format-version: 1.2 data-version: 2012-11-06 date: 06:11:2012 01:32 saved-by: balhoff auto-generated-by: OBO-Edit 2.1.1-beta8 synonymtypedef: PLURAL "PLURAL" default-namespace: vertebrate_skeletal_anatomy treat-xrefs-as-equivalent: UBERON remark: $Revision: 8.04.2012 $ Contact Wasila Dahdul: Wasila.Dahdul@usd.edu. remark: To the extent possible under law, Wasila M. Dahdul has waived all copyright and related or neighboring rights to the Vertebrate Skeletal Anatomy Ontology (VSAO), under CC0 license (http://creativecommons.org/publicdomain/zero/1.0/). This work is published from the United States. ontology: vsao [Term] id: CARO:0000000 name: anatomical entity namespace: caro def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [CARO:MAH, FMA:62955] [Term] id: CARO:0000003 name: anatomical structure namespace: caro def: "Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome." [CARO:MAH, FMA:67135] is_a: CARO:0000006 ! material anatomical entity [Term] id: CARO:0000004 name: portion of organism substance namespace: caro def: "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body." [CARO:MAH, FMA:9669] is_a: CARO:0000006 ! material anatomical entity [Term] id: CARO:0000005 name: anatomical space namespace: caro def: "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures." [CARO:MAH, FMA:5897] is_a: CARO:0000007 ! immaterial anatomical entity [Term] id: CARO:0000006 name: material anatomical entity namespace: caro def: "Anatomical entity that has mass." [CARO:MAH, FMA:67165] is_a: CARO:0000000 ! anatomical entity [Term] id: CARO:0000007 name: immaterial anatomical entity namespace: caro def: "Anatomical entity that has no mass." [CARO:MAH, FMA:67112] is_a: CARO:0000000 ! anatomical entity [Term] id: CARO:0000008 name: anatomical line namespace: caro def: "Non-material anatomical entity of one dimension, whiVSAO forms a boundary of an anatomical surface or is a modulation of an anatomical surface." [CARO:MAH, FMA:9657] is_a: CARO:0000007 ! immaterial anatomical entity [Term] id: CARO:0000009 name: anatomical point namespace: caro def: "Non-material anatomical entity of zero dimension, which forms a boundary of an anatomical line or surface." [CARO:MAH, FMA:9658] is_a: CARO:0000007 ! immaterial anatomical entity [Term] id: CARO:0000010 name: anatomical surface namespace: caro def: "Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures." [CARO:MAH, FMA:24137] is_a: CARO:0000007 ! immaterial anatomical entity [Term] id: CARO:0000011 name: anatomical system namespace: caro def: "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity." [CARO:MAH, FMA:7149] is_a: CARO:0000054 ! anatomical group [Term] id: CARO:0000012 name: multi-cellular organism namespace: caro def: "Anatomical structure that is an individual member of a species and consists of more than one cell." [CARO:MAH, FMA:256135] is_a: CARO:0000003 ! anatomical structure [Term] id: CARO:0000013 name: cell namespace: caro def: "Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:MAH] xref: GO:0005623 is_a: CARO:0000003 ! anatomical structure [Term] id: CARO:0000014 name: cell component namespace: caro def: "Anatomical structure that is a direct part of the cell." [CARO:MAH, FMA:86454] is_a: CARO:0000003 ! anatomical structure relationship: part_of CARO:0000013 ! cell [Term] id: CARO:0000019 name: compound organ component namespace: caro def: "Multi-tissue structure that is part of a compound organ." [CARO:MAH] is_a: CARO:0000055 ! multi-tissue structure relationship: part_of CARO:0000024 ! compound organ [Term] id: CARO:0000021 name: simple organ namespace: caro def: "Multi-tissue structure that is not part of a compound organ." [CARO:MAH] is_a: CARO:0000055 ! multi-tissue structure [Term] id: CARO:0000024 name: compound organ namespace: caro def: "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types." [CARO:MAH] is_a: CARO:0000003 ! anatomical structure [Term] id: CARO:0000027 name: male organism namespace: caro def: "Gonochoristic organism that can produce male gametes." [CARO:MAH] is_a: CARO:0000048 ! gonochoristic organism [Term] id: CARO:0000028 name: female organism namespace: caro def: "Gonochoristic organism that can produce female gametes." [CARO:MAH] is_a: CARO:0000048 ! gonochoristic organism [Term] id: CARO:0000029 name: hermaphroditic organism namespace: caro def: "Multi-cellular organism that can produce both male and female gametes." [CARO:MAH] synonym: "dioecious organism" RELATED [] is_a: CARO:0000012 ! multi-cellular organism [Term] id: CARO:0000030 name: asexual organism namespace: caro def: "Multi-cellular organism that does not produce gametes." [CARO:MAH] is_a: CARO:0000012 ! multi-cellular organism [Term] id: CARO:0000032 name: organism subdivision namespace: caro def: "Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism." [CARO:MAH] is_a: CARO:0000003 ! anatomical structure [Term] id: CARO:0000040 name: acellular anatomical structure namespace: caro def: "Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue." [CARO:MAH, FMA:63863] is_a: CARO:0000003 ! anatomical structure [Term] id: CARO:0000041 name: anatomical cluster namespace: caro def: "Anatomical group that has its parts adjacent to one another." [CARO:MAH, FMA:49443] is_a: CARO:0000054 ! anatomical group [Term] id: CARO:0000042 name: extraembryonic structure namespace: caro def: "Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo." [CARO:MAH] is_a: CARO:0000003 ! anatomical structure [Term] id: CARO:0000043 name: tissue namespace: caro def: "Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships." [CARO:MAH, FMA:9637] synonym: "portion of tissue" EXACT [] is_a: CARO:0000003 ! anatomical structure [Term] id: CARO:0000045 name: sequential hermaphroditic organism namespace: caro def: "Hermaphroditic organism that produces gametes first of one sex, and then later of the other sex." [CARO:MAH] synonym: "consecutive hermaphroditic organism" RELATED [] is_a: CARO:0000029 ! hermaphroditic organism [Term] id: CARO:0000046 name: synchronous hermaphroditic organism namespace: caro def: "Hermaphroditic organism that produces both male and female gametes at the same time." [CARO:MAH] synonym: "serially hermaphroditic organism" RELATED [] is_a: CARO:0000029 ! hermaphroditic organism [Term] id: CARO:0000048 name: gonochoristic organism namespace: caro def: "Multi-cellular organism that has male and female sexes." [CARO:MAH] synonym: "monoecious organism" RELATED [] is_a: CARO:0000012 ! multi-cellular organism [Term] id: CARO:0000049 name: protandrous hermaphroditic organism namespace: caro def: "Sequential hermaphroditic organism that produces\ngametes first of the male sex, and then later of the\nfemale sex." [CARO:MAH] is_a: CARO:0000045 ! sequential hermaphroditic organism [Term] id: CARO:0000050 name: protogynous hermaphroditic organism namespace: caro def: "Sequential hermaphroditic organism that produces\ngametes first of the female sex, and then later of the\nmale sex." [CARO:MAH] is_a: CARO:0000045 ! sequential hermaphroditic organism [Term] id: CARO:0000054 name: anatomical group namespace: caro def: "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue." [CARO:MAH] is_a: CARO:0000003 ! anatomical structure [Term] id: CARO:0000055 name: multi-tissue structure namespace: caro def: "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types." [CARO:MAH] is_a: CARO:0000003 ! anatomical structure [Term] id: CARO:0000062 name: cell space namespace: caro def: "Anatomical space that is part of a cell." [CARO:mah] is_a: CARO:0000005 ! anatomical space [Term] id: CARO:0000063 name: portion of cell substance namespace: caro def: "Portion of organism substance located within a cell." [CARO:mah] is_a: CARO:0000004 ! portion of organism substance [Term] id: CARO:0000064 name: single cell organism namespace: caro def: "Cell that is an individual member of a species." [CARO:MAH] is_a: CARO:0000013 ! cell [Term] id: CARO:0000065 name: basal lamina namespace: caro def: "Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue." [CARO:MAH] is_a: CARO:0000040 ! acellular anatomical structure [Term] id: CARO:0000066 name: epithelium namespace: caro def: "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina." [CARO:MAH, FMA:9639] is_a: CARO:0000043 ! tissue [Term] id: CARO:0000067 name: simple cuboidal epithelium namespace: caro def: "Unilaminar epithelium that consists of a single layer of cuboidal cells." [CARO:MAH, FMA:45566] is_a: CARO:0000073 ! unilaminar epithelium [Term] id: CARO:0000068 name: simple columnar epithelium namespace: caro def: "Unilaminar epithelium that consists of a single layer of columnar cells." [CARO:MAH, FMA:45567] is_a: CARO:0000073 ! unilaminar epithelium [Term] id: CARO:0000069 name: multilaminar epithelium namespace: caro def: "Epithelium that consists of more than one layer of epithelial cells." [CARO:MAH, FMA:45562] is_a: CARO:0000066 ! epithelium [Term] id: CARO:0000070 name: simple squamous epithelium namespace: caro def: "Unilaminar epithelium that consists of a single layer of squamous cells." [CARO:MAH, FMA:45565] is_a: CARO:0000073 ! unilaminar epithelium [Term] id: CARO:0000071 name: atypical epithelium namespace: caro def: "Epithelium that consists of epithelial cells not arranged in one ore more layers." [CARO:MAH] is_a: CARO:0000066 ! epithelium [Term] id: CARO:0000072 name: cavitated compound organ namespace: caro def: "Compound organ that contains one or more macroscopic anatomical spaces." [CARO:MAH] is_a: CARO:0000024 ! compound organ [Term] id: CARO:0000073 name: unilaminar epithelium namespace: caro def: "Epithelium that consists of a single layer of epithelial cells." [CARO:MAH, FMA:45561] is_a: CARO:0000066 ! epithelium [Term] id: CARO:0000074 name: solid compound organ namespace: caro def: "Compound organ that does not contain macroscopic anatomical spaces." [CARO:MAH] is_a: CARO:0000024 ! compound organ [Term] id: CARO:0000077 name: epithelial cell namespace: caro def: "Cell which has as its part a cytoskeleton that allows for tight cell to cell contact and which has apical-basal cell polarity." [CARO:MAH] is_a: CARO:0000013 ! cell [Term] id: CARO:0001000 name: multi-cell-component structure namespace: caro def: "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." [FBC:DOS] is_a: CARO:0000003 ! anatomical structure [Term] id: CARO:0001001 name: neuron projection bundle namespace: caro def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [FBC:DOS] synonym: "nerve fiber bundle" EXACT [FBC:DOS] is_a: CARO:0001000 ! multi-cell-component structure [Term] id: CARO:0001500 name: neuron projection bundle segment namespace: caro def: "A fiber-shaped subdivision of a neuron projection along its long axis." [CAROC:DOS] is_a: CARO:0001000 ! multi-cell-component