/Gray968.png/200px-Gray968.png
pericardium serosum
serous portion of pericardium
uberon
peritoneum
A serous membrane that forms the lining of the abdominal cavity or the coelom — it covers most of the intra-abdominal (or coelomic) organs — in higher vertebrates and some invertebrates (annelids, for instance). It is composed of a layer of mesothelium supported by a thin layer of connective tissue. The peritoneum both supports the abdominal organs and serves as a conduit for their blood and lymph vessels and nerves[WP]. The smooth transparent serous membrane that lines the cavity of the abdomen of a mammal and is folded inward over the abdominal and pelvic viscera[BTO]. The endothelial lining of the ABDOMINAL CAVITY. The parietal peritoneum covers the inside of the ABDOMINAL WALL and the visceral peritoneum covers the bowel, the MESENTERY, and certain of the organs. The portion that covers the bowel becomes the serosal layer of the bowel wall[GAID].
AAO:0010814
An epithelium that lines the peritoneal cavity.[TAO]
BTO:0001472
EV:0100087
FMA:9584
GAID:18
MESH:A01.047.025.600
OpenCyc:Mx4rvjJ72ZwpEbGdrcN5Y29ycA
Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO]
TAO:0005120
TODO - in ZFA is_a epithelium
UBERON:0002358
UMLS:C0031153
VHOG:0001257
XAO:0000139
ZFA:0005120
galen:Peritoneum
http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png
http://upload.wikimedia.org/wikipedia/commons/thumb/5/5f/Gray1040.png/200px-Gray1040.png
ncithesaurus:Peritoneum
peritonaeum
peritoneal
uberon
fibrous pericardium
EMAPA:19029
FMA:9586
MA:0002738
Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA]
SCTID:243953008
This class was created automatically from a combination of ontologies
UBERON:0002359
fibrous portion of pericardium
http://upload.wikimedia.org/wikipedia/commons/1/16/Gray968.png
http://upload.wikimedia.org/wikipedia/commons/thumb/1/16/Gray968.png/200px-Gray968.png
pericardium fibrosum
uberon
exocrine gland
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
AEO:0000097
BTO:0000765
EHDAA2:0003097
Editor's note: Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
FMA:9596
GAID:34
MA:0002564
MESH:A10.336
UBERON:0002365
UMLS:C0015282
ducted gland
glandula exocrina
ncithesaurus:Exocrine_Gland
uberon
prostate gland
BTO:0001129
EFO:0000858
EMAPA:19287
EV:0100104
FMA:9600
GAID:392
MA:0000404
MAT:0000078
MESH:A05.360.444.575
MIAA:0000078
OpenCyc:Mx4rv6trqZwpEbGdrcN5Y29ycA
SCTID:181422007
TODO - FMA treats the gland as part of the prostate - see also FMA:74119.
The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
UBERON:0002367
UMLS:C0033572
VHOG:0001261
galen:ProstateGland
http://upload.wikimedia.org/wikipedia/commons/a/a1/Prostatelead.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/a/a1/Prostatelead.jpg/200px-Prostatelead.jpg
male prostate
ncithesaurus:Prostate_Gland
prostata
prostate
prostatic
uberon
endocrine gland
AEO:0000098
BTO:0001488
EHDAA2:0003098
Endocrine glands are glands of the endocrine system that secrete their products, hormones, directly into the blood rather than through a duct. The main endocrine glands include the pituitary gland, pancreas, ovaries, testes, thyroid gland, and adrenal glands. The hypothalamus is a neuroendocrine organ. Other organs which are not so well known for their endocrine activity include the stomach, which produces such hormones as ghrelin[WP].
FMA:9602
GAID:335
MA:0002563
MESH:A06.407
OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA
SCTID:40818001
UBERON:0002368
UMLS:C0014133
ductless gland
ductless gland
glandula endocrina
glandulae endocrinae
http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png
ncithesaurus:Endocrine_Gland
uberon
adrenal gland
AAO:0010551
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]
Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO]
BTO:0000047
EFO:0000238
EMAPA:18426
EV:0100135
Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO].
FMA:9604
GAID:446
MA:0000116
MAT:0000071
MESH:A06.407.071
MIAA:0000071
OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA
SCTID:181127006
Taxon notes: The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole
UBERON:0002369
UMLS:C0001625
VHOG:0001141
XAO:0000164
adrenal
adrenal capsule
adrenal medulla cell
atrabiliary capsule
epinephric gland
epinephros
galen:AdrenalGland
glandula adrenalis
glandula suprarenalis
glandula suprarenalis
http://upload.wikimedia.org/wikipedia/commons/9/9d/Illu_endocrine_system_New.png
http://upload.wikimedia.org/wikipedia/commons/thumb/c/c6/Illu_endocrine_system.jpg/200px-Illu_endocrine_system.jpg
interrenal gland
ncithesaurus:Adrenal_Gland
suprarenal capsule
suprarenal gland
uberon
thymus
A thymus develops in all vertebrates from the endodermal epithelium of certain pharyngeal pouches and from the adjacent ectodermal epithelium. In fishes, all the pouches, or the first four, contribute to thymus formation, but in tetrapods, the number is more restricted. In mammals, only the third and fourth are involved, and the contribution of the third is by far the greater.[well established][VHOG]
AAO:0010548
Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop.
Anatomical structure which originates as several paired thickenings on the dorsal side of the pharyngeal pouches and secretes thymosin.[AAO]
BTO:0001374
EFO:0000860
EHDAA2:0002017
EHDAA:9119
EMAPA:18768
EV:0100138
FMA:9607
GAID:464
MA:0000142
MAT:0000080
MESH:A06.407.850
MIAA:0000080
OpenCyc:Mx4rvpIympwpEbGdrcN5Y29ycA
SCTID:118507000
TAO:0001078
UBERON:0002370
UMLS:C0040113
VHOG:0000253
XAO:0000163
ZFA:0001078
check - a subtype of gland? not in GO. NCIT has thymus and thymus gland. EHDAA2 has ductless gland.
http://upload.wikimedia.org/wikipedia/commons/c/cf/Illu_thymus.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/c/cf/Illu_thymus.jpg/200px-Illu_thymus.jpg
ncithesaurus:Thymus_Gland
thymic
thymus gland
uberon
bone marrow
AAO:0011007
BTO:0000141
BTO:0000829
EFO:0000868
EV:0100046
FMA:9608
GAID:1287
MA:0000134
MAT:0000084
MESH:A15.382.216
MIAA:0000084
OpenCyc:Mx4rvVm-FpwpEbGdrcN5Y29ycA
SCTID:421320006
TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs
The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]
UBERON:0002371
UMLS:C0005953
VHOG:0001218
XAO:0000123
anterior kidney
flexible tissue found in the hollow interior of bones. In adults, marrow in large bones produces new blood cells[WP].
galen:BoneMarrow
head kidney
http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg
kidney marrow
medulla of bone
medulla ossea
medulla ossium
ncithesaurus:Bone_Marrow
uberon
tonsil
BTO:0001387
EFO:0001401
EV:0100052
FMA:9609
GAID:341
MA:0000143
MESH:A03.867.603.925
Mandel
OpenCyc:Mx4rvVivrZwpEbGdrcN5Y29ycA
Portion of lymphoid tissue on either side of the throat.
UBERON:0002372
UMLS:C0836921
UMLS:C1519547
UMLS:C1519548
Usage notes: the term 'tonsil' can be ambiguous, sometimes refering specifically to the palatine tonsil, sometimes generically to include the cecal tonsils of avians. This class represents lymphoid tissue that is part of the tonsillar ring, in the mouth/throat region
VHOG:0001139
ncithesaurus:Tonsil
ncithesaurus:Tonsilar_Tissue
ncithesaurus:Tonsillar_Lymphoid_Tissue
uberon
connective tissue
AAO:0000098
AO notes: MA also has set of connective tissues
BTO:0000421
Bindegewebe
EFO:0000952
FMA:9640
GAID:100
MA:0000011
MAT:0000301
MESH:A10.165
MIAA:0000301
One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]
OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA
Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]
SCTID:361919005
TAO:0001641
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibres and ground substance.
UBERON:0002384
UMLS:C0009780
VSAO:0000017
XAO:0001017
ZFA:0001632
galen:ConnectiveTissue
ncithesaurus:Connective_Tissue
portion of connective tissue
textus connectivus
uberon
muscle tissue
AAO:0000306
AEO:0000122
EHDAA2:0003122
FMA:9641
MA:0002437
MESH:A02.633
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]
SCTID:91727004
UBERON:0002385
UMLS:C2328219
Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
galen:MuscleTissue
muscular tissue
ncithesaurus:Muscle_Tissue
portion of muscle tissue
textus muscularis
uberon
pes
BTO:0000476
EFO:0003065
EHDAA2:0000546
EMAPA:17459
Editors note: consider renaming using less human-centric terminology
FMA:9664
GAID:40
MA:0000044
MESH:A01.378.610.250
OpenCyc:Mx4rvVi-k5wpEbGdrcN5Y29ycA
SCTID:302545001
UBERON:0002387
UMLS:C0016504
VHOG:0000350
distal portion of the hind limb, including tarsal region, metatarsal region and digits.
foot
galen:Foot
hind foot
hind limb autopodium
hind paw
hind-paw
hindfoot
hindfoot of quadruped
hindlimb autopod
hindlimb autopodium
hindlimb distal free limb segment
http://upload.wikimedia.org/wikipedia/commons/a/ae/Male_Right_Foot_1.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/a/ae/Male_Right_Foot_1.jpg/200px-Male_Right_Foot_1.jpg
ncithesaurus:Foot
pedal
pes
terminal segment of free lower limb
uberon
hematopoietic system
AAO:0011002
Anatomical system that consists of the blood and blood forming tissues.[AAO]
BTO:0000570
Blutbildungssystem
EFO:0000798
EV:0100045
FMA:9667
GAID:1008
MA:0002434
MAT:0000022
MESH:A15.378
MIAA:0000022
SCTID:362587009
TAO:0005023
The tissues concerned in production of the blood, including the bone marrow, liver, lymph nodes, spleen, and thymus[BTO]. Anatomical system that consists of the blood and blood forming tissues. The bodily system of organs and tissues, primarily the bone marrow, spleen, tonsils, and lymph nodes, involved in the production of blood[FD].
This class was created automatically from a combination of ontologies
UBERON:0002390
UMLS:C0018957
VHOG:0001624
XAO:0000122
ZFA:0005023
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
haematological system
haematopoietic system
haemopoietic system
hematological system
hematolymphoid system
hemopoietic system
ncithesaurus:Hematopoietic_System
organa haemopoietica
uberon
lymph
BTO:0000855
EFO:0000871
ENVO:02000041
EV:0100049
FMA:9671
GAID:1186
MA:0002520
MAT:0000055
MESH:A12.207.630
MIAA:0000055
OpenCyc:Mx4rvpDOU5wpEbGdrcN5Y29ycA
This class was created automatically from a combination of ontologies
Transudate contained in the lumen of lymphatic vessel[FMA]. Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system[WP].
UBERON:0002391
UMLS:C0024202
VHOG:0001590
ZFA:0005658
galen:Lymph
http://upload.wikimedia.org/wikipedia/commons/1/19/Illu_lymph_capillary.png
lympha
ncithesaurus:Lymph
uberon
talus
BTO:0002354
EMAPA:18503
EMAPA:19135
FMA:9708
GAID:196
MA:0001351
MESH:A02.835.232.300.710.780
Os trigonum, Astralagus
SCTID:182098005
Taxon notes: The talus is apparently derived from the fusion of three separate bones in the feet of primitive amphibians; the tibiale, articulating with tibia, the intermedium, between the bases of the tibia and fibula, and the fourth centrale, lying in the mid-part of the tarsus. These bones are still partially separate in modern amphibians, which therefore do not have a true talus. The talus forms a considerably more flexible joint in mammals than it does in reptiles. This reaches its greatest extent in artiodactyls, where the distal surface of the bone has a smooth keel to allow greater freedom of movement of the foot, and thus increase running speed[WP]
UBERON:0002395
UMLS:C0039277
astragaloid bone
astragalus
astragalus bone
galen:Talus
http://upload.wikimedia.org/wikipedia/commons/a/a9/Subtalar_Joint.PNG
http://upload.wikimedia.org/wikipedia/commons/thumb/a/a9/Subtalar_Joint.PNG/250px-Subtalar_Joint.PNG
ncithesaurus:Talus
os tarsi tibiale
os trigonum
proximal tarsal bone resulting from fusion of intermedium and fibulare.
uberon
immune system
AAO:0011003
Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.
BILA:0000104
FMA:9825
GAID:328
MA:0002711
MESH:A15.382
OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA
SCTID:362590003
TAO:0001159
The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]
This class was created automatically from a combination of ontologies
UBERON:0002405
UMLS:C0020962
VHOG:0001247
XAO:0003152
ZFA:0001159
ncithesaurus:Immune_System
uberon
pericardial sac
FMA:9868
RETIRED_EHDAA2:0001443
SCTID:361326002
Serous sac, which has as parts the serous pericardium and the pericardial cavity [FMA].
TAO:0000054
UBERON:0002406
We follow FMA in dividing pericardial sac in pericardium and pericardial cavity
http://upload.wikimedia.org/wikipedia/commons/thumb/7/7e/Gray489.png/200px-Gray489.png
pericardium
uberon
pericardium
AAO:0010817
BTO:0000717
EFO:0000820
EHDAA:5376
EMAPA:17174
EV:0100023
FMA:9869
GAID:569
MA:0000099
MAT:0000454
MESH:A07.541.795
OpenCyc:Mx4rvoCLgJwpEbGdrcN5Y29ycA
Peritoneum that surrounds the heart.[AAO]
RETIRED_EHDAA2:0001443
SCTID:181295003
TAO:0000054
The outer membrane/wall of the developing heart, surrounding the myocardium.
UBERON:0002407
UMLS:C0031050
VHOG:0001280
We follow FMA in dividing pericardial sac in pericardium and pericardial cavity
XAO:0004182
ZFA:0000054
galen:Pericardium
http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png
http://upload.wikimedia.org/wikipedia/commons/thumb/7/7e/Gray489.png/200px-Gray489.png
ncithesaurus:Pericardium
pericardial
uberon
autonomic nervous system
AAO:0000033
ANS
BTO:0002507
EHDA:10095
EHDAA:3767
EMAPA:16984
FMA:9905
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]
GAID:706
MA:0000219
MESH:A08.800.050
NIF_GrossAnatomy:birnlex_1123
Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO]
SCTID:362481007
TAO:0001574
The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO].
This class was created automatically from a combination of ontologies
UBERON:0002410
UMLS:C0004388
VHOG:0000396
ZFA:0001574
divisio autonomica systematis nervosi peripherici
http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png
http://upload.wikimedia.org/wikipedia/commons/thumb/f/f7/Gray839.png/200px-Gray839.png
ncithesaurus:Autonomic_Nervous_System
uberon
visceral nervous system
clitoris
BTO:0002020
EHDAA2:0000255
EHDAA:9360
EMAPA:30819
FMA:9909
GAID:385
MA:0000382
MESH:A05.360.319.887.436
OpenCyc:Mx4rvVjr6ZwpEbGdrcN5Y29ycA
SCTID:181442003
The clitoris is a sexual organ that is present only in female mammals. In humans, the visible button-like portion is located near the anterior junction of the labia minora, above the opening of the urethra and vagina. Unlike the penis, which is homologous to the clitoris, the clitoris does not contain the distal portion of the urethra. The only known exception to this is in the Spotted Hyena. In this species, the urogenital system is unique in that the female urinates, mates and gives birth via an enlarged, erectile clitoris, known as a pseudo-penis. In humans, the clitoris is the most sensitive erogenous zone of a woman, the stimulation of which may produce sexual excitement and clitoral erection; its continuing stimulation may produce sexual pleasure in the woman and orgasm. [WP,unvetted].
UBERON:0002411
UMLS:C0008984
VHOG:0000700
clitoral
galen:Clitoris
http://upload.wikimedia.org/wikipedia/commons/c/cf/Clitoris_anatomy_labeled-en.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/c/cf/Clitoris_anatomy_labeled-en.svg/200px-Clitoris_anatomy_labeled-en.svg.png
ncithesaurus:Clitoris
uberon
integumental system
(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]
EFO:0000807
EHDAA2:0000836
EHDAA:6520
EMAPA:17524
EV:0100151
FBbt:00004969
FMA:72979
HAO:0000421
MA:0000014
MAT:0000033
MESH:A17
MIAA:0000033
SCTID:361692004
TADS:0000108
UBERON:0002416
UMLS:C0037267
VHOG:0000403
XAO:0000176
dermal system
in FMA, integumentary system = integument + certain glands. Note that here we use integumental system in a general sense, covering a variety of metazoans
integumentary system
integumentum commune
ncithesaurus:Integumentary_System
organ system that protects the body from damage, comprising the skin and its adnexa (including hair, scales, and nails). The integumentary system has a variety of functions; it may serve to waterproof, cushion and protect the deeper tissues, excrete wastes, regulate temperature and is the location of receptors for pain, sensation, pressure and temperature. In humans the integumentary system additionally provides vitamin D synthesis[WP].
uberon
abdominal segment of trunk
FMA:259211
MA:0000021
SCTID:362875007
UBERON:0002417
abdomen/pelvis/perineum
lower body
lumbar region
the abdominal segment of the torso.
uberon
cartilage tissue
A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO]
AAO:0000060
AEO:0000087
BTO:0000206
EFO:0000949
EHDAA2:0003087
EV:0100141
FMA:37377
GAID:99
MA:0000104
MAT:0000189
MESH:A02.165
MIAA:0000189
OpenCyc:Mx4rvVjeOZwpEbGdrcN5Y29ycA
Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG]
Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO]
Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W]
SCTID:309312004
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts[VSAO].
TAO:0001501
UBERON:0002418
UMLS:C0007301
VHOG:0001207
VSAO:0000040
XAO:0000170
ZFA:0005622
cartilage tissue
cartilages
cartilaginous tissue
chondrogenic tissue
galen:Cartilage
http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg
ncithesaurus:Cartilage
ncithesaurus:Cartilagenous_Tissue
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
uberon
skin gland
A gland that is part of a skin of body [Automatically generated definition].
FMA:71878
MA:0000146
UBERON:0002419
check FMA, use plural for now as general class not there
glandulae cutis
set of skin glands
skin glands
skin glands set
uberon
basal ganglion
BTO:0000235
EFO:0000904
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 set 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.
FMA:62514
SCTID:244434001
UBERON:0002420
basal ganglia
basal ganglion of telencephalon
basal nucleus
http://upload.wikimedia.org/wikipedia/commons/1/1b/Basal_Ganglia_and_Related_Structures.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/1/1b/Basal_Ganglia_and_Related_Structures.svg/200px-Basal_Ganglia_and_Related_Structures.svg.png
nuclei basales
one of a group of nuclei in the brains of vertebrates, situated at the base of the forebrain and strongly connected with the cerebral cortex, thalamus and other areas.ganglion in the head. The main components of the basal ganglia are the striatum, pallidum, substantia nigra, and subthalamic nucleus[WP]. Subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum[NIF].
uberon
hippocampal formation
ABA:HPF
BM:Tel-HF
BTO:0000601
FMA:74038
Hippocampus (proper) plus dentate gyrus and subiculum[definition derived from NIF comments and ontology alignment].
MA:0000189
NIF_GrossAnatomy:birnlex_715
SCTID:422867004
UBERON:0002421
Usage notes: The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum[NIF]. BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says "hippocampus" it means "hippocampal formation". In ABA HPF = (.. subiculum) + HIP, HIP = DG + AH.
archipallium
hippocampus
hippocampus (crosby)
major hippocampus
primal cortex
uberon
hepatobiliary system
AAO:0011056
EFO:0000800
EHDAA2:0000998
EHDAA:2189
EMAPA:16840
EV:0100088
MA:0000324
MAT:0000024
MIAA:0000024
TAO:0000036
The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct
UBERON:0002423
UMLS:C1711359
VHOG:0000294
XAO:0000132
ZFA:0000036
hepaticobiliary system
liver and biliary system
liver/biliary system
ncithesaurus:Hepatobiliary_System
uberon
chest muscle
A muscle organ that is part of a chest [Automatically generated definition].
BTO:0000508
FMA:9619
MA:0000548
UBERON:0002426
anterior thoracic region muscle organ
anterolateral part of thorax muscle organ
chest muscle organ
front of thorax muscle organ
muscle of thorax
muscle organ of anterior thoracic region
muscle organ of anterolateral part of thorax
muscle organ of chest
muscle organ of front of thorax
musculus thoracicus
thoracic muscle
uberon
limb bone
A bone that is part of a limb [Automatically generated definition].
AO notes: NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle // Note that the formal definition is very inclusive, and includes sesamoids
EFO:0000880
EFO:0000945
MAT:0000151
MIAA:0000151
SCTID:304149004
UBERON:0002428
UMLS:C0582791
bone of extremity
bone of limb
free limb bone
ncithesaurus:Bone_of_the_Extremity
uberon
lateral hypothalamic area
ABA:LHA
BM:Die-Hy-HLA
FMA:62030
GAID:640
MA:0000834
MESH:A08.186.211.730.385.357.300
NIF_GrossAnatomy:birnlex_4037
The lateral hypothalamus or lateral hypothalamic area is a part of the hypothalamus. It is concerned with hunger. Damage to this area can cause reduced food intake. Stimulating the lateral hypothalamus causes a desire to eat, while stimulating the ventromedial hypothalamus causes a desire to stop eating. [WP,unvetted].
UBERON:0002430
area hypothalamica lateralis
http://upload.wikimedia.org/wikipedia/commons/thumb/8/8c/HypothalamicNuclei.PNG/200px-HypothalamicNuclei.PNG
lateral division of hypothalamus
lateral group of hypothalamic nuclei
lateral hypothalamic group
lateral hypothalamic nucleus
lateral hypothalamic region
lateral hypothalamic zone (crosby)
uberon
striatum
A region of the forebrain consisting of the caudate nucleus, putamen and fundus striati.[GO].
ABA:STR
AO notes: FMA divides striatum of neuraxis into 4, neostriatum is seperate class. In NIF these are synonyms. TODO - check striatum vs corpus striatum see http://en.wikipedia.org/wiki/Striatum#History. Check caudoputamen
BM:N
BTO:0000418
EFO:0000109
FMA:77618
FMA:83683
MA:0000891
MESH:A08.186.211.730.885.105.487.550
NIF_GrossAnatomy:birnlex_1672
UBERON:0002435
corpus striatum
http://upload.wikimedia.org/wikipedia/commons/3/33/BrainCaudatePutamen.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/3/33/BrainCaudatePutamen.svg/200px-BrainCaudatePutamen.svg.png
ncithesaurus:Striatum
neostriatum
neuraxis striatum
striatal
striate nucleus
striatum of neuraxis
uberon
cerebral white matter
BTO:0000236
FMA:241998
MA:0000945
NIF_GrossAnatomy:birnlex_711
SCTID:361691006
UBERON:0002437
UMLS:C0152295
Usage notes: sometimes the term 'cerebral white matter' may be used generically but here is refers specifically to the white matter in a hemisphere. AO notes: The BTO class is inconsistent as it is part of the brain and spinal cord.
White matter that is part of a cerebral hemisphere.
cerebral hemisphere white matter
hemisphere white matter
ncithesaurus:Cerebral_White_Matter
uberon
ventral tegmental nucleus
ABA:VTN
AO notes: ventral and anterior tegmental nucleus are synonyms in FMA, but we split these into seperate classes. This is consistent with MA, ABA and neuronames, which treat these as distinct (NN suggest the anterior is a rodent specific structure). Location notes: this is part of pons and brainstem in MA, but this leads to an inconsistency with ABA. We err on the side of safety, and exclude the relationship to the pons here.
FMA:72435
MA:0001031
NIF_GrossAnatomy:birnlex_1421
SCTID:369244006
TAO:0000275
UBERON:0002438
ZFA:0000275
anterior tegmental nuclei
anterior tegmental nucleus
deep tegmental nucleus of Gudden
nucleus of Gudden
nucleus tegmentales anteriores
nucleus tegmentalis anterior
rostral tegmental nucleus
uberon
ventral raphe tegmental nucleus
ventral tegmental nuclei
ventral tegmental nucleus (gudden)
ventral tegmental nucleus of gudden
patella
A large sesamoid bone found in the distal femur/proximal tibial region of the hindlimb of tetrapods. The patella is the attachment site for proximal hindlimb tendons.[PHENOSCAPE:ad]
FMA:24485
GAID:203
MA:0001374
MESH:A02.835.232.500.624
SCTID:182083008
The patella, also known as the knee cap or kneepan, is the largest sesamoid bone in the human body. The primary functional role of the patella is knee extension. The patella has convergently evolved in placental mammals and birds; marsupials have only rudimentary, non-ossified patellae. In more primitive tetrapods, including living amphibians and reptiles, the muscle tendons from the upper leg are attached directly to the tibia, and the patella is not present. See also: fabella.
UBERON:0002446
UMLS:C0030647
galen:Patella
http://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/9/9a/Knee_diagram.svg/200px-Knee_diagram.svg.png
knee bone
knee cap
ncithesaurus:Patella
patella
patellar
uberon
lymphoid system
EFO:0000870
EHDAA2:0001043
EHDAA:8677
FMA:74594
GAID:931
MA:0002435
MAT:0000197
MIAA:0000197
OpenCyc:Mx4rwQAKT5wpEbGdrcN5Y29ycA
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]
SCTID:362589007
TAO:0000385
Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG]
The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system (Wikipedia).
UBERON:0002096
UBERON:0002465
UMLS:C0024235
VHOG:0000842
We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments.
XAO:0003199
ZFA:0000385
http://upload.wikimedia.org/wikipedia/commons/b/b3/TE-Lymphatic_system_diagram.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/3/36/Illu_capillary_microcirculation.jpg/200px-Illu_capillary_microcirculation.jpg
lymphatic circulatory system
lymphatic system
ncithesaurus:Lymphatic_System
systema lymphoideum
uberon
autopod region
BTO:0004359
EFO:0000877
FMA:83015
MA:0002714
MAT:0000091
MIAA:0000091
Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton.
SCTID:95936004
Terminal segment of free upper limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot
UBERON:0002470
UMLS:C0687080
autopod
autopodial limb segment
autopodial segment
autopodium
autopodium region
distal free limb segment
distal segment of free limb
ncithesaurus:Paw
paw
pod
uberon
zeugopod
EFO:0000878
FMA:83016
MA:0002716
MAT:0000092
MIAA:0000092
The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus).
There exists some controversy about which podial segments are present in some fishes, e.g. if the autopod is not newly evolved in tetrapods, there is a question as to which segments are actually present in basal vertebrate taxa.[PHENOSCAPE:curators]
UBERON:0002471
epipodium
middle free limb segment
middle limb segment
middle part of limb
middle segment of free limb
uberon
zeugopod limb segment
zeugopodial
zeugopodial limb segment
zeugopodium
zygopod
zygopodium
stylopod
EFO:0000879
FMA:83014
MA:0002717
MAT:0000093
MIAA:0000093
Naming conventions for pod terms under discussion within phenoscape group
The proximal free limb segment. Includes as parts the stylopod skeleton.
UBERON:0002472
propodium
proximal free limb segment
proximal part of limb
proximal segment of free limb
stylopodial
stylopodial limb segment
stylopodium
uberon
intercerebral commissure
Class of unpaired telencephalic white matter structures consisting of fiber pathways which project across the midsagittal plane and which serve to interconnect telencephalic structures lying within the contralateral cerebral hemisphere[FMA].
FMA:67930
MA:0002721
UBERON:0002473
brain commissure
interhemispheric commissure
uberon
bone tissue
FMA:224804
MA:0002780
MESH:A02.835.232
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts[VSAO].
UBERON:0002481
UMLS:C0391978
VSAO:0000047
ZFA:0005621
calcium tissue
galen:BoneTissue
ncithesaurus:Bone_Tissue
osseous tissue
osteogenic tissue
uberon
long bone
BTO:0004256
Endochondral_ossification is an essential process during the rudimentary formation of long bones, with the exception of the clavicle[Wikipedia:Endochondral_ossification]. The medial and and lateral ends undergo EO, the mid-portion is formed by a process with features of EO & IO (the process is shared by the mandible)[ISBN:9780397517251]
FMA:7474
Long bone is a limb bone that is subcylindrical and has a shaft with periosteum separating the ends of the bones. Long bones are present only in the limbs[VSAO].
MA:0002802
OpenCyc:Mx4rv6axr5wpEbGdrcN5Y29ycA
SCTID:332709000
UBERON:0002495
UMLS:C0222647
galen:LongBone
ncithesaurus:Long_Bone
uberon
endochondral bone
AAO:0010776
AEO:0000083
BTO:0002157
EHDAA2:0003083
Replacement bone that forms within cartilage.
Replacement bone that forms within cartilage.[VSAO]
TAO:0001591
UBERON:0002513
VSAO:0000145
XAO:0004018
ZFA:0001591
cartilaginous bone
http://purl.obolibrary.org/obo/uberon/references/reference_0000009
http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg
note that some structures, e.g. in ZFA are both intramembrane and endochondral. Editor notes: placement in this class to be inferred
ossified chondrogenic bone
uberon
intramembranous bone
Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO]
Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP].
TAO:0001644
UBERON:0002514
ZFA:0001635
[In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO]
membrane bone
uberon
limb segment
A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles.
FMA:241863
MA:0002889
UBERON:0002529
UMLS:C1268195
extremity part
free limb segment
limb region
ncithesaurus:Extremity_Part
note FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z
region of limb
segment of limb
subdivision of limb
uberon
gland
A gland is an organ in an animal's body that synthesizes a substance for release such as hormones or breast milk, often into the bloodstream (endocrine gland) or into cavities inside the body or its outer surface (exocrine gland). A gland is an organ specialised for secretion[GO].
AAO:0000212
AEO:0000096
BTO:0000522
Druese
EFO:0000797
EHDAA2:0003096
EHDAA:2161
EHDAA:4475
EHDAA:6522
EMAPA:18425
FBbt:00100317
FMA:86294
HAO:0000375
MAT:0000021
MIAA:0000021
OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA
SCTID:134358001
UBERON:0002530
UBERON:MIAA_0000021
UMLS:C1285092
WikipediaCategory:Glands
galen:Gland
glandula
glandular
http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png
ncithesaurus:Gland
uberon
epiblast (generic)
BTO:0004593
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]
In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]
MAT:0000067
MIAA:0000067
MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class
UBERON:0002532
VHOG:0000243
blastocyst
ectoblast
epiblast
epiblastus
http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png
primitive ectoderm
uberon
pharyngeal arch
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.[well established][VHOG]
AAO:0010359
BTO:0001785
EFO:0000959
EHDAA:571
EMAPA:16117
GAID:1292
MAT:0000242
MESH:A16.254.160
MIAA:0000242
Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering
One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches
One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
SCTID:308766004
TAO:0001306
UBERON:0002539
UMLS:C0080322
VHOG:0000155
XAO:0000096
ZFA:0001306
arcus pharyngei
branchial arch
http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png
http://upload.wikimedia.org/wikipedia/commons/thumb/8/8b/Gray41.png/200px-Gray41.png
ncithesaurus:Pharyngeal_Arch
pharyngeal arches
uberon
visceral arch
digit
AAO:0011126
EFO:0000881
EMAPA:32725
FMA:85518
MA:0000690
MAT:0000285
MIAA:0000285
OpenCyc:Mx4rvzLD_ZwpEbGdrcN5Y29ycA
Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG]
SCTID:361367007
UBERON:0002544
UMLS:C0582802
VHOG:0000944
XAO:0003032
digital
galen:Digit
limb digit
ncithesaurus:Digit
one of several most distal parts of a limb, such as fingers or toes, present in many vertebrates[WP].
todo homology ZFA:0001588-pectoral fin distal radial. Note: This term is a GAT in FMA. Note: we elect to place a strict taxon constraint on this class - this is controversial, and may be weakened later on - see [Wikipedia:Digit_(anatomy)#Evolution]. AO notes: EMAPA mapping from TH
uberon
cranial placode
AAO:0010466
EFO:0001650
Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.
Editor note: to avoid confusion, we include neurogenic placode as a subclass. Do not merge. Terminological notes: The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. Taxon notes: Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons[PMID:11523831].
MAT:0000369
MIAA:0000369
UBERON:0002546
XAO:0000305
placode
uberon
anatomical cavity
Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.
FMA:67552
NIF_GrossAnatomy:birnlex_1011
UBERON:0002553
cavity
galen:Cavity
uberon
limbic lobe
FMA:72719
NIF_GrossAnatomy:birnlex_1128
SCTID:279215006
The limbic lobe (also known as the Cingulate) is a portion of the brain associated with functions such as olfaction and emotion. It contains parts of other lobes, including the frontal, parietal, and temporal. Its main components are the fornicate gyrus, the hippocampus, and the amygdala It is related to the term limbic system, but unlike that term, 'limbic lobe' is a part of the Terminologia Anatomica, and there is less disagreement over what is included in the 'limbic lobe' than there is over what is included in the 'limbic system'. [WP,unvetted].
UBERON:0002600
fornicate gyrus
grande lobe limbique of broca
http://upload.wikimedia.org/wikipedia/commons/7/7e/Human_brain_inferior-medial_view_description.JPG
http://upload.wikimedia.org/wikipedia/commons/thumb/7/7e/Human_brain_inferior-medial_view_description.JPG/200px-Human_brain_inferior-medial_view_description.JPG
limbic lobe (carpenter)
lobus limbicus
uberon
fasciolar gyrus
ABA:FC
BTO:0002497
FMA:61921
NIF_GrossAnatomy:birnlex_1129
SCTID:279210001
TODO - existing definitions, synonyms and relationships in existing AOs seem contradictory; to be resolved. We take the dentate gyrus relationship from BTO, and it is also implied by the FMA synonym. However, FMA says archiortex (embryonic archicortex corresponds to the cortex of the dentate gyrus and hippocampus) and NIF says limbic lobe (which is more general than hippocampus). ABA xref made on basis of BTO related synonym
UBERON:0002601
a small paired band that passes around the splenium of the corpus callosum from the lateral longitudinal stria to the dentate gyrus[Biology-Online]. A posterior and upward extension of the dentate gyrus, forming a transitional area between the dentate gyrus and the indusium griseum[BTO].
fasciola cinerea
gyrus fasciolaris
retrosplenial gyrus of hippocampus
uberon
regional part of brain
A multi-tissue structure that is part of a brain [Automatically generated definition].
FMA:55676
NIF_GrossAnatomy:birnlex_1167
SCTID:384763002
UBERON:0002616
UMLS:C0445620
anatomical structure of brain
biological structure of brain
brain anatomical structure
brain biological structure
brain part
ncithesaurus:Brain_Part
neuraxis segment
segment of brain
uberon
regional part of cerebral cortex
A regional part of brain that is part of a cerebral cortex [Automatically generated definition].
FMA:242193
MA:0000187
NIF_GrossAnatomy:birnlex_1173
SCTID:119408004
UBERON:0002619
UBERON:0003208
cerebral cortex part
cerebral cortex region
neocortex region
region of cerebral cortex
segment of cerebral cortex
todo - check MA term
uberon
cerebral peduncle
BM:CP
BTO:0004676
EFO:0001987
FMA:62394
NIF_GrossAnatomy:birnlex_1202
SCTID:362391000
The cerebral peduncle, by most classifications, is everything in the mesencephalon except the tectum. The region includes the midbrain tegmentum, crus cerebri, substantia nigra and pretectum. By this definition, the cerebral peduncles are also known as the basis pedunculi, while the large ventral bundle of efferent fibers is referred to as the crus cerebri or the pes pedunculi There are numerous nerve tracts located within this section of the brainstem. Of note, in the cerebral peduncular loop fibers from motor areas of the brain project to the cerebral peduncle and then project to various thalamic nuclei. In as much as the peduncles are an anatomic landmark, for details regarding the function of this area interested readers are referred to the individual referenced articles. On a broad scale, though, this area contains many nerve tracts conveying motor information to and from the brain to the rest of the body. Important fibers running through the cerebral peduncles include the corticospinal tract and the corticobulbar tract, among others. [WP,unvetted].
UBERON:0002623
UMLS:C0007793
cerebral peduncle
http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray689.png
http://upload.wikimedia.org/wikipedia/commons/thumb/e/e9/Gray689.png/200px-Gray689.png
ncithesaurus:Cerebral_Peduncle
peduncle of midbrain
pedunculus cerebri
pedunculus cerebri
uberon
regional part of midbrain tegmentum
A multi-tissue structure that is part of a midbrain tegmentum.
FMA:62399
NIF_GrossAnatomy:birnlex_1227
UBERON:0002635
midbrain tegmentum segment
segment of midbrain tegmentum
uberon
regional part of metencephalon
A regional part of brain that is part of a metencephalon [Automatically generated definition].
FMA:67942
NIF_GrossAnatomy:birnlex_1361
UBERON:0002680
metencephalon subdivision
segment of metencephalon
uberon
ventral tegmental area
ABA:VTA
BM:MB-VTA
EFO:0001935
FMA:72438
GAID:587
MESH:A08.186.211.132.659.822.820
NIF_GrossAnatomy:birnlex_1415
The ventral tegmentum (tegmentum is Latin for covering), better known as the ventral tegmental area (VTA), is a group of neurons located close to the midline on the floor of the midbrain. The VTA, the origin of dopaminergic cell bodies that comprise the mesocorticolimbic dopamine system, is widely implicated in the drug and natural reward circuitry of the brain, cognition, motivation, drug addiction, and several psychiatric disorders. The VTA contains neurons that project to numerous areas of the brain, from the prefrontal cortex (PFC) to the caudal brainstem and everywhere in between. [WP,unvetted].
UBERON:0002691
http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png
http://upload.wikimedia.org/wikipedia/commons/thumb/b/b6/Gray712.png/200px-Gray712.png
uberon
ventral tegmental area of tsai
ventral tegmental nucleus (tsai)
ventral tegmental nucleus of tsai
cuneiform nucleus
ABA:CUN
BM:MB-CNF
FMA:72427
NIF_GrossAnatomy:birnlex_1430
UBERON:0002696
parabigeminal area (mai)
uberon
trochlear nucleus
ABA:IV
BM:MB-IV
EV:0100251
FMA:54518
MA:0001075
NIF_GrossAnatomy:birnlex_1488
SCTID:280163001
TAO:0000450
The nucleus of the trochlear nerve is located in the midbrain, at the level of the inferior colliculus. It is a motor nucleus, so located near the midline. Oddly, fibers from the trochlear nucleus cross over in the midbrain at the superior medullary velum and exit posteriorly, (this is the only cranial nerve to do so). The nerve then goes around the midbrain, and is visible coming out the sides. [WP,unvetted].
UBERON:0002722
ZFA:0000450
fourth cranial nerve nucleus
http://upload.wikimedia.org/wikipedia/commons/c/c6/Drn.png
http://upload.wikimedia.org/wikipedia/en/thumb/c/c6/Drn.png/200px-Drn.png
motor nucleus IV
nIV
nucleus nervi trochlearis
nucleus nervi trochlearis
nucleus of trochlear nerve
trochlear IV nucleus
trochlear motor nucleus
uberon
regional part of thalamus
A regional part of brain that is part of a thalamus [Automatically generated definition].
FMA:67705
NIF_GrossAnatomy:birnlex_1517
SCTID:119406000
UBERON:0002730
segment of thalamus
thalamus segment
uberon
regional part of forebrain
A regional part of brain that is part of a forebrain [Automatically generated definition].
FMA:61996
NIF_GrossAnatomy:birnlex_1677
UBERON:0002780
forebrain segment
segment of forebrain
uberon
regional part of diencephalon
A regional part of brain that is part of a diencephalon [Automatically generated definition].
FMA:62005
NIF_GrossAnatomy:birnlex_1685
SCTID:119264001
UBERON:0002784
diencephalon segment
uberon
regional part of telencephalon
A regional part of brain that is part of a telencephalon [Automatically generated definition].
FMA:62374
NIF_GrossAnatomy:birnlex_1700
UBERON:0002791
segment of telencephalon
telencephalon segment
uberon
regional part of midbrain
A regional part of brain that is part of a midbrain [Automatically generated definition].
FMA:61997
NIF_GrossAnatomy:birnlex_763
SCTID:119239004
UBERON:0002950
midbrain segment
segment of midbrain
uberon
regional part of midbrain tectum
A regional part of brain that is part of a midbrain tectum [Automatically generated definition].
FMA:62398
NIF_GrossAnatomy:birnlex_795
UBERON:0002966
midbrain tectum segment
segment of midbrain tectum
uberon
cingulate gyrus
A gyrus in the medial part of the brain. It partially wraps around the corpus callosum and is limited above by the cingulate sulcus. The cortical part of the cingulate gyrus is referred to as cingulate cortex.[Wikipedia]. The cingulate gyrus receives inputs from the anterior nucleus of the thalamus and the neocortex, as well as from somatosensory areas of the cerebral cortex. It projects to the entorhinal cortex via the cingulum. It functions as an integral part of the limbic system, which is involved with emotion formation and processing, learning, and memory. Also, executive control needed to suppress inappropriate unconscious priming is known to involve the anterior cingulate gyrus. It is also involved in respiratory control.
BM:Tel-CG
BTO:0003976
FMA:62434
NIF_GrossAnatomy:birnlex_798
SCTID:279208003
UBERON:0002967
UMLS:C0018427
cingulate area
cingulate region
falciform lobe
http://upload.wikimedia.org/wikipedia/commons/thumb/d/dc/Gray727_cingulate_gyrus.png/200px-Gray727_cingulate_gyrus.png
ncithesaurus:Cingulate_Gyrus
uberon
upper limbic gyrus
substantia nigra pars lateralis
ABA:SNI
FMA:76844
MA:0001065
NIF_GrossAnatomy:birnlex_866
Regional part of substantia nigra consisting of loosely packed cells, generally located ventral and lateral to the pars compacta. Many cells in this region use GABA as a neurotransmitter (MM).
Substantia nigra, lateral part
UBERON:0002995
disjointness violation - relationship: part_of UBERON:0001966
lateral part of substantia nigra
pars lateralis
uberon
lobe parts of cerebral cortex
FMA:68603
NIF_GrossAnatomy:birnlex_922
UBERON:0003022
cerebral cortical segment
check w.r.t regional part of cerebreal cortex
regional organ part of cerebral cortex
segment of cerebral cortex
uberon
central gray substance of midbrain
ABA:PAG
BM:MB-PAG
BTO:0002701
EFO:0002470
EV:0100249
FMA:74510
GAID:585
MA:0000209
MA:0002895
MESH:A08.186.211.132.659.822.595
NIF_GrossAnatomy:birnlex_973
Periaqueductal gray (PAG; also called the 'central gray') is the gray matter located around the cerebral aqueduct within the midbrain. It plays a role in the descending modulation of pain and in defensive behaviour. The ascending pain and temperature fibers of the spinothalamic tract also send information to the PAG via the spinomesencephalic tract. The spinomesencephalic tract is so-named because the fibers originate in the spine and terminate in the mesencephalon, another name for the midbrain, the part of the brain in which the PAG resides. [WP,unvetted].
SCTID:369233003
TAO:0000518
TODO - resolve MA - see tracker
UBERON:0003040
ZFA:0000518
anulus of cerebral aqueduct
central (periaqueductal) gray
central grey
griseum centrale
http://upload.wikimedia.org/wikipedia/commons/d/da/Cn3nucleus.png
http://upload.wikimedia.org/wikipedia/commons/thumb/d/da/Cn3nucleus.png/200px-Cn3nucleus.png
midbrain periaqueductal grey
periaquectuctal grey
periaqueductal gray
periaqueductal gray matter
periaqueductal gray of tegmentum
periaqueductal grey
periaqueductal grey matter
periaqueductal grey substance
s. grisea centralis
substantia grisea centralis
uberon
regional part of hypothalamus
A regional part of brain that is part of a hypothalamus [Automatically generated definition].
FMA:67706
NIF_GrossAnatomy:birnlex_995
SCTID:360454003
UBERON:0003048
hypothalamus segment
segment of hypothalamus
uberon
olfactory placode
A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity.
AAO:0011076
EFO:0003420
EHDAA2:0001232
EHDAA:1504
EMAPA:16543
Olfactory placodes are the only ectodermal placodes to produce glia, a cell type typically derived from neural crest // Note that NBK53171 classifies this as non-neurogenic
TAO:0000048
UBERON:0003050
VHOG:0000186
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG]
XAO:0000005
ZFA:0000048
nasal I placode
nasal placode
olfactory placodes
placoda nasalis
placoda olfactoria
uberon
periderm
A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis.
EHDAA2:0001846
EHDAA:6538
EVL
Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)
TAO:0001185
The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]
UBERON:0003055
UMLS:C1518973
VHOG:0001680
XAO:0000029
ZFA:0001185
epidermis epithelial layer
epidermis outer layer
ncithesaurus:Periderm
periderm
relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]
skin periderm
uberon
pre-chordal neural plate
(...) 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]
AAO:0011084
TAO:0007016
The portion of neural plate anterior to the mid-hindbrain junction.
This class was created automatically from a combination of ontologies
UBERON:0003056
VHOG:0001200
XAO:0000045
ZFA:0007016
anterior neural plate
uberon
chordal neural plate
(...) 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]
TAO:0007017
The portion of neural plate posterior to the mid-hindbrain junction.
This class was created automatically from a combination of ontologies
UBERON:0003057
VHOG:0001201
XAO:0000046
ZFA:0007017
posterior neural plate
uberon
presomitic mesoderm
AAO:0011086
EFO:0001982
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]
PSM
TAO:0000279
UBERON:0003059
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. <a href='http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-PUB-961014-576'>Kimmel et al, 1995.</a>
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]
VHOG:0000559
XAO:0000057
ZFA:0000279
presumptive somite mesoderm
segmental plate
somitogenic mesoderm
uberon
unsegmented mesenchyme
unsegmented paraxial mesoderm
pronephric duct
(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]
AAO:0011088
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]
In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP].
SCTID:361406002
TAO:0000150
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]
UBERON:0003060
UMLS:C1283945
VHOG:0000082
XAO:0000063
ZFA:0000150
archinephric duct
ductus pronephricus
ncithesaurus:Pronephric_Duct
uberon
blood island
AAO:0011006
AO notes: EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac
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].
EFO:0003489
EHDAA:207
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]
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]
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]
TAO:0000094
TE:E5.11.2.0.0.0.4
UBERON:0003061
UMLS:C1511224
VBI
VHOG:0000085
XAO:0000067
ZFA:0000094
blood islands
caudal hematopoietic tissue
ncithesaurus:Blood_Island
posterior ICM
posterior blood island
relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]
uberon
ventral blood island
ventral lateral plate mesoderm
intermediate mesoderm
(...)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]
AAO:0010575
EMAPA:16178
IM
Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]
SCTID:361476001
TAO:0001206
The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads.
UBERON:0003064
UMLS:C1284010
VHOG:0000087
XAO:0000085
ZFA:0001206
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Gray19_with_color.png/200px-Gray19_with_color.png
intermediate mesenchyme
intermediate plate mesoderm
mesenchyma intermedium
ncithesaurus:Intermediate_Mesoderm
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').
uberon
pharyngeal arch 2
2
2nd arch
2nd pharyngeal arch
2nd visceral arch
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]
AAO:0010363
EHDAA2:0000050
EHDAA:611
EMAPA:16272
In XAO, develops from visceral pouch 2
SCTID:308768003
TAO:0001596
The second of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
UBERON:0003066
VHOG:0000297
XAO:0000098
ZFA:0001611
arcus pharyngeus secundus
assists in forming the side and front of the neck.
branchial arch 2
http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png
http://upload.wikimedia.org/wikipedia/commons/thumb/8/8b/Gray41.png/200px-Gray41.png
hyoid arch
hyoid bars
ncithesaurus:Second_Pharyngeal_Arch
pharyngeal arch 2
pharyngeal arches 2
second branchial arch
second pharyngeal arch
second visceral arch
uberon
visceral arch 2
axial mesoderm
AAO:0011017
EFO:0003647
TAO:0001204
The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.
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]
UBERON:0003068
VHOG:0000107
XAO:0000205
ZFA:0001204
chordamesoderm
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Gray19_with_color.png/200px-Gray19_with_color.png
uberon
eye primordium
AAO:0011038
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
EFO:0003541
EHDAA2:0004431
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.
TAO:0000570
UBERON:0003071
UBERON:0005060
XAO:0000227
XAO:0004090
ZFA:0000570
eye anlage
eye field
eye placode
occular primordium
ocular primordium
optic field
optic placode
optic placode of camera-type eye
optic primordium
uberon
optic cup
(...) 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]
EHDAA2:0001303
EHDAA:2912
EMAPA:16674
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].
SCTID:308789007
TAO:0001202
UBERON:0003072
UMLS:C0231109
VHOG:0000167
ZFA:0001202
eye cup
ncithesaurus:Optic_Cup
ocular cup
uberon
lens placode
(...) 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]
A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP].
AAO:0011055
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]
EFO:0003494
EHDAA2:0000982
EHDAA:2908
EMAPA:16672
Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]
TAO:0000122
UBERON:0003073
UMLS:C1517770
VHOG:0000166
XAO:0000240
ZFA:0000122
http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png
ncithesaurus:Lens_Placodes
placoda lentis
uberon
mesonephric duct
(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]
AAO:0000637
Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO]
EHDAA2:0001243
EHDAA:1590
EMAPA:16577
GAID:1315
Leydig's duct
MESH:A16.254.940
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].
SCTID:308800003
TAO:0000546
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.
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]
UBERON:0003074
UMLS:C0043204
VHOG:0000082
Wolffian duct
XAO:0000242
ZFA:0000546
archinephric duct
ductus mesonephricus; ductus Wolffi
http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png
http://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Gray1109.png/200px-Gray1109.png
ncithesaurus:Mesonephric_Duct
renal duct
uberon
neural plate
(...) 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]
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]
AAO:0011072
BTO:0001765
EHDAA:346
EHDAA:902
EMAPA:16095
EMAPA:16527
EMAPA:16756
RETIRED_EHDAA2:0001252
TAO:0000132
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]
UBERON:0003075
UMLS:C0920623
VHOG:0000068
XAO:0000249
ZFA:0000132
http://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png
lamina neuralis
ncithesaurus:Neural_Plate
presumptive central nervous system
uberon
posterior neural tube
(...) 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]
AAO:0011082
TAO:0007037
This class was created automatically from a combination of ontologies
UBERON:0003076
VHOG:0001383
XAO:0000250
ZFA:0007037
uberon
paraxial mesoderm
AAO:0010568
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)
EFO:0003515
EMAPA:16183
EMAPA:16751
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]
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]
SCTID:361475002
TAO:0000255
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]
UBERON:0003077
UMLS:C1284009
VHOG:0000114
XAO:0000259
ZFA:0000255
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Gray19_with_color.png/200px-Gray19_with_color.png
mesoderma paraxiale
ncithesaurus:Paraxial_Mesoderm
paraxial mesenchyme
somitic mesoderm
uberon
floor plate
A ventral region of glial cells in the neural tube that provides inductive signals for the specification of neuronal cell types. The floor plate is evident at the ventral midline by the neural fold stage[GO]. A structure integral to the developing nervous system of vertebrate organisms. Located on the ventral midline of the embryonic neural tube, the floor plate is a specialized glial structure that spans the anteroposterior axis from the midbrain to the tail regions. It has been shown that the floor plate is conserved among vertebrates with homologous structures in invertebrates such as the fruit fly Drosophila and the nematode C. elegans. Functionally, the structure serves as an organizer to ventralize tissues in the embryo as well as to guide neuronal positioning and differentiation along the dorsoventral axis of the neural tube[WP].
AAO:0011041
BTO:0001720
EFO:0003473
FP
Note that although this is classically defined as being located on the neural tube, in many AOs the floor plate continues post-embryonically after the neural tube has ceased to exist. Consider 'floor plate of neural tube'.
Organizing center consisting of a small group of cells located at the ventral midline of the neural tube that influences the development of the nervous system, governing the specification of neuronal cell types and directing axonal trajectories.[AAO]
RETIRED_EHDAA2:0000545
TAO:0000022
UBERON:0003079
ZFA:0000022
bodenplatte
floorplate
http://upload.wikimedia.org/wikipedia/commons/8/89/Gray642.png
http://upload.wikimedia.org/wikipedia/commons/thumb/8/89/Gray642.png/200px-Gray642.png
uberon
ventral plate
anterior neural tube
(...) 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]
AAO:0011012
TAO:0007038
UBERON:0003080
VHOG:0001384
XAO:0000307
ZFA:0007038
editor note: TODO - add grouping class for the anterior end of the neural tube at all stages
uberon
lateral plate mesoderm
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]
AAO:0010574
AO notes: subclass of mesoderm in ZFA.
EHDAA2:0000919
EHDAA:379
EMAPA:16179
Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]
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].
SCTID:361477005
TAO:0000121
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]
UBERON:0003081
UBERON:0006258
UMLS:C1517749
VHOG:0000118
XAO:0000311
ZFA:0000121
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
http://upload.wikimedia.org/wikipedia/commons/thumb/6/64/Gray19_with_color.png/200px-Gray19_with_color.png
lateral mesoderm
lateral plate
lateral plate mesenchyme
mesoderma laminae lateralis
ncithesaurus:Lateral_Mesoderm
uberon
myotome
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]
AAO:0011067
AEO:0001018
BTO:0000742
EHDAA2:0003431
EHDAA:1721
EHDAA:1727
EHDAA:1733
EHDAA:1739
Editors note: The term "myotome" is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class.
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]
Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]
SCTID:344535001
TAO:0001056
UBERON:0003082
UMLS:C1513802
VHOG:0001244
XAO:0000315
ZFA:0001056
http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png
http://upload.wikimedia.org/wikipedia/commons/thumb/9/96/Gray65.png/200px-Gray65.png
muscle plate
myomere
myomeres
myotome region
myotomes
myotomus
ncithesaurus:Myotome_Region
uberon
trunk neural crest
AAO:0010582
EFO:0003605
EHDAA2:0001901
Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO]
TAO:0001024
This class was created automatically from a combination of ontologies
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].
UBERON:0003083
VHOG:0000062
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
XAO:0000319
ZFA:0001024
trunk crest
uberon
heart primordium
AAO:0011044
BTO:0001887
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]
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.
TAO:0000028
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]
UBERON:0003084
UMLS:C1514450
XAO:0000336
ZFA:0000028
editor note: should probably be fused with heart rudiment.
fused heart primordium
ncithesaurus:Primordium_of_the_Heart
relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]
uberon
sclerotome
AAO:0010571
AEO:0000212
AO notes: part_of somite in XAO
EHDAA2:0003439
Skeletogenic portion of somites.[AAO]
TAO:0001080
The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]
UBERON:0003089
UMLS:C0183176
VHOG:0000680
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].
XAO:0000397
ZFA:0001080
http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png
http://upload.wikimedia.org/wikipedia/commons/thumb/9/96/Gray65.png/200px-Gray65.png
ncithesaurus:Sclerotome
sclerotomes
sclerotomus
uberon
thyroid primordium
AAO:0011106
BTO:0004709
EHDAA2:0002033
EHDAA:952
EMAPA:16361
EMAPA:16558
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
TAO:0001081
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.
UBERON:0003091
UMLS:C1519512
XAO:0000444
ZFA:0001081
ncithesaurus:Thyroid_Primordium
uberon
cranial neural crest
AAO:0010580
Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]
EFO:0003645
EHDAA2:0004420
EMAPA:16091
Neural crest that is part of the head.[TAO]
TAO:0001194
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].
This class was created automatically from a combination of ontologies
UBERON:0003099
VHOG:0000063
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
XAO:0001001
ZFA:0001194
cephalic neural crest
crista neuralis cranialis
head crest
head neural crest
uberon
female organism
AAO:0010030
BILA:0000028
CARO:0000028
FBbt:00007011
FMA:67812
Gonochoristic organism that can produce female gametes.
HAO:0000028
SCTID:362608006
TAO:0000303
TGMA:0001839
UBERON:0003100
XAO:0003005
ZFA:0000303
female
female human body
uberon
male organism
AAO:0010033
BILA:0000027
CARO:0000027
FBbt:00007004
FMA:67811
Gonochoristic organism that can produce male gametes.
HAO:0000027
SCTID:362609003
TAO:0000242
TGMA:0001838
UBERON:0003101
WBbt:0007850
XAO:0003006
ZFA:0000242
male
male human body
uberon
surface structure
AAO:0010337
AEO:0000010
EHDAA2:0003010
Organism subdivision that is the collection of anatomical structures on the body surface[ZFA].
Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]
TAO:0000292
UBERON:0003102
VSAO:0000001
XAO:0003028
ZFA:0000292
anatomical surface feature
galen:SurfaceRegion
surface feature
surface region
uberon
compound organ
AAO:0010015
AEO:0000024
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.
BILA:0000024
CARO:0000024
EHDAA2:0003024
HAO:0000024
TADS:0000598
TAO:0000496
TGMA:0001837
UBERON:0003103
VHOG:0001723
XAO:0003041
ZFA:0000496
organ
uberon
mesenchyme
A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]
AAO:0010427
AEO:0000145
BTO:0001393
EHDAA2:0003145
EV:0100007
Editors notes: the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense
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]
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].
TAO:0000393
UBERON:0003104
UMLS:C0162415
VHOG:0000170
XAO:0003046
ZFA:0000393
http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/f/f4/Mesenchymal_Stem_Cell.jpg/200px-Mesenchymal_Stem_Cell.jpg
mesenchyma
mesenchymal
mesenchymal tissue
mesenchyme tissue
ncithesaurus:Mesenchyme
portion of mesenchymal tissue
portion of mesenchyme tissue
uberon
dermatocranium
AAO:0010154
Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO]
Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO]
Editor notes: wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007
Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified].
TAO:0000863
UBERON:0003113
VHOG:0001665
XAO:0003169
ZFA:0000863
dendrocranium
dermal bone cranium
dermal part of skull
exocranium
roof of skull
roofing bones of the skull
skull roof
uberon
pharyngeal arch 3
3
3rd arch
3rd pharyngeal arch
3rd visceral arch
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]
AAO:0010365
EHDAA2:0000069
EHDAA:1080
EMAPA:16399
SCTID:308769006
TAO:0001598
The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[AAO]
The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus.
UBERON:0003114
VHOG:0000298
XAO:0000447
ZFA:0001606
branchial arch 1
first branchial arch
first gill arch
gill arch 1
in XAO, called branchial arch 1 and df VP3
third pharyngeal arch
third visceral arch
uberon
visceral arch 3
chorion
BTO:0000252
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"].
EFO:0002780
EHDAA2:0000245
EHDAA:150
EMAPA:16112
EV:0100121
FMA:80224
GAID:1299
MESH:A16.254.403.473
Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]
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.
The outer membrane enclosing the embryo in reptiles, birds, and mammals. [TFD][VHOG]
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].
UBERON:0003124
UMLS:C0008503
UMLS:C1516505
VHOG:0000200
chorion (vertebrates)
chorion frondosum
chorionic
chorionic sac
embryonic chorion
fetal chorion
http://upload.wikimedia.org/wikipedia/commons/5/51/Gray24.png
ncithesaurus:Chorion
ncithesaurus:Chorionic_Sac
uberon
trachea
AAO:0010140
An elongated tube which carries air to and from the lungs.[AAO]
BTO:0001388
EFO:0000935
EHDAA2:0002066
EHDAA:3078
EMAPA:16853
EV:0100040
FMA:7394
GAID:361
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]
MA:0000441
MAT:0000137
MESH:A04.889
MIAA:0000137
OpenCyc:Mx4rvViOX5wpEbGdrcN5Y29ycA
SCTID:181213009
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.
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]
The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph].
UBERON:0003126
UMLS:C0040578
VHOG:0000371
XAO:0000118
cartilaginous trachea
http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/c/c3/Illu_conducting_passages.jpg/200px-Illu_conducting_passages.jpg
ncithesaurus:Trachea
tracheal
tracheal tubule
uberon
vertebrate trachea
windpipe
cranium
BTO:0001328
EFO:0000831
EHDAA:6029
FMA:71325
MA:0000316
MAT:0000340
MIAA:0000340
OpenCyc:Mx4rvVlEyJwpEbGdrcN5Y29ycA
SCTID:181889008
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
UBERON:0003128
Upper portion of the skull that excludes the mandible (when present in the organism).
VHOG:0000334
bones of cranium
calvarium
cranial
epicranial plate
ossa cranii
set of bones of cranium
skeletal system of head
skull minus mandible
uberon
upper part of skull
skull
Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
BTO:0001295
EHDAA2:0000325
EMAPA:17680
FMA:46565
GAID:82
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
MESH:A02.835.232.781
OpenCyc:Mx4rvVjOsZwpEbGdrcN5Y29ycA
SCTID:110530005
UBERON:0003129
UMLS:C0037303
WikipediaCategory:Skull
cranial skeleton
galen:Skull
ncithesaurus:Skull
skeletal system of head
uberon
reproductive organ
An organ involved in reproduction
EMAPA:17381
GO uses genitalia for the singular organ
MA:0001752
MESH:A05.360
OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA
SCTID:128181006
TGMA:0000591
UBERON:0003133
UMLS:C0017420
WBbt:0008422
genital organ
genitalia
ncithesaurus:Genitalia
reproductive system organ
sex organ
uberon
female reproductive organ
A female organ involved in reproduction
EMAPA:17959
MA:0000544
UBERON:0003134
female organism reproductive organ
female organism reproductive structure
female organism reproductive system organ
female organism sex organ
female reproductive gland/organ
female reproductive system organ
female sex organ
reproductive organ of female organism
reproductive structure of female organism
reproductive system organ of female organism
sex organ of female organism
uberon
male reproductive organ
A male organ involved in reproduction
MA:0000545
UBERON:0003135
male organism reproductive organ
male organism reproductive structure
male organism reproductive system organ
male organism sex organ
male reproductive gland/organ
male reproductive system organ
male sex organ
reproductive organ of male organism
reproductive structure of male organism
reproductive system organ of male organism
sex organ of male organism
uberon
phalanx
Endochondral bones that are often elongate and arranged in rows of articulating elements, and form the visible part of the digits.
MA:0000304
OpenCyc:Mx4rvolPZpwpEbGdrcN5Y29ycA
SCTID:290029003
Taxon notes: In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three[WP]
UBERON:0003221
UMLS:C0222682
VSAO:0000199
digit long bone
galen:Phalanx
long bone of digit
ncithesaurus:Phalanx
phalange
phalangeal
phalanges
phalanx bone
uberon
endoderm of foregut
An endoderm that is part of a foregut [Automatically generated definition].
EHDAA2:0000566
EHDAA:524
TODO - check
UBERON:0003258
foregut endoderm
uberon
chorionic mesoderm
EHDAA2:0003245
EHDAA:154
EMAPA:16114
EMAPA:16266
RETIRED_EHDAA2:0000247
TODO - check
UBERON:0003265
UBERON:0003423
VHOG:0000620
chorion mesenchyme
chorion mesoderm
chorionic mesenchyme
mesenchyme of chorion
mesenchyme of chorion (vertebrates)
uberon
skeleton of lower jaw
A subdivision of skeleton that is part of a lower jaw [Automatically generated definition].
AAO:0000274
EHDAA2:0004606
EHDAA:8005
EMAPA:17910
FMA:54398
MA:0001906
TAO:0001273
The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]
The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO]
UBERON:0003278
VHOG:0000428
XAO:0003084
ZFA:0001273
in EHDAA2, this does not include the mandible; it includes the teeth and Meckel's cartilage
lower jaw
lower jaw skeleton
mandible
mandibles
mandibular series
relationship type change: subclass anatomical cluster (CARO:0000041) CHANGED TO: develops_from anatomical cluster (UBERON:0000477)[TAO]
relationship type change: subclass anatomical cluster (CARO:0000041) CHANGED TO: overlaps anatomical cluster (UBERON:0000477)[TAO]
relationship type change: subclass anatomical cluster (CARO:0000041) CHANGED TO: part_of anatomical cluster (UBERON:0000477)[TAO]
relationship type change: subclass anatomical cluster (CARO:0000041) CHANGED TO: subdivision_of anatomical cluster (UBERON:0000477)[TAO]
uberon
mesentery of stomach
EHDAA2:0001922
EHDAA:2999
EMAPA:17024
EMAPA:18902
MA:0001617
SCTID:261623000
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.
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]
UBERON:0003281
VHOG:0000358
mesentery of ventriculus
mesogaster
mesogastium
mesogastrium
stomach mesentery
todo - check primitive vs developed
uberon
ventriculus mesentery
mesentery of oesophagus
A mesentery that is part of a esophagus [Automatically generated definition].
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]
EHDAA2:0001288
EHDAA:2943
EMAPA:16836
EMAPA:18864
MA:0001569
UBERON:0003283
VHOG:0000415
esophagus mesentery
gullet mesentery
mesentery of esophagus
mesentery of gullet
oesophagus mesentery
uberon
gland of foregut
A gland that is part of a foregut [Automatically generated definition].