structure relationship: part_of CARO:0001001 ! neuron projection bundle created_by: djs93 creation_date: 2011-09-10T04:22:25Z [Term] id: CARO:0001501 name: neuron projection bundle subsegment namespace: caro def: "A subdivision of a neuron projection along its long axis that is sufficiently short that it is not fiber-shaped." [CAROC:DOS] is_a: CARO:0001000 ! multi-cell-component structure relationship: part_of CARO:0001001 ! neuron projection bundle created_by: djs93 creation_date: 2011-09-10T04:24:17Z [Term] id: CL:0000003 name: native cell namespace: cell def: "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)." [CARO:mah] comment: To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). synonym: "cell in vivo" NARROW [] xref: CARO:0000013 is_a: CARO:0000013 ! cell [Term] id: CL:0000008 name: migratory cranial neural crest cell namespace: cell is_a: CL:0000333 ! migratory neural crest cell [Term] id: CL:0000055 name: non-terminally differentiated cell namespace: cell def: "A precursor cell with a limited number of potential fates." [SANBI:mhl] comment: define using PATO mulit-potent or oligopotent? synonym: "blast cell" EXACT [] xref: BTO:0000125 xref: FMA:84782 is_a: CL:0000003 ! native cell [Term] id: CL:0000058 name: chondroblast namespace: cell def: "Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell." [GO_REF:0000034, GOC:tfm, ISBN:0618947256] synonym: "chrondoplast" EXACT [] xref: BTO:0003607 xref: FMA:66783 is_a: CL:0002320 ! connective tissue cell relationship: develops_from CL:0007009 ! prechondroblast relationship: produces VSAO:0000040 ! cartilage tissue relationship: produces VSAO:0000059 ! avascular GAG-rich matrix [Term] id: CL:0000059 name: ameloblast namespace: cell alt_id: CL:0000053 alt_id: CL:0000139 def: "Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell." [GO_REF:0000034, GOC:tfm, MESH:A.11.436.107] comment: Legacy definition: A cylindrical epithelial cell in the innermost layer of the enamel organ. Their functions include contribution to the development of the dentinoenamel junction by the deposition of a layer of the matrix, thus producing the foundation for the prisms (the structural units of the dental enamel), and production of the matrix for the enamel prisms and interprismatic substance. (From Jablonski's Dictionary of Dentistry, 1992). synonym: "amelocyte" EXACT [] synonym: "enamel secreting cell" EXACT [] xref: BTO:0001663 xref: FMA:70576 is_a: CL:0000151 ! secretory cell relationship: adjacent_to VSAO:0000025 ! odontogenic papilla relationship: develops_from CL:0007000 ! preameloblast relationship: produces VSAO:0000065 ! enamel [Term] id: CL:0000060 name: odontoblast namespace: cell def: "Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell." [GO_REF:0000034, ISBN:0618947256] comment: legacy def: One of the cells forming the outer surface of dental pulp that produces tooth dentin. xref: BTO:0001769 xref: FMA:62999 is_a: CL:0000055 ! non-terminally differentiated cell relationship: develops_from CL:0007003 ! preodontoblast relationship: part_of VSAO:0000025 ! odontogenic papilla relationship: produces VSAO:0000069 ! dentine [Term] id: CL:0000061 name: cementoblast namespace: cell alt_id: CL:0000859 def: "Skeletogenic cell that produces cementum (a bony substance that covers the root of a tooth), is part of the odontogenic papilla, and develops from a precementoblast cell." [GO_REF:0000034, ISBN:0781733901] comment: Legacy def: A cell of ectomesenchymal origin that aids in the formation the cementum layer on the roots of teeth. synonym: "cementum secreting cell" EXACT [] xref: FMA:63002 is_a: CL:0000062 ! osteoblast relationship: develops_from CL:0007002 ! precementoblast relationship: part_of VSAO:0000025 ! odontogenic papilla relationship: produces VSAO:0000062 ! cementum [Term] id: CL:0000062 name: osteoblast namespace: cell def: "Skeletogenic cell that secretes osteoid, is capable of producing mineralized (hydroxyapatite) matrix, is located adjacent to or within osteoid tissue, and arises from the transformation of a preosteoblast cell." [GO_REF:0000034, MESH:A.11.329.629] comment: non-encoded relationships from VSAO - capable_of_producing mineralized extracellular matrix. part_of osteoid xref: BTO:0001593 xref: FMA:66780 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0002320 ! connective tissue cell relationship: develops_from CL:0007010 ! preosteoblast relationship: produces VSAO:0000046 ! osteoid [Term] id: CL:0000134 name: mesenchymal cell namespace: cell alt_id: CL:0002452 def: "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. This cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." [FB:ma, GOC:dsd, http://en.wikipedia.org/wiki/Mesenchymal_stem_cell, http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells, PMCID:PMC2613570, PMID:10102814j, PMID:16923606, PMID:17986482, PMID:19960544] comment: Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. synonym: "BMSC" EXACT [] synonym: "bone marrow stromal cells" EXACT [] synonym: "CFU-F" EXACT [] synonym: "colony-forming unit-fibroblast" EXACT [] synonym: "marrow stromal cells" EXACT [PMID:11378515] synonym: "mesenchymal precursor cell" EXACT [] synonym: "mesenchymal progenitor cells" EXACT [MESH:D044982] synonym: "mesenchymal stem cell" EXACT [] synonym: "mesenchymal stromal cell" EXACT [] synonym: "mesenchymal stromal cells" EXACT [] synonym: "MSC" EXACT [PMID:11378515] synonym: "stem cells, mesenchymal" EXACT [MESH:D044982] xref: BTO:0002625 xref: BTO:0003298 xref: FMA:70546 is_a: CL:0002320 ! connective tissue cell [Term] id: CL:0000137 name: osteocyte namespace: cell def: "A mature osteoblast that has become embedded in the bone matrix. They occupy a small cavity, called lacuna, in the matrix and are connected to adjacent osteocytes via protoplasmic projections called canaliculi." [GOC:tfm, MESH:A.11.329.629.500] comment: need to add non-terminally differentiated osteoblast to CL and use that for the develops from. synonym: "bone cell" BROAD [] xref: BTO:0002038 xref: FMA:66779 is_a: CL:0001035 ! bone cell relationship: develops_from CL:0001040 ! non-terminally differentiated osteoblast relationship: integral_part_of VSAO:0000118 ! cellular bone tissue [Term] id: CL:0000138 name: chondrocyte namespace: cell def: "Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell." [GO_REF:0000034, MESH:A.11.329.171] synonym: "cartilage cell" EXACT [] xref: BTO:0000249 xref: FMA:66782 is_a: CL:0002320 ! connective tissue cell relationship: develops_from CL:0000058 ! chondroblast relationship: part_of VSAO:0000040 ! cartilage tissue relationship: produces VSAO:0000059 ! avascular GAG-rich matrix [Term] id: CL:0000140 name: odontocyte namespace: cell def: "Skeletogenic cell that secretes dentine matrix, is derived from odontogenic papilla. Embedded in dentine tissue, and is the transformation of a non-terminally differentiated odontoblast cell." [GO_REF:0000034] comment: develops_from differs from CL as need to add the non-terminally differentiated odontoblast class to CL is_a: CL:0002320 ! connective tissue cell relationship: develops_from CL:0000134 ! mesenchymal cell relationship: develops_from CL:0007012 ! non-terminally differentiated odontoblast relationship: produces VSAO:0000069 ! dentine [Term] id: CL:0000141 name: cementocyte namespace: cell def: "An osteocytelike cell with numerous processes, trapped in a lacuna in the cement of the tooth." [ISBN:0781733901] comment: CHECK: wikipedia says that cementocytes no longer produce cementum, but the phenoscape def is: Skeletogenic cell that produces cementum, is part of the odontogenic papilla, and is a transformation of a cementoblast cell (no change to existing def). xref: FMA:63003 is_a: CL:0000137 ! osteocyte relationship: develops_from CL:0000061 ! cementoblast relationship: part_of VSAO:0000025 ! odontogenic papilla [Term] id: CL:0000151 name: secretory cell namespace: cell def: "A cell that specializes in controlled release of one or more substances." [GOC:tfm, ISBN:0721662544] xref: BTO:0003659 xref: FMA:86916 is_a: CL:0000003 ! native cell intersection_of: CL:0000003 ! native cell intersection_of: capable_of GO:0032940 ! secretion by cell relationship: capable_of GO:0032940 ! secretion by cell [Term] id: CL:0000222 name: mesodermal cell namespace: cell def: "A cell of the middle germ layer of the embryo." [MESH:A.16.254.425.660] synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 is_a: CL:0002321 ! embryonic cell [Term] id: CL:0000333 name: migratory neural crest cell namespace: cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [MESH:A.16.254.600] xref: FMA:86667 is_a: CL:0002321 ! embryonic cell relationship: develops_from CL:0007004 ! premigratory neural crest cell [Term] id: CL:0000742 name: periarticular chondrocyte namespace: cell def: "A round chondrocyte that first differentiates in the late embryonic growth plate of bone." [PMID:15951842] is_a: CL:0000138 ! chondrocyte [Term] id: CL:0000743 name: hypertrophic chondrocyte namespace: cell def: "Chondrocyte that is terminally differentiated, produces type X collagen, is large in size, and often associated with the replacement of cartilage by bone (endochondral ossification)." [GO_REF:0000034, PMID:15951842] comment: is hypertrophic pathological or normal? and can it be described using a pato term? is_a: CL:0000138 ! chondrocyte [Term] id: CL:0001035 name: bone cell namespace: cell def: "A connective tissue cell found in bone." [GO_REF:0000034, GOC:add] is_a: CL:0000003 ! native cell relationship: part_of VSAO:0000057 ! bone element created_by: adiehl creation_date: 2011-11-16T04:28:16Z [Term] id: CL:0001039 name: terminally differentiated osteoblast def: "Osteoblast that is terminally differentiated, located adjacent to acellular or cellular bone tissue within periosteum, and is capable of mineralizing the matrix." [VSAO:curator] xref: VSAO:0000116 is_a: CL:0000062 ! osteoblast [Term] id: CL:0001040 name: non-terminally differentiated osteoblast def: "Osteoblast that is non-terminally differentiated and located in cellular bone tissue or under the periosteum in acellular bone." [VSAO:curator] comment: VSAO relationship simplified OBO_REL:integral_part_of cellular bone tissue xref: VSAO:0000117 is_a: CL:0000062 ! osteoblast relationship: integral_part_of VSAO:0000047 ! bone tissue [Term] id: CL:0002320 name: connective tissue cell namespace: cell alt_id: CL:1000406 def: "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." [GOC:tfm, ISBN:0618947256] xref: FMA:63875 is_a: CL:0000003 ! native cell created_by: tmeehan creation_date: 2010-09-15T03:01:54Z [Term] id: CL:0002321 name: embryonic cell namespace: cell def: "A cell of the embryo." [FMA:0618947256] xref: FMA:82840 xref: FMA:82841 xref: WBbt:0007028 is_a: CL:0000003 ! native cell created_by: tmeehan creation_date: 2010-09-15T03:39:21Z [Term] id: CL:0007000 name: preameloblast namespace: cell def: "Skeletogenic cell that has the potential to develop into an ameloblast. Located in the inner enamel epithelium, these cells elongate, their nuclei shift distally (away from the dental papilla), and their cytoplasm becomes filled with organelles needed for synthesis and secretion of enamel proteins." [GO_REF:0000034, PMCID:PMC2737325] is_a: CL:0000055 ! non-terminally differentiated cell relationship: adjacent_to VSAO:0000025 ! odontogenic papilla relationship: develops_from CL:0000008 ! migratory cranial neural crest cell created_by: haendel creation_date: 2012-06-15T01:27:01Z [Term] id: CL:0007001 name: skeletogenic cell namespace: cell def: "Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized)." [GO_REF:0000034] comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. \n\nNOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. http://www.copewithcytokines.de/cope.cgi?key=scleroblasts synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000003 ! native cell relationship: produces VSAO:0000013 ! mineralized tissue relationship: produces VSAO:0000020 ! mineralized extracellular matrix created_by: haendel creation_date: 2012-06-15T02:51:27Z [Term] id: CL:0007002 name: precementoblast namespace: cell def: "Skeletogenic cell that has the potential to develop into a cementoblast." [GO_REF:0000034] is_a: CL:0000055 ! non-terminally differentiated cell relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of VSAO:0000025 ! odontogenic papilla created_by: haendel creation_date: 2012-06-15T04:37:13Z [Term] id: CL:0007003 name: preodontoblast namespace: cell def: "Skeletogenic cell that has the potential to form an odontoblast, deposits predentine, and arises from a cranial neural crest cell." [GO_REF:0000034] is_a: CL:0000055 ! non-terminally differentiated cell relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of VSAO:0000025 ! odontogenic papilla relationship: produces VSAO:0000071 ! pre-dentine created_by: haendel creation_date: 2012-06-15T05:15:11Z [Term] id: CL:0007004 name: premigratory neural crest cell namespace: cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] is_a: CL:0000003 ! native cell created_by: haendel creation_date: 2012-06-27T08:27:35Z [Term] id: CL:0007005 name: notochordal cell namespace: cell def: "Cell that is part of the notochord." [GO_REF:0000034] comment: NOTE: TO DO, notochord development still needs work. is_a: CL:0000003 ! native cell relationship: develops_from CL:0007006 ! chordamesodermal cell relationship: part_of VSAO:0000032 ! notochord created_by: haendel creation_date: 2012-06-27T08:47:31Z [Term] id: CL:0007006 name: chordamesodermal cell namespace: cell def: "Mesodermal cell that is axially located and gives rise to the cells of the notochord." [GO_REF:0000034] is_a: CL:0000222 ! mesodermal cell created_by: haendel creation_date: 2012-06-27T08:52:41Z [Term] id: CL:0007007 name: notochordal sheath cell namespace: cell def: "Notochordal cell that is part of the outer epithelium of the notochord and surrounds the vacuolated notochord cells." [CL:MAH] is_a: CL:0007005 ! notochordal cell created_by: haendel creation_date: 2012-06-27T09:26:37Z [Term] id: CL:0007008 name: notochordal vacuole cell namespace: cell def: "Notochordal cell that is inner portion of the notochord and becomes vacuolated as development proceeds." [CL:MAH] synonym: "chordablast" EXACT [GO_REF:0000034] synonym: "chordoblast" EXACT [PMID:14574572] is_a: CL:0007005 ! notochordal cell relationship: part_of VSAO:0000032 ! notochord created_by: haendel creation_date: 2012-06-27T09:29:30Z [Term] id: CL:0007009 name: prechondroblast namespace: cell def: "Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells." [GO_REF:0000034] is_a: CL:0000055 ! non-terminally differentiated cell created_by: haendel creation_date: 2012-06-27T10:44:01Z [Term] id: CL:0007010 name: preosteoblast namespace: cell def: "Skeletogenic cell that has the potential to transform into an osteoblast, and develops from neural crest or mesodermal cells." [GO_REF:0000034] synonym: "osteoprogenitor cell" EXACT [] is_a: CL:0000055 ! non-terminally differentiated cell relationship: develops_from CL:0000222 ! mesodermal cell relationship: develops_from CL:0000333 ! migratory neural crest cell relationship: part_of VSAO:0000046 ! osteoid created_by: haendel creation_date: 2012-06-27T10:57:21Z [Term] id: CL:0007012 name: non-terminally differentiated odontoblast def: "Odontoblast that non-terminally differentiated, located in the odontogenic papilla and dentine tissue, and transforms from a odontoblast cell." [GO_REF:0000034] is_a: CL:0000060 ! odontoblast [Term] id: CL:0007013 name: terminally differentiated odontoblast def: "Odontoblast that is terminally differentiated and derived from an odontogenic papilla and associated with dentine." [GO_REF:0000034] is_a: CL:0000060 ! odontoblast [Term] id: GO:0001503 name: ossification namespace: biological_process def: "The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance." [GOC:mtg_mpo, PMID:17572649] comment: Note that this term does not have a 'developmental process' parent because ossification isn't necessarily developmental, can also occur as part of bone remodeling. Instead use 'ossification involved in bone maturation ; GO:0043931'. synonym: "bone biosynthesis" EXACT [] synonym: "bone formation" EXACT [] synonym: "osteogenesis" EXACT [] xref: Wikipedia:Ossification is_a: GO:0008150 ! biological_process [Term] id: GO:0001649 name: osteoblast differentiation namespace: biological_process def: "The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone." [CL:0000062, GO_REF:0000034, GOC:jid] synonym: "osteoblast cell differentiation" EXACT [] is_a: GO:0008150 ! biological_process relationship: part_of GO:0001503 ! ossification [Term] id: GO:0001957 name: intramembranous ossification namespace: biological_process def: "Direct ossification that occurs within mesenchyme or an accumulation of relatively unspecialized cells." [ISBN:0878932437] comment: An instance of intramembranous ossification may also be classified as metaplastic; the former classifies based on tissue type location, and the latter based on mechanism/cell division. synonym: "dermal ossification" NARROW [GO_REF:0000034] xref: Wikipedia:Intramembranous_ossification is_a: GO:0036072 ! direct ossification [Term] id: GO:0001958 name: endochondral ossification namespace: biological_process def: "Replacement ossification wherein bone tissue replaces cartilage." [GO_REF:0000034, ISBN:0878932437] xref: Wikipedia:Endochondral_ossification is_a: GO:0036075 ! replacement ossification relationship: part_of GO:0060350 ! endochondral bone morphogenesis [Term] id: GO:0008150 name: biological_process namespace: biological_process alt_id: GO:0000004 alt_id: GO:0007582 def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. synonym: "biological process" EXACT [] synonym: "biological process unknown" NARROW [] synonym: "physiological process" EXACT [] xref: Wikipedia:Biological_process [Term] id: GO:0030282 name: bone mineralization namespace: biological_process def: "The deposition of calcium phosphate in bone tissue." [GOC:mah] synonym: "bone calcification" NARROW [] is_a: GO:0031214 ! biomineral tissue development relationship: part_of GO:0001503 ! ossification [Term] id: GO:0031214 name: biomineral tissue development namespace: biological_process def: "Formation of hard tissues that consist mainly of inorganic compounds, and also contain a small amounts of organic matrices that are believed to play important roles in their formation." [PMID:15132736] synonym: "biomineral formation" RELATED [GOC:dph, GOC:tb] synonym: "biomineralization" EXACT [] synonym: "mineralization" EXACT [] xref: Wikipedia:Biomineralisation is_a: GO:0008150 ! biological_process [Term] id: GO:0032940 name: secretion by cell namespace: biological_process def: "The controlled release of a substance by a cell." [GOC:mah] synonym: "cellular secretion" EXACT [] xref: Wikipedia:Secretion is_a: GO:0008150 ! biological_process [Term] id: GO:0035630 name: bone mineralization involved in bone maturation namespace: biological_process def: "The deposition of calcium phosphate in bone tissue, involved in the progression of the skeleton from its formation to its mature state." [GOC:bf, GOC:BHF] comment: Bone mineralization can also occur after a fracture and as a response to stress; in these cases, consider using the term 'bone mineralization ; GO:0030282'. is_a: GO:0030282 ! bone mineralization relationship: part_of GO:0043931 ! ossification involved in bone maturation [Term] id: GO:0036072 name: direct ossification namespace: biological_process def: "The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance, that does not require the replacement of preexisting tissues." [GO_REF:0000034] is_a: GO:0001503 ! ossification [Term] id: GO:0036073 name: perichondral ossification namespace: biological_process def: "Intramembranous ossification from the surface of a cartilage element as the perichondrium becomes a periosteum, without replacement of cartilage." [GO_REF:0000034] is_a: GO:0001957 ! intramembranous ossification [Term] id: GO:0036074 name: metaplastic ossification namespace: biological_process def: "Direct ossification in which bone formation occurs as result of the direct transformation of non-bone cells into bone cells without cell division." [GO_REF:0000034] comment: Some intramembranous ossification may also be classified as metaplastic; the former classifies based on tissue type location, and the latter based on mechanism/cell division. synonym: "metaplasia" RELATED [GO_REF:0000034] is_a: GO:0036072 ! direct ossification [Term] id: GO:0036075 name: replacement ossification namespace: biological_process def: "Ossification that requires the replacement of a preexisting tissue prior to bone tissue formation." [GO_REF:0000034] synonym: "indirect ossification" EXACT [GO_REF:0000034] is_a: GO:0001503 ! ossification [Term] id: GO:0036076 name: ligamentous ossification namespace: biological_process def: "Ossification wherein bone tissue forms within ligamentous tissue." [GO_REF:0000034] comment: Ligamentous ossification may occur via replacement ossification or metaplastic ossification or both in any one instance. is_a: GO:0001503 ! ossification [Term] id: GO:0036077 name: intratendonous ossification namespace: biological_process def: "Ossification wherein bone tissue forms within tendonous tissue." [GO_REF:0000034] comment: Tendonous ossification may occur via replacement ossification or metaplastic ossification or both in any one instance. is_a: GO:0001503 ! ossification [Term] id: GO:0043931 name: ossification involved in bone maturation namespace: biological_process def: "The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone, involved in the progression of the skeleton from its formation to its mature state." [GOC:dph, GOC:mah, GOC:mtg_mpo] synonym: "ossification involved in bone modeling" NARROW [GO_REF:0000034] synonym: "ossification involved in skeletal development" EXACT [GOC:dph] is_a: GO:0001503 ! ossification relationship: part_of GO:0070977 ! bone maturation [Term] id: GO:0060348 name: bone development namespace: biological_process def: "The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components." [GOC:dph] is_a: GO:0008150 ! biological_process [Term] id: GO:0060349 name: bone morphogenesis namespace: biological_process def: "The process in which bones are generated and organized." [GOC:dph] is_a: GO:0008150 ! biological_process [Term] id: GO:0060350 name: endochondral bone morphogenesis namespace: biological_process def: "The process in which bones are generated and organized as a result of the conversion of initial cartilaginous anlage into bone." [GOC:dph, PMID:11680679] is_a: GO:0060349 ! bone morphogenesis [Term] id: GO:0070977 name: bone maturation namespace: biological_process def: "A developmental process, independent of morphogenetic (shape) change, that is required for bone to attain its fully functional state." [GOC:dph, GOC:mah] is_a: GO:0008150 ! biological_process relationship: part_of GO:0060348 ! bone development [Term] id: PATO:0000001 name: quality namespace: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities." [PATOC:GVG] synonym: "trait" EXACT [] [Term] id: PATO:0001448 name: ossified def: "A composition quality inhering in an bearer by virtue of the bearer's being hardened by the deposition of calcium into bone." [MAMMALOGY:MAMMALOGY] is_a: PATO:0000001 ! quality [Term] id: PATO:0001449 name: cartilaginous def: "A composition quality inhering in an bearer by virtue of the bearer's cartilage quantities." [Wikipedia:http://en.wikipedia.org/wiki/Cartilaginous] comment: Cartilage is a type of dense connective tissue. It is composed of specialized cells called chondrocytes (CL:0000138) that produce a large amount of extracellular matrix composed of collagen fibers, abundant ground substance rich in proteoglycan, and elastin fibers is_a: PATO:0000001 ! quality [Term] id: VSAO:0000000 name: cartilage element def: "Skeletal element that is composed of cartilage tissue and may be permanent or transient." [GO_REF:0000034] synonym: "cartilage" RELATED [] synonym: "cartilaginous element" EXACT [] synonym: "chondrogenic element" EXACT [] is_a: VSAO:0000128 ! skeletal element intersection_of: VSAO:0000128 ! skeletal element intersection_of: develops_from VSAO:0000092 ! chondrogenic condensation intersection_of: has_part VSAO:0000040 ! cartilage tissue intersection_of: part_of VSAO:0000037 ! endoskeleton relationship: develops_from VSAO:0000092 ! chondrogenic condensation relationship: has_part VSAO:0000040 ! cartilage tissue relationship: part_of VSAO:0000037 ! endoskeleton [Term] id: VSAO:0000001 name: surface structure def: "Organism subdivision which is the collection of anatomical structures on the body surface." [ZFIN:curator] is_a: CARO:0000032 ! organism subdivision [Term] id: VSAO:0000002 name: mode of ossification def: "The formation of bone or of a bony substanc, or the conversion of fibrous tissue or of cartilage into bone or a bony substance." [GOC:mtg_mpo\, PMID:17572649] xref: GO:0001503 is_obsolete: true replaced_by: GO:0001503 [Term] id: VSAO:0000003 name: permanent cartilage def: "Chondrogenic element that is composed of cartilage that is not replaced." [GO_REF:0000034] is_a: VSAO:0000000 ! cartilage element [Term] id: VSAO:0000004 name: opercle bone def: "Dermal bone that forms the postero-dorsal part of the opercular series. The opercle articulates with the hyomandibula antero-dorsally and with the subopercle ventrally. The opercle is a paired bone." [TAO:curator] comment: Term resides in TAO. is_obsolete: true replaced_by: TAO:0000250 [Term] id: VSAO:0000005 name: basihyal element comment: Term resides in TAO. is_obsolete: true replaced_by: TAO:0001891 [Term] id: VSAO:0000006 name: cell condensation def: "Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995)." [GO_REF:0000034] is_a: CARO:0000003 ! anatomical structure [Term] id: VSAO:0000007 name: basihyal bone def: "Endochondral bone that is median and is the anterior-most bone of the ventral hyoid arch." [TAO:curator] comment: Term resides in TAO. is_obsolete: true replaced_by: TAO:0000316 [Term] id: VSAO:0000008 name: neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [VSAO:curator] xref: CL:0000333 is_obsolete: true replaced_by: CL:0000333 [Term] id: VSAO:0000009 name: notochordal cell def: "Cell of the notochord, often vacuolated or resembles a chondrocyte." [VSAO:curator] is_obsolete: true replaced_by: CL:0007005 [Term] id: VSAO:0000010 name: notochordal mesodermal cell is_obsolete: true replaced_by: CL:0007006 [Term] id: VSAO:0000011 name: mesodermal cell def: "Cell derived from mesoderm." [VSAO:curator] xref: CL:0000222 is_obsolete: true replaced_by: CL:0000222 [Term] id: VSAO:0000012 name: skeletogenic cell def: "Cell that has the potential to form a skeletal cell type (e.g., cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized)." [VSAO:curator] is_obsolete: true replaced_by: CL:0007001 [Term] id: VSAO:0000013 name: mineralized tissue is_a: VSAO:0000015 ! skeletal tissue [Term] id: VSAO:0000014 name: basihyal cartilage def: "Pharyngeal arch cartilage that is median and is the anterior-most cartilage of the ventral hyoid arch." [TAO:curator] comment: Term resides in TAO. is_obsolete: true replaced_by: TAO:0001510 [Term] id: VSAO:0000015 name: skeletal tissue def: "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support." [GO_REF:0000034] is_a: VSAO:0000017 ! connective tissue relationship: develops_from CL:0007001 ! skeletogenic cell [Term] id: VSAO:0000016 name: basihyal condensation is_obsolete: true [Term] id: VSAO:0000017 name: connective tissue def: "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance." [GO_REF:0000034] synonym: "portion of connective tissue" EXACT [] is_a: CARO:0000043 ! tissue [Term] id: VSAO:0000018 name: ventral hyoid arch comment: Term resides in TAO. is_obsolete: true replaced_by: TAO:0001402 [Term] id: VSAO:0000019 name: chordablast def: "Epithelial cell that is large, vacuolated, and part of the notochord." [VSAO:curator] is_obsolete: true replaced_by: CL:0007008 [Term] id: VSAO:0000020 name: mineralized extracellular matrix def: "Extracellular matrix that is mineralized." [GO_REF:0000034] is_a: VSAO:0000021 ! proteinaceous extracellular matrix [Term] id: VSAO:0000021 name: proteinaceous extracellular matrix def: "A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus. [GOC:mtg_sensu, ISBN:0198547684]." [GO:[GOC:mtg_sensu\, ISBN:0198547684\], GO_REF:0000034, VSAO:curator] is_a: VSAO:0000022 ! extracellular matrix [Term] id: VSAO:0000022 name: extracellular matrix def: "Combination of protein fibers, ground substance and tissue fluid; typically has embedded cells." [GO_REF:0000034] synonym: "ECM" EXACT [VSAO:curator] is_a: CARO:0000040 ! acellular anatomical structure [Term] id: VSAO:0000023 name: membrane bone def: "Bone element that arises as a result of intramembranous ossification." [GO_REF:0000034] is_a: VSAO:0000057 ! bone element intersection_of: VSAO:0000057 ! bone element intersection_of: participates_in GO:0001957 ! intramembranous ossification relationship: participates_in GO:0001957 ! intramembranous ossification [Term] id: VSAO:0000024 name: intercalar def: "Small membrane bone homologous with a cartilage bone in more basal fishes (Patterson, 1977). Situated between the exoccipital and the pterotic at point of attachment of short ligament that originates on the ventral arm of the posttemporal." [TAO:curator] comment: Term resides in TAO. is_obsolete: true replaced_by: TAO:0000474 [Term] id: VSAO:0000025 name: odontogenic papilla def: "Cell condensation that is a well-defined population of densely organized mesenchymal cells that aggregates adjacent to an epithelium." [GO_REF:0000034] synonym: "dental papilla" EXACT [VSAO:curator] synonym: "odontogenic condensation" EXACT [VSAO:curator] is_a: VSAO:0000006 ! cell condensation [Term] id: VSAO:0000026 name: skeleton def: "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body." [GO_REF:0000034] is_a: CARO:0000041 ! anatomical cluster relationship: part_of VSAO:0000027 ! skeletal system [Term] id: VSAO:0000027 name: skeletal system def: "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system." [GO_REF:0000034] is_a: CARO:0000011 ! anatomical system relationship: part_of VSAO:0000031 ! musculoskeletal system [Term] id: VSAO:0000028 name: integumentary papilla def: "Odontogenic papilla that is located in the integument." [GO_REF:0000034] synonym: "scale papilla" EXACT [VSAO:curator] is_a: VSAO:0000025 ! odontogenic papilla relationship: has_location VSAO:0000029 ! integument [Term] id: VSAO:0000029 name: integument def: "Surface structure that is the outer protective covering of the body." [GO_REF:0000034] is_a: VSAO:0000001 ! surface structure [Term] id: VSAO:0000030 name: oropharyngeal papilla def: "Odontogenic papilla located along the jaws or pharyngeal skeleton." [GO_REF:0000034] synonym: "oropharyngeal dental papilla" EXACT [VSAO:curator] is_a: VSAO:0000025 ! odontogenic papilla relationship: has_location VSAO:0000034 ! oropharynx [Term] id: VSAO:0000031 name: musculoskeletal system def: "Anatomical system that consists of the muscular and skeletal systems." [VSAO:curator] is_a: CARO:0000011 ! anatomical system [Term] id: VSAO:0000032 name: notochord def: "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue." [GO_REF:0000034] is_a: CARO:0000055 ! multi-tissue structure [Term] id: VSAO:0000033 name: muscular system def: "Anatomical system that consists of the muscles of the body." [VSAO:curator] synonym: "musculature system" EXACT [VSAO:curator] is_a: CARO:0000011 ! anatomical system relationship: part_of VSAO:0000031 ! musculoskeletal system [Term] id: VSAO:0000034 name: oropharynx is_a: CARO:0000041 ! anatomical cluster [Term] id: VSAO:0000035 name: dermal skeleton def: "Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements." [GO_REF:0000034] synonym: "dermal skeletal system" RELATED [VSAO:curator] synonym: "dermoskeleton" RELATED [VSAO:curator] synonym: "desmoskeleton" RELATED [VSAO:curator] synonym: "exoskeleton" RELATED [VSAO:curator] is_a: VSAO:0000042 ! skeletal subdivision [Term] id: VSAO:0000036 name: perichondrium def: "Fibrous connective tissue that surrounds cartilage." [GO_REF:0000034] is_a: VSAO:0000017 ! connective tissue [Term] id: VSAO:0000037 name: endoskeleton def: "Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues." [GO_REF:0000034] synonym: "replacement skeleton" EXACT [VSAO:curator] is_a: VSAO:0000042 ! skeletal subdivision [Term] id: VSAO:0000038 name: preameloblast def: "Skeletogenic cell that has the potential to develop into an ameloblast." [VSAO:curator] is_obsolete: true replaced_by: CL:0007000 [Term] id: VSAO:0000039 name: chordoblast def: "Skeletogenic cell that is derived from the notochordal mesoderm and produces notochordal tissue (and cartilage tissue in some taxa)." [VSAO:curator] is_obsolete: true replaced_by: CL:0007008 [Term] id: VSAO:0000040 name: cartilage tissue def: "Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts." [GO_REF:0000034] synonym: "cartilage" RELATED [VSAO:curator] synonym: "chondrogenic tissue" EXACT [VSAO:curator] is_a: VSAO:0000015 ! skeletal tissue relationship: part_of VSAO:0000037 ! endoskeleton [Term] id: VSAO:0000041 name: preodontoblast def: "Skeletogenic cell that has the potential to form an odontoblast, deposits predentine, and arises from a neural crest cell." [VSAO:curator] is_obsolete: true replaced_by: CL:0007003 [Term] id: VSAO:0000042 name: skeletal subdivision def: "Anatomical cluster consisting of the skeletal elements that are part of the skeleton." [VSAO:curator] is_a: CARO:0000041 ! anatomical cluster relationship: part_of VSAO:0000026 ! skeleton [Term] id: VSAO:0000043 name: precementoblast def: "Skeletogenic cell that has the potential to develop into a cementoblast." [VSAO:curator] is_obsolete: true replaced_by: CL:0007002 [Term] id: VSAO:0000044 name: prechondroblast def: "Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells." [VSAO:curator] is_obsolete: true replaced_by: CL:0007009 [Term] id: VSAO:0000045 name: preosteoblast def: "Skeletogenic cell that has the potential to transform into an osteoblast, and develops from neural crest or mesodermal cells." [VSAO:curator] is_obsolete: true replaced_by: CL:0007010 [Term] id: VSAO:0000046 name: osteoid def: "Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue." [GO_REF:0000034] synonym: "pre-bone" EXACT [GO_REF:0000034] synonym: "prebone" EXACT [VSAO:curator] is_a: VSAO:0000021 ! proteinaceous extracellular matrix is_a: VSAO:0000047 ! bone tissue [Term] id: VSAO:0000047 name: bone tissue def: "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." [GO_REF:0000034] synonym: "bone" RELATED [VSAO:curator] synonym: "osteogenic tissue" EXACT [VSAO:curator] is_a: VSAO:0000015 ! skeletal tissue relationship: part_of VSAO:0000035 ! dermal skeleton relationship: part_of VSAO:0000037 ! endoskeleton relationship: part_of VSAO:0000057 ! bone element [Term] id: VSAO:0000048 name: scale relationship: part_of VSAO:0000026 ! skeleton [Term] id: VSAO:0000049 name: cranial skeleton def: "Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus." [GO_REF:0000034] is_a: VSAO:0000042 ! skeletal subdivision relationship: part_of VSAO:0000056 ! axial skeleton [Term] id: VSAO:0000050 name: dense regular connective tissue def: "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts)." [GO_REF:0000034] is_a: VSAO:0000017 ! connective tissue [Term] id: VSAO:0000051 name: lepidosteoid scale def: "Multi-layer ganoid scale composed of ganoine and cellular bone." [GO_REF:0000034] is_a: VSAO:0000052 ! ganoid scale [Term] id: VSAO:0000052 name: ganoid scale def: "Thick, rhomboid-shaped integumentary skeletal element composed of multiple tissues including ganoine and bone." [GO_REF:0000034] is_a: VSAO:0000048 ! scale [Term] id: VSAO:0000053 name: vacuolated notochordal tissue def: "Connective tissue that is matrix-poor with large number of vacuolated cells." [GO_REF:0000034] synonym: "notochord proper" EXACT [VSAO:curator] is_a: VSAO:0000017 ! connective tissue relationship: part_of VSAO:0000032 ! notochord [Term] id: VSAO:0000054 name: perichordal tissue def: "Fibrous connective tissue that surrounds the notochord; includes a layer of elastin." [GO_REF:0000034] comment: Derived from cells surrounding the notochord (possibly the slerotome). Disparate from (not derived from) notochord. synonym: "notochord" RELATED [VSAO:curator] synonym: "perichordal connective tissue" EXACT [VSAO:curator] synonym: "perichordal sheath" EXACT [VSAO:curator] synonym: "perichordal sheath tissue" EXACT [VSAO:curator] is_a: VSAO:0000017 ! connective tissue relationship: part_of VSAO:0000032 ! notochord [Term] id: VSAO:0000055 name: polypteroid scale def: "Multi-tissue structure composed of ganoine, dentine, elasmodine and cellular bone." [GO_REF:0000034] synonym: "polypterid scale" EXACT [VSAO:curator] is_a: VSAO:0000052 ! ganoid scale [Term] id: VSAO:0000056 name: axial skeleton def: "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum." [GO_REF:0000034] synonym: "axial skeletal system" EXACT [VSAO:curator] is_a: VSAO:0000042 ! skeletal subdivision [Term] id: VSAO:0000057 name: bone element def: "Skeletal element that is composed of bone tissue." [GO_REF:0000034] synonym: "bone" RELATED [] synonym: "bone organ" EXACT [] is_a: VSAO:0000128 ! skeletal element intersection_of: VSAO:0000128 ! skeletal element intersection_of: has_part VSAO:0000047 ! bone tissue relationship: has_part VSAO:0000047 ! bone tissue [Term] id: VSAO:0000058 name: chondroblast def: "Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell." [VSAO:curator] xref: CL:0000058 is_obsolete: true replaced_by: CL:0000058 [Term] id: VSAO:0000059 name: avascular GAG-rich matrix def: "Proteinaceous extracellular matrix that is avascular and consists primarily of glycosaminoglycans." [GO_REF:0000034] synonym: "avascular glycosaminoglycan-rich matrix" EXACT [VSAO:curator] synonym: "cartilage matrix" EXACT [VSAO:curator] synonym: "cartilage-like matrix" EXACT [VSAO:curator] is_a: VSAO:0000021 ! proteinaceous extracellular matrix [Term] id: VSAO:0000060 name: osteoblast def: "Skeletogenic cell that secretes osteoid, is capable of producing mineralized (hydroxyapatite) matrix, is located adjacent to or within osteoid tissue, and arises from the transformation of a preosteoblast cell." [VSAO:curator] xref: CL:0000062 is_obsolete: true replaced_by: CL:0000062 [Term] id: VSAO:0000061 name: cementoblast def: "Skeletogenic cell that produces cementum (= bone of attachment), is part of the odontogenic papilla, and develops from a precementoblast cell." [VSAO:curator] xref: CL:0000061 is_obsolete: true replaced_by: CL:0000061 [Term] id: VSAO:0000062 name: cementum def: "Odontoid tissue that is deposited by cementoblasts onto dentine tissue and functions to attach teeth, odontodes and other odontogenic derivatives to bone tissue and the integument." [GO_REF:0000034] synonym: "bone of attachment" EXACT [VSAO:curator] is_a: VSAO:0000063 ! odontoid tissue [Term] id: VSAO:0000063 name: odontoid tissue def: "Skeletal tissue that is part of the exoskeleton and derived from an odontogenic papilla." [GO_REF:0000034] synonym: "dental tissue" RELATED [VSAO:curator] synonym: "odontogenic tissue" EXACT [VSAO:curator] is_a: VSAO:0000015 ! skeletal tissue relationship: develops_from VSAO:0000025 ! odontogenic papilla relationship: part_of VSAO:0000035 ! dermal skeleton [Term] id: VSAO:0000064 name: ameloblast def: "Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell." [VSAO:curator] xref: CL:0000059 is_obsolete: true replaced_by: CL:0000059 [Term] id: VSAO:0000065 name: enamel def: "Skeletal tissue that consists of an avascular, noncollagenous, hypermineralized matrix that is deposited by ameloblasts that are excluded from the matrix. Enamel develops from organic pre-enamel tissue that is replaced by a largely inorganic matrix." [GO_REF:0000034] synonym: "enamel tissue" EXACT [VSAO:curator] is_a: VSAO:0000063 ! odontoid tissue relationship: develops_from VSAO:0000066 ! pre-enamel [Term] id: VSAO:0000066 name: pre-enamel def: "Odontogenic tissue that is avascular non-mineralized matrix that is deposited by preameloblast and ameloblasts that are excluded from the matrix." [GO_REF:0000034] synonym: "pre-enamel tissue" EXACT [VSAO:curator] synonym: "preenamel tissue" EXACT [VSAO:curator] is_a: VSAO:0000063 ! odontoid tissue [Term] id: VSAO:0000067 name: paired appendage is_a: VSAO:0000075 ! appendage [Term] id: VSAO:0000068 name: odontoblast def: "Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell." [VSAO:curator] xref: CL:0000060 is_obsolete: true replaced_by: CL:0000060 [Term] id: VSAO:0000069 name: dentine def: "Collagen-rich odontogenic tissue characteristic of teeth and tooth-like skeletal elements (e.g., odontodes); mature dentine is mineralized and develops from predentine tissue; often (but not always) tubular and acellular." [GO_REF:0000034] synonym: "dental tissue" EXACT [VSAO:curator] is_a: VSAO:0000063 ! odontoid tissue relationship: develops_from VSAO:0000071 ! pre-dentine [Term] id: VSAO:0000070 name: elasmoid scale def: "Multi-tissue integumentary element composed dentine, elasmodine, and hypermineralized tissue." [GO_REF:0000034] is_a: VSAO:0000048 ! scale relationship: has_part VSAO:0000069 ! dentine [Term] id: VSAO:0000071 name: pre-dentine def: "Odontogenic tissue that is collagen-rich and characteristic of vertebrate teeth and tooth-like structures (e.g., odontodes) deposited by preodontoblasts and odontoblasts that are typically excluded from the matrix." [GO_REF:0000034] synonym: "pre-dentine tissue" EXACT [VSAO:curator] synonym: "predentine tissue" EXACT [VSAO:curator] is_a: VSAO:0000063 ! odontoid tissue [Term] id: VSAO:0000072 name: ligament def: "Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ." [GO_REF:0000034] is_a: VSAO:0000050 ! dense regular connective tissue [Term] id: VSAO:0000073 name: tendon def: "Dense regular connective tissue that connects muscle to bone." [GO_REF:0000034] is_a: VSAO:0000050 ! dense regular connective tissue [Term] id: VSAO:0000074 name: palaeoniscoid scale def: "Multi-tissue structure composed of ganoine, dentine and bone; not known in extant taxa." [GO_REF:0000034] synonym: "Palaeoniscus-type scale" EXACT [VSAO:curator] is_a: VSAO:0000052 ! ganoid scale [Term] id: VSAO:0000075 name: appendage is_a: CARO:0000032 ! organism subdivision [Term] id: VSAO:0000076 name: appendicular skeleton def: "Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes." [GO_REF:0000034, UBERON:cjm] synonym: "appendicular skeletal system" RELATED [VSAO:curator] is_a: VSAO:0000042 ! skeletal subdivision relationship: part_of VSAO:0000214 ! appendage/girdle complex relationship: part_of VSAO:0000306 ! appendicular skeletal system [Term] id: VSAO:0000077 name: non-mineralized chondroid tissue is_a: VSAO:0000015 ! skeletal tissue [Term] id: VSAO:0000078 name: chondroid tissue