EHDAA2:0000567
EHDAA:950
EMAPA:16557
UBERON:0003294
VHOG:0000650
foregut gland
uberon
pharyngeal gland
BTO:0004849
EHDAA2:0001461
EHDAA:2967
FMA:55075
Racemose mucous glands beneath the mucous membrane of the pharynx.
UBERON:0003295
glandulae pharyngeae
pharynx gland
uberon
gland of diencephalon
A gland that is part of a diencephalon [Automatically generated definition].
EHDAA2:0000395
EHDAA:4475
EMAPA:16646
EMAPA:16897
UBERON:0003296
VHOG:0000653
between brain gland
diencephalon gland
gland of between brain
gland of interbrain
gland of mature diencephalon
interbrain gland
mature diencephalon gland
uberon
gland of integumental system
A gland that is part of a integumental system [Automatically generated definition].
EHDAA2:0000837
EHDAA:6522
EMAPA:17758
MA:0000144
UBERON:0003297
VHOG:0000654
integumental system gland
uberon
floor plate of diencephalon
A floor plate that is part of a diencephalon [Automatically generated definition].
EHDAA2:0000388
EHDAA:1975
EHDAA:2651
EHDAA:3480
EMAPA:16645
EMAPA:16903
In summary, the available data for tunicates, amphioxus, and vertebrates indicate that a floorplate-like structure was already present in the proximate invertebrate ancestor of the vertebrates and that the genetic mechanisms for DV patterning of the nerve cord were also largely in place.[well established][VHOG]
TAO:0000871
UBERON:0003309
VHOG:0000782
ZFA:0000871
between brain floor plate
between brain floorplate
diencephalon floor plate
diencephalon floorplate
floor plate diencephalic region
floor plate diencephalon
floor plate of between brain
floor plate of interbrain
floor plate of mature diencephalon
floorplate diencephalon
floorplate of between brain
floorplate of diencephalon
floorplate of interbrain
floorplate of mature diencephalon
interbrain floor plate
interbrain floorplate
mature diencephalon floor plate
mature diencephalon floorplate
uberon
mesenchyme of knee
EHDAA2:0000898
EHDAA:5163
EHDAA:6188
EMAPA:17495
Mesenchyme that is part of a knee [Automatically generated definition].
UBERON:0003321
VHOG:0001070
knee mesenchyme
uberon
mesenchyme of lower jaw
EHDAA2:0001024
EHDAA:8003
EMAPA:17916
Mesenchyme that is part of a lower jaw [Automatically generated definition].
UBERON:0003324
VHOG:0001069
lower jaw mesenchyme
mesenchyme of ventral mandibular arch
uberon
ventral mandibular arch mesenchyme
mesenchyme of footplate
EHDAA2:0000549
EHDAA:5149
EHDAA:6172
EMAPA:17252
Mesenchyme that is part of a footplate.
UBERON:0003328
UBERON:0005260
VHOG_RETIRED:0001055
foot plate mesenchyme
uberon
ganglion of peripheral nervous system
A ganglion that is part of a peripheral nervous system [Automatically generated definition].
BTO:0001123
EMAPA:18371
MA:0001161
UBERON:0003338
We follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS
peripheral nervous system ganglion
uberon
epithelium of mucosa
A layer of epithelial cells on the surface of the mucosa.
BTO:0003752
EMAPA:18668
EMAPA:18835
EMAPA:18857
EMAPA:18862
EMAPA:18868
EMAPA:18893
EMAPA:18899
EMAPA:18912
EMAPA:18917
EMAPA:18927
EMAPA:18934
EMAPA:18941
EMAPA:19078
EMAPA:26961
EMAPA:26985
EMAPA:27019
EMAPA:27033
EMAPA:27047
EMAPA:27061
EMAPA:27075
EMAPA:27089
EMAPA:27103
EMAPA:27131
EMAPA:27145
EMAPA:27159
EMAPA:27175
EMAPA:27191
EMAPA:27207
EMAPA:27219
EMAPA:27229
EMAPA:27307
UBERON:0003350
lamina epithelialis mucosa
lamina epithelialis mucosae
uberon
pharyngeal epithelium
An epithelium that is part of a pharynx [Automatically generated definition].
EMAPA:16551
EMAPA:16708
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]
MA:0002725
RETIRED_EHDAA2:0001460
TAO:0001174
UBERON:0003351
XAO:0003202
ZFA:0001174
epithelial tissue of pharynx
epithelium of pharynx
pharynx epithelial tissue
pharynx epithelium
uberon
epithelium of hindgut
An epithelium that is part of a hindgut [Automatically generated definition].
EHDAA2:0000782
EMAPA:16717
UBERON:0003353
epithelial tissue of hindgut
hindgut epithelial tissue
hindgut epithelium
uberon
chorionic ectoderm
BTO:0005145
EMAPA:16113
UBERON:0003374
chorion ectoderm
chorion epithelium
chorionic epithelium
uberon
gland of gut
A gland that is part of a digestive tract [Automatically generated definition].
EMAPA:18815
UBERON:0003408
digestive tract gland
gland of digestive tract
gland of lower gastrointestinal tract
gut gland
lower gastrointestinal tract gland
uberon
pelvic appendage bud mesenchyme
EHDAA2:0001035
EMAPA:17255
Mesenchyme that is part of a pelvic appendage bud.
Mesoderm part of pelvic fin bud.[TAO]
TAO:0001386
UBERON:0003412
ZFA:0001386
leg mesenchyme
lower limb bud mesenchyme
mesoderm pelvic fin bud
pelvic fin bud mesenchyme
uberon
mesenchyme of umbilical cord
EMAPA:26127
SCTID:368069009
UBERON:0003422
Wharton's jelly
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]
todo - check
uberon
umbilical cord mesenchyme
leg nerve
A nerve that is part of a leg [Automatically generated definition].
MA:0000673
UBERON:0003431
nerve of leg
uberon
limb nerve
A nerve that is part of a limb [Automatically generated definition].
MA:0000693
SCTID:359923002
UBERON:0003440
nerve of limb
uberon
hindlimb nerve
A nerve that is part of a hindlimb [Automatically generated definition].
MA:0000664
UBERON:0003442
hind limb nerve
inferior member nerve
lower extremity nerve
nerve of hind limb
nerve of hindlimb
nerve of inferior member
nerve of lower extremity
uberon
head bone
A bone that is part of a head [Automatically generated definition].
MA:0000576
SCTID:118646007
UBERON:0003457
adult head bone
adult head bone organ
bone of adult head
bone of head
bone organ of adult head
bone organ of head
head bone organ
uberon
facial bone
A bone that is part of a facial skeleton [Automatically generated definition].
EMAPA:19019
Editors note: test whether 'facial bone' is an exact synonym
MA:0001482
SCTID:181799005
UBERON:0003462
UMLS:C0015455
bone of facial skeleton
bone of viscerocranium
facial bone
facial skeleton bone
ncithesaurus:Facial_Bone
uberon
viscerocranium bone
hindlimb bone
A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle)
EFO:0003842
GAID:198
Note that the MA class is actually bone of pelvic complex; in contrast the NCIT class excludes ilium etc
SCTID:361370006
UBERON:0003464
UMLS:C0448188
bone of hind limb
bone of hindlimb
bone of inferior member
bone of lower extremity
bone organ of hind limb
bone organ of hindlimb
bone organ of inferior member
bone organ of lower extremity
hind limb bone
hind limb bone organ
hindlimb bone organ
inferior member bone
inferior member bone organ
lower extremity bone
lower extremity bone organ
ncithesaurus:Bone_of_the_Lower_Extremity
uberon
respiratory system artery
An artery that is part of a respiratory system [Automatically generated definition].
MA:0001804
UBERON:0003469
uberon
head blood vessel
A blood vessel that is part of a head [Automatically generated definition].
MA:0000575
SCTID:127865000
UBERON:0003496
adult head blood vessel
blood vessel of adult head
blood vessel of head
uberon
respiratory system blood vessel
A blood vessel that is part of a respiratory system [Automatically generated definition].
MA:0001799
UBERON:0003504
apparatus respiratorius blood vessel
blood vessel of apparatus respiratorius
blood vessel of respiratory system
uberon
arterial blood vessel
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
MA:0000061
UBERON:0003509
only in MA - supertype of artery, arteriole, aorta.
uberon
trunk blood vessel
A blood vessel that is part of a trunk [Automatically generated definition].
MA:0000511
UBERON:0003513
blood vessel of torso
blood vessel of trunk
torso blood vessel
uberon
brain grey matter
A gray matter of neuraxis that is part of a brain [Automatically generated definition].
MA:0000810
UBERON:0003528
UMLS:C1707348
brain gray matter
brain gray matter of neuraxis
brain grey substance
gray matter of brain
gray matter of neuraxis of brain
grey matter of brain
grey substance of brain
ncithesaurus:Cerebral_Gray_Matter
uberon
brain white matter
MA:0000820
UBERON:0003544
UMLS:C1706995
brain white matter of neuraxis
brain white substance
ncithesaurus:Brain_White_Matter
the regions of the brain that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites.
uberon
white matter of brain
white matter of neuraxis of brain
white substance of brain
leg connective tissue
A portion of connective tissue that is part of a leg [Automatically generated definition].
MA:0000671
UBERON:0003569
connective tissue of leg
leg portion of connective tissue
leg textus connectivus
portion of connective tissue of leg
textus connectivus of leg
uberon
limb connective tissue
A portion of connective tissue that is part of a limb [Automatically generated definition].
MA:0000689
UBERON:0003587
connective tissue of limb
limb portion of connective tissue
limb textus connectivus
portion of connective tissue of limb
textus connectivus of limb
uberon
hindlimb connective tissue
A portion of connective tissue that is part of a hindlimb [Automatically generated definition].
MA:0000661
UBERON:0003589
connective tissue of hind limb
connective tissue of hindlimb
connective tissue of inferior member
connective tissue of lower extremity
hind limb connective tissue
hind limb portion of connective tissue
hind limb textus connectivus
hindlimb portion of connective tissue
hindlimb textus connectivus
inferior member connective tissue
inferior member portion of connective tissue
inferior member textus connectivus
lower extremity connective tissue
lower extremity portion of connective tissue
lower extremity textus connectivus
portion of connective tissue of hind limb
portion of connective tissue of hindlimb
portion of connective tissue of inferior member
portion of connective tissue of lower extremity
textus connectivus of hind limb
textus connectivus of hindlimb
textus connectivus of inferior member
textus connectivus of lower extremity
uberon
limb long bone
A long bone that is part of a limb [Automatically generated definition].
MA:0000298
UBERON:0003606
long bone of limb
uberon
hindlimb long bone
A long bone that is part of a hindlimb [Automatically generated definition].
MA:0000300
UBERON:0003608
hind limb long bone
inferior member long bone
long bone of hind limb
long bone of hindlimb
long bone of inferior member
long bone of lower extremity
lower extremity long bone
uberon
pedal digit 1
1st digit of the hind autopod.
AAO:0010644
BTO:0002349
EHDAA2:0002037
EMAPA:17460
FMA:25047
GAID:45
MA:0000465
MESH:A01.378.610.250.300.792.380
SCTID:302546000
UBERON:0003631
UMLS:C1708079
VSAO:0000201
big toe
digit 1 of hind-paw
digit 1 of pes
digitus primus (I) pedis
foot digit 1
foot digit 1
great toe
hallex
hallux
hallux; digitus primus [I]
hind digit I
hind limb digit 1
http://upload.wikimedia.org/wikipedia/commons/a/ab/RightFootToes.jpg
ncithesaurus:Foot_Digit_1
pedal digit 1
preaxial digit of hindlimb
toe 1
uberon
pedal digit 1 phalanx
A phalanx that is part of a foot digit 1 [Automatically generated definition].
EMAPA:19124
FMA:32884
MA:0001381
SCTID:361798006
UBERON:0003640
UMLS:C1708080
big toe phalanx
digit long bone of foot digit 1
digit long bone of hallux
foot digit 1 digit long bone
foot digit 1 long bone of digit
foot digit 1 phalanx
foot digit 1 phalanx
hallux digit long bone
hallux long bone of digit
hallux phalanx
hind limb digit 1 phalanx
long bone of digit of foot digit 1
long bone of digit of hallux
ncithesaurus:Foot_Digit_1_Phalanx
phalanx of big toe
phalanx of first digit of foot
phalanx of foot digit 1
phalanx of great toe
phalanx of hallux
uberon
respiratory system arterial blood vessel
An arterial blood vessel that is part of a respiratory system [Automatically generated definition].
MA:0001800
UBERON:0003643
uberon
metatarsal bone of digit 1
1
A metatarsal bone that distally_connected_to a proximal phalanx of pedal digit 1.
AAO:0000925
Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with the prepollex and tarsal 1 proximally and with the proximal phalanx of digit I distally.[AAO]
EMAPA:19123
FMA:24502
MA:0001369
SCTID:182121005
The first metatarsal bone is the bone in the body of the foot just behind the big toe. It is remarkable for its great thickness, and is the shortest of the metatarsal bones. The body is strong, and of well-marked prismoid form. The base presents, as a rule, no articular facets on its sides, but occasionally on the lateral side there is an oval facet, by which it articulates with the second metatarsal. Its proximal articular surface is of large size and kidney-shaped; its circumference is grooved, for the tarsometatarsal ligaments, and medially gives insertion to part of the tendon of the Tibialis anterior; its plantar angle presents a rough oval prominence for the insertion of the tendon of the Peronæus longus. The head is large; on its plantar surface are two grooved facets, on which glide sesamoid bones; the facets are separated by a smooth elevation[Wikipedia:First_metatarsal_bone].
UBERON:0003650
UMLS:C1708999
first metatarsal bone
foot digit 1 metatarsal bone
hallux metatarsal bone
metatarsal 1
metatarsal I
metatarsal bone digit 1
metatarsal bone of foot digit 1
metatarsal bone of hallux
ncithesaurus:Metatarsal_Bone_Digit_1
toe 1 metatarsal
toe 1 metatarsus
uberon
mesopodium bone
A bone that is part of a mesopodium skeleton[cjm]. The carpus (wrist) and tarsus (ankle) of land vertebrates primitively had three rows of carpal or tarsal bones. Often some of these have become lost or fused in evolution. Three proximals. In the hand humans has all three. In the foot the middle proximal appears in 5-15% of people as an os trigonum. Centrale or os centrale, on the medial side. In humans and our closest relatives the African apes (chimpanzees and gorillas) it fuses to the scaphoid where it forms the articulation with the trapezoid bone; occasionally it stays separate. In Man's foot it is the navicular. Some early land vertebrates had more than one (up to three) os centrale per hand or foot. Distals, one per finger / toe at the base of each metacarpal or metatarsal. In mammals the 4th and 5th fuse. In the horse the 1st is lost[WP].
MA:0000295
UBERON:0003656
basipodium bone
carpal/tarsal bone
mesopod bone
mesopodial bone
uberon
limb joint
Any joint that is part of a (free) limb.
MA:0000691
Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses
SCTID:312683002
UBERON:0003657
galen:LimbJoint
joint of limb
joint of limb skeletal system
skeletal limb joint
uberon
limb muscle
A muscle organ that is part of a limb [Automatically generated definition].
MA:0000692
UBERON:0003661
limb muscle organ
muscle organ of limb
uberon
hindlimb muscle
A muscle organ that is part of a hindlimb [Automatically generated definition].
AAO:0000222
EFO:0001928
FMA:37368
UBERON:0003663
free lower limb muscle
hind limb muscle organ
hindlimb muscle organ
inferior member muscle organ
lower extremity muscle organ
muscle of free lower limb
muscle of posterior limb
muscle organ of hind limb
muscle organ of hindlimb
muscle organ of inferior member
muscle organ of lower extremity
uberon
abdominal cavity
EFO:0000213
FMA:12266
GAID:17
MESH:A01.047.025
OpenCyc:Mx4rvZR1TJwpEbGdrcN5Y29ycA
SCTID:361294009
UBERON:0003684
UMLS:C0230168
body cavity of the human body (and animal bodies) that holds the bulk of the viscera. It is located below (or inferior to) the thoracic cavity, and above the pelvic cavity. It is a part of the abdominopelvic cavity. Organs of the abdominal cavity include the stomach, liver, gallbladder, spleen, pancreas, small intestine, kidneys, and large intestine. The abdominal cavity is lined with a protective membrane termed the peritoneum. The kidneys are located in the abdominal cavity behind the peritoneum, in the retroperitoneum. The viscera are also covered, in the front, with a layer of peritoneum called the greater omentum (or omental apron).
cavitas abdominis
cavity of abdominal compartment
cavity of compartment of abdomen
galen:AbdominalCavity
http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/e/ee/Scheme_body_cavities-en.svg/200px-Scheme_body_cavities-en.svg.png
ncithesaurus:Abdominal_Cavity
space of abdominal compartment
uberon
abdominal wall
FMA:10429
FMA:259054
GAID:26
MESH:A01.047.050
SCTID:181613000
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).
UBERON:0003697
UMLS:C0836916
http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg
layers of the abdominal wall
ncithesaurus:Abdominal_Wall
paries abdominalis
paries abdominalis
uberon
wall of abdomen
wall of abdomen proper
calcaneal tendon
AO notes: in FMA this is a ligament, and part of the muscle
Achille's tendon
Achilles tendon
Achilles' tendon
FMA:51061
GAID:277
MA:0002993
MESH:A02.880.176
OpenCyc:Mx4rvVjNX5wpEbGdrcN5Y29ycA
SCTID:181705009
The Achilles tendon is a tendon of the posterior leg. It serves to attach the plantaris, gastrocnemius (calf) and soleus muscles to the calcaneus (heel) bone.
UBERON:0003701
UMLS:C0001074
calcaneal tendon
http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg
ncithesaurus:Achilles_Tendon
tendo Achillis
tendo calcaneus
uberon
neural tissue
AAO:0000325
AEO:0000123
EHDAA2:0003123
FMA definition includes vasculature
FMA:9642
GAID:609
MESH:A08.561
One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
OpenCyc:Mx4rVmfYCsQ_QdeM_bFAeS8NRQ
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].
SCTID:91728009
UBERON:0003714
UMLS:C0027757
ncithesaurus:Nervous_Tissue
nerve tissue
nervous tissue
portion of neural tissue
uberon
mediastinum
EFO:0003057
FMA:9826
GAID:94
MESH:A01.911.800.500
OpenCyc:Mx4rv2OKJ5wpEbGdrcN5Y29ycA
SCTID:181217005
The mediastinum is a non-delineated group of structures in the thorax, surrounded by loose connective tissue. It is the central compartment of the thoracic cavity. It contains the heart, the great vessels of the heart, esophagus, trachea, phrenic nerve, cardiac nerve, thoracic duct, thymus, and lymph nodes of the central chest. The mediastinum lies between the right and left pleura in and near the median sagittal plane of the chest. It extends from the sternum in front to the vertebral column behind, and contains all the thoracic viscera except the lungs. It may be divided for purposes of description into two parts:an upper portion, above the upper level of the pericardium, which is named the superior mediastinum with its superior limit at the superior thoracic opening and its inferior limit at the plane from the sternal angle to the disc of T4-T5 (Plane of Ludwig at Angle of Louis); and a lower portion, below the upper level of the pericardium. This lower portion is again subdivided into three parts, viz. that in front of the pericardium, the anterior mediastinum; that containing the pericardium and its contents, the middle mediastinum; and that behind the pericardium, the posterior mediastinum. It is surrounded by the chest wall anteriorly, the lungs laterally and the spine posteriorly. It is continuous with the loose connective tissue of the neck, and extends inferiorly onto the diaphragm.
UBERON:0003728
UMLS:C0025066
http://upload.wikimedia.org/wikipedia/commons/a/ab/Mediastinum.png
http://upload.wikimedia.org/wikipedia/commons/thumb/a/ab/Mediastinum.png/200px-Mediastinum.png
mediastinal
mediastinal part of chest
ncithesaurus:Mediastinum
uberon
mouth mucosa
BTO:0002860
FMA:59660
GAID:951
MA:0002794
MESH:A10.615.550.599
UBERON:0003729
UMLS:C0026639
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)
buccal mucosa
mouth mucosa
mouth mucous membrane
mouth organ mucosa
mucosa of mouth
mucosal lining of mouth
mucous membrane of mouth
ncithesaurus:Oral_Mucosa
oral mucosa
oral mucous membrane
oral part of viscerocranial mucosa
the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized.
tunica mucosa oris
tunica mucosa oris
uberon
prostate bud
A region of the fetal urogenital sinus epithelium destined to become the prostate[GO].
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]
UBERON:0003820
prostate ductal progenitor
prostatic bud
uberon
metapodium bone
A bone of the metapodial skeleton
MA:0000301
UBERON:0003821
metacarpal or metatarsal bone
metacarpal/metatarsal
metacarpal/metatarsal bone
metapodi bone
metapodial bone
metapodium bone
uberon
hindlimb zeugopod
EFO:0003051
EHDAA2:0001030
EHDAA:5165
EHDAA:6190
EMAPA:17496
FMA:24979
FMA:24984
MA:0000051
MESH:A01.378.610.500
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
OpenCyc:Mx4rvczZBpwpEbGdrcN5Y29ycA
SCTID:244015008
The middle limb segment of the pelvic free limb, between the autopod and stylopod segments. Includes as parts the hindlimb zeugopodial skeleton, which includes as parts the tibia and fibula, or their cartilage precursors, or evolutionary variants.
UBERON:0003823
UMLS:C1140621
VHOG:0000348
VSAO:0005060
calf
calf of leg
crus
crus of hindlimb
galen:Leg
hind epipodium
hind limb middle limb segment
hind limb zeudopodium
hind limb zeugopod
hindlimb epipodium
hindlimb middle limb segment
hindlimb zeudopodium
hindlimb zeugopod
hindlimb zeugopodium
hindlimb zygopod
intermediate segment of free lower limb
leg
lower extremity middle limb segment
lower extremity zeugopod
lower leg
middle limb segment of hind limb
middle limb segment of hindlimb
ncithesaurus:Leg
note that FMA:24979 denotes the middle segment (zeugopod), its placement here is correct. See obo-anatomy archives for discussion // Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here
posterior curral region
posterior leg region
posterior part of leg
posterior region of leg
regio cruris posterior
regio surae
shank
sura
sural
sural region
uberon
zeugopod of hind limb
zeugopod of hindlimb
upper leg bone
A bone that is part of a hindlimb stylopod [Automatically generated definition].
MA:0000682
UBERON:0003826
uberon
thoracic segment muscle
A muscle organ that is part of a thorax [Automatically generated definition].
MA:0000561
UBERON:0003830
muscle organ of thorax
thorax muscle organ
uberon
upper body muscle
respiratory system muscle
A muscle organ that is part of a respiratory system [Automatically generated definition].
MA:0001828
UBERON:0003831
apparatus respiratorius muscle organ
muscle organ of apparatus respiratorius
muscle organ of respiratory system
respiratory system muscle organ
uberon
hindlimb joint
A limb joint that is part of a hindlimb [Automatically generated definition].
MA:0000662
SCTID:304573000
UBERON:0003840
hind limb joint of limb
hind limb limb joint
hindlimb joint of limb
hindlimb limb joint
inferior member joint of limb
inferior member limb joint
joint of limb of hind limb
joint of limb of hindlimb
joint of limb of inferior member
joint of limb of lower extremity
joint of lower limb
limb joint of hind limb
limb joint of hindlimb
limb joint of inferior member
limb joint of lower extremity
lower extremity joint of limb
lower extremity limb joint
uberon
neural tube lumen
(...) 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]
AAO:0011073
An anatomical space that surrounded_by a neural tube.
EHDAA2:0001269
EHDAA:2889
EHDAA:914
EMAPA:16167
EMAPA:16533
TODO - check
UBERON:0003842
UBERON:0005713
VHOG:0001119
XAO:0000252
cavity of neural tube
lumen of neural tube
neural lumen
neural tube neural lumen
neurocoel
uberon
mesencephalic neural crest
A neural crest that developmentally_contributes_to a midbrain.
EFO:0003591
EHDAA2:0001101
EHDAA:360
TAO:0000935
UBERON:0003849
VHOG:0000796
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
ZFA:0000935
mesencephalic neural crest
neural crest midbrain
uberon
telencephalon neural crest
A neural crest that developmentally_contributes_to a telencephalon.
Cranial neural crest that is part of the telencephalon.[TAO]
EFO:0003574
RETIRED_EHDAA2:0001991
TAO:0000812
UBERON:0003850
VHOG:0000799
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
ZFA:0000812
neural crest telencephalon
uberon
diencephalon neural crest
A neural crest that developmentally_contributes_to a diencephalon.
EFO:0003573
EHDAA2:0000603
EMAPA:16518
TAO:0000811
UBERON:0003851
VHOG:0000798
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
ZFA:0000811
diencephalic neural crest
future diencephalon neural crest
neural crest diencephalon
neural crest of future diencephalon
uberon
rhombencephalon neural crest
A neural crest that developmentally_contributes_to a hindbrain.
Cranial neural crest that is part of the hindbrain.[TAO]
EHDAA2:0001628
EHDAA:362
TAO:0007063
UBERON:0003852
VHOG:0001210
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
ZFA:0007063
neural crest hindbrain
rhombencephalic neural crest
uberon
spinal cord neural crest
A neural crest that developmentally_contributes_to a spinal cord.
EHDAA:696
EMAPA:16094
EMAPA:16163
EMAPA:16529
EMAPA:16881
UBERON:0003853
VHOG:0001006
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]
neural crest spinal cord
spinal neural crest
uberon
odontogenic mesenchyme
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
Mesenchyme enclosed by dental organ.[TAO]
Mesenchyme that gives rise to an odontogenic papilla.
TAO:0005139
UBERON:0003856
VHOG_RETIRED:0001444
ZFA:0005139
dental mesenchyme
dental organ mesenchyme
enamel organ mesenchyme
tooth enamel organ mesenchyme
tooth mesenchyme
uberon
hindlimb mesenchyme
Mesenchyme that is part of a hindlimb [Automatically generated definition].
UBERON:0003860
VHOG:0001074
hind limb mesenchyme
inferior member mesenchyme
lower extremity mesenchyme
mesenchyme of hind limb
mesenchyme of hindlimb
mesenchyme of inferior member
mesenchyme of lower extremity
uberon
proximal phalanx of pes
A proximal phalanx that is part of a pedal digit [Automatically generated definition].
FMA:75828
MA:0001387
SCTID:85533000
UBERON:0003868
UMLS:C0224020
foot proximal phalanx
ncithesaurus:Proximal_Phalanx_of_Foot
proximal pedal phalanx
proximal phalanx of foot
proximal phalanx of foot digit
proximal phalanx of hind digit
proximal phalanx of pes
proximal phalanx of toe
uberon
presumptive ganglion
A presumptive structure that develops_into a ganglion.
UBERON:0003869
uberon
body cavity precursor
An anatomical cavity that develops_into a coelemic cavity lumen.
UBERON:0003886
uberon
intraembryonic coelom
(...) 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]
EHDAA:251
EMAPA:16088
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
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].
UBERON:0003887
UMLS:C1512940
VHOG:0000316
ncithesaurus:Intraembryonic_Coelom
somatic coelom
uberon
fallopian tube
EFO:0000974
EHDAA2:0000504
EV:0100112
FMA:18245
GAID:365
MA:0000385
MESH:A05.360.319.114.373
OpenCyc:Mx4rvViVeZwpEbGdrcN5Y29ycA
SCTID:181463001
Two very fine tubes lined with ciliated epithelia, leading from the ovaries of female mammals into the uterus, via the utero-tubal junction[WP]. Embryos have two pairs of ducts to let gametes out of the body; one pair (the Mullerian ducts) develops in females into the Fallopian tubes, uterus and vagina, while the other pair (the Wolffian ducts) develops in males into the epididymis and vas deferens.
UBERON:0003889
UMLS:C0015560
fallopian tubes
female paramesonephric duct
galen:FallopianTube
http://en.wikipedia.org/wiki/Talk:Fallopian_tube#Homology
http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/6/68/Scheme_female_reproductive_system-en.svg/200px-Scheme_female_reproductive_system-en.svg.png
mammalian oviduct
ncithesaurus:Fallopian_Tube
tuba uterina
uberon
uterine tube
Mullerian duct
AAO:0010141
Development notes: Sertoli cells secrete anti-Mullerian hormone (AMH) inducing the demise of this duct
EHDAA2:0004048
EMAPA:27665
Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG]
GAID:1309
In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG]
MESH:A16.254.570
Muellerian duct
Müllerian duct
RETIRED_EHDAA2:0001399
SCTID:308802006
Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO]
UBERON:0003890
UBERON:0005318
UMLS:C0026732
VHOG:0001199
XAO:0000330
ductus paramesonephricus
early paramesonephric duct
http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png
http://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Gray1109.png/200px-Gray1109.png
ncithesaurus:Mullerian_Duct
paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM].
paramesonephric duct
uberon
liver primordium
A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum.
AAO:0011058
BTO:0003391
EFO:0002577
EFO:0003428
EHDAA2:0000744
EHDAA:973
EMAPA:16847
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
TAO:0000124
UBERON:0003894
UMLS:C0734013
UMLS:C1514451
XAO:0003266
ZFA:0000124
embryological hepatic plate
hepatic plate
liver bud
liver endoderm
ncithesaurus:Hepatic_Cord
ncithesaurus:Primordium_of_the_Liver
primordium of the liver
uberon
skeletal muscle of trunk
A skeletal muscle of the trunk.
SCTID:244848007
UBERON:0003898
skeletal muscle of torso
skeletal muscle tissue of torso
skeletal muscle tissue of trunk
torso skeletal muscle
torso skeletal muscle tissue
trunk skeletal muscle
trunk skeletal muscle tissue
uberon
retinal neural layer
(...) 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]
AAO:0011095
BTO:0000929
EHDAA2:0001253
EHDAA:4763
EMAPA:17171
EMAPA:18590
FMA:58628
MA:0000277
TAO:0000046
The layer of nerve cells in the retina[XAO]. The part of the retina that contains neurons and photoreceptor cells[GO].
UBERON:0003902
UMLS:C1518263
VHOG:0000535
XAO:0003216
ZFA:0000046
editor note - we follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers; the neural layers are further divided into 9 layers. Note that in MA this class is a leaf node.
ncithesaurus:Neural_Retina
neural layer of retina
neural retina
neural retinal epithelium
neuroretina
stratum nervosum (retina)
uberon
tooth-like structure
HAO:0001019
UBERON:0003913
hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food.
see dermal denticle
tooth-like organ
uberon
epithelial tube
AEO:0000114
EHDAA2:0003114
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.
FBbt:00007474
UBERON:0003914
epithelial or endothelial tube
uberon
endothelial tube
Any endothelium that has the quality of being cylindrical [Automatically generated definition].
UBERON:0003915
uberon
kidney mesenchyme
Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO].
UBERON:0003918
check this
mesenchyme of kidney
uberon
venous blood vessel
Compare to: vein
FMA:86188
MA:0000066
UBERON:0003920
a blood vessel that carries blood from the capillaries toward the heart
segment of venous tree organ
uberon
venous tree organ segment
pancreas primordium
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'
EFO:0002579
EFO:0003434
EHDAA2:0001382
EHDAA:2163
EMAPA:17066
FMA:79792
TAO:0000254
UBERON:0003921
XAO:0001101
ZFA:0000254
embryonic structure that develops into pancreatic bud.
http://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Gray982.png/200px-Gray982.png
pancreatic anlage
pancreatic endoderm
pancreatic primordium
primordial pancreas
uberon
pancreatic bud
EFO:0003470
SCTID:360398004
TAO:0001390
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].
UBERON:0003922
UMLS:C1283285
ZFA:0001390
http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png
http://upload.wikimedia.org/wikipedia/commons/thumb/4/49/Suckale08FBS_fig1_pancreas_development.jpeg/300px-Suckale08FBS_fig1_pancreas_development.jpeg
http://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Gray982.png/200px-Gray982.png
ncithesaurus:Pancreatic_Bud
pancreatic anlage
pancreatic buds
uberon
dorsal pancreatic bud
AAO:0011031
EFO:0003465
EHDAA2:0001385
EMAPA:17067
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]
SCTID:361435005
TAO:0001370
The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO]
UBERON:0003923
VHOG:0001428
XAO:0000467
ZFA:0001370
dorsal pancreas anlage
dorsal pancreatic anlage
http://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Gray982.png/200px-Gray982.png
pancreas dorsal primordium duct bud
pancreas primordium dorsal bud
pancreatic bud that gives rise to the accessory pancreatic duct.
posterior pancreatic anlage
posterior pancreatic bud
uberon
ventral pancreatic bud
AAO:0011111
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]
EFO:0003464
EHDAA2:0001389
EMAPA:17256
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]
SCTID:361437002
TAO:0001369
UBERON:0003924
VHOG:0001429
XAO:0001103
ZFA:0001369
anterior pancreatic anlage
anterior pancreatic bud
http://upload.wikimedia.org/wikipedia/commons/thumb/d/db/Gray982.png/200px-Gray982.png
pancreas primordium ventral bud
pancreas ventral primordium duct bud
pancreatic bud that gives rise to the major pancreatic duct.
uberon
ventral pancreas anlage
ventral pancreatic anlage
gut epithelium
An epithelium that is part of a digestive tract [Automatically generated definition].