def: "Skeletal tissue that is mineralized, has large chondrocyte-like cells, sparse extracellular matrix, and minimal perichondrium; develops from non-mineralized chondroid tissue." [GO_REF:0000034, TAO:curator] synonym: "chondroid bone tissue" EXACT [VSAO:curator] is_a: VSAO:0000015 ! skeletal tissue relationship: develops_from VSAO:0000077 ! non-mineralized chondroid tissue [Term] id: VSAO:0000079 name: odontode scale def: "Multi-tissue structure composed of enameloid, dentine surrounding a pulp cavity, and bone of attachment anchoring the element into the dermis." [GO_REF:0000034] synonym: "placoid scale" EXACT [VSAO:curator] is_a: VSAO:0000048 ! scale [Term] id: VSAO:0000080 name: keratin-based scale def: "Fold or elevation of the epidermis rich in keratin proteins; possibly calcified but does not contain skeletal elements." [GO_REF:0000034] is_a: VSAO:0000048 ! scale [Term] id: VSAO:0000081 name: cosmoid scale def: "Multi-tissue integumentary element composed of enamel or enameloid, dentine and lamellar bone, and characterized by pore-canal system." [GO_REF:0000034] is_a: VSAO:0000048 ! scale [Term] id: VSAO:0000082 name: craniofacial skeleton def: "Cranial skeleton derived from neural crest cells." [GO_REF:0000034] synonym: "Cranio-facial skeleton" EXACT [VSAO:curator] is_a: VSAO:0000049 ! cranial skeleton relationship: has_location VSAO:0000083 ! craniofacial region [Term] id: VSAO:0000083 name: craniofacial region is_a: CARO:0000041 ! anatomical cluster [Term] id: VSAO:0000084 name: cementocyte def: "Skeletogenic cell that produces cementum, is part of the odontogenic papilla, and is a transformation of a cementoblast cell." [VSAO:curator] xref: CL:0000141 is_obsolete: true replaced_by: CL:0000141 [Term] id: VSAO:0000085 name: chondrocyte def: "Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell." [VSAO:curator] xref: CL:0000138 is_obsolete: true replaced_by: CL:0000138 [Term] id: VSAO:0000086 name: secondary cartilage tissue def: "Cartilage tissue that is part of the exoskeleton, deposited adjacent to bone after bone formation." [GO_REF:0000034] is_a: VSAO:0000040 ! cartilage tissue relationship: part_of VSAO:0000035 ! dermal skeleton [Term] id: VSAO:0000087 name: cosmine synonym: "cosmoid scale tissue" EXACT [GO_REF:0000034] is_a: VSAO:0000063 ! odontoid tissue [Term] id: VSAO:0000088 name: mineralized cartilage tissue def: "Cartilage tissue that is mineralized." [GO_REF:0000034] is_a: VSAO:0000040 ! cartilage tissue [Term] id: VSAO:0000089 name: non-mineralized cartilage tissue def: "Cartilage tissue that is not mineralized." [GO_REF:0000034] is_a: VSAO:0000040 ! cartilage tissue [Term] id: VSAO:0000090 name: integumentary skeleton def: "Skeletal subdivision that is part of the extra-oral dermal skeletal system that develops and remains invested within the integument, primarily the dermis." [GO_REF:0000034] is_a: VSAO:0000042 ! skeletal subdivision relationship: has_location VSAO:0000029 ! integument relationship: part_of VSAO:0000035 ! dermal skeleton [Term] id: VSAO:0000091 name: elastic cartilage tissue def: "Cartilage tissue that is flexible and contains abundant elastic fibers." [GO_REF:0000034] is_a: VSAO:0000089 ! non-mineralized cartilage tissue relationship: develops_from VSAO:0000092 ! chondrogenic condensation [Term] id: VSAO:0000092 name: chondrogenic condensation def: "Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes." [GO:curator] synonym: "cartilaginous condensation" EXACT [] is_a: VSAO:0000006 ! cell condensation [Term] id: VSAO:0000093 name: postcranial axial skeleton def: "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum." [GO_REF:0000034] is_a: VSAO:0000042 ! skeletal subdivision relationship: part_of VSAO:0000056 ! axial skeleton [Term] id: VSAO:0000094 name: hyaline cartilage tissue def: "Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance." [GO_REF:0000034] synonym: "hyaline cartilage" EXACT [VSAO:curator] is_a: VSAO:0000040 ! cartilage tissue [Term] id: VSAO:0000095 name: non-terminally differentiated odontoblast def: "Odontoblast that non-terminally differentiated, located in the odontogenic papilla and dentine tissue, and transforms from a odontoblast cell." [GO_REF:0000034] is_obsolete: true replaced_by: CL:00007012 [Term] id: VSAO:0000096 name: terminally differentiated odontoblast def: "Odontoblast that is terminally differentiated and derived from an odontogenic papilla and associated with dentine." [VSAO:curator] is_obsolete: true replaced_by: CL:00007013 [Term] id: VSAO:0000097 name: orthodentine def: "Odontoid tissue that typically contains tubules and is acellular." [GO_REF:0000034] is_a: VSAO:0000063 ! odontoid tissue [Term] id: VSAO:0000098 name: hypertrophic chondrocyte def: "Chondrocyte that is terminally differentiated, produces type X collagen, is large in size, and often associated with the replacement of cartilage by bone (endochondral ossification)." [VSAO:curator] xref: CL:0000743 is_obsolete: true replaced_by: CL:0000743 [Term] id: VSAO:0000099 name: fin def: "Surface structure involved in locomotion." [TAO:curator] xref: UBERON:0008897 is_a: VSAO:0000075 ! appendage [Term] id: VSAO:0000100 name: periarticular chondrocyte def: "Chondrocyte that is located on a joint surface; part of articular cartilage." [VSAO:curator] xref: CL:0000742 is_obsolete: true replaced_by: CL:0000742 [Term] id: VSAO:0000101 name: joint def: "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue." [GO_REF:0000034] synonym: "articulation" EXACT [] is_a: CARO:0000041 ! anatomical cluster [Term] id: VSAO:0000102 name: osteodentine is_a: VSAO:0000063 ! odontoid tissue [Term] id: VSAO:0000103 name: fibrocartilage def: "Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns." [GO_REF:0000034] is_a: VSAO:0000040 ! cartilage tissue [Term] id: VSAO:0000104 name: ganoine def: "Odontogenic tissue that is hypermineralized acellular, noncollagenous, covered by an epidermis and often deposited in multiple layers." [GO_REF:0000034] is_a: VSAO:0000063 ! odontoid tissue relationship: part_of VSAO:0000052 ! ganoid scale [Term] id: VSAO:0000105 name: limiting layer of elasmoid scale def: "Hypermineralized tissue lacking collagen (except Sharpey's fibres), developing in close proximity to the basal cells of the overlying epithelium." [GO_REF:0000034] relationship: part_of VSAO:0000070 ! elasmoid scale [Term] id: VSAO:0000106 name: vasodentine def: "Dentine tissue that lacks dentine tubules and that is penetrated by blood capillaries." [GO_REF:0000034] synonym: "vascular dentine" EXACT [VSAO:curator] is_a: VSAO:0000063 ! odontoid tissue [Term] id: VSAO:0000107 name: elasmodine def: "Odontogenic tissue that consists of multiple layers of collagen fibers organized in orthogonal or twisted arrangements." [GO_REF:0000034] is_a: VSAO:0000063 ! odontoid tissue relationship: part_of VSAO:0000070 ! elasmoid scale [Term] id: VSAO:0000108 name: non-mineralized hyaline cartilage tissue def: "Hyaline cartilage tissue that is not mineralized." [GO_REF:0000034] is_a: VSAO:0000089 ! non-mineralized cartilage tissue is_a: VSAO:0000094 ! hyaline cartilage tissue [Term] id: VSAO:0000109 name: mineralized hyaline cartilage tissue def: "Hyaline cartilage tissue that is mineralized." [GO_REF:0000034] is_a: VSAO:0000013 ! mineralized tissue is_a: VSAO:0000088 ! mineralized cartilage tissue is_a: VSAO:0000094 ! hyaline cartilage tissue relationship: develops_from VSAO:0000094 ! hyaline cartilage tissue [Term] id: VSAO:0000110 name: columnar chondrocyte def: "Chondrocyte that is linearly arranged with other columnar chondrocytes." [GO_REF:0000034] xref: CL:0000744 is_a: CL:0000138 ! chondrocyte [Term] id: VSAO:0000111 name: paired fin def: "Fin that is one of a pair located ventrally on the organism." [TAO:curator] synonym: "artioptérygie (French)" EXACT [PSPUB:0000140] synonym: "nageoire paire (French)" EXACT [PSPUB:0000164] xref: UBERON:0000151 is_a: VSAO:0000067 ! paired appendage is_a: VSAO:0000099 ! fin [Term] id: VSAO:0000112 name: odontocyte def: "Skeletogenic cell that secretes dentine matrix, is derived from odontogenic papilla. Embedded in dentine tissue, and is the transformation of a non-terminally differentiated odontoblast cell." [VSAO:curator] xref: CL:0000140 is_obsolete: true replaced_by: CL:0000140 [Term] id: VSAO:0000113 name: enameloid def: "Skeletal tissue that is hypermineralized and aprismatic and deposited by a combination of ameloblasts and odontoblasts that are excluded from the matrix. Enameloid develops from pre-enameloid tissue." [GO_REF:0000034] synonym: "bitypic enamel" EXACT [VSAO:curator] synonym: "durodentine" EXACT [VSAO:curator] synonym: "enameloid tissue" EXACT [VSAO:curator] synonym: "vitrodentine" EXACT [VSAO:curator] is_a: VSAO:0000063 ! odontoid tissue relationship: develops_from VSAO:0000114 ! pre-enameloid [Term] id: VSAO:0000114 name: pre-enameloid def: "Odontoid tissue that is avascular non-mineralized matrix that is deposited by odontoblasts and ameloblasts that are excluded from the matrix." [GO_REF:0000034] synonym: "non-mineralized enameloid tissue" EXACT [VSAO:curator] is_a: VSAO:0000063 ! odontoid tissue [Term] id: VSAO:0000115 name: mineralized bone tissue def: "Bone tissue mineralized with hydroxyapatite." [GO_REF:0000034] is_a: VSAO:0000013 ! mineralized tissue is_a: VSAO:0000047 ! bone tissue relationship: develops_from VSAO:0000046 ! osteoid relationship: part_of VSAO:0000020 ! mineralized extracellular matrix [Term] id: VSAO:0000116 name: terminally differentiated osteoblast def: "Osteoblast that is terminally differentiated, located adjacent to acellular or cellular bone tissue within periosteum, and is capable of mineralizing the matrix." [VSAO:curator] is_obsolete: true replaced_by: CL:0001039 [Term] id: VSAO:0000117 name: non-terminally differentiated osteoblast def: "Osteoblast that is non-terminally differentiated and located in cellular bone tissue or under the periosteum in acellular bone." [VSAO:curator] is_obsolete: true replaced_by: CL:0001040 [Term] id: VSAO:0000118 name: cellular bone tissue def: "Mineralized bone tissue that always includes non-terminally differentiated osteoblasts and osteocytes." [GO_REF:0000034] is_a: VSAO:0000115 ! mineralized bone tissue [Term] id: VSAO:0000119 name: non-mineralized avascular GAG-rich matrix def: "Avascular GAG-rich matrix that is not mineralized." [GO_REF:0000034] synonym: "non-mineralized cartilage" EXACT [VSAO:curator] is_a: VSAO:0000059 ! avascular GAG-rich matrix relationship: part_of VSAO:0000089 ! non-mineralized cartilage tissue [Term] id: VSAO:0000120 name: mineralized avascular GAG-rich matrix def: "Avascular GAG-rich matrix that is mineralized." [GO_REF:0000034] is_a: VSAO:0000020 ! mineralized extracellular matrix is_a: VSAO:0000059 ! avascular GAG-rich matrix relationship: part_of VSAO:0000088 ! mineralized cartilage tissue [Term] id: VSAO:0000121 name: free limb is_a: VSAO:0000067 ! paired appendage [Term] id: VSAO:0000122 name: acellular bone tissue def: "Mineralized bone tissue that has terminally differentiated osteoblasts but lacks osteocytes." [GO_REF:0000034] is_a: VSAO:0000115 ! mineralized bone tissue relationship: has_part CL:0001039 ! terminally differentiated osteoblast [Term] id: VSAO:0000123 name: odontode tissue def: "Skeletal tissue that is avascular tubular mineralized matrix, primarily made of dentine that is deposited by odontoblasts that are excluded from the matrix; develops from pre-dentine tissue." [GO_REF:0000034] synonym: "dental tissue" RELATED [VSAO:curator] is_a: VSAO:0000063 ! odontoid tissue relationship: develops_from VSAO:0000071 ! pre-dentine [Term] id: VSAO:0000124 name: osteocyte def: "Skeletogenic cell that secretes and is embedded in lacunae within mineralized bone matrix and that arises from the transformation of non-terminally differentiated osteoblasts. Interconnected with other osteocytes in lacunae by canaliculi." [VSAO:curator] xref: CL:0000137 is_obsolete: true replaced_by: CL:0000137 [Term] id: VSAO:0000125 name: pectoral appendage synonym: "anterior paired appendage" EXACT [] is_a: VSAO:0000067 ! paired appendage intersection_of: VSAO:0000067 ! paired appendage intersection_of: part_of VSAO:0000213 ! pectoral appendage/girdle complex relationship: part_of VSAO:0000213 ! pectoral appendage/girdle complex [Term] id: VSAO:0000126 name: pelvic appendage synonym: "posterior paired appendage" EXACT [] is_a: VSAO:0000067 ! paired appendage intersection_of: VSAO:0000067 ! paired appendage intersection_of: part_of VSAO:0000215 ! pelvic appendage/girdle complex relationship: part_of VSAO:0000215 ! pelvic appendage/girdle complex [Term] id: VSAO:0000127 name: gastralium def: "Dermal element that arises via intramembranous ossification and are developmentally distinct from true ribs that articulate with the vertebral column." [GO_REF:0000034] synonym: "abdominal rib" EXACT [VSAO:curator] synonym: "belly rib" EXACT [VSAO:curator] synonym: "gastralia" EXACT PLURAL [] is_a: VSAO:0000130 ! dermal bone [Term] id: VSAO:0000128 name: skeletal element def: "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages." [GO_REF:0000034] is_a: CARO:0000024 ! compound organ intersection_of: CARO:0000024 ! compound organ intersection_of: part_of VSAO:0000026 ! skeleton relationship: part_of VSAO:0000026 ! skeleton [Term] id: VSAO:0000129 name: pelvic fin def: "Paired fin located in the abdominal position of the body." [TAO:curator] synonym: "ischioptérygie (French)" EXACT [PSPUB:0000142] synonym: "nageoire pelvienne (French)" EXACT [PSPUB:0000164] xref: UBERON:0000152 is_a: VSAO:0000111 ! paired fin is_a: VSAO:0000126 ! pelvic appendage intersection_of: VSAO:0000111 ! paired fin intersection_of: part_of VSAO:0000215 ! pelvic appendage/girdle complex relationship: part_of VSAO:0000215 ! pelvic appendage/girdle complex [Term] id: VSAO:0000130 name: dermal bone def: "Skeletal element that forms superficially in the organism, usually in association with the ectoderm." [GO_REF:0000034] synonym: "dermal element" EXACT [VSAO:curator] synonym: "membrane bone" RELATED [VSAO:curator] is_a: VSAO:0000023 ! membrane bone relationship: part_of VSAO:0000035 ! dermal skeleton [Term] id: VSAO:0000131 name: appendicular ossicle def: "Ossicle that is part of the appendicular skeleton." [PSPUB:0000169] comment: Examples of appendicular ossicles include the patella and meniscus of the knee joint. is_a: VSAO:0000132 ! ossicle [Term] id: VSAO:0000132 name: ossicle def: "Skeletal element that is often isolated, small, and variable in composition." [PSPUB:0000169] comment: 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. is_a: VSAO:0000128 ! skeletal element [Term] id: VSAO:0000133 name: axial ossicle def: "Ossicle that is part of the axial skeleton." [PSPUB:0000169] comment: Examples of axial ossicles include the ossified tendons adjacent to the neural spines of the vertebral column. is_a: VSAO:0000132 ! ossicle [Term] id: VSAO:0000134 name: ossified tendon def: "Sesamoid that develops within a tendon, distal to an articulation or joint." [PSPUB:0000169] synonym: "intratendonous ossification" RELATED [] is_a: VSAO:0000137 ! sesamoid [Term] id: VSAO:0000135 name: replacement element def: "Skeletal element that forms as a replacement or substitution of another element or tissue." [GO_REF:0000034] is_a: VSAO:0000128 ! skeletal element intersection_of: VSAO:0000128 ! skeletal element intersection_of: participates_in GO:0036075 ! replacement ossification relationship: participates_in GO:0036075 ! replacement ossification [Term] id: VSAO:0000136 name: direct ossification def: "Ossification that does not require the replacement of pre-existing tissues, most often a cartilaginous model." [GO_REF:0000034] is_obsolete: true replaced_by: GO:0036072 [Term] id: VSAO:0000137 name: sesamoid def: "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." [PSPUB:0000169] comment: 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. is_a: VSAO:0000132 ! ossicle relationship: develops_in VSAO:0000050 ! dense regular connective tissue [Term] id: VSAO:0000138 name: ligamentous replacement element def: "Replacement element that forms as a replacement of a ligament." [GO_REF:0000034] is_a: VSAO:0000135 ! replacement element [Term] id: VSAO:0000139 name: endochondral element def: "A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification." [GO_REF:0000034] synonym: "endochondral replacement element" EXACT [] is_a: VSAO:0000135 ! replacement element intersection_of: VSAO:0000128 ! skeletal element intersection_of: participates_in GO:0001958 ! endochondral ossification relationship: participates_in GO:0001958 ! endochondral ossification [Term] id: VSAO:0000140 name: replacement ossification def: "Ossification that requires the replacement of a pre-existing tissue prior to bone tissue formation." [VSAO:curator] synonym: "indirect ossification" EXACT [] is_obsolete: true replaced_by: GO:0036075 [Term] id: VSAO:0000141 name: intramembranous ossification def: "Direct ossification that occurs within mesenchyme with the formation of an osteogenic condensation not associated with a perichondrium." [VSAO:curator] xref: GO:0001957 is_obsolete: true replaced_by: GO:0001957 [Term] id: VSAO:0000142 name: metaplastic ossification def: "Direct ossification in which transformation of the pre-existing tissue occurs without dedifferentiation of cells or reinitiation of cell division; direct transformation of a non-bone tissue into a bone tissue." [VSAO:curator] synonym: "metaplasia" EXACT [] is_obsolete: true replaced_by: GO:0036074 [Term] id: VSAO:0000143 name: endochondral ossification def: "Replacement ossification wherein bone tissue replaces cartilage." [VSAO:curator] is_obsolete: true replaced_by: GO:0001958 [Term] id: VSAO:0000144 name: perichondral ossification def: "Intramembranous ossification on the surface of a cartilage element as the perichondrium becomes a periosteum, without replacement of cartilage." [VSAO:curator] is_obsolete: true replaced_by: GO:0036073 [Term] id: VSAO:0000145 name: endochondral bone def: "Replacement bone that forms within cartilage." [GO_REF:0000034] synonym: "ossified chondrogenic bone" EXACT [] is_a: VSAO:0000057 ! bone element is_a: VSAO:0000139 ! endochondral element intersection_of: VSAO:0000057 ! bone element intersection_of: develops_from VSAO:0000000 ! cartilage element relationship: develops_from VSAO:0000000 ! cartilage element [Term] id: VSAO:0000146 name: transient cartilaginous element def: "Chondrogenic element that is composed of cartilage during development and has the potential to become replaced by another tissue." [GO_REF:0000034] synonym: "endochondral replacement cartilage" EXACT [] is_a: VSAO:0000000 ! cartilage element is_a: VSAO:0000139 ! endochondral element relationship: participates_in GO:0001958 ! endochondral ossification [Term] id: VSAO:0000147 name: pectoral fin def: "Paired fin that is located in the thoracic region of the body." [TAO:curator] synonym: "forefin" EXACT [] synonym: "nageoire pectorale (French)" EXACT [PSPUB:0000164] synonym: "omoptérygie (French)" EXACT [PSPUB:0000154] synonym: "thoracoptérygie (French)" EXACT [PSPUB:0000140] xref: UBERON:0000151 is_a: VSAO:0000111 ! paired fin is_a: VSAO:0000125 ! pectoral appendage intersection_of: VSAO:0000111 ! paired fin intersection_of: part_of VSAO:0000213 ! pectoral appendage/girdle complex relationship: part_of VSAO:0000213 ! pectoral appendage/girdle complex [Term] id: VSAO:0000148 name: forelimb synonym: "pectoral limb" EXACT [] is_a: VSAO:0000121 ! free limb is_a: VSAO:0000125 ! pectoral appendage intersection_of: VSAO:0000121 ! free limb intersection_of: part_of VSAO:0000213 ! pectoral appendage/girdle complex relationship: part_of VSAO:0000213 ! pectoral appendage/girdle complex [Term] id: VSAO:0000149 name: pharyngeal arch relationship: part_of VSAO:0000049 ! cranial skeleton [Term] id: VSAO:0000150 name: hindlimb synonym: "hind limb" EXACT [] synonym: "hind-limb" EXACT [] is_a: VSAO:0000121 ! free limb is_a: VSAO:0000126 ! pelvic appendage intersection_of: VSAO:0000121 ! free limb intersection_of: part_of VSAO:0000215 ! pelvic appendage/girdle complex relationship: part_of VSAO:0000215 ! pelvic appendage/girdle complex [Term] id: VSAO:0000151 name: forelimb skeleton is_a: VSAO:0000300 ! free limb skeleton relationship: part_of VSAO:0000148 ! forelimb [Term] id: VSAO:0000152 name: hindlimb skeleton synonym: "hind limb skeleton" EXACT [] synonym: "hind-limb skeleton" EXACT [] is_a: VSAO:0000300 ! free limb skeleton relationship: part_of VSAO:0000150 ! hindlimb [Term] id: VSAO:0000153 name: pectoral fin skeleton def: "Paired fin skeleton that consists of the supporting endochondral proximal and distal radials and the dermal fins rays or lepidotrichia. The pectoral fin skeleton is located in the thoracic region of the body and articulates with the scapula and coracoid." [TAO:curator] synonym: "forefin skeleton" EXACT [] is_a: VSAO:0000169 ! paired fin skeleton relationship: part_of VSAO:0000147 ! pectoral fin [Term] id: VSAO:0000154 name: pelvic fin skeleton def: "Paired fin skeleton located in the abdominal position that consists of supporting endochondral radials and dermal fin rays or lepidotrichia." [TAO:GA_TG] is_a: VSAO:0000169 ! paired fin skeleton relationship: part_of VSAO:0000129 ! pelvic fin [Term] id: VSAO:0000155 name: pelvic girdle skeleton def: "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." [UBERON:cjm] is_a: VSAO:0000302 ! girdle skeleton relationship: part_of