BTO:0000956
EHDAA2:0004567
Epithelium lining the lumen of the gut.[TAO]
TAO:0005123
UBERON:0003929
UMLS:C0836205
XAO:0003200
ZFA:0005123
digestive tract epithelial tissue
digestive tract epithelium
epithelial tissue of digestive tract
epithelial tissue of gut
epithelial tissue of lower gastrointestinal tract
epithelium of digestive tract
epithelium of gut
epithelium of lower gastrointestinal tract
gut epithelial tissue
lower gastrointestinal tract epithelial tissue
lower gastrointestinal tract epithelium
ncithesaurus:Gut_Epithelium
uberon
sex gland
MA:0001751
UBERON:0003937
any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction
genitalia gland
gland of genitalia
gland of reproductive system
reproductive gland
reproductive system gland
uberon
rete testis
An anastomosing network of delicate tubules located in the hilum of the testicle (mediastinum testis) that carries sperm from the seminiferous tubules to the vasa efferentia[WP].
EMAPA:18332
Editors note: add more specific classification e.g. anastomosing network - consider FMA:3726
FMA:19834
GAID:399
Haller's rete
MESH:A05.360.444.849.600
SCTID:279617009
UBERON:0003959
UMLS:C0035278
http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/b/b5/Hodenschema.svg/200px-Hodenschema.svg.png
ncithesaurus:Rete_Testis
uberon
internal female genitalia
BTO:0003099
FMA:45654
SCTID:303518005
UBERON:0003975
female internal genitalia
internal female genital organ
internal genitalia of female reproductive system
organa genitalia feminina interna
the internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina.
uberon
dermatome
AAO:0011028
AEO:0001017
EHDAA2:0003428
EHDAA:1719
EHDAA:1725
EHDAA:1731
EHDAA:1737
Not to be confused with 'dermatome segment of skin'.
UBERON:0004016
UMLS:C0180383
XAO:0000220
cutis plate
dermatomal mesenchyme
http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png
mesenchyma dermatomiale
ncithesaurus:Dermatome
the mesoderm that is derived from the somite that is fated to become the dermis[MP]
uberon
subplate
The transient fetal subplate zone, together with the marginal zone and the cortical plate, represents the developmental anlage of the mammalian cerebral cortex. It serves as a waiting compartment for growing cortical afferents; its cells are involved in the establishment of pioneering cortical efferent projections and transient fetal circuitry, and apparently have a number of other developmental roles. The subplate zone is a phylogenetically recent structure and it is most developed in the human brain. Subplate neurons are among the first generated neurons in the mammalian cerebral cortex [1]. These neurons disappear during postnatal development and are important in establishing the correct wiring [2][3] and functional maturation [4] of the cerebral cortex. Subplate neurons appear to be selectively sensitive to injury (such as hypoxia) which in humans are associated with motor and cognitive defects[WP].
UBERON:0004035
the transient outer neural tube region that contains the first generated post-mitotic neurons that receive synaptic input from thalamic axons and in turn project axons to the developing cortical plate
uberon
external male genitalia
BTO:0003097
EMAPA:30977
FMA:45642
SCTID:362264000
UBERON:0004053
external male genital organ
galen:MaleExternalGenitalia
male external genitalia
organa genitalia masculina externa
the external masculine genital organs, including the penis and scrotum
uberon
internal male genitalia
BTO:0003096
Editor note: consider splitting genitalia from genital organ
FMA:45655
SCTID:310536002
UBERON:0004054
internal male genital organ
male internal genitalia
organa genitalia masculina interna
the internal masculine genital organs, including the testes, epididymides, deferent ducts, seminal vesicles, prostate, ejaculatory ducts, and bulbourethral glands
uberon
neural tube ventricular layer
EMAPA:16783
EMAPA:17152
UBERON:0004060
consider merging with 'ventricular zone'
neural tube ependymal zone
neural tube ventricular zone
the layer of undifferentiated, proliferating cells that line the neural tube lumen
uberon
neural tube mantle layer
EMAPA:17148
UBERON:0004061
neural tube intermediate zone
the layer of glia and differentiating neurons that will form the gray matter of the spinal cord; this lies between the ventricular and marginal layers and includes the basal and alar plates
uberon
neural tube marginal layer
EMAPA:17151
UBERON:0004062
neural tube marginal zone
the outermost layer of the neural tube that contains nerve fibers and will form the white matter
uberon
frontonasal prominence
An unpaired facial process in the embryo formed from the tissues surrounding the forebrain vesicle that develops into the forehead and bridge of the nose/snout[MP]. During embryonic development, two areas of thickened ectoderm, the olfactory areas, appear immediately under the fore-brain in the anterior wall of the stomodeum, one on either side of a region termed the frontonasal prominence (or process)[WP]. By the upgrowth of the surrounding parts these areas are converted into pits, the olfactory pits, which indent the frontonasal prominence and divide it into a medial and two lateral nasal processes[WP].
EHDAA2:0000578
EHDAA:4778
EMAPA:16681
SCTID:361486000
UBERON:0004066
UBERON:0006237
UMLS:C1517321
VHOG:0001319
http://upload.wikimedia.org/wikipedia/commons/9/98/Gray44.png
http://upload.wikimedia.org/wikipedia/commons/thumb/9/98/Gray44.png/200px-Gray44.png
ncithesaurus:Frontonasal_Prominence
prominentia frontonasalis
uberon
lateral nasal prominence
EHDAA2:0000916
EHDAA:4786
EMAPA:16805
SCTID:308880000
UBERON:0004067
http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png
http://upload.wikimedia.org/wikipedia/commons/thumb/2/2d/Gray48.png/200px-Gray48.png
lateral nasal process
lateral nasal swelling
latero-nasal process
prominentia nasalis lateralis
the lateral area of the two branches of a horseshoe-shaped mesenchymal swelling in the future nasal region of the embryo; it separates the olfactory pit from the developing eye and the ala of the nose/snout develops from it
uberon
medial nasal prominence
EHDAA2:0001076
EHDAA:4792
EMAPA:16808
Fusion of right and left medial nasal processes forms a primary palate rostrally and the nasal septum caudally. The incisive bone, including upper incisor teeth and the rostral up- per lip, are derived from the primary palate. The nasal septum consists of bone, cartilage, and a patch of soft tissue membrane that separates right & left halves of the nasal cavity.
SCTID:308877001
UBERON:0004068
VHOG:0000804
http://upload.wikimedia.org/wikipedia/commons/8/85/Gray45.png
http://upload.wikimedia.org/wikipedia/commons/thumb/8/85/Gray45.png/200px-Gray45.png
medial nasal process
medial nasal swelling
medial-nasal process
nasomedial prominence
prominentia nasalis medialis
the central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the formation of half of the upper jaw, and the nasal tip and philtrum of the upper lip develop from it
uberon
brain ventricle
BTO:0001442
EFO:0001914
FMA:78447
MA:0000818
MESH:A08.186.211.276
NIF_GrossAnatomy:birnlex_1356
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.
OpenCyc:Mx4rvmTY65wpEbGdrcN5Y29ycA
SCTID:180929003
UBERON:0004086
UMLS:C0007799
cerebral ventricle
ncithesaurus:Ventricle_Brain
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
region of ventricular system of brain
uberon
ocular region
.
FMA:260119
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.
UBERON:0004088
content of orbital part of eye
eye region
orbital content
uberon
midface
MA:0001910
UBERON:0004089
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.
lower face
midface/lower face
midfacial
snout
the middle of the face including the nose and its associated bony structures[MW].
uberon
anatomical conduit
AEO:0000080
EHDAA2:0003080
FMA:242873
UBERON:0004111
any opening in the body.
foramen
foramina
note that FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
uberon
pharyngeal pouch
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]
AAO:0011113
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]
EFO:0003627
EHDAA:1086
EHDAA:1669
EHDAA:579
EHDAA:617
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]
SCTID:34674002
TAO:0001106
UBERON:0004117
UMLS:C0231067
VHOG:0001203
XAO:0000282
ZFA:0001106
branchial pouch
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].
ncithesaurus:Pharyngeal_Pouch
pharyngeal pouches
uberon
visceral pouch
visceral pouches
endoderm-derived structure
An anatomical structure that develops (entirely or partially) from the endoderm.
Grouping term for query purposes
UBERON:0004119
uberon
mesoderm-derived structure
An anatomical structure that develops (entirely or partially) from the mesoderm.
Grouping term for query purposes
UBERON:0004120
uberon
ectoderm-derived structure
An anatomical structure that develops (entirely or partially) from the ectoderm.
Grouping term for query purposes
UBERON:0004121
uberon
genitourinary system
AAO:0000624
An anatomical system that has_part a reproductive system and has_part a excretory system.
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]
BILA:0000122
BTO:0003091
EFO:0003864
EHDAA:1013
EMAPA:16367
EV:0100094
GAID:362
GU tract
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]
MESH:A05
OpenCyc:Mx4rQRpVMgAKEdyHxgDggVfs8g
SCTID:278861008
UBERON:0004122
UMLS:C0042066
Urogenitalsystem
VHOG:0000286
XAO:0000140
galen:GenitoUrinarySystem
genitourinary
genitourinary tract
ncithesaurus:Genitourinary_System
relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]
uberon
urogenital
urogenital system
urogenital tract
optic vesicle
(...) 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]
AAO:0011039
EHDAA2:0001320
EMAPA:16540
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
SCTID:362864008
TAO:0000050
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].
UBERON:0004128
UMLS:C0231106
VHOG:0000165
XAO:0000228
ZFA:0000050
evagination
http://upload.wikimedia.org/wikipedia/commons/thumb/e/e0/Gray863.png/200px-Gray863.png
ncithesaurus:Optic_Vesicle
ocular vesicle
uberon
cardiogenic plate
(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]
EHDAA2:0000215
EMAPA:16106
TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO
The first recognizable structure derived from the heart field
UBERON:0004139
VHOG:0000975
cardiogenic crescent
heart rudiment
myocardial plate
uberon
heart field
UBERON:0004140
XAO:0004185
a specific region of the lateral mesoderm in which the heart will develop.
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]
primary heart field
uberon
heart tube
AAO:0010411
Cavitated compound organ that will become the adult heart following looping morphogenesis and valve formation[ZFA].
EFO:0003526
EHDAA:424
EMAPA:16208
TAO:0000360
UBERON:0004141
XAO:0000337
ZFA:0000360
early primitive heart tube
embryonic heart tube
uberon
cardiac chamber
A cardiac chamber surrounds an enclosed cavity within the heart
FMA:7095
OpenCyc:Mx4rmexpjPdAEduAAAAOpmP6tw
SCTID:276456008
UBERON:0004151
chamber of heart
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
heart chamber
uberon
septum transversum
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]
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].
EHDAA2:0001829
EHDAA:736
EMAPA:16318
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]
Note that in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum
SCTID:308819008
UBERON:0004161
UMLS:C0231004
VHOG:0000019
ncithesaurus:Septum_Transversum
transverse septum
uberon
internal genitalia
FMA:45652
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
UBERON:0004175
internal genitalia
internal genitals
internal reproductive organ
internal sex organ
uberon
external genitalia
FMA:45643
SCTID:362207005
The external genitalia are the outer sex organs, such as the penis or vulva in mammals
UBERON:0004176
external genitalia
external reproductive organ
external sex organ
uberon
hemopoietic organ
BTO:0004605
FMA:7143
Organ that is part of the hematopoietic system.
SCTID:361338006
UBERON:0004177
haematological system organ
haemopoietic system organ
hematopoeitic or lymphoid organ
hematopoietic system organ
lymphoid organ
note that the FMA class 'lymphoid organ' is a general anatomical term
organ of haematological system
organ of haemopoietic system
organ of hematopoietic system
organ of organa haemopoietica
organa haemopoietica organ
uberon
endodermal gut
A portions of the gut that is derived from endoderm.
UBERON:0004185
uberon
pedal digit bone
A bone that is part of a hindlimb digit. Typically phalanges but may include sesamoids.
MA:0000646
UBERON:0004248
bone of digit of foot
bone of digit of terminal segment of free lower limb
bone of digitus pedis
bone of foot digit
bone of terminal segment of free lower limb digit
bone of toe
bone organ of digit of foot
bone organ of digit of terminal segment of free lower limb
bone organ of digitus pedis
bone organ of foot digit
bone organ of terminal segment of free lower limb digit
bone organ of toe
digit of foot bone
digit of foot bone organ
digit of terminal segment of free lower limb bone
digit of terminal segment of free lower limb bone organ
digital bone of foot
digitus pedis bone
digitus pedis bone organ
foot digit bone
foot digit bone
foot digit bone organ
hind limb digit bone
terminal segment of free lower limb digit bone
terminal segment of free lower limb digit bone organ
toe bone
toe bone organ
uberon
hindlimb zeugopod bone
A bone that is part of a lower leg [Automatically generated definition].
MA:0000676
UBERON:0004251
bone of hind limb middle limb segment
bone of hind limb zeugopod
bone of hindlimb middle limb segment
bone of hindlimb zeugopod
bone of inferior member middle limb segment
bone of inferior member zeugopod
bone of intermediate segment of free lower limb
bone of lower extremity middle limb segment
bone of lower extremity zeugopod
bone of lower leg
bone of middle limb segment of hind limb
bone of middle limb segment of hindlimb
bone of middle limb segment of inferior member
bone of middle limb segment of lower extremity
bone of zeugopod of hind limb
bone of zeugopod of hindlimb
bone of zeugopod of inferior member
bone of zeugopod of leg
bone of zeugopod of lower extremity
bone organ of hind limb middle limb segment
bone organ of hind limb zeugopod
bone organ of hindlimb middle limb segment
bone organ of hindlimb zeugopod
bone organ of inferior member middle limb segment
bone organ of inferior member zeugopod
bone organ of intermediate segment of free lower limb
bone organ of lower extremity middle limb segment
bone organ of lower extremity zeugopod
bone organ of lower leg
bone organ of middle limb segment of hind limb
bone organ of middle limb segment of hindlimb
bone organ of middle limb segment of inferior member
bone organ of middle limb segment of lower extremity
bone organ of zeugopod of hind limb
bone organ of zeugopod of hindlimb
bone organ of zeugopod of inferior member
bone organ of zeugopod of leg
bone organ of zeugopod of lower extremity
hind limb middle limb segment bone
hind limb middle limb segment bone organ
hind limb zeugopod bone
hind limb zeugopod bone organ
hindlimb middle limb segment bone
hindlimb middle limb segment bone organ
hindlimb zeugopod bone
hindlimb zeugopod bone organ
inferior member middle limb segment bone
inferior member middle limb segment bone organ
inferior member zeugopod bone
inferior member zeugopod bone organ
intermediate segment of free lower limb bone
intermediate segment of free lower limb bone organ
lower extremity middle limb segment bone
lower extremity middle limb segment bone organ
lower extremity zeugopod bone
lower extremity zeugopod bone organ
lower leg bone
middle limb segment of hind limb bone
middle limb segment of hind limb bone organ
middle limb segment of hindlimb bone
middle limb segment of hindlimb bone organ
middle limb segment of inferior member bone
middle limb segment of inferior member bone organ
middle limb segment of lower extremity bone
middle limb segment of lower extremity bone organ
uberon
zeugopod of hind limb bone
zeugopod of hind limb bone organ
zeugopod of hindlimb bone
zeugopod of hindlimb bone organ
zeugopod of inferior member bone
zeugopod of inferior member bone organ
zeugopod of leg bone
zeugopod of leg bone organ
zeugopod of lower extremity bone
zeugopod of lower extremity bone organ
hindlimb zeugopod muscle
A muscle organ that is part of a hindlimb zeugopod (lower leg) [Automatically generated definition].
Editor notes: the FMA class "muscle of leg" belongs here, do not move. See notes on UBERON:0000978 for possible terminological confusion over term 'leg'
FMA:22471
MA:0000678
SCTID:265806001
UBERON:0004256
calf muscle
lower leg muscle
muscle of leg
uberon
lower leg connective tissue
A portion of connective tissue that is part of a lower leg [Automatically generated definition].
MA:0000677
UBERON:0004270
connective tissue of hind limb middle limb segment
connective tissue of hind limb zeugopod
connective tissue of hindlimb middle limb segment
connective tissue of hindlimb zeugopod
connective tissue of inferior member middle limb segment
connective tissue of inferior member zeugopod
connective tissue of intermediate segment of free lower limb
connective tissue of lower extremity middle limb segment
connective tissue of lower extremity zeugopod
connective tissue of lower leg
connective tissue of middle limb segment of hind limb
connective tissue of middle limb segment of hindlimb
connective tissue of middle limb segment of inferior member
connective tissue of middle limb segment of lower extremity
connective tissue of zeugopod of hind limb
connective tissue of zeugopod of hindlimb
connective tissue of zeugopod of inferior member
connective tissue of zeugopod of leg
connective tissue of zeugopod of lower extremity
hind limb middle limb segment connective tissue
hind limb middle limb segment portion of connective tissue
hind limb middle limb segment textus connectivus
hind limb zeugopod connective tissue
hind limb zeugopod portion of connective tissue
hind limb zeugopod textus connectivus
hindlimb middle limb segment connective tissue
hindlimb middle limb segment portion of connective tissue
hindlimb middle limb segment textus connectivus
hindlimb zeugopod connective tissue
hindlimb zeugopod portion of connective tissue
hindlimb zeugopod textus connectivus
inferior member middle limb segment connective tissue
inferior member middle limb segment portion of connective tissue
inferior member middle limb segment textus connectivus
inferior member zeugopod connective tissue
inferior member zeugopod portion of connective tissue
inferior member zeugopod textus connectivus
intermediate segment of free lower limb connective tissue
intermediate segment of free lower limb portion of connective tissue
intermediate segment of free lower limb textus connectivus
lower extremity middle limb segment connective tissue
lower extremity middle limb segment portion of connective tissue
lower extremity middle limb segment textus connectivus
lower extremity zeugopod connective tissue
lower extremity zeugopod portion of connective tissue
lower extremity zeugopod textus connectivus
lower leg portion of connective tissue
lower leg textus connectivus
middle limb segment of hind limb connective tissue
middle limb segment of hind limb portion of connective tissue
middle limb segment of hind limb textus connectivus
middle limb segment of hindlimb connective tissue
middle limb segment of hindlimb portion of connective tissue
middle limb segment of hindlimb textus connectivus
middle limb segment of inferior member connective tissue
middle limb segment of inferior member portion of connective tissue
middle limb segment of inferior member textus connectivus
middle limb segment of lower extremity connective tissue
middle limb segment of lower extremity portion of connective tissue
middle limb segment of lower extremity textus connectivus
portion of connective tissue of hind limb middle limb segment
portion of connective tissue of hind limb zeugopod
portion of connective tissue of hindlimb middle limb segment
portion of connective tissue of hindlimb zeugopod
portion of connective tissue of inferior member middle limb segment
portion of connective tissue of inferior member zeugopod
portion of connective tissue of intermediate segment of free lower limb
portion of connective tissue of lower extremity middle limb segment
portion of connective tissue of lower extremity zeugopod
portion of connective tissue of lower leg
portion of connective tissue of middle limb segment of hind limb
portion of connective tissue of middle limb segment of hindlimb
portion of connective tissue of middle limb segment of inferior member
portion of connective tissue of middle limb segment of lower extremity
portion of connective tissue of zeugopod of hind limb
portion of connective tissue of zeugopod of hindlimb
portion of connective tissue of zeugopod of inferior member
portion of connective tissue of zeugopod of leg
portion of connective tissue of zeugopod of lower extremity
textus connectivus of hind limb middle limb segment
textus connectivus of hind limb zeugopod
textus connectivus of hindlimb middle limb segment
textus connectivus of hindlimb zeugopod
textus connectivus of inferior member middle limb segment
textus connectivus of inferior member zeugopod
textus connectivus of intermediate segment of free lower limb
textus connectivus of lower extremity middle limb segment
textus connectivus of lower extremity zeugopod
textus connectivus of lower leg
textus connectivus of middle limb segment of hind limb
textus connectivus of middle limb segment of hindlimb
textus connectivus of middle limb segment of inferior member
textus connectivus of middle limb segment of lower extremity
textus connectivus of zeugopod of hind limb
textus connectivus of zeugopod of hindlimb
textus connectivus of zeugopod of inferior member
textus connectivus of zeugopod of leg
textus connectivus of zeugopod of lower extremity
uberon
zeugopod of hind limb connective tissue
zeugopod of hind limb portion of connective tissue
zeugopod of hind limb textus connectivus
zeugopod of hindlimb connective tissue
zeugopod of hindlimb portion of connective tissue
zeugopod of hindlimb textus connectivus
zeugopod of inferior member connective tissue
zeugopod of inferior member portion of connective tissue
zeugopod of inferior member textus connectivus
zeugopod of leg connective tissue
zeugopod of leg portion of connective tissue
zeugopod of leg textus connectivus
zeugopod of lower extremity connective tissue
zeugopod of lower extremity portion of connective tissue
zeugopod of lower extremity textus connectivus
skeleton
AEO:0000168
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]
EFO:0000806
EHDAA2:0001843
EHDAA:5047
FMA:23875
GAID:177
MA:0003006
MAT:0000032
MESH:A02.835
MIAA:0000032
Note that the source FMA definition has been modified here to include cartilage skeletons. We may wish to introduce subclasses for bony/cartilage skeletons.
OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA
SCTID:361378004
UBERON:0004288
VSAO:0000026
XAO:0004053
all the bones and/or cartilaginous elements in the body. Together with the articular system, this comprises the skeletal system.
galen:Skeleton
http://purl.obolibrary.org/obo/uberon/references/reference_0000025
set of all bones
set of bones of body
skeletal
uberon
dermomyotome
AAO:0010572
AEO:0000214
EHDAA2:0003259
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.
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]
Portion of somites that gives rise to dermis and muscles.[AAO]
TAO:0001513
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]
UBERON:0004290
UMLS:C1511786
VHOG:0000676
ZFA:0001513
dermamyotome
dermomyotomes
ncithesaurus:Dermomyotome
uberon
heart rudiment
TAO:0000115
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]
UBERON:0004291
ZFA:0000115
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.
heart cone
rudimentary heart
uberon
proximal phalanx
1
AAO:0010680
MA:0002916
Proximal-most phalanx within a digit[CJM]. Proximal phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones at the base of a toe or finger, the prominent, knobby ends of which are often called the knuckles. In other vertebrates, proximal phalanges have a similar placement in the corresponding limbs, be they paw, wing or fin. In many species, they are the longest and thickest phalanx ('finger' bone)[WP].
SCTID:299708005
UBERON:0004302
phalanx 1
phalanx I
proximal-most phalanx
uberon
proximal phalanx of pedal digit 1
A proximal phalanx that is part of a pedal digit 1 [Automatically generated definition].
FMA:43252
SCTID:182150003
UBERON:0004332
foot digit 1 proximal phalanx
hallux proximal phalanx
proximal phalanx of big toe
proximal phalanx of foot digit 1
proximal phalanx of great toe
proximal phalanx of hallux
proximal phalanx of the 1st toe
uberon
allantois
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]
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].
BTO:0000474
EHDAA2:0000113
EMAPA:16084
EMAPA:16107
EMAPA:28547
MESH:A16.254.403.147
RETIRED_EHDAA2:0000114
SCTID:308825007
Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]
UBERON:0004340
UMLS:C0002084
VHOG:0000738
a diverticulum of the hindgut endoderm [ISBN10:0073040584 "Vertebrates, Kardong"]. AO notes: part_of embryo in EHDAA2 - note differences in humans
allantoic
http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray25.png
ncithesaurus:Allantois
uberon
primitive streak
(...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG]
AO notes: VHOG includes a very broad grouping here based on PMID:9609826
EHDAA2:0001525
EHDAA:185
EMAPA:16072
SCTID:361438007
The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP]
UBERON:0004341
UMLS:C0033153
VHOG:0001202
http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png
http://upload.wikimedia.org/wikipedia/commons/thumb/f/f4/Gray13.png/200px-Gray13.png
ncithesaurus:Primitive_Streak
primitive streak - blastopore - germ ring
uberon
trophectoderm
(...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates.[well established][VHOG]
BTO:0001840
EHDAA2:0002091
EHDAA:56
EMAPA:16046
Editor notes: distinction between trophectoderm and trophoblast unclear/inconsistent in many sources. AO notes: BTO has this has part of the trophoblast
The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG]
UBERON:0004345
VHOG:0000979
outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition
trophectodermal
uberon
limb bud
AAO:0010375
An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
BTO:0001640
Early outgrowth of presumptive limb.[AAO]
GAID:1307
MESH:A16.254.462
UBERON:0004347
UMLS:C0282505
XAO:0003161
gemmae membrorum
induced_by Fgf10, capable of initiating limb forming interactions between endoderm and mesoderm
limb buds
limbbud
ncithesaurus:Limb_Bud
uberon
apical ectodermal ridge
AAO:0010760
AER
Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO]
EMAPA:32744
Proliferative region that is part of the developing fin fold or fin.[TAO]
TAO:0002146
UBERON:0004356
UMLS:C1516037
Usage notes: note that media, dorsal fins etc have AERs. Taxon/development notes: The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold[PMID:20574421]. Function notes: maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop
XAO:0004121
ZFA:0001702
crista ectodermalis apicalis
http://upload.wikimedia.org/wikipedia/commons/5/56/Limbbuddiagram.jpg
multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP].
ncithesaurus:Apical_Ectodermal_Ridge
relationship loss: subclass proliferative region (TAO:0000098)[TAO]
uberon
limb/fin bud
An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056]
The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG]
UBERON:0004357
VHOG:0001258
limb - fin bud
paired appendage bud
uberon
pharyngeal arch 1
1
1st arch
1st pharyngeal arch
1st visceral arch
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]
AAO:0010364
EHDAA2:0000006
EHDAA:573
EMAPA:16118
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.
SCTID:308767008
TAO:0001595
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]
UBERON:0004362
UMLS:C1517197
VHOG:0000296
XAO:0000097
ZFA:0001612
arcus pharyngeus primus
branchial arch 1
first branchial arch
first pharyngeal arch
first visceral arch
http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png
http://upload.wikimedia.org/wikipedia/commons/thumb/2/2d/Gray48.png/200px-Gray48.png
mandibular arch
ncithesaurus:First_Pharyngeal_Arch
uberon
visceral arch 1
aortic arch
AAO:0010414
EFO:0003695
EHDAA2:0000186
EHDAA:398
EHDAA:7327
EMAPA:16684
One of a series of paired embryological vascular structures which give rise to several major arteries.
Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG]
TAO:0005004
UBERON:0004342
UBERON:0004363
UMLS:C0003489
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
VHOG:0000122
When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]
XAO:0000341
ZFA:0005004
aa. arcuum pharyngeorum
aortic arches
branchial aortic arches
branchial arch artery
embryonic aortic arch artery
http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png
http://upload.wikimedia.org/wikipedia/commons/thumb/8/84/Gray473.png/200px-Gray473.png
ncithesaurus:Aortic_Arch
pharyngeal arch artery
uberon
bone of free limb or fin
A bone that is part of an appendage [Automatically generated definition].
UBERON:0004375
appendage bone
bone of appendage
bone of free segment of appendicular skeleton
uberon
distal metaphysis
A metaphysis that is in_distal_side_of a diaphysis.
FMA:32824
UBERON:0004377
distal diaphyseal end of long bone
uberon
distal epiphysis
An epiphysis that adjacent_to a distal metaphysis.
FMA:32822
SCTID:279999006
UBERON:0004379
distal end of long bone
uberon
skeleton of limb
EHDAA2:0002221
Note that EHDAA2 considers hip and shoulder joints part of limb skeleton.
Skeletal subdivision that is part of the limb.[VSAO]
The collection of all skeletal elements in an individual limb.
UBERON:0004381
VSAO:0000300
free limb skeleton
limb skeleton
set of bones of limb
uberon
epiphysis of femur
An epiphysis that is part of a femur [Automatically generated definition].
FMA:32838
SCTID:314625005
UBERON:0004384
femoral epiphysis
uberon
distal epiphysis of femur
A distal epiphysis that is part of a femur [Automatically generated definition].
AAO:0000893
FMA:32844
Head of the femur that articulates with the tibia and fibula.[AAO]
SCTID:280016000
UBERON:0004406
distal femoral epiphysis
distal head of femur
uberon
tarsal region
CALOHA:TS-2219
EFO:0001409
EMAPA:19133
FMA:9665
GAID:41
MA:0000043
MESH:A01.378.610.250.149
MESH:A13.473.821
OpenCyc:Mx4rvVi-R5wpEbGdrcN5Y29ycA
SCTID:361292008
UBERON:0002388
UBERON:0004454
ankle
ankle region
articulatio talocruralis
galen:Ankle
hind basipodium
hind mesopodium
hock
http://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/b/bf/Ankle_en.svg/200px-Ankle_en.svg.png
mesopodial segment of the pes, including the tarsal skeleton and associated tissues.
note that this term refers to the limb segment. See also: tarsal bones and tarsal skeleton. AO notes: MA has both tarsus (part of foot, has tarsal bone) and ankle (part of hindlimb, has joint, nerve, skin).
tarsal limb segment
uberon
entire sense organ system
FMA:78499
Sum of all sensory systems in an organism.
UBERON:0004456
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
sense organ system
uberon
cavity lining
Editor notes: consider merging with serous membrane. AO notes: in MA this groups pericardium, pleura and periotoneal cavity lining
MA:0002448
UBERON:0004457
uberon
body cavity or lining
EMAPA:16060
MA:0000005
Note that this class may be merged into 'serous sac'. See notes for 'cavity lining'
UBERON:0004458
uberon
musculature of trunk
A musculature that is part of a trunk [Automatically generated definition].
AAO:0011572
EFO:0003531
FMA:50187
UBERON:0004479
muscle group of trunk
set of muscles of trunk
uberon
cardiac muscle tissue of atrium
A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition].
FMA:7283
UBERON:0004490
uberon
cardiac muscle tissue of myocardium
A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition].
Editors note: Note placement of MA class based on parthood relationship
FMA:261726
MA:0002441
UBERON:0004493
uberon
cardiovascular system
AAO:0011001
Anatomical system that has as its parts the heart and blood vessels.
BILA:0000016
BTO:0000088
CV system
EFO:0000791
EHDAA2:0000216
EHDAA:394
EMAPA:16104
EMAPA:16370
EV:0100017
FMA:7161
GAID:467
Herz und Gefaesssystem
MA:0000010
MAT:0000016
MESH:A07
MIAA:0000016
OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA
SCTID:278198007
TAO:0000010
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]
UBERON:0004535
UMLS:C0007226
Usage notes: we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
VHOG:0000302
WikipediaCategory:Cardiovascular_system
XAO:0000100
XAO:0001010
ZFA:0000010
ncithesaurus:Cardiovascular_System
uberon
lymph vasculature
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]
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.
FMA:63815
TAO:0005105
UBERON:0004536
ZFA:0005105
lymphatic trunks and ducts
lymphatic vasculature
lymphatic vessel network
lymphatic vessels set
set of lymphatic vessels
trunci et ductus lymphatici
uberon
blood vasculature
TAO:0001079
UBERON:0004537
ZFA:0001079
a vascular network consisting of blood vessels.
blood vascular network
blood vessels
set of blood vessels
uberon
systemic arterial system
FMA:45623
UBERON:0004571
systemic arterial circulatory system
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.
uberon
arterial system
BTO:0004690
EHDAA2:0000143
EHDAA:396
EMAPA:16201
EMAPA:16371
MA:0002719
SCTID:362030008
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]
The part of the cardiovascular system consisting of all arteries.
UBERON:0004572
VHOG:0000273
uberon
systemic artery
FMA:66464
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.
UBERON:0004573
systemic arterial subtree
uberon
venous system
BTO:0004692
EHDAA2:0002171
EHDAA:486
EMAPA:16240
MA:0002720
SCTID:362060003
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]
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:0004582
UMLS:C1267406
VHOG:0000277
ncithesaurus:Venous_System
uberon
vein system
sphincter muscle
AO notes: FMA class is not a subtype of muscle
FMA:75004
UBERON:0004590
UMLS:C1409894
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.
circular muscle
ncithesaurus:Sphincter
sphincter
uberon
blood vessel endothelium
An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart
BTO:0000766
MA:0000709
TAO:0005257
UBERON:0004638
UMLS:C1706972
ZFA:0005257
ncithesaurus:Blood_Vessel_Endothelium
uberon
arterial system endothelium
An endothelium that is part of an arterial system [Automatically generated definition].
MA:0000703
UBERON:0004700
UMLS:C1706849
ncithesaurus:Arterial_System_Endothelium
uberon
dorsal thalamus
BM:Die-Th
EHDAA2:0000692
MA and ZFA think there is a distinct dorsal thalamus, but FMA says its an exact synonym. TODO. http://www.ncbi.nlm.nih.gov/pubmed/8167659
MA:0000180
TAO:0000653
UBERON:0004703
ZFA:0000653
dorsal thalamus
ncithesaurus:Dorsal_Thalamus
thalamus, pars dorsalis
uberon
limb/fin
An appendage that is part of a appendage girdle complex.
UBERON:0004708
UBERON:0009872
VSAO:0000067
girdle-associated appendage
jointed paired lateral appendage
limb or fin
paired appendage
pectoral or pelvic appendage
pelvic/pectoral appendage
this class is the union of the classes limb, pectoral fin and pelvic fin.
uberon
pelvic appendage
Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues.
UBERON:0004709
UBERON:0009876
VSAO notes - in contrast to VSAO, we include separate subclasses for limbs and fins
VSAO:0000126
hindlimb/pelvic fin
pelvic appendage
pelvic limb/fin
posterior paired appendage
uberon
conceptus
AEO:0000194
BTO:0003834
EHDAA2:0000001
EHDAA2:0003235
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].
UBERON:0004716
UMLS:C1516779
Wikipedia:Conceptus
embryo plus adnexa
ncithesaurus:Conceptus
uberon
segmental subdivision of nervous system
An organ segment that is part of a nervous system [Automatically generated definition].
Editor note: revisit this after CARO is revised and/or we have defined metameric segment
FBbt:00005140
UBERON:0004732
neuromere
uberon
segmental subdivision of hindbrain
An organ segment that is part of a hindbrain [Automatically generated definition].
FMA:61998
UBERON:0004733
hindbrain segment
segment of hindbrain
uberon
dentary
AAO:0000124
Dermal bone that is usually the anteriormost bone of the lower jaw, and that articulates with the angular, or anguloarticular bone, posteriorly, and carries part of the mandibular sensory canal and pore openings of the mandibular sensory canal on its lateral surface. The dentary is a paired bone.[TAO]
EFO:0003508
Of all these bones [dentary, splenials, coronoids, angular, surangular and prearticular], only the dentary remains in the lower jaw of a mammal.[well established][VHOG]
Ossified element of intramembranous origin that invests the lateral margin of Meckel's cartilage thereby forming the lateral side of the mandible in anurans and salamanders (Duellman & Trueb, 1994:293). In caecilians, the dentary is part of a compound bone termed the pseudodentary.[AAO]
TAO:0000191
Taxon notes: In lobe-finned fishes and the early fossil tetrapods, the bone homologous to the mandible of mammals is merely the largest of several bones in the lower jaw. In such animals, it is referred to as the dentary bone, and forms the body of the outer surface of the jaw. It is bordered below by a number of splenial bones, while the angle of the jaw is formed by a lower angular bone and a suprangular bone just above it. The inner surface of the jaw is lined by a prearticular bone, while the articular bone forms the articulation with the skull proper. Finally a set of three narrow coronoid bones lie above the prearticular bone. As the name implies, the majority of the teeth are attached to the dentary, but there are commonly also teeth on the coronoid bones, and sometimes on the prearticular as well. This complex primitive pattern has, however, been simplified to various degrees in the great majority of vertebrates, as bones have either fused or vanished entirely. In teleosts, only the dentary, articular, and angular bones remain, while in living amphibians, the dentary is accompanied only by the prearticular, and, in salamanders, one of the coronoids. The lower jaw of reptiles has only a single coronoid and splenial, but retains all the other primitive bones except the prearticular.
The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified].
The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians. In mammals the lower jaw consists entirely of the dentary bone. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, ZFA:0000191_and_Liem_KF, p.248][VHOG]
UBERON:0004742
VHOG:0001022
ZFA:0000191
dentale
dentaries
dentary bone
http://palaeos.com/vertebrates/bones/dermal/images/Dentary1.gif
os dentale
relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO]
sur-angulaire
uberon
skeletal tissue
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]
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]
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
SCTID:309311006
UBERON:0004755
VSAO:0000015
XAO:0004038
ZFA:0005619
mineralized tissue
uberon
skeletal element
AAO:0011129
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
TAO:0001890
TODO - add more general class for other kinds of mineralized tissue
UBERON:0004765
VSAO:0000128
XAO:0004012
ZFA:0005494
galen:SkeletalStructure
uberon
bone of lower jaw
Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular
Editor notes: Do not manually classify under here - bones are automatically classified
UBERON:0004768
lower jaw bone
uberon
diaphysis
FMA:24013
GAID:189
MESH:A02.835.232.169
SCTID:361729006
Subdivision of long bone which forms the part of the bone between the two epiphyses, excluding the metaphyses[FMA,modified].
Subdivision of long bone which forms the part of the bone between the two epiphyses; together with other the subdivisions of long bone, it constitutes the long bone. Examples: diaphysis of humerus, diaphysis of femur[FMA].
The main or mid section (shaft) of a long bone. It is made up of cortical bone and usually contains bone marrow and adipose tissue (fat)[WP][FMA:24013, Wikipedia:Diaphysis].
UBERON:0004769
body of long bone
http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/9/94/Illu_long_bone.jpg/200px-Illu_long_bone.jpg
long bone diaphysis
shaft of long bone
uberon
articular system
Anatomical system that consists of all the joints of the body.
FMA:23878
MA:0003007
SCTID:361827000
UBERON:0004770
VSAO:0000181
joint system
set of all joints
set of all joints of body
set of joints of body
uberon
gastrointestinal system serosa
A serous membrane that is part of a digestive system [Automatically generated definition].
MA:0001522
UBERON:0004782
digestive system serosa
digestive system serous membrane
gastrointestinal system serous membrane
serosa of digestive system
serosa of gastrointestinal system
serous membrane of digestive system
serous membrane of gastrointestinal system
uberon
respiratory system mucosa
A mucosa that is part of a respiratory system [Automatically generated definition].
BTO:0000973
EMAPA:18334
GAID:304
MA:0001827
MESH:A04.760
TODO - split respiratory tract mucosa from respiratory system mucosa
UBERON:0004785
apparatus respiratorius mucosa
apparatus respiratorius mucosa of organ
apparatus respiratorius mucous membrane
mucosa of apparatus respiratorius
mucosa of organ of apparatus respiratorius
mucosa of organ of respiratory system
mucosa of respiratory system
mucous membrane of apparatus respiratorius
mucous membrane of respiratory system
respiratory mucosa
respiratory system mucosa of organ
respiratory system mucous membrane
uberon
gastrointestinal system mucosa
A mucosa that is part of a gastrointestinal system.
BTO:0000546
MA:0001521
SCTID:410433007
The gut mucosa of amphioxus has insulin-secreting cells. PMID:16417468
UBERON:0004786
digestive tract mucosa
gut mucosa
gut mucuous membrane
mucosa of gut
uberon
respiratory tract epithelium
An epithelium that is part of a respiratory tract [Automatically generated definition].
BTO:0000419
MA:0001480
SCTID:321764001
UBERON:0004802
VHOG:0000981
airway epithelium
epithelial tissue of respiratory tract
epithelium of respiratory tract
respiratory epithelium
respiratory tract epithelial tissue
uberon
respiratory system epithelium
An epithelium that is part of a respiratory system [Automatically generated definition].
MA:0001823
UBERON:0004807
VHOG:0000981
apparatus respiratorius epithelial tissue
apparatus respiratorius epithelium
epithelial tissue of apparatus respiratorius
epithelial tissue of respiratory system
epithelium of apparatus respiratorius
epithelium of respiratory system
respiratory system epithelial tissue
uberon
gastrointestinal system epithelium
An epithelium that is part of a digestive system [Automatically generated definition].
MA:0001520
UBERON:0004808
digestive system epithelial tissue
digestive system epithelium
epithelial tissue of digestive system
epithelial tissue of gastrointestinal system
epithelium of digestive system
epithelium of gastrointestinal system
gastrointestinal system epithelial tissue
uberon
lower respiratory tract epithelium
An epithelium that is part of a lower respiratory tract [Automatically generated definition].
MA:0001481
UBERON:0004815
epithelial tissue of lower respiratory tract
epithelium of lower respiratory tract
lower respiratory tract epithelial tissue
uberon
kidney epithelium
An epithelium that is part of a kidney [Automatically generated definition].
BTO:0000059
MA:0002846
UBERON:0004819
epithelial tissue of kidney
epithelium of kidney
kidney epithelial tissue
uberon
respiratory system skeletal muscle
A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition].
MA:0001829
UBERON:0004830
respiratory system skeletal muscle tissue
skeletal muscle of apparatus respiratorius
skeletal muscle of respiratory system
skeletal muscle tissue of apparatus respiratorius
skeletal muscle tissue of respiratory system
uberon
aorta endothelium
An endothelium that is part of an aorta [Automatically generated definition].
BTO:0000394
EFO:0002597
MA:0000701
UBERON:0004851
UMLS:C1706824
adult aorta endothelium
endothelium of adult aorta
endothelium of aorta
endothelium of trunk of aortic tree
endothelium of trunk of systemic arterial tree
ncithesaurus:Aorta_Endothelium
trunk of aortic tree endothelium
trunk of systemic arterial tree endothelium
uberon
cardiovascular system endothelium
An endothelium that is part of the cardiovascular system.
BTO:0001853
GAID:519
MA:0000717
MESH:A07.231.330
TAO:0002171
UBERON:0004852
VHOG:0001217
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
XAO:0000356
ZFA:0001639
consider merging with 'endothelium'
uberon
gastrointestinal system mesentery
A mesentery that is part of a digestive system [Automatically generated definition].
MA:0001900
UBERON:0004854
digestive system mesentery
mesentery of digestive system
mesentery of gastrointestinal system
uberon
eye gland
A gland that is part of a eye [Automatically generated definition].
Example: harderian gland
MA:0000267
UBERON:0004859
gland of eye
uberon
somatic layer of lateral plate mesoderm
AAO:0011100
BILA:0000047
Layer of lateral plate mesoderm that forms the future body wall - underlies the ectoderm[WP].
UBERON:0004871
XAO:0000271
check BILA
outer layer of lateral plate mesoderm
parietal mesoderm
somatic mesoderm
uberon
splanchnic layer of lateral plate mesoderm
AAO:0011102
AO notes: We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors
BILA:0000044
Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].
UBERON:0004872
XAO:0000276
inner layer of lateral plate mesoderm
splanchnic mesoderm
uberon
visceral mesoderm
somatopleure
EHDAA2:0001847
EHDAA:381
EMAPA:16180
UBERON:0004874
UMLS:C1519423
VHOG:0000557
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].
http://upload.wikimedia.org/wikipedia/commons/thumb/2/28/Gray16.png/200px-Gray16.png
ncithesaurus:Somatopleure
todo - check relationship to LPM
uberon
nephrogenic cord
FMA:72168
SCTID:361405003
UBERON:0004875
UMLS:C1283944
a portion of the urogenital ridge which is the source of much of the urinary system[WP].
chorda nephrogenica
ncithesaurus:Nephrogenic_Cord
part_of or develops_from urogenital ridge?
uberon
urogenital ridge
BTO:0001402
EHDAA2:0004022
EMAPA:30888
EMAPA:30899
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]
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].
SCTID:308801004
UBERON:0004876
UMLS:C0231047
ncithesaurus:Urogenital_Ridge
uberon
urethral fold
urogenital fold
chordamesoderm
AAO:0000478
EFO:0003426
TAO:0000091
The central region of trunk mesoderm. This tissue forms the notochord
UBERON:0004880
ZFA:0000091
axial chorda mesoderm
chorda mesoderm
dorsal mesoderm
note that WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord.
presumptive notochord
uberon
urogenital sinus epithelium
EHDAA2:0004061
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
UBERON:0004902
UGE
epithelium of urogenital sinus
uberon
we follow EHDAA2 in dividing the UGS into epithelium and lumen
articulation
FBbt:00005811
UBERON:0004905
anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
uberon
ectodermal gut
A portion of the gut that is derived from ectoderm.
UBERON:0004906
uberon
lower digestive tract
EHDAA2:0000726
FMA:49179
MA:0000917
SCTID:279973004
UBERON:0004907
UMLS:C0226875
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
galen:LowerGastrointestinalTract
gut
lower GI tract
lower gastrointestinal tract
ncithesaurus:Lower_Gastrointestinal_Tract
the region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition].
uberon
epithelium of gonad
An epithelium surrounding a gonad.
EHDAA:4032
EHDAA:5931
FBbt:00004859
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
UBERON:0004909
UMLS:C1517534
gonad epithelium
gonadal epithelium
ncithesaurus:Germinal_Epithelium
uberon
epithelium of male gonad
An epithelium surrounding a testis.
BTO:0001364
EMAPA:17973
FBbt:00004955
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
UBERON:0004910
testis epithelium
testis sheath
uberon
biliary bud
EHDAA2:0000171
EMAPA:16561
EMAPA:16565
UBERON:0004912
VHOG:0001351
hepatic diverticulum
http://upload.wikimedia.org/wikipedia/commons/thumb/4/4f/Gray1088.png/200px-Gray1088.png
uberon
subdivision of digestive tract
FBbt:00100315
FMA:71131
UBERON:0004921
alimentary system subdivision
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
subdivision of alimentary system
uberon
organ component layer
FMA:82485
UBERON:0004923
uberon
mucosa of pylorus
A mucosa that is part of a pylorus [Automatically generated definition].
BTO:0002984
EMAPA:27199
EMAPA:27499
FMA:17461
UBERON:0004998
antropyloric mucosa
mucosa of organ of pyloric part of stomach
mucosa of organ of pylorus
mucosa of organ of stomach pyloric region
mucosa of pyloric part of stomach
mucosa of stomach pyloric region
mucous membrane of pyloric part of stomach
mucous membrane of pylorus
mucous membrane of stomach pyloric region
organ mucosa of pyloric part of stomach
organ mucosa of pylorus
organ mucosa of stomach pyloric region
pyloric part of stomach mucosa
pyloric part of stomach mucosa of organ
pyloric part of stomach mucous membrane
pyloric part of stomach organ mucosa
pylorus mucosa
pylorus mucosa of organ
pylorus mucous membrane
pylorus organ mucosa
stomach pyloric region mucosa
stomach pyloric region mucosa of organ
stomach pyloric region mucous membrane
stomach pyloric region organ mucosa
uberon
mucosa of tongue
A mucosa that is part of a tongue [Automatically generated definition].
EFO:0002553
FMA:54807
SCTID:362092002
UBERON:0005020
lingual mucosa
mucosa of organ of tongue
mucous membrane of tongue
organ mucosa of tongue
tongue mucosa
tongue mucosa of organ
tongue mucous membrane
tongue organ mucosa
tunica mucosa linguae
uberon
mediastinum testis
EMAPA:18331
FMA:19812
SCTID:362279007
The mediastinum testis is a network of fibrous connective tissue that extends from the upper to near the lower extremity of the testis, and is wider above than below. From its front and sides numerous imperfect septa (trabeculæ) are given off, which radiate toward the surface of the organ, and are attached to the tunica albuginea. They divide the interior of the organ into a number of incomplete spaces, called lobules. These are somewhat cone-shaped, being broad at their bases at the surface of the gland, and becoming narrower as they converge to the mediastinum. The mediastinum supports the rete testis and blood vessels of the testis in their passage to and from the substance of the gland[WP]
UBERON:0005051
body of highmore
hilum of testicle
http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/b/b5/Hodenschema.svg/200px-Hodenschema.svg.png
mediastinum of testis
testis mediastinum
uberon
zone of long bone
An organ part that is part of a long bone [Automatically generated definition].
FMA:24008
UBERON:0005055
long bone zone
uberon
external female genitalia
An external genitalia that is part of a female reproductive system [Automatically generated definition].
BTO:0003100
EMAPA:30984
FMA:45649
SCTID:362234008
UBERON:0005056
external female genital organ
external genitalia of female reproductive system
female external genitalia
galen:FemaleExternalGenitalia
organa genitalia feminina externa
uberon
immune organ
An organ that is part of a immune system [Automatically generated definition].
UBERON:0005057
uberon
hemolymphoid system gland
A gland that is part of a hemolymphoid system [Automatically generated definition].
MA:0002962
UBERON:0005058
hemopoietic or lymphoid gland
hemopoietic or lymphoid organ
uberon
neural fold
EHDAA2:0001249
EMAPA:16093
EMAPA:16142
EMAPA:16146
EMAPA:16151
EMAPA:16155
EMAPA:16159
EMAPA:16162
EMAPA:16288
EMAPA:16292
EMAPA:16295
EMAPA:16299
EMAPA:16303
EMAPA:16307
EMAPA:16528
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].
One of the two elevated edges of the neural groove[GO,MP].
SCTID:361461009
UBERON:0005062
UMLS:C0814993
XAO:0004087
medullary fold
ncithesaurus:Neural_Fold
uberon
neural rod
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]
EFO:0003498
TAO:0000133
UBERON:0005068
ZFA:0000133
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].
uberon
tube lumen
A hole in a tube[GO].
AEO:0000078
EHDAA2:0004618
RETIRED_EHDAA2:0003078
UBERON:0005082
uberon
ectodermal placode
An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]
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
UBERON:0005085
uberon
tooth placode
An tooth placode is a thickening of the ectoderm that will give rise to the tooth bud[GO].
BTO:0001511
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.
Placode that develops into a tooth. The placode is a thickening of the pharyngeal epithelium.[TAO]
TAO:0001153
UBERON:0005087
ZFA:0001153
dental placode
dental primordium
odontogenic placode
tooth germ
uberon
sebaceous gland placode
A sebaceous gland placode is a thickening of the ectoderm that will give rise to the sebaceous gland bud[GO].
UBERON:0005088
todo - add bud
uberon
muscle structure
FBbt:00005073
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
UBERON:0005090
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
muscle
muscle element
uberon
kidney rudiment
.
Editor notes: class added for consistency with GO - consider merging with kidney mesenchyme.
UBERON:0005095
kidney anlage
uberon
mesonephric epithelium
An epithelium that is part of a mesonephros [Automatically generated definition].
UBERON:0005103
uberon
epithelial bud
A bud is a protrusion that forms from an epithelial sheet by localized folding.
BTO:0001639
UBERON:0005153
uberon
epithelial cord
AEO:0000216
EHDAA2:0004052
TODO - add superclass of developing structure
UBERON:0005154
uberon
reproductive structure
An anatomical structure that is part of the reproductive system.
UBERON:0005156
reproductive system structure
uberon
epithelial fold
An epithelial sheet bent on a linear axis.
UBERON:0005157
uberon
multi cell component structure
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
AAO:0011000
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."
CARO:0001000
FBbt:00007060
FMA:83115
UBERON:0005162
cell part cluster
multi-cell-component structure
uberon
abdomen organ
An organ that is part of an abdomen [Automatically generated definition].
MA:0000522
SCTID:272631008
UBERON:0005172
uberon
abdominal segment organ
An organ that is part of a abdominal segment of trunk.
Includes abdomen organ and pelvis organ
MA:0000529
UBERON:0005173
uberon
back organ
An organ that is part of a back [Automatically generated definition].
MA:0001901
UBERON:0005174
uberon
chest organ
An organ that is part of a chest [Automatically generated definition].
MA:0000552
UBERON:0005175
uberon
tooth enamel organ
.
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]
BTO:0001722
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]
MA:0001604
MESH:A14.254.900.720.265
SCTID:362863002
TAO:0005138
UBERON:0005176
ZFA:0005138
dental organ
enamel organ
odontogenic organ
organum enameleum
uberon
trunk organ
An organ that is part of a trunk [Automatically generated definition].
MA:0000516
UBERON:0005177
uberon
thoracic cavity organ
An organ that is part of a thoracic cavity [Automatically generated definition].
MA:0000557
UBERON:0005178
uberon
thoracic segment organ
An organ that is part of a thoracic segment of trunk.
MA:0000563
UBERON:0005181
uberon
upper body organ
head mesenchyme
EFO:0003492
EHDAA2:0000732
EHDAA:179
EMAPA:16098
EMAPA:16269
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]
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.
TAO:0000113
UBERON:0005253
VHOG:0000332
ZFA:0000113
cephalic mesenchyme
uberon
upper leg mesenchyme
EHDAA2:0002132
EMAPA:17501
Mesenchyme that is part of a hindlimb stylopod [Automatically generated definition].
UBERON:0005254
VHOG:0000506
uberon
pedal digit mesenchyme
Mesenchyme that is part of a toe [Automatically generated definition].
UBERON:0005255
VHOG:0000463
foot digit mesenchyme
hind limb digit mesenchyme
toe mesenchyme
uberon
trunk mesenchyme
EFO:0003485
EHDAA2:0002092
EHDAA:377
EMAPA:16177
Mesenchyme that is part of a trunk.
TAO:0000081
UBERON:0005256
VHOG:0000281
ZFA:0000081
uberon
lower leg mesenchyme
EHDAA2:0001032
EMAPA:17498
Mesenchyme that is part of a lower leg [Automatically generated definition].
UBERON:0005259
VHOG:0000752
uberon
ventricular system of central nervous system
CNS ventricular system
EFO:0003650
EHDAA2:0004362
EV:0100306
FMA:242675
TAO:0001261
UBERON:0005281
ZFA:0001261
a set of structures containing cerebrospinal fluid in the brain. It is continuous with the central canal of the spinal cord[WP].
http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png
http://upload.wikimedia.org/wikipedia/commons/thumb/7/7d/Gray734.png/200px-Gray734.png
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'
uberon
ventricle system
ventricular system
ventricular system of neuraxis
ventriculi cerebri
ventricular system of brain
FMA:242787
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]
UBERON:0005282
VHOG:0000005
brain ventricular system
uberon
myelencephalon
BTO:0000758
EHDAA2:0001207
EHDAA:5526
EMAPA:17082
MA:0000205
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]
The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]
The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP].
UBERON:0005290
VHOG:0000456
http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg
http://upload.wikimedia.org/wikipedia/commons/thumb/5/54/EmbryonicBrain.svg/200px-EmbryonicBrain.svg.png
the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes
uberon
embryonic tissue
A portion of tissue that is part of an embryo.
UBERON:0005291
developing tissue
portion of embryonic tissue
uberon
extraembryonic tissue
BTO:0003360
EFO:0001406
MAT:0000061
MIAA:0000061
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:0005292
extra-embryonic tissue
uberon
genital ridge
AAO:0011047
EFO:0001414
EHDAA2:0004044
SCTID:361399001
TODO - check developmental relationships. merge with urogenital ridge?
The precursor to the gonads.
UBERON:0005294
UMLS:C1512243
XAO:0000018
crista gonadalis
gonadal ridge
http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1106.png
http://upload.wikimedia.org/wikipedia/commons/thumb/3/30/Gray1106.png/200px-Gray1106.png
ncithesaurus:Gonadal_Ridge
uberon
sex cord
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.
EHDAA2:0004051
RETIRED_EHDAA2:0001523
SCTID:343823004
UBERON:0005295
UMLS:C1512242
gonad cord
gonadal cord
ncithesaurus:Gonadal_Cord
primitive sex cord
uberon
testis sex cord
EHDAA2:0002011
EHDAA:8152
EMAPA:29098
The testis cords are precursors to the rete testis. They play several different roles in the development of the male genitals[WP].
UBERON:0005297
VHOG:0001321
check primary vs testis
primary sex cord
testis cord
testis primary sex cords
testis primitive sex cord
uberon
male preputial gland
BTO:0001111
EMAPA:30502
EMAPA:30640
EMAPA:30659
FMA:19653 was previously placed here, but ISBN10:0123813611 states that no true equivalent in humans. See also https://sourceforge.net/tracker/index.php?func=detail&aid=3588536&group_id=76834&atid=1109502
MA:0000403
One of the sebaceous glands of the corona and neck of the glans penis.
UBERON:0005301
UMLS:C0227956
gland of Tyson
ncithesaurus:Preputial_Gland
preputial gland
preputial gland of male
preputial gland of penis
uberon
mammary placode
TODO develops_from
The mammary placode is a transient lens shaped structure that will give rise to the mammary bud proper[GO].
UBERON:0005311
uberon
mammary bud
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].
UBERON:0004181
UBERON:0005333
mammary gland bud
milk bud
uberon
dorsal telencephalic commissure
UBERON:0005340
dorsal commissure
the fiber tracts that connect the dorsal region of the two cerebral hemispheres and span the longitudinal fissure, including the corpus callosum and hippocampal commissure[MP].
uberon
cortical plate
ABA:CTXpl
UBERON:0005343
the outer neural tube region in which post-mitotic neuroblasts migrate along radial glia to form the adult cortical layers[MP].
uberon
spermatic cord
FMA:19937
GAID:395
MESH:A05.360.444.777
SCTID:181433005
The cord-like structure in males comprising the vas deferens and associated tissue that runs from the abdomen down to each testis[MP].
UBERON:0005352
UMLS:C0037855
funiculus spermaticus
http://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png
http://upload.wikimedia.org/wikipedia/commons/thumb/3/35/Male_anatomy.png/200px-Male_anatomy.png
ncithesaurus:Spermatic_Cord
spermatic chord
uberon
ventricle of nervous system
FMA:242770
UBERON:0005358
region of wall of ventricular system of neuraxis
uberon
olfactory lobe
(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]
BTO:0001362
EFO:0000108
EHDAA2_RETIRED:0001294
EHDAA:5480
EMAPA:17778
MA:0002413
MIAA:0000116
Olfactory apparatus on the lower surface of the frontal lobe of the brain. It consists of the olfactory bulb, tract, and trigone[BTO].
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].
UBERON:0005366
UMLS:C0178780
VHOG:0000833
ncithesaurus:Olfactory_Lobe
uberon
dorsal striatum
ABA:STRd
According to BrainInfo it is a part of the basal ganglia comprising the globus pallidus and striatum
According to the 1917 version of Gray's Anatomy, it is the combination of the lentiform nucleus and the caudate nucleus
BTO:0004701
FMA:77620
It may also refer to both the basal ganglia and the internal capsule collectively.
It may also refer to the putamen and caudate collectively.
MA:0002971
NIF_GrossAnatomy:nlx_anat_1010001
Those portions of the caudate nucleus and especially the putamen located generally superior to a plane representing the anterior commissure; also called the dorsal basal ganglia; may function in motor activities with cognitive origins.
UBERON:0005382
caudoputamen
corpus striatum
dorsal basal ganglia
dorsal basal ganglion
striated body
striatum dorsale
uberon
caudate-putamen
ABA:CP
BM:Tel-C-Pu
BTO:0000212
CHECK - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM)
EFO:0001912
EMAPA:19095
MA:0000893
NIF_GrossAnatomy:nlx_anat_100312
Regional part of telencephalon in some species, e.g., rodent, equivalent to the dorsal striatum (caudate nucleus and putamen). Unlike the dorsal striatum of primates, for example, the caudoputamen is not split into separate nuclei by the fibers of the internal capsule. Rather, the internal capsule splits into fiber bundles which course through the structure.
UBERON:0005383
caudate putamen
caudateputamen
caudoputamen
uberon
photoreceptor array
An array of photoreceptors and any supporting cells found in an eye.
FBbt:00004200
UBERON:0005388
light-sensitive tissue
uberon
transparent eye structure
UBERON:0005389
lens
transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array
uberon
female reproductive gland
A sex gland that is part of a female reproductive system.
BTO:0000254
MA:0000383
UBERON:0005398
uberon
male reproductive gland
A sex gland that is part of a male reproductive system.
BTO:0000080
MA:0000399
UBERON:0005399
uberon
cerebral grey matter
AO notes: BTO may actually be a more generic structure; FMA may represent a more specific structure. Consider merging with gray matter of telencephalon
BTO:0000823
FMA:61821
MA:0000944
UBERON:0005401
cerebral gray matter
uberon
ventral striatum
ABA:STRv
BTO:0004702
EFO:0001936
FMA:77614
MA:0002972
The ventral striatum is a portion of the striatum. It consists of the nucleus accumbens and the olfactory tubercle. Some sources also include the ventromedial parts of the caudate nucleus and putamen. It is considered a reward center.
UBERON:0005403
uberon
circumventricular organ
AO notes: MA subdivides into sensory and secretory
Brain region located around or in relation to the ventricular system that is highly vascularized and distinguished by the lack of a blood brain barrier.
CVO
FMA:84081
MA:0002942
NIF_GrossAnatomy:nlx_anat_20090312
UBERON:0005408
circumventricular organ
circumventricular organ of neuraxis
http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png
uberon
gastrointestinal system
All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]
BTO:0000058
EHDAA2:0000110
EHDAA:514
EMAPA:16246
EV:0100056
FMA:71132
GAID:294
GI tract
MA:0000323
MESH:A03.492
SCTID:373871007
UBERON:0005409
UMLS:C0012240
VHOG:0000412
alimentary system
alimentary tract
galen:GastrointestinalTract
gastro-intestinal system
gastrointestinal (GI) tract
gastrointestinal system
gastrointestinal tract
ncithesaurus:Gastrointestinal_System
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
uberon
hindlimb bud
A limb bud that develops into a hindlimb.
AAO:0010382
EHDAA:2358
EMAPA:16779
Genes: Tbx4 specifies hindlimbs. Wnt8c restricts Fgf10 in chick.
MIAA:0000256
RETIRED_EHDAA2:0003197
SCTID:346164003
The bilateral thickening of the ectoderm in the region of the first noticeable at NF stage 47, and innervated by NF stage 51. The hind limb buds develop before the forelimb buds.[AAO]
UBERON:0005418
XAO:0003066
hind limb bud
leg bud
limb bud - hindlimb
posterior limb bud
uberon
pelvic appendage bud
A limb bud that develops into a hindlimb or pelvic fin.
EFO:0003469
Fin bud that develops into the pelvic fin.[TAO]
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
TAO:0001384
UBERON:0005420
VHOG:0001260
ZFA:0001384
at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future
hindlimb/pelvic fin bud
pelvic fin bud
uberon
developing anatomical structure
AEO:0000125
CALOHA:TS-2122
EHDAA2:0003125
FBbt:00007006
MIAA:0000019
UBERON:0005423
developing structure
developmental structure
developmental tissue
uberon
presumptive neural retina
(...) 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]
EHDAA2:0001304
EMAPA:16675
Portion of tissue that is the inner layer of the optic cup and will become the neural retina.
TAO:0001071
UBERON:0005425
VHOG:0000490
ZFA:0001071
inner layer optic cup
optic cup inner layer
presumptive retina
presumptive retinas
uberon
lens vesicle
(...) 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]
A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]
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]
EHDAA2:0000983
EHDAA:4737
EMAPA:17163
Portion of tissue that gives rise to the lens.
SCTID:361510002
TAO:0002205
UBERON:0005426
VHOG:0001163
ZFA:0001679
hollow lens vesicle
solid lens vesicle
uberon
vagal neural crest
EHDAA2:0002156
EHDAA:669
TAO:0000818
UBERON:0005428
VHOG:0001208
Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO]
Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA].
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
XAO:0004191
ZFA:0000818
post-otic neural crest
uberon
definitive endoderm
EFO:0002574
EHDAA2:0000337
EHDAA:218
EMAPA:16070
Embryonic endoderm
FMA:85519
UBERON:0005439
VHOG:0000751
uberon
segment of pes
A segment of autopod that is part of a pes.
FMA:24993
SCTID:362887000
UBERON:0005445
foot region
foot subdivision
regio pedis
segment of foot
subdivision of foot
uberon
sulcus limitans of neural tube
A longitudinal groove in the neural tube wall of the embryo; stretches from the mesencephalon caudad[TMD].
UBERON:0005478
neural tube lateral wall sulcus limitans
sulcus limitans
uberon
midbrain lateral wall
EHDAA2:0001171
EHDAA:3700
EMAPA:16976
TAO:0000906
UBERON:0005495
VHOG:0000455
ZFA:0000906
lateral wall mesencephalon
lateral wall midbrain
uberon
neural tube lateral wall
EHDAA2:0001257
EHDAA:2873
EHDAA:912
Portion of tissue on the side of the lumen of the neural tube.
TAO:0001435
UBERON:0005496
VHOG:0000513
ZFA:0001435
lateral wall neural tube
uberon
non-neural ectoderm
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)
EFO:0003643
EHDAA:257
EMAPA:16074
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]
RETIRED_EHDAA2:0001273
TAO:0001178
UBERON:0005497
VHOG:0001372
XAO:0004091
ZFA:0001178
epidermal ectoderm
epithelial ectoderm
non neural ectoderm
surface ectoderm
uberon
ventral ectoderm
primitive heart tube
EHDAA2:0001512
EHDAA:436
EMAPA:16215
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
SCTID:361522004
TAO:0000149
UBERON:0005498
ZFA:0000149
uberon
thymus primordium
A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO]
A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID].
EFO:0003622
EHDAA2:0002023
EHDAA:2969
EMAPA:17523
EMAPA:18536
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]
TAO:0001077
UBERON:0005562
ZFA:0001077
thymic primordium
thymic rudiment
uberon
gonad primordium
EFO:0003651
EHDAA:5927
EMAPA:17204
Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]
Portion of tissue that gives rise to the immature gonad.
RETIRED_EHDAA2:0002148
TAO:0001262
Taxon notes: this is a very broad grouping class
UBERON:0005564
WBbt:0008366
ZFA:0001262
gonadal primordium
uberon
undifferentiated gonad
lung primordium
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.
AAO:0011059
EFO:0002578
UBERON:0005597
XAO:0001002
lateral diverticula
lung endoderm
uberon
dorsal mesogastrium
EHDAA2:0000416
EHDAA:3001
EMAPA:17025
EMAPA:18903
MA:0001618
The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG]
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.
UBERON:0005602
UMLS:C1512038
VHOG:0000352
dorsal mesentery
ncithesaurus:Dorsal_Mesogastrium
uberon
left dorsal aorta
A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG]
Contributes to the arch of aorta in humans[http://emedicine.medscape.com/article/899609-overview]
EHDAA2:0000936
EHDAA:404
EMAPA:16205
MA:0000478
SCTID:361403005
UBERON:0005613
VHOG:0000484
uberon
right dorsal aorta
A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG]
EHDAA2:0001720
EHDAA:406
EMAPA:16206
MA:0000479
Normally regresses in humans[http://emedicine.medscape.com/article/899609-overview]
SCTID:361404004
UBERON:0005622
VHOG:0000485
uberon
extraembryonic membrane
AO notes: EHDAA2 is a mereological sum. Taxon notes: stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN10:0073040584 "Vertebrates, Kardong"]
EHDAA2:0004714
Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo.
SCTID:362840007
UBERON:0005631
http://purl.obolibrary.org/obo/uberon/references/reference_0000010
uberon
pronephric mesoderm
A mesoderm that develops_into a pronephros.
AAO:0011090
EFO:0003479
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]
TAO:0000067
UBERON:0005721
VHOG:0001239
XAO:0000264
ZFA:0000067
pronephric anlage
pronephric bulge
pronephric mesenchyme
pronephric primordium
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
uberon
olfactory system
AAO:0000334
AAO:0000978
BILA:0000144
EFO:0001973
FMA:7190
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
MA:0002445
NIF_GrossAnatomy:nlx_anat_090806
OpenCyc:Mx4rvViw75wpEbGdrcN5Y29ycA
SCTID:362290002
TAO:0001149
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].
The sensory system used for olfaction (the sense of smell).[AAO]
UBERON:0005725
UMLS:C0228065
XAO:0003196
ZFA:0001149
ncithesaurus:Olfactory_System
uberon
extraembryonic mesoderm
.
EHDAA2:0000474
UBERON:0005728
VHOG:0000616
extra-embryonic mesoderm
extraembryonic mesenchyme
uberon
pelvic appendage field
A limb/fin field that develops_into a pelvic appendage bud mesenchyme.
Embryonic region that develops into the pelvic fin bud.[TAO]
TAO:0001454
UBERON:0005730
ZFA:0001454
pelvic appendage field of lateral plate mesoderm
pelvic fin field
uberon
limb/fin field
A ring of cells capable of forming a limb or paired fin[Gilbert,modified].
Editor notes: we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this.
UBERON:0005732
limb/fin field of lateral plate mesoderm
uberon
limb field
A ring of cells capable of forming a limb.
UBERON:0005733
limb field of lateral plate mesoderm
the central portion of the limb field gives rise to the limb proper. mesenchyme cells proliferate from from the somatic layer of limb field lateral plate mesoderm (limb skeletal precursors) and from the somites (limb muscle precursors) . these mesenchymal cells accumulate under the ectedermal tissue to make a limb bud. // The lateral plate mesoderm in the limb field is also special in that it will induce myoblasts to migrate out from the somites and enter the limb bud. No other region of the lateral plate mesoderm will do that (Hayashi and Ozawa 1995)
uberon
rostral part of nephrogenic cord
The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros.
UBERON:0005754
uberon
embryonic uterus
FMA:72173
SCTID:255782009
UBERON:0005795
fetal uterus
uberon
segment of aorta
FMA:13087
SCTID:119203005
UBERON:0005800
UMLS:C0506947
aortic segment
ncithesaurus:Aortic_Segment
uberon
dorsal aorta
AAO:0011029
BTO:0004673
DA
EHDAA:402
EMAPA:18606
Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO]
SCTID:338637006
TAO:0000014
The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch[BTO]. The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once[GO]. Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP].
UBERON:0005805
VHOG:0000264
When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]
XAO:0000051
ZFA:0000014
aortae dorsales
dorsal aort%c3%a6
dorsal aorta root
dorsal aortic root
http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray459.png
relationship loss: part_of axial vasculature (TAO:0001073)[TAO]
uberon
developing mesenchymal condensation
A delimited region of dense mesenchyme within looser mesenchyme.
AEO:0000148
EHDAA2_RETIRED:0003148
EHDAA:8979
EMAPA:25351
UBERON:0005856
mesenchyme condensation
uberon
cartilaginous condensation
AEO:0000147
AO notes: isa cell condensation in VSAO
Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.
EHDAA2:0003147
EMAPA:25353
UBERON:0005863
VSAO:0000092
XAO:0004022
cartilage condensation
cartilagenous condensation
chondrogenic condensation
uberon
pre-muscle condensation
AEO:0000149
EHDAA2_RETIRED:0003149
UBERON:0005865
UBERON:0008714
pre muscle mass
premuscle mass
uberon
pre-cartilage condensation
A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage.
AEO:0000150
EHDAA2:0003150
UBERON:0005866
pre-chondrogenic condensation
precartilage condensation
precartilagenous condensation
prechondrogenic condensation
uberon
mandibular prominence
EHDAA2:0001061
EHDAA:5871
EMAPA:17355
Editor note: check develops_from
The mandibular prominence is an embryological structure which gives rise to the lower portion of the face. The mandible and lower lip derive from it. It is innervated by the mandibular nerve.
UBERON:0005867
UMLS:C1512982
mandibular process
mandibular swelling
ncithesaurus:Mandibular_Prominence
prominentia mandibularis
uberon
olfactory pit
AAO:0011068
An indentation of the olfactory placode which ends when the pits hollows out to form the nasopharynx[GO].
By the upgrowth of the surrounding parts the olfactory areas are converted into pits, the nasal pits or olfactory pits, which indent the fronto-nasal process and divide it into a medial and two lateral nasal processes[Wikipedia:Nasal_pit].
EFO:0003496
EHDAA2:0001295
EHDAA:4772
EMAPA:16800
SCTID:361485001
UBERON:0005870
XAO:0000275
XAO:0004073
nasal pit
uberon
we represent the relationship as develops from, though in fact the pit is formed as an indentation in the placode
undifferentiated genital tubercle
A genital tubercle is a body of tissue present in the development of the urinary and reproductive organs. It forms in the ventral, caudal region of mammalian embryos of both sexes, and eventually develops into a phallus. In the human fetus the genital tubercle develops around week 4 of gestation, and by week 9 becomes recognizably either a clitoris or penis. This should not be confused with the sinus tubercle which is a proliferation of endoderm induced by paramesonephic ducts. Even after the phallus is developed, the term genital tubercle remains, but only as the terminal end of it[2], which develops into either the glans penis or the glans clitoridis. The genital tubercle is sensitive to dihydrotestosterone and rich in 5-alpha-reductase, so that the amount of fetal testosterone present after the second month is a major determinant of phallus size at birth.[WP].
EHDAA2:0000705
EHDAA:5925
EMAPA:17382
In mammalian embryos, male and female external genitalia develop from the genital tubercle.[well established][VHOG]
SCTID:308798005
Taxon notes: todo - add taxon constraints. AO notes: we assume the EMAPA class is the undifferentiated form based on TS timings
The eminence in the embryo which develops into the clitoris or penis. [TFD][VHOG]
UBERON:0005876
VHOG:0000583
embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin; GT development is indistinguishable in male and female mouse embryos until ~E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP]
genital tubercle
http://upload.wikimedia.org/wikipedia/commons/d/d6/Gray1119.png
phallic tubercle
tuberculum genitale
tuberculum phallicum
uberon
undifferentiated genital tubercle
limb outgrowth
UBERON:0005881
encompasses digits and prepollex. requires review
uberon
alar plate
UBERON:0005882
alar lamina
alar plate of neural tube
dorsal part of neural tube
http://upload.wikimedia.org/wikipedia/commons/2/29/Gray646.png
lamina alaris
lamina dorsolateralis
the mantle layer of the neural tube that lies dorsal to the sulcus limitans and contains primarily sensory neurons and interneurons involved in communication of sensory impulses.
uberon
neural tube lateral wall mantle layer
EHDAA2:0001261
TODO - expand subtypes post EHDAA2-revision, check lateral wall
UBERON:0005883
uberon
coelomic epithelium
AO notes: EHDAA2:0004049 used to be called "coelomic epithelium" but is now "gonadal ridge mesothelium"
The epithelial lining of the surface of the coelom.
UBERON:0005891
XAO:0000329
celomic epithelium
germinal epithelium of Waldeyer
uberon
leg bone
A bone that is part of the region of the hindlimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia. Counter-examples: any pes phalanx
MA:0000670
MESH:A02.835.232.500
UBERON:0005893
uberon
pes bone
A bone that is part of the pes skeleton
GAID:192
MA:0000643
MESH:A02.835.232.300
OpenCyc:Mx4rv5ridZwpEbGdrcN5Y29ycA
SCTID:361371005
UBERON:0005899
UMLS:C0016505
bone of foor proper or tarsal skeleton
bone of foot
bone of pedal skeleton
bone of pes
foot bone
http://purl.obolibrary.org/obo/uberon/references/reference_0000015
ncithesaurus:Foot_Bone
uberon
occipital region
AAO:0010199
An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO]
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles.
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO]
FMA:49187
SCTID:362618001
TAO:0001414
TODO - check
UBERON:0005902
XAO:0003173
ZFA:0001414
back of head
basicranial region
occipital part of head
occipital region of head
uberon
duct of male reproductive system
A duct that is part of a male reproductive system.
UBERON:0005904
groups the individual ducts in a variety of species
uberon
serous sac
FMA:9689
Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]
SCTID:362890006
See notes for serous membrane
UBERON:0005906
uberon
endo-epithelium
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]
FMA:69065
UBERON:0005911
uberon
zone of bone organ
FMA:10483
UBERON:0005913
bone organ zone
uberon
axial skeleton plus cranial skeleton
AAO:0000963
EMAPA:17214
EMAPA:18043
MA:0000308
SCTID:361725000
See [UBERONREF:0000008]
Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
UBERON:0005944
UMLS:C0222645
VSAO:0000056
XAO:0004011
http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg
ncithesaurus:Axial_Skeleton
skeleton axiale
uberon
brain commissure
A commissure that is part of a brain.
UBERON:0005970
any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain[MP]
uberon
amniotic fold
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].
EMAPA:16076
UBERON:0005971
uberon
heart layer
UBERON:0005983
the laminar structure of the heart
uberon
skin adnexa
UBERON:0006003
adnexae cutis
editor note - add subclasses based on resolution of CARO tracker item. Also check: adnexal gland
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
uberon
digit 1
1
MA:00003023
UBERON:0006048
autopod digit 1
dewclaw
limb digit 1
uberon
multi-limb segment region
A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions).
UBERON:0006058
uberon
nerve fiber
A threadlike extension of a nerve cell and consists of an axon and myelin sheath (if existence) in the nervous system. There are nerve fibers in the central nervous system and peripheral nervous system. A nerve fiber may be myelinated and/or unmyelinated. In the central nervous system (CNS), myelin by oligodendroglia cells is formed. Schwann cells form myelin in the peripheral nervous system (PNS). Schwann cells also make a thin covering in an axon without myelin (in the PNS). A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system
FMA:5914
MESH:A08.663.542
SCTID:88545005
UBERON:0006134
nerve fibre
neurofibra
neurofibra
neurofibrum
uberon
myelinated nerve fiber
FMA:5915
GAID:745
MESH:A08.663.542.512
SCTID:362296008
UBERON:0006135
UMLS:C0027750
consider adding link to UBERON:0002316
ncithesaurus:Myelinated_Nerve_Fiber
uberon
rhombic lip
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
TAO:0001440
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]
UBERON:0006215
XAO:0004135
ZFA:0001440
cerebellum primordium
dorsal part of alar plate of metencephalon
uberon
cloacal membrane
A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG]
EHDAA2:0000257
EHDAA:214
EHDAA:2933
EMAPA:16832
In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG]
SCTID:308826008
UBERON:0006217
UMLS:C0231056
VHOG:0001198
embryonic cloacal membrane
http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png
membrana cloacalis
ncithesaurus:Cloacal_Membrane
the membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings.
uberon
future diencephalon
A multi-tissue structure that develops_into a diencephalon.
EFO:0003442
EHDAA2:0000600
EHDAA:844
EMAPA:16514
RETIRED_EHDAA2:0000386
TAO:0000574
UBERON:0006222
ZFA:0000574
presumptive diencephalon
uberon
female genital tubercle
A differentiated genital tubercle that is part of a female reproductive system.
EHDAA:8118
EMAPA:18680
RETIRED_EHDAA2:0000500
UBERON:0006233
VHOG:0000666
genital tubercle of female
uberon
femur pre-cartilage condensation
EHDAA2:0000508
EMAPA:17502
UBERON:0006234
VHOG:0000951
uberon
foregut-midgut junction
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]
An anatomical boundary that adjacent_to a foregut and adjacent_to a midgut.
EHDAA2:0000569
EHDAA:526
EMAPA:16363
UBERON:0006235
VHOG:0000291
uberon
future brain
EFO:0003431
EHDAA:300
EHDAA:830
EMAPA:16089
EMAPA:16471
RETIRED_EHDAA2:0000591
TAO:0000146
UBERON:0006238
Usage notes: this class is restricted to neural-tube derived brains
ZFA:0000146
brain rudiment
presumptive brain
uberon
future forebrain
EFO:0003423
EHDAA2:0000661
EHDAA:2643
EMAPA:16640
TAO:0000062
TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)
UBERON:0006240
ZFA:0000062
presumptive forebrain
presumptive prosencephalon
prosencephalon
uberon
future spinal cord
EFO:0003438
EHDAA2:0000674
EHDAA:898
EMAPA:16092
EMAPA:16525
EMAPA:16755
TAO:0000417
UBERON:0006241
ZFA:0000417
presumptive spinal cord
presumptive spinal cord neural keel
presumptive spinal cord neural plate
presumptive spinal cord neural rod
uberon
gall bladder primordium
EHDAA2:0000700
EHDAA:3047
EMAPA:16713
EMAPA:16842
UBERON:0006242
XAO:0004205
uberon
infundibular recess of 3rd ventricle
EHDAA2:0000827
EHDAA:4479
EMAPA:16648
EMAPA:16899
Editor note: in FMA this is a cavity, whereas in EHDAA2 it is an epithelial sac
FMA:78456
SCTID:369280006
The floor of the third ventricle is prolonged downward as a funnel-shaped recess, the infundibular recess, into the infundibulum, and to the apex of the latter the hypophysis or pititary is attached
UBERON:0006250
http://upload.wikimedia.org/wikipedia/commons/7/75/Gray654.png
infundibular recess
infundibular recess of third ventricle
recessus infundibularis
recessus infundibuli
recessus infundibuli
uberon
knee joint primordium
EHDAA2:0000897
EHDAA:8467
EMAPA:17740
UBERON:0006256
uberon
lingual swellings
EHDAA2:0000996
EMAPA:17186
Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]
Primordium of the tongue; the median swelling and the distal and proximal swellings arise from the ventral aspect of the stomodeum. [TFD][VHOG]
UBERON:0006260
VHOG:0000449
lingual swelling
the collection consisting of the two lateral swellings and the medial swelling
uberon
male genital tubercle
A differentiated genital tubercle that is part of a male reproductive system.
EHDAA:8138
EMAPA:17969
RETIRED_EHDAA2:0001048
UBERON:0006261
VHOG:0000667
genital tubercle of male
uberon
notochordal plate
EHDAA2:0001278
EHDAA:264
EMAPA:16101
TODO - check ordering; awaiting confirmation from JB
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.
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]
UBERON:0006267
UMLS:C1518429
VHOG:0001212
ncithesaurus:Notochordal_Plate
uberon
notochordal process
EHDAA2:0001279
EHDAA:224
EMAPA:16102
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.
UBERON:0006268
UMLS:C1518430
VHOG:0001213
a midline cellular cord formed from the migration of mesenchymal cells from the primitive knot
chordamesoderm
ncithesaurus:Notochordal_Process
presumptive notochord
uberon
early prosencephalic vesicle
EHDAA2:0001571
EHDAA:1356
EMAPA:16521
SCTID:361480006
TAO:0001259
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]
UBERON:0006284
VHOG:0000644
ZFA:0001259
forebrain ventricle
forebrain vesicle
future brain vesicle that gives rise to telencephalic ventricle/lateral ventricles and 3rd ventricle
prosencephalic ventricle
prosencephalic vesicle
uberon
spleen primordium
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].
AO notes: check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme
EHDAA2:0001904
EHDAA:3003
EMAPA:18535
EMAPA:18659
UBERON:0006293
UBERON:0009750
XAO:0000326
left spleen primordium
spleen mesenchyme
splenic mesenchyme
splenic primordium
uberon
submandibular gland primordium
EHDAA2:0001939
EHDAA:9255
EMAPA:17755
UBERON:0006298
uberon
brainstem nucleus
A nucleus of brain that is part of a brainstem.
MA:0000821
UBERON:0006331
uberon
pallidum
ABA:PAL
FMA:83684
MA:0000889
Part of what are called the basal ganglia of the brain which consist of the globus pallidus and the ventral pallidum.
UBERON:0006514
neuraxis pallidum
pallidum of neuraxis
uberon
seminal fluid
BTO:0001232
FMA:62967
MA:0002523
MAT:0000057
MIAA:0000057
The fluid portion of the semen, in which the spermatozoa are suspended[BTO].
UBERON:0006530
Usage notes: we follow FMA and make this class a generic superclass of the secretions of different glands (prostate, bulbo-urethreal, seminal vesicle). MA (and ncit) follows a mixture model, where these secretions are part of the seminal fluid // Taxon notes: This term covers a variety of species. Example: In D. melanogaster, seminal fluid proteins affect female receptivity, ovulation, oogenesis, sperm storage, sperm competition and mating plug formation [doi:10.1046/j.1365-2540.2001.00961.x]. Note that ths intology contains a number of subtypes of seminal fluid, defined according to glands (which are more taxonomically restricted)
male genital fluid
male genital secretion
seminal fluid
seminal plasma
uberon
mammary gland fluid/secretion
A portion of organism substance that secreted_by a mammary gland.
MA:0002505
UBERON:0006539
lactiferous gland fluid
lactiferous gland secretion
mammary gland fluid
mammary gland secretion
secretion of mammary gland
uberon
renal duct
A tube in the kidney that collect and transport urine.
TAO:0005289
UBERON:0006553
ZFA:0005289
in ZFA this is defined as part of mesonephros
uberon
urinary system structure
An anatomical structure that is part of a excretory system.
SCTID:122489005
UBERON:0006554
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
uberon
excretory tube
A tube that is part of a excretory system.
UBERON:0006555
uberon
lymphatic part of lymphoid system
.
AAO:0010522
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
EFO:0000870
EMAPA:18248
FMA:7162
MA:0002961
MESH:A15.382.520
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]
SCTID:362597000
UBERON:0006558
VHOG:0001761
lymphatic system
lymphatic tree system
lymporeticular system
uberon
pharynx
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]
FBbt:00005380
MAT:0000049
MIAA:0000049
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
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
UBERON:0006562
WBbt:0003681
branchial
pharyngeal
pharyngeal tube
uberon
hypothalamic nucleus
A nucleus of brain that is part of a hypothalamus.
BTO:0002449
FMA:258762
MA:0002426
SCTID:279304003
UBERON:0006568
nucleus of hypothalamus
uberon
diencephalic nucleus
A nucleus of brain that is part of a diencephalon.
TAO:0002191
UBERON:0006569
ZFA:0001659
uberon
presumptive endoderm
AAO:0000471
EFO:0003437
TAO:0000416
UBERON:0006595
ZFA:0000416
uberon
presumptive structure
AAO:0000479
TAO:0001116
UBERON:0006598
ZFA:0001116
presumptive structures
uberon
presumptive ectoderm
AAO:0000470
EFO:0003466
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
TAO:0001376
UBERON:0006601
XAO:0004132
ZFA:0001376
presumptive epidermis
uberon
presumptive mesoderm
AAO:0000476
EFO:0003467
Editors note: requires review
TAO:0001377
UBERON:0006603
ZFA:0001377
uberon
glans clitoris
BTO:0003117
EMAPA:19170
EMAPA:30829
Erectile tissue at the end of the clitoris, which is continuous with the intermediate part of the vestibulovaginal bulbs[BTO]. The clitoral glans (glans clitoridis) is an external portion of the clitoris[WP].
FMA:19999
SCTID:362241002
UBERON:0006653
UMLS:C0227769
clitoris glans
glans clitoridis
glans clitoris
glans of clitoris
http://upload.wikimedia.org/wikipedia/commons/8/8c/Clitoris_inner_anatomy.gif
ncithesaurus:Glans_Clitoris
uberon
mesopodium region
Naming conventions for pod terms under discussion within phenoscape group
The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus)
UBERON:0006716
carpus/tarsus
mesopod
mesopodial limb segment
mesopodial segment
uberon
skeleton of autopod
Distal section of the limb skeleton, consisting of the anterior autopodium or posterior autopodium.[VSAO]
Naming conventions for pod terms under discussion within phenoscape group
The collection of all skeletal elements in an autopodium region.
UBERON:0006717
VSAO:0005019
autopod skeleton
autopodial skeleton
autopodium
uberon
median lingual swelling
During the third week of embryological development there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings which rise from the inner surface of the mandibular arch and meet in the middle line. The site of their meeting remains post-embryonically as the median sulcus of the tongue. The tuberculum impar is said to form the central part of the tongue immediately in front of the foramen cecum, but Hammar insists that it is purely a transitory structure and forms no part of the adult tongue[WP, Gray's].
EHDAA2:0001081
EMAPA:17187
Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]
SCTID:308821003
The thyroid initially develops caudal to the tuberculum impar . This embryonic swelling arises from the first pharyngeal arch and occurs midline on the floor of the developing pharynx, eventually helping form the tongue as the 2 lateral lingual swellings overgrow it. [http://emedicine.medscape.com/article/845125-overview]
UBERON:0006756
VHOG:0000730
http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png
median lingual swelling
median tongue bud
tuberculum impar
tuberculum linguale mediale
uberon
lateral lingual swelling
During the third week there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings (or distal tongue bud) which rise from the inner surface of the mandibular arch and meet in the middle line.
EHDAA2:0000911
EMAPA:17189
Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]
Structure notes: paired
UBERON:0006757
VHOG:0000731
http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png
lateral lingual prominence
lateral swellings
tuberculum laterale
tuberculum linguale laterale
uberon
glandular epithelium
BTO:0002991
Editor notes: consider splitting epithelium from epithelial tissue
Epithelium composed of secretory cells.
UBERON:0006799
UMLS:C0682578
UMLS:C1708242
ncithesaurus:Glandular_Epithelial_Tissue
ncithesaurus:Glandular_Epithelium
uberon
anatomical line
AAO:0010267
AEO:0000008
BILA:0000008
CARO:0000008
EHDAA2:0003008
FMA:9657
HAO:0000008
Non-material anatomical entity of one dimension, whiVSAO forms a boundary of an anatomical surface or is a modulation of an anatomical surface.[CARO]
Non-material anatomical entity of one dimension, which forms a boundary of an anatomical surface or is a modulation of an anatomical surface.
TAO:0001837
TGMA:0001828
UBERON:0006800
XAO:0004003
ZFA:0001689
uberon
groove
AAO:0010276
AEO:0000161
Anatomical line that delineates a furrow or depression in an organ or tissue.
EHDAA2:0003161
FMA:75037
TAO:0001838
UBERON:0006846
ZFA:0001690
uberon
adrenal/interrenal gland
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]
Editor notes: keep this grouping class so long as it is required for GO
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]
UBERON:0006858
VHOG:0001141
adrenal - interrenal gland
adrenal gland - interrenal gland
adrenal gland/interrenal tissue
suprarenal gland - interrenal gland
uberon
diaphysis proper
FMA:32688
MA:0002803
Subdivision of long bone which forms the part of the bone between two metaphyses. Note that the diaphysis includes the metaphyses, but the diaphysis proper excludes these.
The MA class is placed here because we assume it means diaphysis proper, because in MA epiphysis is not part of MA:0002803
UBERON:0006861
body proper of long bone
long bone diaphysis
shaft proper of long bone
uberon
terminal part of digestive tract
FBbt:00005756
UBERON:0006866
Usage notes: this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future.
WBbt:0005773
rectal part of digestive tract
rectum
terminal section of digestive tract
uberon
seminal fluid secreting gland
A gland that secretes a seminal fluid.
FBbt:00004958
UBERON:0006868
WBbt:0006870
uberon
footplate
AO notes: EHDAA2 does not have a single class for footplate, but includes epithelium, mesenchyme and AER
An autopod plate that develops_into a pes.
EHDAA:5143
EHDAA:6096
EMAPA:17249
UBERON:0004343
UBERON:0006871
UMLS:C1517291
foot disk
foot plate
ncithesaurus:Foot_Plate
uberon
vasculature of organ
A vasculature that is part of a organ.
FMA:74612
UBERON:0006876
organ vasculature
set of blood vessels of organ
uberon
mandibular process mesenchyme
EHDAA2:0001062
EHDAA:5861
EHDAA:5873
EMAPA:17357
Mesenchyme that is part of a mandibular prominence.
UBERON:0006905
mesenchyme of mandibular process
mesenchyme of mandibular prominence
uberon
lumen of gut
An anatomical space that surrounded_by a digestive tract.
BTO:0000349
FMA:45677
UBERON:0006909
digestive tract lumen
gut cavity
gut lumen
lumen of alimentary tract
lumen of digestive tract
uberon
squamous epithelium
BTO:0002072
SCTID:40118003
UBERON:0006914
UMLS:C0221909
an epithelium characterised by its most superficial layer consisting of squamous epithelial cells.
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
ncithesaurus:Squamous_Epithelium
uberon
stomach glandular epithelium
A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands.
EMAPA:17623
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
FMA:63458
MA:0002784
UBERON:0006924
epithelium of gastric gland
gastric gland epithelium
uberon
digestive gland
A gland, such as the liver or pancreas, that secretes into the alimentary canal substances necessary for digestion.
AAO:0000130
BTO:0000345
UBERON:0006925
digestive system gland
uberon
glandular columnar epithelium
FMA:64800
Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA]
UBERON:0006929
UMLS:C0225337
ncithesaurus:Columnar_Epithelium
uberon
stomach glandular region mucosa
A mucosa of stomach that is part of a stomach glandular region.
MA:0001614
UBERON:0006931
uberon
sensory epithelium
FMA:62410
SCTID:309045006
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.
UBERON:0006934
neuroepithelium
note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical
uberon
efferent duct
AAO:0010532
AO notes: Check EMAPA. Taxon notes: There are two basic designs for efferent ductule structure: a) multiple entries into the epididymis, as seen in most large mammals. In humans and other large mammals, there are approximately 15-20 efferent ducts, which also occupy nearly one third of the head of the epididymis. b) single entry, as seen in most small animals such as rodents, whereby the 3-6 ductules merge into a single small ductule prior to entering the epididymis
Any of a group ranging from one to twelve (varies in species) small seminal ducts per testis which transport sperm from the testes to the kidney.[AAO]
EMAPA:18993
FMA:19081
MA:0000398
The efferent ducts (or efferent ductules or ductuli efferentes) connect the rete testis with the initial section of the epididymis. The ductuli are unilaminar and composed of columnar ciliated and non-ciliated (absorptive) cells. The ciliated cells serve to stir the luminal fluids, possibly to help ensure homogeneous absorption of water from the fluid produced by the testis, which results in an increase in the concentration of luminal sperm. The epithelium is surrounded by a band of smooth muscle that helps to propel the sperm toward the epididymis.
UBERON:0006946
UMLS:C0228013
ductuli efferentes testis
efferent ductule
http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg
ncithesaurus:Efferent_Ductule
uberon
vasa efferentia
male genital duct
A duct or series of ducts that transports sperm from the gonad. In mammals this is from the seminiferous tubules through rete testis, vas efferentia, epididymis, vas deferens, ejeculatory duct to the urethra.
FMA:55678
TAO:0001268
Taxon notes: we use this as a generic grouping class for a number of taxa. AO notes: in FMA includes as parts: seminal vesicle, efferent ductule (vas efferentia), epididymis, deferent duct (vas deferens), ejaculatory duct
UBERON:0006947
UBERON:0010140
ZFA:0001268
sperm duct
sperm ducts
uberon
vascular cord
EFO:0003709
TAO:0005077
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].
UBERON:0006965
ZFA:0005077
uberon
cardiac mesoderm
AAO:0011021
BILA:0000051
EFO:0000315
EHDAA:385
SCTID:360387000
UBERON:0007005
VHOG:0001641
XAO:0000235
cardiogenic mesoderm
consider FBbt:00005541
heart primordia
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].
uberon
cleaving embryo
BILA:0000058
Organism at the cleavage stage.
UBERON:0007010
uberon
primitive gut
BILA:0000084
SCTID:360394002
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]
UBERON:0007026
UMLS:C1514442
ncithesaurus:Primordial_Gut
uberon
mandibular neural crest
Cranial neural crest that migrates into the mandibular arch.
TAO:0007064
UBERON:0007098
XAO:0000024
ZFA:0007064
uberon
circulatory organ
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood[GO].
ANISEED:1235302
FBbt:00003154
TADS:0000147
UBERON:0007100
adult heart
cardiac pump
cardiac structure
dorsal tube
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
heart
heart or heart like organ
http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg
uberon
pharyngeal pouch 2
2nd arch branchial pouch
2nd arch branchial pouch endoderm
2nd arch pouch endoderm
2nd branchial pouch
2nd pharyngeal pouch endoderm
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]
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]
AAO:0011115
EFO:0003633
EHDAA2:0000058
EMAPA:16275
EMAPA:16276
RETIRED_EHDAA2:0000060
SCTID:345349000
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]
TAO:0001130
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]
UBERON:0005715
UBERON:0007123
UMLS:C0231069
VHOG:0000561
VHOG:0000967
XAO:0000247
ZFA:0001130
ncithesaurus:Second_Pharyngeal_Pouch
pharyngeal pouches 2
second arch pharyngeal pouch
second pharyngeal pouch
second visceral pouch
uberon
visceral pouch 2
trunk ganglion
EFO:0000901
Ganglion which is located in the trunk.
MAT:0000344
MIAA:0000344
TAO:0001573
UBERON:0007134
ZFA:0001573
body ganglion
trunk ganglia
uberon
neural keel
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.
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]
EFO:0003497
TAO:0000131
UBERON:0007135
ZFA:0000131
presumptive central nervous system
uberon
tracheobronchial tree
FMA:7393
SCTID:361384001
UBERON:0004102
UBERON:0007196
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.
tracheobronchial system
uberon
mesenchyme derived from head neural crest
EFO:0003572
EHDAA2:0000735
EMAPA:16100
EMAPA:16169
EMAPA:16271
EMAPA_RETIRED:16271
Mesenchyme that develops_from a cranial neural crest.
TAO:0000787
UBERON:0007213
ZFA:0000787
head mesenchyme from cranial neural crest
head mesenchyme from neural crest
head neural crest derived mesenchyme
uberon
1st arch mandibular component
EHDAA2:0000031
EHDAA:583
EMAPA:16382
Editors note: relationship to Meckel's cartilage to be added
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]
UBERON:0007237
VHOG:0000510
uberon
ventral mandibular arch
ventral pharyngeal arch 1
ventral visceral arch 1
nuclear complex of neuraxis
FMA:84059
Internal gray matter component which consists of an assemblage of nuclei of neuraxis. Example: cerebellar nuclear complex, Vestibular nuclear complex.[FMA]
UBERON:0007245
cluster of neural nuclei
neural nuclei
nuclear complex
todo - move existing complex classes currently under nucleus to be under this class
uberon
pelvic appendage skeleton
The collection of all skeletal elements in a pelvic appendage region.
UBERON:0007273
uberon
presumptive hindbrain
CALOHA:TS-2118
EFO:0003440
EHDAA2:0001630
TAO:0000569
TODO - unify naming conventions
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].
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.
UBERON:0007277
ZFA:0000569
embryonic rhombencephalon
future hindbrain
rhombencephalon
uberon
presumptive segmental plate
A presumptive structure that develops_into a presomitic mesoderm.
EFO:0003421
TAO:0000053
UBERON:0007282
ZFA:0000053
uberon
presumptive neural plate
A presumptive structure that develops_into a neural plate.
EFO:0003424
Region of the gastrula which gives rise to the neural plate.[TAO]
TAO:0000063
UBERON:0007284
ZFA:0000063
uberon
presumptive paraxial mesoderm
A presumptive structure that develops_into a paraxial mesoderm.
EFO:0003443
TAO:0000591
UBERON:0007285
XAO:0004134
ZFA:0000591
uberon
presumptive floor plate
A presumptive structure that develops_into a floor plate.
EFO:0003454
TAO:0001218
UBERON:0007286
ZFA:0001218
uberon
presumptive pronephric mesoderm
A presumptive structure that develops_into a pronephric mesoderm.
EFO:0003619
TAO:0001070
UBERON:0007297
ZFA:0001070
nephron primordium
uberon
pharyngeal vasculature
A vasculature that is part of a chordate pharynx.
TAO:0005003
UBERON:0007303
ZFA:0005003
branchial vasculature
uberon
outer epithelial layer
Editor's note: this grouping class exists primarily to align with GO - see GO:0008544.
FBbt:00004993
HAO:0000298
TADS:0000109
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].
UBERON:0007376
WBbt:0005733
epidermis
hypodermis
outer epidermal layer
uberon
enveloping layer of ectoderm
EFO:0003425
EVL
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.
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]
TAO:0000086
UBERON:0007383
ZFA:0000086
enveloping layer
relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]
uberon
nucleus of midbrain tegmentum
A nucleus of brain that is part of a midbrain tegmentum.
FMA:258768
This class groups together any nuclei in the tegmentum region, possibly including disparate structures across species
UBERON:0007414
UBERON:0012277
ZFA:0005577
tegmental nucleus
uberon
peduncle of neuraxis
FMA:83860
UBERON:0007417
neuraxis peduncle
uberon
developing epithelial placode
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
AEO_RETIRED:0000112
Consider merging with ectodermal placode? In EHDAA2 this includes lens, nasal, otic epibranchial and trigeminal placodes
EHDAA2:0003112
EHDAA2_RETIRED:0003112
UBERON:0007497
epithelial placode
uberon
epithelial sac
AEO:0000115
An epithelial tube that is open at one end only.
EHDAA2:0003115
UBERON:0007499
uberon
epithelial tube open at both ends
AEO:0000116
An epithelial tube open at both ends that allows fluid flow.
RETIRED_EHDAA2:0003116
UBERON:0007500
uberon
epithelial vesicle
A closed epithelium with a lumen.
AEO:0000119
EHDAA2:0003119
EHDAA2:0003119
UBERON:0007503
uberon
dense mesenchyme tissue
AEO:0000146
EHDAA2:0003146
EHDAA2:0003146
Mesenchyme with little extracellular matrix.
UBERON:0007524
uberon
migrating mesenchyme population
AEO:0000152
EHDAA2:0003152
EHDAA2:0003152
Editors note: this class will be an important part of the NC reorganization
Mesenchymal cells that are migrating.
UBERON:0007530
uberon
ciliated columnar epithelium
FMA:64798
Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]
UBERON:0007592
uberon
ciliated epithelium
Epithelium bearing vibratile cilia on the free surface.
UBERON:0007601
uberon
kidney field
UBERON:0007687
kidney anlage
region of the embryo into the area in which the kidney rudiment will develop.
uberon
thyroid diverticulum
UBERON:0007689
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].
saccus thyroideus; diverticulum thyroideum
uberon
early pharyngeal endoderm
.
EFO:0003626
EHDAA2:0001457
EHDAA:962
TAO:0001104
UBERON:0007690
ZFA:0001104
early pharyngeal arch endoderm
pharyngeal arch endoderm
pharyngeal endoderm
pharyngeal region endoderm
relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm'
uberon
nucleus of thalamus
A nucleus of brain that is part of a thalamus.
BTO:0002452
FMA:256693
MA:0002992
SCTID:279115000
UBERON:0007692
nuclear complex of thalamus
thalamic nucleus
todo - consider splitting nucleus and complex
uberon
tract of brain
An axon tract that is part of a brain.
Editor notes: we place the NIF class here because it is part of the brain
FMA:83848
NIF_GrossAnatomy:birnlex_1649
UBERON:0007702
brain tract
uberon
epidermis gland
A gland that is part of a epidermis.
FMA:59153
UBERON:0007771
epidermal gland
gland of epidermis
uberon
vascular system
BTO:0001085
EHDAA2:0004520
MA:0002718
UBERON:0007798
UMLS:C0489903
in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
ncithesaurus:Vascular_System
uberon
connecting stalk
A bridge of mesoderm connecting the caudal end of the young embryo with the trophoblastic tissues; the precursor of the umbilical cord.
BTO:0004705
UBERON:0007806
UMLS:C1516792
ncithesaurus:Connecting_Stalk
todo - this is currently defined as a bridge of mesoderm, but in EHDAA2 is extraembryonic structure split into mesoderm and blood vessels
uberon
craniocervical region
CALOHA:TS-2356
EV:0100009
FMA:280881
MA:0000006
SCTID:361355005
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:0007811
UMLS:C0460004
WikipediaCategory:Head_and_neck
galen:HeadAndNeck
head and neck
head or neck
ncithesaurus:Head_and_Neck
uberon
appendage girdle region
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]
FMA:24874
Note that this encompasses non-skeletal tissue
UBERON:0007823
UBERON:0007824
VSAO:0000303
fin girdle
fin girdle region
girdle
girdle region
limb girdle
limb girdle region
uberon
external nose
FMA:59515
SCTID:265785009
Subdivision of face, the exterior of the nose, which consists of a root, dorsum, tip, columella, and right and left alae.
UBERON:0007827
UMLS:C0458561
ncithesaurus:External_Nose
nose
uberon
skeleton of pelvic girdle
AAO:0000426
AAO:0000768
AO notes: Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts. Editor notes: need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)
Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO]
Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO]
EFO:0000947
EHDAA2:0001426
EHDAA:7149
EHDAA:8324
EMAPA:18028
FMA:87592
Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO]
MAT:0000182
MIAA:0000182
Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature.
TAO:0000565
The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]
UBERON:0007832
VHOG:0000305
VSAO:0000155
XAO:0003064
ZFA:0000565
galen:PelvicGirdle
http://people.eku.edu/ritchisong/pectoralgirdles.gif
http://upload.wikimedia.org/wikipedia/commons/thumb/f/fe/Gray242.png/200px-Gray242.png
pelvic girdle
pelvic girdle skeleton
uberon
membrane bone
AEO:0000085
Bone element that arises as a result of intramembranous ossification.
Bone element that arises as a result of intramembranous ossification.[VSAO]
EHDAA2:0003085
Intramembranous bone that forms deep in the organism.[TAO]
TAO:0001645
UBERON:0007842
VSAO:0000023
XAO:0004014
ZFA:0001636
uberon
cartilaginous element
AAO:0011130
AO notes: TAO still mixes tissue and element
FMA:55107
Skeletal element that is composed of cartilage tissue and may be permanent or transient.
UBERON:0007844
VSAO:0000000
XAO:0004013
ZFA:0001501
cartilage
cartilage element
cartilage organ
chondrogenic element
uberon
regular connective tissue
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.
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).
FMA:20103
UBERON:0007845
uberon
dense regular connective tissue
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]
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]
FMA:64781
Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]
SCTID:22560007
UBERON:0007846
UMLS:C0225333
VSAO:0000050
XAO:0004030
dense fibrous connective tissue
dense regular collagenous connective tissue
dense regular collagenous tissue
ncithesaurus:Regular_Dense_Connective_Tissue
regular dense connective tissue
typus regularis (textus connectivus collagenosus compactus)
uberon
head or neck bone
A bone that is part of a craniocervical region.
MA:0000569
UBERON:0007914
uberon
bone of hip region
MA:0000655
SCTID:304907005
UBERON:0008202
in MA, this includes the femur. i.e. pelvic girdle bone or femur; note that this makes the ilium etc in MA hindlimb bones. in MA this is a hindlimb bone
uberon
tibialis
BTO:0000864
Either of two muscles of the calf of the leg.
MA:0002425
UBERON:0008230
UMLS:C1710422
ncithesaurus:Tibialis
tibialis muscle
uberon
erectile tissue
UBERON:0008324
uberon
mammary ridge
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].
EMAPA:18541
UBERON:0008425
mammary fold
milk line
split ridge and milk line?
uberon
inner cell mass derived epiblast
An epiblast (generic) that develops_from a inner cell mass.
EHDAA2:0000444
EHDAA:42
EHDAA:75
EMAPA:16050
UBERON:0008780
UMLS:C1516906
embryonic epiblast
ncithesaurus:Epiblast
uberon
lower limb segment
A limb segment that is part of a hindlimb.
FMA:24877
UBERON:0008784
free lower limb segment
free lower limb subdivision
segment of free lower limb
subdivision of free lower limb
uberon
parotid gland primordium
EHDAA2:0001413
EHDAA:9246
UBERON:0008801
uberon
intromittent organ
AAO:0010255
FBbt:00004850
HAO:0000091
Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO]
TAO:0002036
TGMA:0000585
UBERON:0008811
aedeagus
an external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP].
this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition
uberon
pharyngeal system
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.
EHDAA2:0000187
UBERON:0008814
UMLS:C1519038
ncithesaurus:Pharyngeal_Apparatus
pharyngeal apparatus
pharyngeal arch region
pharyngeal arches and clefts
uberon
embryonic head
A head that is part of a embryo.
FBbt:00000155
UBERON:0008816
uberon
hepatic diverticulum
AAO:0011057
EHDAA2:0000740
EHDAA:1530
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.
UBERON:0008835
UMLS:C1512407
XAO:0000101
diverticulum hepaticum
http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png
liver diverticulum
ncithesaurus:Hepatic_Diverticulum
uberon
liver bud
BTO:0001642
UBERON:0008836
uberon
skeletal ligament
AAO:0010444
AEO:0000090
Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.[VSAO]
EHDAA2:0003232
EV:0100144
Editor notes: logical definition deliberately made strict to avoid classifying MA:spiral ligament as both nonskeletal and skeletal. see https://sourceforge.net/tracker/?group_id=76834&atid=1205376
FMA:25624
GAID:118
Ligament organ that primarily consists of regular dense connective tissue aggregated into fasciculi; connects bone and cartilage organs. Examples: sutural ligament, ligament of pinna, tarsal ligament.
MA:0003005
SCTID:410744003
UBERON:0008846
VSAO:0000072
articular larua
articular ligament
http://upload.wikimedia.org/wikipedia/commons/thumb/9/9a/Knee_diagram.svg/200px-Knee_diagram.svg.png
ligament
true ligament
uberon
pyloric canal
FMA:14580
SCTID:245417002
UBERON:0008858
canalis pyloricus
canalis pyloricus
http://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg
the short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter
uberon
pyloric gastric gland
Editors note: check relationship to pylorus vs antrum
FMA:14922
SCTID:70710007
UBERON:0008861
UMLS:C0227239
glandula pylorica
http://upload.wikimedia.org/wikipedia/commons/b/bf/Gray1054.png
ncithesaurus:Pyloric_Gland
pyloric antrum gland
pyloric gland
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].
uberon
splanchnocranium
AAO:0010157
AO notes: VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton. Editor/AO notes: many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO]
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO]
Subdivision of endoskeleton derived from pharyngeal arches
TAO:0001216
The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG]
The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG]
UBERON:0008895
VHOG:0000315
VSAO:0000149
XAO:0003176
ZFA:0001216
branchial arch skeleton
gill arch skeleton
http://upload.wikimedia.org/wikipedia/commons/thumb/7/77/Illu_facial_bones.jpg/200px-Illu_facial_bones.jpg
pharyngeal arch
pharyngeal arch skeleton
pharyngeal skeleton
uberon
visceral skeleton
viscerocranium
dermal bone
AAO:0010769
Intramembranous bone that forms superficially in the organism.[TAO]
Note that other AOs are not yet in sync with this classification
Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO].
TAO:0001590
UBERON:0008907
VSAO:0000130
XAO:0004015
ZFA:0001590
uberon
respiratory primordium
EHDAA2:0004069
UBERON:0008947
UMLS:C1514898
ncithesaurus:Respiratory_Primordium
uberon
stomach region
An organ part that is part of a stomach.
MA:0002561
SCTID:245415005
UBERON:0009034
uberon
thymic region
UBERON:0009113
uberon
indifferent gonad
A gonad prior to differentiating into a definitive testis or ovary.
EHDAA2:0000716
UBERON:0009117
UMLS:C1512703
ncithesaurus:Indifferent_Gonad
typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321]
uberon
adenohypophyseal placode
EFO:0000229
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)
TAO:0001198
The adenohypophyseal placode forms the anterior lobe of the pituitary gland and gives rise to the endocrine secretory cells of the pituitary
UBERON:0009122
XAO:0004208
ZFA:0001198
pituitary placode
uberon
entire mesenchyme
EHDAA2:0001113
EHDAA:177
EMAPA:16097
UBERON:0003313
UBERON:0009142
consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)
uberon
developing esophageal region
EMAPA:16700
RETIRED_EHDAA2:0000654
SCTID:245404000
UBERON:0009143
consider merging into esophagus
esophageal region
oesophageal region
oesophageal region
uberon
pharyngeal region
EMAPA:16549
RETIRED_EHDAA2:0001454
UBERON:0009145
uberon
indifferent external genitalia
EHDAA2:0004021
UBERON:0009196
uberon
nephric duct
A nephric duct is a tube that drains a primitive kidney[GO].
UBERON:0009201
pronephric duct or mesonephric duct
uberon
embryonic nasal process
EHDAA2:0000581
EHDAA:4776
EMAPA:16680
SCTID:308881001
UBERON:0009292
medial or lateral; in EHDAA2 also frontonasal or intermaxillary
nasal placode
uberon
pharyngeal arch mesenchymal region
A portion of mesenchymal tissue associated with an individual pharyngeal arch.
Editor notes: this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. [MP:0011262]
UBERON:0009494
branchial arch mesenchyme
pharyngeal arch mesenchyme
uberon
epithelium of foregut-midgut junction
An epithelium that is part of a foregut-midgut junction.
EHDAA2:0000573
EMAPA:16564
UBERON:0009497
uberon
endoderm of foregut-midgut junction
An endoderm that is part of a foregut-midgut junction.
EHDAA2:0000572
EMAPA:18403
UBERON:0009550
uberon
subdivision of trunk
FMA:25054
SCTID:22943007
UBERON:0009569
region of trunk
trunk subdivision
uberon
midbrain mantle layer
EHDAA2:0001172
EMAPA:16977
UBERON:0009581
VHOG:0000910
mantle layer lateral wall mesencephalon
mantle layer lateral wall midbrain
midbrain lateral wall mantle layer
uberon
1st arch mandibular mesenchyme
EHDAA2:0000034
EMAPA:16385
Mesenchyme that is part of a 1st arch mandibular component.
UBERON:0009584
UBERON:0010043
mandibular component mesenchyme
mandibular mesenchyme
mesenchymal region of mandibular component of first pharyngeal arch
mesenchyme of mandibular component
uberon
presumptive midbrain
A presumptive structure that develops_into a midbrain.
EFO:0003432
EHDAA2:0000615
TAO:0000148
TODO - unify naming conventions
UBERON:0009616
ZFA:0000148
early midbrain
future midbrain
mesencephalon
presumptive mesencephalon
uberon
trunk paraxial mesoderm
EHDAA2:0002094
UBERON:0009618
trunk and cervical paraxial mesenchyme
trunk paraxial mesenchyme
uberon
spinal nerve root
FMA:14060
GAID:717
MESH:A08.800.800.720.725
SCTID:362436008
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.
UBERON:0009623
UMLS:C0037940
ZFA has part_of to spinal cord but this causes spatial disjointness violations (CNS/PNS)
ZFA:0005578
ncithesaurus:Spinal_Nerve_Root
root of spinal nerve
spinal neural root
uberon
midbrain nucleus
Nucleus located in the midbrain.
SCTID:279285003
TAO:0002209
UBERON:0009661
ZFA:0001665
uberon
telencephalic nucleus
A nucleus of brain that is part of a telencephalon.
TAO:0002178
UBERON:0009663
ZFA:0001660
uberon
gut mesentery
EHDAA2:0004566
UBERON:0009664
uberon
early telencephalic vesicle
EFO:0003562
EHDAA2:0001981
EHDAA:1993
EHDAA:2671
EMAPA:16914
UBERON:0009676
early telencephalic ventricle
early telencephalic vesicle
uberon
intermaxillary process
EHDAA2:0000868
EHDAA:7856
Editors note: requires verification. Note EHDAA2 has this as coming from both lateral and medial prominences. See also: median cleft lip
UBERON:0009714
globular process
globular processes of his
intermaxillary segment
the primordial mass of tissue formed by the merging of the medial nasal prominences of the embryo; it contributes to the intermaxillary portion of the upper jaw, the prolabial portion of the upper lip, and the primary palate.
uberon
entire pharyngeal arch endoderm
EHDAA2:0004621
UBERON:0009722
pharyngeal arch endoderm
uberon
limb mesenchyme
AO notes: EMAPA mapping from TH
EMAPA:32705
UBERON:0009749
limb mesoderm
the primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells.
uberon
embryonic midbrain hindbrain boundary
UBERON:0009774
merge with presumptive midbrain hindbrain boundary?
uberon
acinus
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.
FMA:55588
UBERON:0009842
acinar
acini
glandular acinus
http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png
uberon
urogenital sinus mesenchyme
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
Mesenchyme that surrounds primitive urogenital sinus.
UBERON:0009845
UGM
uberon
embryonic cloacal epithelium
An epithelium that is part of a embryonic cloaca.
EHDAA2:0004585
UBERON:0009846
cloacal epithelium
uberon
prostate field
UBERON:0009847
a specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop.
prostate primordium
uberon
digestive tract diverticulum
Branch or outpocketing of the digestive tract.
FBbt:00100316
UBERON:0009854
diverticulum of gut
intestinal pouch
uberon
sac
UBERON:0009856
diverticulum
galen:Diverticulum
pouch
uberon
zone of stomach
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.
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
FMA:14558
SCTID:245415005
UBERON:0009870
gastric zone
http://upload.wikimedia.org/wikipedia/commons/thumb/2/29/Regions_of_stomach.svg/500px-Regions_of_stomach.svg.png
region of stomach
section of stomach
uberon
metapodium region
Intermediate segment of the autopod, between the mesopodial region and and acropodial region. Examples: metacarpal region, metatarsal region
Naming conventions for pod terms under discussion within phenoscape group. Editors note: considering adding 'acropodial region'
UBERON:0009877
metacarpal or metatarsal part of limb
metacarpus/metatarsus
metacarpus/metatarsus region
metapodial segment
metapodium
uberon
mesopodium skeleton
Limb skeleton subdivision consisting of endochondral bones increasing the freedom of movement of the autopodia, and located between zeugopodia and autopodia.[VSAO]
The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton
UBERON:0009878
VSAO:0005022
basipodium
basipodium skeleton
carpal/tarsal skeleton
mesopodial skeleton
mesopodium
mesopodium skeleton
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: transitively_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: transitively_distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
uberon
tarsal skeleton
AAO:0000220
EMAPA:25072
FMA:71339
GAID:1223
MA:0000050
SCTID:264228001
SCTID:361796005
Segment of the leg corresponding to the tarsus. It consists of several elements that articulate with the tibia and fibula at one end and the metatarsals at the other end.[AAO]
Subdivision of skeleton that consists of endochondral elements distal to the zeugopodial skeletal elements which constitute the proximal region of the posterior autopod skeleton[PHENOSCAPE:ad].
Taxon notes: Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present[PHENOSCAPE:ad]. AO notes: we assume MA:tarsus belongs here, as there is a distinct class MA:ankle, with the tarsal bone being part of the former. XAO:tarsus is part of the hindlimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent.
The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG]
UBERON:0009879
VHOG:0001160
VSAO:0005024
XAO:0003211
basipodium
hind mesopodium
hind mesopodium skeleton
mesopodium
set of tarsal bones
tarsal bones
tarsal bones set
tarsus
uberon
anterior lateral plate mesoderm
ALPM
EFO:0003704
TAO:0005041
UBERON:0009881
ZFA:0005041
uberon
vomeronasal system
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]
UBERON:0009954
a vertebrate nasal chemosensory system that is responsible for detecting intraspecific pheromonal cues as well as environmental odorants
uberon
neurogenic placode
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]
EFO:0003460
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]
TAO:0001309
UBERON:0009955
ZFA:0001309
neurogenic placodes
placodae neurogenicae
uberon
condyle
FMA:75434
Protuberance on a bone that participates in a joint with another bone.[TAO]
SCTID:91737009
TAO:0002259
UBERON:0009979
UMLS:C0524414
condylar
galen:Condyle
ncithesaurus:Condyle
the round prominence at the end of a bone, most often part of a joint - an articulation with another bone[WP].
uberon
condyle of femur
A condyle that is part of a distal epiphysis of femur.
AAO:0000900
Convex articular facet of the distal head of the femur that articulates with the proximal head of the fibula.[AAO]
FMA:32855
SCTID:304912006
UBERON:0009980
condylus femoralis
condylus femoris
femoral condyle
fibular condyle
galen:FemoralCondyle
uberon
medial condyle of femur
FMA:32858
SCTID:182056007
The medial condyle is one of the two projections on the lower extremity of femur. The medial condyle is larger than the lateral (outer) condyle due to more weight bearing caused by the center of gravity being medial to the knee. On the posterior surface of the condyle the linea aspera (a ridge running down the posterior shaft of the femur) turns into the medial supracondylar ridge. The outermost protrusion on the medial surface of the medial condyle is referred to as the "medial epicondyle" and can be palpated by running fingers medially from the patella with the knee in flexion.
UBERON:0009984
c. medialis femoris
http://upload.wikimedia.org/wikipedia/commons/5/53/Gray246.png
medial condyle of the femur
uberon
aggregate regional part of brain
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].
FMA:256381
NIF_GrossAnatomy:nlx_anat_20090509
UBERON:0010009
set of nuclei of neuraxis
uberon
collection of basal ganglia
All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates.[well established][VHOG]
BM:Tel-BG
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.
FMA:84013
GAID:617
MA:0000184
MESH:A08.186.211.730.885.105
NIF_GrossAnatomy:birnlex_826
UBERON:0010011
UMLS:C0004781
VHOG:0001696
basal ganglia
basal ganglia set
ncithesaurus:Basal_Ganglia
set of basal ganglia
uberon
food storage organ
An organ of the digestive tract that is capable of retaining and storing food
TADS:0000172
TGMA:0001041
This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates
UBERON:0010039
uberon
1st arch mesenchyme
EMAPA:16128
Mesenchyme that is part of a pharyngeal arch 1.
UBERON:0010042
mesenchyme of 1st arch
uberon
entire pharyngeal arch associated mesenchyme
EHDAA2:0001459
EMAPA:16550
The sum total of mesenchymal tissue in the pharyngeal arch region.
UBERON:0010046
associated mesenchyme of pharyngeal region
entire branchial arch associated mesenchyme
pharyngeal arch associated mesenchyme
uberon
oral gland
EHDAA2:0001327
EHDAA:2181
EMAPA:16572
EMAPA:16723
Gland of the epithelium lining the oral cavity. The most common are the salivary glands.
Note that Kardong classifies lacrimal glands here
SCTID:25421004
UBERON:0003293
UBERON:0010047
VHOG:0000652
buccal gland
gland of oral opening
gland of oral part of face
gland of subdivision of mouth
oral cavity gland
oral opening gland
oral part of face gland
oral region gland
subdivision of mouth gland
uberon
future tongue
A compound organ that develops_into a tongue.
EHDAA2:0000696
EHDAA:2951
UBERON:0010056
uberon
open anatomical space
AEO:0000221
An anatomical space with at least one opening to another space or the exterior.
EHDAA2:0004616
UBERON:0010064
uberon
future corpus striatum
A multi-tissue structure that develops_into a corpus striatum.
EHDAA2:0000596
UBERON:0010082
uberon
future dermis
EHDAA2:0000598
Editor notes: check development
Mesenchyme that develops_into a dermis.
UBERON:0010083
uberon
future diaphragm
A skeletal muscle tissue that develops_into a diaphragm.
EHDAA2:0000599
UBERON:0010084
uberon
future metencephalon
A developing anatomical structure that develops_into a metencephalon.
EHDAA2:0000623
UBERON:0010092
uberon
future myelencephalon
A developing anatomical structure that develops_into a myelencephalon.
EHDAA2:0000640
UBERON:0010096
uberon
future caudate nucleus
A nucleus of brain that develops_into a caudate nucleus.
EHDAA2:0004461
UBERON:0010122
uberon
femur cartilage condensation
EMAPA:17742
TODO - request EHDAA2
UBERON:0010129
femoral cartilage condensation
uberon
autopod plate
UBERON:0010130
limb plate
the distal elements of the developing limb of vertebrates that will give rise to the pedal appendages (e.g. manus, pes, paw)
uberon
conducting tissue of heart
EHDAA2:0004528
FMA:83378
UBERON:0010131
specialized conducting tissue of heart
specialized muscle tissue of heart
uberon
neuroendocrine gland
An endocrine gland that is part of a nervous system.
MA:0000720
UBERON:0010133
uberon
secretory circumventricular organ
MA:0002943
UBERON:0010134
uberon
primitive sex cord of indifferent gonad
A sex cord that is part of a indifferent gonad.
EHDAA2:0004051
UBERON:0010141
Usage notes: note that this represents the indifferent structure.
indifferent sex cord
primitive sex cords
uberon
seminal vesicle fluid
A bodily secretion that secreted_by a seminal vesicle.
AO notes: in ncit, seminal fluid is a subtype of seminal vesicle secretion
FMA:62969
MA:0002526
UBERON:0010143
UMLS:C0036614
UMLS:C0227987
ncithesaurus:Seminal_Fluid
ncithesaurus:Seminal_Vesicle_Secretion
secretion of seminal vesicle
seminal fluid
seminal vesicle secretion
uberon
vesicular fluid
male accessory sex gland
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
UBERON:0010147
uberon
protuberance
A roughly circular bulge in a surface.
AEO:0000205
EHDAA2:0003250
FMA:82506
UBERON:0010188
uberon
aortic system
EHDAA2:0004512
UBERON:0010191
uberon
thalamic complex
EHDAA2:0004469
FMA:258745
UBERON:0010225
uberon
future cardiac ventricle
FMA:71006
Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle.
TAO:0002231
UBERON:0010226
ZFA:0001719
presumptive cardiac ventricle heart tube
primordial cardiac ventricle
primordial ventricle
uberon
future cardiac atrium
FMA:71005
Multi-tissue structure that is part of the heart tube and will become the cardiac atrium.
TAO:0002228
UBERON:0010227
ZFA:0001718
presumptive atrium heart tube
primordial atrium
primordial cardiac atrium
uberon
eyeball of camera-type eye
FMA:12513
MIAA:0000283
SCTID:244486005
See notes for camera-type eye
The camera-type eye apart from its appendages/adnexa.
UBERON:0010230
VHOG:0001616
bulbus oculi
eye
eye globe
eyeball
globe
uberon
1st arch mandibular mesenchyme from neural crest
EHDAA2:0000037
Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme.
UBERON:0010252
uberon
mesenchyme from rhombencephalic neural crest
EHDAA2:0004423
Mesenchyme that develops_from a rhombencephalon neural crest.
UBERON:0010258
uberon
1st arch mesenchyme from neural crest
EMAPA:16129
Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme.
UBERON:0010259
branchial arch 1 mesenchyme from neural crest
mesenchyme derived from neural crest of mesenchyme of 1st arch
neural crest derived arch 1 mesenchyme
pharyngeal arch 1 mesenchyme from neural crest
uberon
umbilical blood vessel
A blood vessel that overlaps a umbilical cord.
SCTID:408728001
UBERON:0010260
uberon
umbilical cord blood vessel
midbrain basal plate
EFO:0003567
EHDAA2:0004375
Portion of tissue that is dorsolateral to the floor plate and part of the midbrain.
TAO:0000761
UBERON:0010285
ZFA:0000761
basal plate midbrain
uberon
midbrain neural tube
Portion of neural tube that gives rise to the midbrain.
TAO:0007039
UBERON:0010286
ZFA:0007039
uberon
extraembryonic epithelium
An epithelium that is part of a extraembryonic structure.
UBERON:0010303
extra-embryonic epithelium
uberon
immature eye
Developing anatomical structure that develops into the eyeball and associated structures.
Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]
TAO:0002201
UBERON:0010312
ZFA:0001678
future eye
uberon
neural crest-derived structure
An anatomical structure that develops from the neural crest.
Grouping term for query purposes
UBERON:0010313
uberon
structure with developmental contribution from neural crest
An anatomical structure that has some part that develops from the neural crest.
Grouping term for query purposes
UBERON:0010314
uberon
germ layer / neural crest
UBERON:0010316
uberon
cranial skeletal system
AAO:0000109
AAO:0000971
AAO:0010185
Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO]
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)
Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.
Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO]
TAO:0000737
UBERON:0010323
VSAO:0000049
XAO:0003075
ZFA:0000737
cranial skeleton
cranium
osteocranium
uberon
limb/fin bud mesenchyme
Mesenchyme that is part of a limb/fin bud.
UBERON:0010329
uberon
extraembryonic membrane mesenchyme
Mesenchyme that is part of a extraembryonic membrane.
UBERON:0010333
uberon
mandibular process mesenchyme from neural crest
EHDAA2:0004603
Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme.
UBERON:0010336
uberon
pharyngeal arch mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme.
Partially implements UBERONREF:0000002 NC meeting scheme
UBERON:0010359
arch mesenchyme from neural crest
branchial arch mesenchyme from neural crest
neural crest derived arch mesenchyme
uberon
endochondral element
A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
UBERON:0010363
VSAO:0000139
XAO:0004017
ZFA:0005620
endochondral replacement element
http://purl.obolibrary.org/obo/uberon/references/reference_0000009
uberon
dermal skeleton
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.
This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO
UBERON:0010364
VSAO:0000035
XAO:0004025
dermal skeletal system
dermoskeleton
desmoskeleton
exoskeleton
uberon
odontoid tissue
Skeletal tissue that is part of the exoskeleton and derived from an odontogenic papilla.
UBERON:0010365
UMLS:C1519551
VSAO:0000063
XAO:0004046
ZFA:0005623
dental tissue
ncithesaurus:Tooth_Tissue
odontogenic tissue
tooth tissue
uberon
ecto-epithelium
Epithelium that derives from the ectoderm. Examples: epithelium of acinus of lactiferous duct, subscapular lens epithelium, epithelium of posterior surface of cornea.
FMA:69064
UBERON:0010371
ectoderm-derived epithelium
uberon
pancreas dorsal primordium
Consider merging with dorsal pancreatic bud. Starts at CS12 in human (EHDAA2, embryology.ch 'bud anlagen')
EHDAA2:0001384
FMA:79793
UBERON:0010375
dorsal pancreas
uberon
pancreas ventral primordium
EHDAA2:0001387
FMA:79794
Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen')
UBERON:0010376
uberon
ventral pancreas
mesenchyme from somatopleure
EHDAA2:0001120
Editor notes: the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives
Mesenchyme that develops_from a somatopleure.
UBERON:0010377
uberon
eye surface
MA:0002486
UBERON:0010409
uberon
pseudostratified columnar epithelium
A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels.
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.
FMA:45572
UBERON:0010498
UMLS:C0836138
UMLS:C1514590
ncithesaurus:Pseudostratified_Columnar_Epithelium
ncithesaurus:Pseudostratified_Epithelium
uberon
pseudostratified ciliated columnar epithelium
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.
FMA:13146
UBERON:0010499
UMLS:C0506992
epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)
ncithesaurus:Pseudostratified_Columnar_Ciliated_Epithelium
uberon
microcirculatory vessel
A portion of tissue that consists of a tube composed of epithelial cells that connects larger vessels.
TAO:0005251
UBERON:0010523
ZFA:0005251
microcirculatory vessels
uberon
limb/fin segment
An appendage segment that is part of a limb/fin.
UBERON:0010538
uberon
tarsus pre-cartilage condensation
A pre-cartilage condensation that develops_into a tarsal bone.
EHDAA2:0001978
UBERON:0010540
uberon
tarsus cartilage condensation
A cartilaginous condensation that develops_into a tarsal bone.
EHDAA2:0001977
UBERON:0010541
uberon
skeleton of acropodium
FMA:231315
The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the autopodium - i.e. the bones of the digits or their cartilaginous precursors[VSAO,modified].
UBERON:0010543
VSAO:0005028
acropodial skeleton
acropodium
acropodium skeleton
digit skeleton
digital skeleton
set of phalanges
skeleton of digits
uberon
metatarsus skeleton
AAO:0000221
FMA:71340
Limb segment that consists of the long bones of the pes. The metatarsals are analogous to the metacarpal bones of the manus.
MESH:A01.378.610.250.300.480
OpenCyc:Mx4rva_rBJwpEbGdrcN5Y29ycA
Segment of the leg corresponding to the metatarsus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO]
UBERON:0010545
VSAO:0005027
XAO:0003212
http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png
http://upload.wikimedia.org/wikipedia/commons/thumb/5/52/Gray291.png/200px-Gray291.png
metatarsal bones set
metatarsal skeleton
metatarsalia
metatarsals [I-V]
ossa metatarsalia
posterior metapodium
posterior metapodium skeleton
set of metatarsal bones
set of metatarsals [I-V]
skeleton of metatarsus
uberon
metapodium skeleton
Endochondral bone complex located between the mesopodium and the acropodium and consisting of the metacarpals or metatarsals.[VSAO]
Subdivision of skeleton that corresponds to metapodium region, between acropodial skeleton and mesopdoial skeleton.
UBERON:0010546
VSAO:0005025
metacarpal/metatarsal skeleton
metapodial skeleton
metapodium
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: transitively_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
skeleton of metapodium
uberon
pedal digit 1 metatarsal pre-cartilage condensation
A pedal digit metatarsal pre-cartilage condensation that is part of a pedal digit 1 mesenchyme.
EHDAA2:0002040
EMAPA:17725
UBERON:0010547
foot digit 1 metatarsal pre-cartilage condensation
hind limb digit 1 metatarsal pre-cartilage condensation
toe 1 metatarsal pre-cartilage condensation
uberon
pedal digit 1 metatarsal cartilage condensation
A pedal digit metatarsal cartilage condensation that is part of a pedal digit 1 mesenchyme.
EMAPA:18106
UBERON:0010557
foot digit 1 metatarsal cartilage condensation
hind limb digit 1 metatarsal cartilage condensation
toe 1 metatarsal cartilage condensation
uberon
pedal digit 1 mesenchyme
EHDAA2:0002039
EMAPA:17462
Mesenchyme that is part of a pedal digit 1.
UBERON:0010562
foot digit 1 mesenchyme
hind limb digit 1 mesenchyme
uberon
pedal digit 1 phalanx pre-cartilage condensation
A pre-cartilage condensation that is part of a pedal digit 1 mesenchyme.
EHDAA2:0002041
EMAPA:17726
UBERON:0010580
foot digit 1 phalanx pre-cartilage condensation
hind limb digit 1 phalanx pre-cartilage condensation
uberon
pedal digit phalanx pre-cartilage condensation
A pre-cartilage condensation that is part of a pedal digit mesenchyme.
UBERON:0010585
VHOG:0000952
foot digit phalanx pre-cartilage condensation
foot phalanx pre-cartilage condensation
hind limb digit phalanx pre-cartilage condensation
hindlimb phalanx pre-cartilage condensation
pes phalanx pre-cartilage condensation
uberon
pedal digit 1 phalanx cartilage condensation
A cartilaginous condensation that is part of a pedal digit 1 mesenchyme.
EMAPA:18107
UBERON:0010680
foot digit 1 phalanx cartilage condensation
hind limb digit 1 phalanx cartilage condensation
uberon
pedal digit phalanx cartilage condensation
A cartilaginous condensation that is part of a pedal digit mesenchyme.
UBERON:0010685
foot digit phalanx cartilage condensation
hind limb digit phalanx cartilage condensation
uberon
pedal digit metatarsal pre-cartilage condensation
UBERON:0010687
VHOG:0000948
foot digit metatarsal pre-cartilage condensation
hind limb digit metatarsal pre-cartilage condensation
metatarsal bone pre-cartilage condensation
metatarsus pre-cartilage condensation
uberon
mesenchyme of tarsal region
EMAPA:18500
Mesenchyme of the carpal region that conributes to the tarsal skeleton.
UBERON:0010695
uberon
skeleton of pedal acropodium
FMA:78512
The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the pedal autopodium - i.e. the bones of the foot or their cartilaginous precursors[cjm].
UBERON:0010696
VSAO:0005030
all phalanges in hindlimb autopod
foot digit skeleton
hind acropodium skeleton
pedal phalanges
phalanges of foot
phalanges of pes
posterior acropodium
posterior acropodium skeleton
set of pedal phalanges
set of phalanges of foot
set of phalanges of pes
uberon
pedal digit metatarsal cartilage condensation
UBERON:0010697
foot digit metatarsal cartilage condensation
hind limb digit metatarsal cartilage condensation
uberon
phalanx pre-cartilage condensation
A pre-cartilage condensation that is part of a digit mesenchyme.
UBERON:0010700
uberon
phalanx cartilage condensation
A cartilaginous condensation that is part of a digit mesenchyme.
UBERON:0010701
uberon
digit mesenchyme
Mesenchyme that is part of a digit.
UBERON:0010702
uberon
appendage girdle complex
2012-04-23T10:46:51Z
An organism subdivision that includes both an appendage and its accociated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]
FMA:7182
It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]
It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] AO notes: note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)
UBERON:0010707
VSAO:0000214
appendage complex
appendage-girdle complex
appendage/girdle complex
girdle plus limb or fin
haendel
limb
uberon
pelvic complex
AO notes: note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here
Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO]
Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle.
FMA:7184
SCTID:416631005
UBERON:0010709
VSAO:0000215
lower limb
pelvic appendage/girdle complex
pelvic girdle plus pelvic limb or fin
pelvic girdle plus posterior limb or fin
uberon
limb skeleton subdivision
Editor notes - note the distinction between this and skeleton of limb
Skeletal subdivision that is a segment of the limb skeleton.
UBERON:0010712
VSAO:0005018
uberon
girdle skeleton
AAO:0010686
Skeletal subdivision that is part of the appendage girdle region.[VSAO]
The subdivision of the skeleton of either the pectoral or pelvic girdle.
UBERON:0010719
VSAO:0000302
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: transitively_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
skeleton of girdle
uberon
hindlimb zeugopod skeleton
AAO:0000216
Segment of the leg corresponding to the tibia and fibula.[AAO]
Subdivision of skeleton consisting of all skeletal elements in an hindlimb zeugopod region.
UBERON:0010720
VSAO:0005014
crus skeleton
hind epipodium
hindlimb epipodium
hindlimb zygopod skeleton
posterior zeugopodium
posterior zeugopodium skeleton
uberon
distal tarsal bone
AAO:0000914
FMA:24517
SCTID:182102002
Series of elements that articulate with the metatarsals.[AAO]
There are three cuneiform bones in the human foot: the medial cuneiform the intermediate cuneiform also known as the middle the lateral cuneiform. They are located between the navicular bone and the first, second and third metatarsal bones and are medial to the cuboid bone[WP, unvetted, human specific].
UBERON:0010721
UMLS:C1511560
cuneiform
cuneiform bone
distal tarsal
distal tarsal bone
http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray268.png
ncithesaurus:Cuneiform_Bone_of_the_Foot
os cuneiform
os cuneiforme
uberon
bone of appendage girdle complex
A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle).
MA:0000688
UBERON:0010740
bone of extended limb/fin region
limb bone
uberon
bone of pelvic complex
A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle.
MA:0000660
Note that the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle
UBERON:0010742
hindlimb bone
uberon
appendage segment
FBbt:00007018
UBERON:0010758
uberon
calcaneum pre-cartilage condensation
EMAPA:17736
UBERON:0010801
calcaneous pre-cartilage condensation
uberon
calcaneum cartilage condensation
EMAPA:18143
UBERON:0010842
calcaneous cartilage condensation
uberon
tibia cartilaginous condensation
A cartilaginous condensation that develops_into a tibia.
EMAPA:18155
UBERON:0010849
uberon
tibia pre-cartilage condensation
A pre-cartilage condensation that develops_into a tibia.
EHDAA2:0002036
UBERON:0010850
uberon
fibula cartilaginous condensation
A cartilaginous condensation that develops_into a fibula.
EMAPA:18154
UBERON:0010851
fibulal cartilage condensation
fibular cartilage condensation
uberon
fibula pre-cartilage condensation
A pre-cartilage condensation that develops_into a fibula.
EHDAA2:0000509
EHDAA:6196
UBERON:0010852
fibulal pre-cartilage condensation
fibular pre-cartilage condensation
uberon
limb bone cartilaginous condensation
A cartilaginous condensation that develops_into a limb bone.
UBERON:0010881
uberon
limb bone pre-cartilage condensation
A pre-cartilage condensation that develops_into a limb bone.
UBERON:0010882
uberon
hindlimb bone cartilaginous condensation
A cartilaginous condensation that develops_into a hindlimb bone.
UBERON:0010885
uberon
hindlimb bone pre-cartilage condensation
A pre-cartilage condensation that develops_into a hindlimb bone.
UBERON:0010886
uberon
pelvic complex muscle
AAO:0000218
FMA:9622
MA:0000663
Muscles of the pelvic girdle, hindlimb or pelvic fin.
Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO]
UBERON:0010890
lower limb muscle
muscle of lower limb
muscle of pelvic girdle and leg
pelvic girdle and hind limb muscles
pelvic girdle or hind limb muscle
pelvic girdle or posterior limb muscle
uberon
ossicle
Ossicles are composed of a combination skeletal tissues, including bone, calcified cartilage, hyaline cartilage, etc, and exhibit variable development across species. Ossicles are not necessarily jointed, and examples include the menisci of synovial joints, "Panda's thumb" (radial sesamoid), cardiac skeletal elements, sclerotic bones, middle ear ossicles, and sesamoids.
Skeletal element that is often isolated, small, and variable in composition.[VSAO]
Skeletal element that is small dermal or endochondral bone.
UBERON:0010911
VSAO:0000132
uberon
subdivision of skeleton
AO notes: VSAO def logically wrong
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.
Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]
FMA:23879
SCTID:129140006
UBERON:0010912
VSAO:0000042
skeletal subdivision
subdivision of skeleton (in vivo)
uberon
trunk and cervical myotome group
EHDAA2:0003425
UBERON:0010963
isa row in EHDAA2
uberon
flexor pre-muscle mass
EHDAA2:0000543
UBERON:0010977
uberon
nonsynovial joint
FMA:7491
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.
UBERON:0011134
solid joint
uberon
axial skeletal system
FMA:7483
Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
UBERON:0011137
uberon
post-cranial axial skeletal system
Subdivision of the skeletal system which consists of the post-cranial axial skeleton plus associated joints.
UBERON:0011138
axial skeletal system
http://purl.obolibrary.org/obo/uberon/references/reference_0000003
uberon
synovial limb joint
Any synovial joint that is part of a (free) limb.
FMA:258776
Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses.
UBERON:0011139
synovial joint of free limb segment
uberon
appendicular ossicle
Examples of appendicular ossicles include the patella and meniscus of the knee joint.
Ossicle that is part of the appendicular skeleton.
UBERON:0011141
VSAO:0000131
XAO:0004194
ossicle of appendicular skeleton
uberon
upper urinary tract
FMA:45658
SCTID:181413006
Subdivision of urinary system which consists of the kidney and the ureters.
UBERON:0011143
galen:UpperUrinaryTract
uberon
facial skeleton
EHDAA2:0002206
EHDAA:8361
EMAPA:18022
FMA:53673
MA:0000318
Subdivision of skull that consists of the facial bones.
UBERON:0011156
facial bone
facial skeleton
http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg
ossa facialia
ossa faciei
uberon
viscerocranium
primary subdivision of skull
FMA:54964
The skull can be divided into two: the neurocranium and the facial skeleton
UBERON:0011158
skull subdivision
subdivision of skull
uberon
primary subdivision of cranial skeletal system
UBERON:0011159
uberon
gastrointestinal sphincter
A sphincter muscle that is part of the gastrointestinal system
UBERON:0011185
UMLS:C1517464
ncithesaurus:Gastrointestinal_Sphincter
uberon
nucleus of midbrain tectum
A neural nucleus that is part of a midbrain tectum.
FMA:258766
UBERON:0011214
nucleus of tectum
tectal nucleus
uberon
cell part cluster of neuraxis
A multi cell component structure that is part of a central nervous system.
FMA:83143
UBERON:0011215
neuraxis layer
uberon
organ system subdivision
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.
FBbt:00007330
FMA:67509
SCTID:91690000
UBERON:0011216
uberon
appendicular skeletal system
FMA:7484
Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]
Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints.
UBERON:0011249
VHOG:0001666
VSAO:0000306
uberon
autopod bone
A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones.
UBERON:0011250
http://purl.obolibrary.org/obo/uberon/references/reference_0000015
uberon
embryonic skin basal layer
EHDAA2:0001845
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'
UBERON:0011272
basal cell layer of skin
outer epithelium of body
uberon
white matter of telencephalon
A partion of white matter that is part of a telencephalon. This can be further subdivided in some species, for example, into hemisphere white matter and the corpus callosum.
CNS white matter that is part of the telencephalon[ZFA:0000597].
FMA:83930
TAO:0000597
UBERON:0011299
UBERON:0013202
ZFA:0000597
telencephalic tract/commissure
telencephalic tracts
uberon
gray matter of telencephalon
A portion of gray matter of neuraxis that is part of a telencephalon.
FMA:83911
UBERON:0011300
uberon
cranial blood vasculature
A blood vasculature that is part of a head.
Blood vessel part of cranial vasculature.[TAO]
TAO:0005297
UBERON:0011362
ZFA:0005297
cranial blood vessels
set of blood vessels of head
uberon
prepuce
UBERON:0011374
Usage notes: this is a generic sex-neutral grouping class for the male and female prepuce. Note that this structure is a combination of skin and other tissue
ncithesaurus:Prepuce
preputial
uberon
skeleton of limb/fin
Skeletal subdivision that is part of the paired limb/fin.[VSAO]
The collection of all skeletal elements in an individual limb or fin.
UBERON:0011582
VSAO:0000301
limb/fin skeleton
uberon
stylopodial skeleton
Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified].
Proximal element of the limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively.[VSAO]
UBERON:0011583
VSAO:0005007
propodial
propodial skeleton
propodium
stylopod
stylopodial
stylopodium
stylopodium skeleton
uberon
zeugopodial skeleton
Section of the forelimb skeleton located between the stylopodium and the autopodium.
UBERON:0011584
VSAO:0005010
epipodium
skeleton of zeugopod
uberon
zeugopod skeleton
zeugopodial
zygopodial
zygopodium
cell condensation
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).
Editor notes: consider obsoleting, coordinate with VSAO
UBERON:0011585
VSAO:0000006
XAO:0004021
uberon
pre-dentine
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].
UBERON:0011587
VSAO:0000071
XAO:0004052
pre-dentine tissue
predentin
predentine tissue
uberon
jaw region
UBERON:0011595
http://eol.org/collections/11578
there are two jaw regions: the upper and lower. Each jaw region can be subdivided into left and right halves
uberon
axial subdivision of organism
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:0011676
uberon
hindlimb intermedium
AAO:0000923
UBERON:0011678
intermedium (hind)
uberon
proximal tarsal bone
A tarsal bone that connected_to a hindlimb zeugopod skeleton.
UBERON:0011679
uberon
differentiated genital tubercle
.
UBERON:0011757
UMLS:C1514448
ncithesaurus:Primordial_Phallus
phallus
phallus primordialis
primordial phallus
uberon
non-neurogenic ectodermal placode
UBERON:0011814
uberon
irregular connective tissue
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
UBERON:0011821
uberon
dense irregular connective tissue
FMA:20109
Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.
Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]
UBERON:0011822
UMLS:C0738366
irregular dense connective tissue
ncithesaurus:Irregular_Dense_Connective_Tissue
typus irregularis (textus connectivus collagenosus compactus)
uberon
dense connective tissue
AAO:0000121
Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]
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
UBERON:0011823
UMLS:C1511770
ncithesaurus:Dense_Connective_Tissue
uberon
gastrocnemius externus
.
M. gastrocnemius externus
UBERON:0011910
musculus gastrocnemius externus
uberon
stomach glandular region
A stomach region that has_part a stomach glandular epithelium.
MA:0001613
SCTID:27633001
UBERON:0011953
UMLS:C0227197
glandular stomach
ncithesaurus:Glandular_Stomach
uberon
coelom
EHDAA2:0004731
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.
The structure that contains the coelemic cavity.
UBERON:0011997
coelem
coelomic
coelomic cavity
uberon
epithelium-associated lymphoid tissue
FMA:62811
UBERON:0012069
uberon
centrale
Endochondral bone located between the proximal and distal rows of carpals or tarsals and thus representing the central carpals or tarsals[PHENOSCAPE].
FMA:77232
UBERON:0012131
Usage notes: This term corresponds both to the navicular bone in the pes and the similar central carpals in the manus. AO notes: the FMA term is under 'general anatomical term'.
central mesopodium bone
os centrale
uberon
segment of autopod
UBERON:0012139
uberon
digitopodium region
A segment of the autopod consisting of both acropodial region and metapodial region, but excluding the mesopodial/basopodial region.
Terminology notes: some sources call this the acropodium. see http://purl.obolibrary.org/obo/uberon/references/reference_0000019
UBERON:0012140
acropodium (Wagner)
autopod proper
http://purl.obolibrary.org/obo/uberon/references/reference_0000019
uberon
pedal digitopodium region
A digitopodium region that is part of a pes[Obol]. This includes the toes and metatarsal region, but excludes the tarsals region.
FMA:73084
Terminology notes: some sources call this the acropodium. see http://purl.obolibrary.org/obo/uberon/references/reference_0000019
UBERON:0012142
foot proper
http://purl.obolibrary.org/obo/uberon/references/reference_0000019
uberon
skeleton of digitopodium
A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton.
Terminology notes: some sources call this the acropodium. see http://purl.obolibrary.org/obo/uberon/references/reference_0000019
UBERON:0012150
autopod proper skeleton
digitopodium
http://purl.obolibrary.org/obo/uberon/references/reference_0000019
uberon
skeleton of pedal digitopodium
A subdivision of the pes skeleton consisting of both pedal acropodial skeleton and metatarsal skeleton, but excluding the tarsal skeleton.
Terminology notes: some sources call this the acropodium. see http://purl.obolibrary.org/obo/uberon/references/reference_0000019
UBERON:0012152
foot proper skeleton
http://purl.obolibrary.org/obo/uberon/references/reference_0000019
pedal digitopodium
skeleton of foot proper
uberon
head or neck skin
A zone of skin that is part of a craniocervical region.
MA:0000574
UBERON:0012180
UMLS:C1522650
ncithesaurus:Skin_of_the_Scalp_and_Neck
uberon
columnar epithelium
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]
UBERON:0012274
uberon
meso-epithelium
Epithelium that derives from the mesoderm. [Automatically generated definition].
FMA:86452
UBERON:0012275
uberon
embryonic cloacal fold
EHDAA2:0004009
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
UBERON:0012292
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
cloacal fold
uberon
embryonic facial prominence
One of five swellings formed during the development of the face
SCTID:89066004
UBERON:0012314
uberon
holocrine gland
A gland whose discharged secretion contains entire secreting cells.
BTO:0002325
UBERON:0012344
uberon
acropodium region
Note this class refers to an entire limb segment, not just the bones
The segment of the autopod that consists of the digits.
UBERON:0012354
acropodial limb segment
acropodial region
acropodial segment of autopod
set of digits
uberon
digitopodium bone
A bone that is part of a the digitopodium skeleton - i.e. the acropodial skeleton or the metapodial skeleton.
UBERON:0012357
uberon
pedal digitopodium bone
A bone that is part of a the pedal digitopodium skeleton - i.e. the toes or the metatarsal skeleton.
UBERON:0012359
bone of foot proper
bone of hindlimb digitopodium
uberon
bone of jaw
Editor notes: Do not manually classify under here - bones are automatically classified
SCTID:369003004
UBERON:0012360
jaw bone
uberon
internal anal region
EHDAA2:0004588
UBERON:0012361
uberon
hemopoietic tissue
Blood-forming tissue, consisting of reticular fibers and cells. Also known as hemopoietic tissue
Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue
CALOHA:TS-2142
FMA:14073
UBERON:0012429
UMLS:C0229619
haemopoietic tissue
hematopoietic tissue
ncithesaurus:Hematopoietic_Tissue
textus haemopoieticus
uberon
external anal region
EHDAA2:0004589
UBERON:0012469
uberon
skeleton of pelvic complex
FMA:24140
The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle.
UBERON:0012476
bones of lower limb
lower limb skeleton
ossa membri inferioris
pelvic complex skeleton
set of bones of lower limb
skeleton of posterior limb/fin and girdle
uberon
cloacal epithelium
An epithelium that is part of a cloaca.
UBERON:0012481
uberon
future brain vesicle
SCTID:360409004
UBERON:0013150
brain vesicle
early brain vesicle
primary brain vesicle
primitive brain vesicle
secondary brain vesicle
todo - resolve space vs structure inconsistency; consider adding all secondary vesicles (e.g. diencephalic; my/metencephalic. See http://www.dartmouth.edu/~rswenson/NeuroSci/chapter_4.html). Note that some sources may treat the term vesicle as the progenitor of the whole brain region; for example 'The retina develops directly from the neural tube as an outpouching from the diencephalic vesicle'
uberon
future glans
UBERON:0013238
uberon
future glans penis
EMAPA:29288
UBERON:0013239
glans of male genital tubercle
uberon
future glans clitoris
EMAPA:19170
UBERON:0013240
glans of female genital tubercle
uberon
space surrounding organism
UBERON:0013514
external to organism
outside of body
the space that surrounds an organism.
uberon
subdivision of uterine tube
FMA:18302
UBERON:0013515
subdivision of fallopian tube
subdivision of oviduct
uberon
uterine tube zone
zone of uterine tube
subdivision of tube
UBERON:0013522
uberon
length unit
A unit which is a standard measure of the distance between two points.
length unit
mass unit
A unit which is a standard measure of the amount of matter/energy of a physical object.
mass unit
time unit
A unit which is a standard measure of the dimension in which events occur in sequence.
time unit
temperature unit
A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
temperature unit
substance unit
A unit which is a standardised quantity of an element or compound with uniform composition.
substance unit
meter
A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
meter
kilogram
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
kilogram
second
A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
second
kelvin
A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water.
kelvin
mole
A substance unit which is equal to the amount of substance of a molecular system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12.
mole
centimeter
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
centimeter
millimeter
A length unit which is equal to one thousandth of a meter or 10^[-3] m.
millimeter
micrometer
A length unit which is equal to one millionth of a meter or 10^[-6] m.
micrometer
nanometer
A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
nanometer
gram
A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
gram
milligram
A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
milligram
microgram
A mass unit which is equal to one millionth of a gram or 10^[-6] g.
microgram
nanogram
A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
nanogram
picogram
A mass unit which is equal to 10^[-12] g.
picogram
degree Celsius
A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
degree Celsius
millisecond
A time unit which is equal to one thousandth of a second or 10^[-3] s.
millisecond
microsecond
A time unit which is equal to one millionth of a second or 10^[-6] s.
microsecond
minute
A time unit which is equal to 60 seconds.
minute
hour
A time unit which is equal to 3600 seconds or 60 minutes.
hour
day
A time unit which is equal to 24 hours.
day
week
A time unit which is equal to 7 days.
week
month
A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
month
year
A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
year
micromole
A substance unit equal to a millionth of a mol or 10^[-6] mol.
micromole
nanomole
A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.
nanomole
picomole
A substance unit equal to 10^[-12] mol.
picomole
femtomole
A substance unit equal to 10^[-15] mol.
femtomole
attomole
A substance unit equal to 10^[-18] mol.
attomole
base unit
A unit which is one of a particular measure to which all measures of that type can be related.
base unit
concentration unit
A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
concentration unit
mass density unit
A density unit which is a standard measure of the mass of a substance in a given volume.
mass density unit
unit of molarity
A concentration unit which is a standard measure of the number of moles of a given substance per liter of solution.
unit of molarity
molar
A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
molar
millimolar
A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
millimolar
micromolar
A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
micromolar
picomolar
A unit of molarity which is equal to 10^[-12] M.
picomolar
volume unit
A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
volume unit
cubic centimeter
A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
cubic centimeter
milliliter
A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
milliliter
liter
A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.
liter
microliter
A volume unit which is equal to one millionth of a liter or 10^[-6] L.
microliter
nanoliter
A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.
nanoliter
picoliter
A volume unit which is equal to 10^[-12] L.
picoliter
femtoliter
A volume unit which is equal to 10^[-15] L.
femtoliter
radiation unit
A unit which is a standard measure of the amount of radiation emitted by a given radiation source as well as the amount of radiation absorbed or deposited in a specific material by a radiation source.
radiation unit
activity (of a radionuclide) unit
A unit which is a standard measure of the transformation (disintegration) rate of a radioactive substance.
activity (of a radionuclide) unit
curie
An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which there are 3.7 x 10^[10] atom disintegration per second (dps).
curie
roentgen
An exposure unit which is equal to the amount of radiation required to liberate positive and negative charges of one electrostatic unit of charge in 1 cm^[3] of air at standard temperature and pressure (STP). This corresponds to the generation of approximately 2.0810^[9] ion pairs.
roentgen
Roentgen equivalent man
A dose equivalent unit which when multiplied by hundred is equal to one sievert or 1 Sv. 1 Sv is equal to 100 rem.
Roentgen equivalent man
disintegrations per minute
An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per minute or there is one atom disintegration per minute.
disintegrations per minute
counts per minute
An activity (of a radionuclide) unit which is equal to the number of light emissions produced by ionizing radiation in one minute.
counts per minute
light unit
A unit which is a standard measure of the intensity of light.
light unit
mass percentage
A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
mass percentage
mass volume percentage
A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
mass volume percentage
volume percentage
A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
volume percentage
gram per liter
A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
gram per liter
milligram per milliliter
A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
milligram per milliliter
dimensionless unit
A unit which is a standard measure of physical quantity consisting of only a numerical number without any units.
dimensionless unit
percent
A dimensionless ratio unit which denotes numbers as fractions of 100.
percent
count unit
A dimensionless unit which denotes a simple count of things.
count unit
degree Fahrenheit
A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius.
degree Fahrenheit
pH
A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
pH
volume per unit volume
A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution.
volume per unit volume
milliliter per liter
A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
milliliter per liter
gram per deciliter
A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
gram per deciliter
deciliter
A volume unit which is equal to one tenth of a liter or 10^[-1] L.
deciliter
colony forming unit per milliliter
A colony forming unit which a measure of viable bacterial numbers in one milliliter.
colony forming unit per milliliter
bit
An information unit which refers to a digit in the binary numeral system, which consists of base 2 digits (ie there are only 2 possible values: 0 or 1).
bit
acute lymphoblastic leukemia
acute lymphoblastic leukemia
acute myeloid leukemia
acute myeloid leukemia
acute promyelocytic leukemia
acute promyelocytic leukemia
asthma
asthma
Burkitts lymphoma
Burkitts lymphoma
cancer
cancer
chronic myelogenous leukemia
chronic myelogenous leukemia
colorectal adenocarcinoma
colorectal adenocarcinoma
diabetes mellitus
diabetes mellitus
disease
disease
family history
family history
insulinoma
insulinoma
leukemia
leukemia
neoplasm
neoplasm
experiment performer
experiment performer
type I diabetes mellitus
type I diabetes mellitus
type II diabetes mellitus
type II diabetes mellitus
lymphoid neoplasm
lymphoid neoplasm
data analyst
data analyst
investigator
investigator
submitter
submitter
myeloid neoplasm
myeloid neoplasm
mouse prenatal
mouse prenatal
Theiler stage 11
Theiler stage 11
Theiler stage 17
Theiler stage 17
Theiler stage 21
Theiler stage 21
Theiler stage 22
Theiler stage 22
Theiler stage 24
Theiler stage 24
Theiler stage 26
Theiler stage 26
Theiler stage 28
Theiler stage 28
International Unit
International Unit
mouse postnatal
mouse postnatal
Theiler stage 27
Theiler stage 27
Theiler stage 1
Theiler stage 1
Theiler stage 2
Theiler stage 2
Theiler stage 3
Theiler stage 3
Theiler stage 4
Theiler stage 4
Theiler stage 5
Theiler stage 5
Theiler stage 6
Theiler stage 6
Theiler stage 7
Theiler stage 7
Theiler stage 8
Theiler stage 8
Theiler stage 9
Theiler stage 9
Theiler stage 10
Theiler stage 10
Theiler stage 12
Theiler stage 12
Theiler stage 13
Theiler stage 13
Theiler stage 14
Theiler stage 14
Theiler stage 15
Theiler stage 15
Theiler stage 16
Theiler stage 16
Theiler stage 18
Theiler stage 18
Theiler stage 19
Theiler stage 19
Theiler stage 20
Theiler stage 20
Theiler stage 23
Theiler stage 23
Theiler stage 25
Theiler stage 25
Feature Extraction Software
Feature Extraction Software
embryonic day 15.5
15.5 days after fertilization
Person: Chris Stoeckert, Jie Zheng
embryonic day 16.5
16.5 days after fertilization
Person: Chris Stoeckert, Jie Zheng
embryonic day 8.5
Person: Chris Stoeckert, Jie Zheng
8.5 days after fertilization
embryonic day 17.5
Person: Chris Stoeckert, Jie Zheng
17.5 days after fertilization
embryonic day 8.25
8.25 days after fertilization
Person: Chris Stoeckert, Jie Zheng
embryonic day 18.5
Person: Chris Stoeckert, Jie Zheng
18.5 days after fertilization
embryonic day 8
8 days after fertilization
Person: Chris Stoeckert, Jie Zheng
embryonic day 18
18 days after fertilization
Person: Chris Stoeckert, Jie Zheng
embryonic day 11.5
Person: Chris Stoeckert, Jie Zheng
11.5 days after fertilization
postnatal day 0
0 day after birth
embryonic day 12.5
12.5 days after fertilization
Person: Chris Stoeckert, Jie Zheng
postnatal day 4
4 days after birth
embryonic day 9.5
Person: Chris Stoeckert, Jie Zheng
9.5 days after fertilization
postnatal day 12
12 days after birth
embryonic day 10.5
Person: Chris Stoeckert, Jie Zheng
10.5 days after fertilization
postnatal day 60
60 days after birth
embryonic day 13.5
Person: Chris Stoeckert, Jie Zheng
13.5 days after fertilization
embryonic day 14.5
Person: Chris Stoeckert, Jie Zheng
14.5 days after fertilization
example to be eventually removed
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
PERSON:Alan Ruttenberg
term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
to be replaced with external ontology term
Alan Ruttenberg
Terms with this status should eventually replaced with a term from another ontology.
group:OBI
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Alan Ruttenberg
group:OBI
Helicos
Helicos
Philippe Rocca-Serra
Roche
Philippe Rocca-Serra
Roche
Illumina
Illumina
Philippe Rocca-Serra
Li-Cor
Li-Cor
Philippe Rocca-Serra
Applied Biosystems
Applied Biosystems
Philippe Rocca-Serra
Barry Smith and Pierre Grenon: "The Cornucopia of Formal Ontological Relations"
Pierre Grenon: "Nuts in BFO's Nutshell: Revisions to the Bi-categorial Axiomatization of BFO"
Institute for Formal Ontology and Medical Information Science (IFOMIS)
Barry Smith: "Basic Tools of Formal Ontology"
Pierre Grenon
Pierre Grenon: "BFO in a Nutshell: A Bi-categorial Axiomatization of BFO and Comparison with DOLCE"
Pierre Grenon, Barry Smith and Louis Goldberg: "Biodynamic Ontology: Applying BFO in the Biomedical Domain"
Barry Smith: "Beyond Concepts: Ontology as Reality Representation"
Barry Smith: "Against Fantology"
Pierre Grenon: "Spatio-temporality in Basic Formal Ontology: SNAP and SPAN, Upper-Level Ontology, and Framework for Formalization"