VSAO:0000304 ! pelvic girdle region [Term] id: VSAO:0000156 name: pectoral girdle skeleton def: "Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature." [UBERON:cjm] is_a: VSAO:0000302 ! girdle skeleton relationship: part_of VSAO:0000305 ! pectoral girdle region [Term] id: VSAO:0000157 name: scapula is_a: VSAO:0000145 ! endochondral bone relationship: part_of VSAO:0000156 ! pectoral girdle skeleton [Term] id: VSAO:0000158 name: coracoid is_a: VSAO:0000145 ! endochondral bone relationship: part_of VSAO:0000156 ! pectoral girdle skeleton [Term] id: VSAO:0000159 name: ossified ligament def: "Sesamoid that develops within a ligament, distal to an articulation or joint." [GO_REF:0000034, PSPUB:0000169] is_a: VSAO:0000137 ! sesamoid [Term] id: VSAO:0000160 name: anocleithrum def: "Dermal bone of pectoral girdle that is dorsal to and articulates with the cleithrum." [VSAO:curator] comment: In sarcopterygians; analogous in position to postcleithrum in actinopterygians. synonym: "anocleithra" EXACT PLURAL [] is_a: VSAO:0000130 ! dermal bone relationship: part_of VSAO:0000156 ! pectoral girdle skeleton [Term] id: VSAO:0000161 name: interclavicle def: "Dermal bone of pectoral girdle that is median and ventral in position." [VSAO:curator] is_a: VSAO:0000130 ! dermal bone relationship: part_of VSAO:0000156 ! pectoral girdle skeleton [Term] id: VSAO:0000162 name: median fin def: "Fin that is an unpaired fin located in the sagittal plane of the organism." [TAO:curator] synonym: "nageoire impaire (French)" EXACT [PSPUB:0000164] synonym: "périssoptérygie (French)" EXACT [PSPUB:0000140] is_a: VSAO:0000099 ! fin [Term] id: VSAO:0000163 name: anal fin def: "Median fin that is located posterior to the anus." [TAO:curator] synonym: "nageoire anale (French)" EXACT [PSPUB:0000164] synonym: "proctoptère (French)" EXACT [PSPUB:0000136] synonym: "proctoptérygie (French)" EXACT [PAPUB:0000142, PSPUB:0000140] is_a: VSAO:0000162 ! median fin [Term] id: VSAO:0000164 name: caudal fin def: "The caudal fin is the most posterior median fin. It is composed of a complex of three modified centra and modified neural and hemal arches and spines. Mabee and Bird, 2001." [ZFIN:curator] synonym: "nageoire caudale (French)" EXACT [PSPUB:0000164] synonym: "tail" EXACT [] synonym: "tail fin" EXACT [] synonym: "uroptère (French)" EXACT [PSPUB:0000135] synonym: "uroptérygie (French)" EXACT [PSPUB:0000140] is_a: VSAO:0000162 ! median fin [Term] id: VSAO:0000165 name: dorsal fin def: "Median fin located on the dorsal surface of the organism." [TAO:curator] synonym: "nageoire dorsale (French)" EXACT [PSPUB:0000164] synonym: "notoptère (French)" EXACT [PSPUB:0000163] synonym: "notoptérygie (French)" EXACT [PSPUB:0000140] is_a: VSAO:0000162 ! median fin [Term] id: VSAO:0000166 name: anal fin skeleton def: "Median fin skeleton that is located posterior to the anus." [TAO:curator] is_a: VSAO:0000170 ! median fin skeleton relationship: part_of VSAO:0000163 ! anal fin [Term] id: VSAO:0000167 name: caudal fin skeleton def: "Median fin skeleton supporting the caudal fin." [TAO:curator] is_a: VSAO:0000170 ! median fin skeleton relationship: part_of VSAO:0000164 ! caudal fin [Term] id: VSAO:0000168 name: dorsal fin skeleton def: "Median fin skeleton located on the dorsal surface of the organism." [TAO:curator] is_a: VSAO:0000170 ! median fin skeleton relationship: part_of VSAO:0000165 ! dorsal fin [Term] id: VSAO:0000169 name: paired fin skeleton def: "Skeletal system that consists of the paired fins (pectoral or pelvic fins)." [TAO:curator] is_a: VSAO:0000301 ! limb/fin skeleton relationship: part_of VSAO:0000111 ! paired fin [Term] id: VSAO:0000170 name: median fin skeleton def: "Postcranial axial skeleton that is unpaired and located on the sagittal plane of the organism." [TAO:curator] synonym: "axial fin skeleton" EXACT [] synonym: "unpaired fin skeleton" EXACT [] is_a: VSAO:0000042 ! skeletal subdivision relationship: part_of VSAO:0000162 ! median fin [Term] id: VSAO:0000171 name: scapular complex def: "Skeletal subdivision of dermal bones that may include the anterolateral plate (AL), the spinal process (Sp), and anteroventral plate (AV) and other dermal bones that are part of the pectoral girdle." [VSAO:curator] comment: A scapular complex is described in placoderms (Goujet and Young, 1995). is_a: VSAO:0000042 ! skeletal subdivision relationship: part_of VSAO:0000156 ! pectoral girdle skeleton [Term] id: VSAO:0000172 name: lepidotrichium def: "Dermal bone that is rod-like, formed and usually contained in a fin membrane, and jointed to or adjacent to distal radials. Lepidotrichia are formed from paired hemitrichia surrounding actinotrichia. There are usually two more lepidotrichia than distal radials." [TAO:curator] synonym: "fin ray" EXACT [] is_a: VSAO:0000130 ! dermal bone [Term] id: VSAO:0000173 name: pelvic fin lepidotrichium def: "Lepidotrichium that is part of the pelvic fin skeleton." [TAO:curator] synonym: "pelvic fin lepidotrichia" EXACT PLURAL [] synonym: "pelvic fin ray" EXACT [] is_a: VSAO:0000172 ! lepidotrichium relationship: part_of VSAO:0000154 ! pelvic fin skeleton [Term] id: VSAO:0000174 name: caudal fin lepidotrichium def: "Lepidotrichium that is part of the caudal fin skeleton." [TAO:curator] synonym: "caudal fin ray" EXACT [] is_a: VSAO:0000172 ! lepidotrichium relationship: part_of VSAO:0000167 ! caudal fin skeleton [Term] id: VSAO:0000175 name: pectoral fin lepidotrichium def: "Lepidotrichium that is part of the pectoral fin skeleton." [TAO:curator] comment: Each pectoral lepidotrichium may be unsegmented (e.g., spine), segmented but unbranched (e.g., leading ray) or segmented and branched. Definition of lepidotrichium by Schultze and Arratia (1989: 217). For additional information about lepidotrichia see Arratia et al. 2001 and Arratia 2008. synonym: "pectoral fin lepidotrichia" EXACT PLURAL [] synonym: "pectoral fin ray" EXACT [] is_a: VSAO:0000172 ! lepidotrichium relationship: part_of VSAO:0000153 ! pectoral fin skeleton [Term] id: VSAO:0000176 name: anal fin lepidotrichium def: "Lepidotrichium that is part of the anal fin skeleton." [TAO:curator] synonym: "anal fin lepidotrichia" EXACT PLURAL [] synonym: "anal fin ray" EXACT [] is_a: VSAO:0000172 ! lepidotrichium relationship: part_of VSAO:0000166 ! anal fin skeleton [Term] id: VSAO:0000177 name: dorsal fin lepidotrichium def: "Lepidotrichium that is part of the dorsal fin skeleton." [TAO:curator] synonym: "dorsal fin lepidotrichia" EXACT PLURAL [] synonym: "dorsal fin ray" EXACT [] is_a: VSAO:0000172 ! lepidotrichium relationship: part_of VSAO:0000168 ! dorsal fin skeleton [Term] id: VSAO:0000178 name: embryonic structure def: "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells." [ZFIN:curator] is_a: CARO:0000003 ! anatomical structure [Term] id: VSAO:0000179 name: fin bud synonym: "fin buds" EXACT PLURAL [] is_a: VSAO:0000001 ! surface structure is_a: VSAO:0000178 ! embryonic structure [Term] id: VSAO:0000180 name: process def: "Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc." [TAO:curator] synonym: "bony projection" RELATED [] synonym: "flange" EXACT [] synonym: "flanges" EXACT PLURAL [] synonym: "lamella" EXACT [] synonym: "lamellae" EXACT PLURAL [] synonym: "lamina" EXACT [] synonym: "laminae" EXACT [] synonym: "processes" EXACT PLURAL [] synonym: "projection" EXACT [] synonym: "projections" EXACT PLURAL [] synonym: "ridge" EXACT [] synonym: "ridges" EXACT PLURAL [] synonym: "shelf" EXACT [] synonym: "shelves" EXACT PLURAL [] is_a: CARO:0000003 ! anatomical structure [Term] id: VSAO:0000181 name: articular system def: "Anatomical system that consists of all the joints of the body." [VSAO:curator] synonym: "joint system" EXACT [] is_a: VSAO:0000027 ! skeletal system [Term] id: VSAO:0000182 name: suprabranchial fin def: "Paired fin that is a bilaterally paired anterior outgrowth located high on the side of the animal, not far behind the orbit, with the posterior extremity corresponding with the expected posterior end of the branchial region." [PSPUB:0000172] comment: Suprabranchial fins are anterior outgrowths from the cephalothorax of thelodonts. Typically scale covered. They do not appear to contain skeletal tissues or elements. is_a: VSAO:0000111 ! paired fin [Term] id: VSAO:0000183 name: vertebral centrum def: "Skeletal element that surrounds the notochord." [VSAO:curator] comment: The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification. synonym: "centrum" EXACT [] is_a: VSAO:0000128 ! skeletal element relationship: part_of VSAO:0000184 ! vertebral element [Term] id: VSAO:0000184 name: vertebral element def: "Skeletal element that forms around the notochord and is part of the vertebral column." [TAO:curator] is_a: VSAO:0000128 ! skeletal element relationship: part_of VSAO:0000185 ! vertebral column [Term] id: VSAO:0000185 name: vertebral column def: "Anatomical cluster that consists of all the vertebra in the body." [VSAO:curator] is_a: VSAO:0000042 ! skeletal subdivision relationship: part_of VSAO:0000093 ! postcranial axial skeleton [Term] id: VSAO:0000186 name: femur def: "Endochondral longbone connecting the pelvic girdle with posterior zeugopodium." [VSAO:NI] is_a: VSAO:0000145 ! endochondral bone created_by: haendel creation_date: 2012-03-08T09:23:01Z [Term] id: VSAO:0000213 name: pectoral appendage/girdle complex def: "Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle." [VSAO:MAH] is_a: VSAO:0000214 ! appendage/girdle complex created_by: haendel creation_date: 2012-04-23T10:37:01Z [Term] id: VSAO:0000214 name: appendage/girdle complex def: "Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper." [GO_REF:0000034] comment: 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. is_a: CARO:0000054 ! anatomical group created_by: haendel creation_date: 2012-04-23T10:46:51Z [Term] id: VSAO:0000215 name: pelvic appendage/girdle complex def: "Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle." [VSAO:MAH] is_a: VSAO:0000214 ! appendage/girdle complex created_by: haendel creation_date: 2012-04-23T10:51:37Z [Term] id: VSAO:0000300 name: free limb skeleton def: "Skeletal subdivision that is part of the limb." [GO_REF:0000034] is_a: VSAO:0000301 ! limb/fin skeleton relationship: part_of VSAO:0000121 ! free limb created_by: haendel creation_date: 2012-06-26T07:29:11Z [Term] id: VSAO:0000301 name: limb/fin skeleton def: "Skeletal subdivision that is part of the paired limb/fin." [GO_REF:0000034] is_a: VSAO:0000042 ! skeletal subdivision relationship: part_of VSAO:0000076 ! appendicular skeleton created_by: haendel creation_date: 2012-06-26T07:42:15Z [Term] id: VSAO:0000302 name: girdle skeleton def: "Skeletal subdivision that is part of the appendage girdle region." [GO_REF:0000034] is_a: VSAO:0000042 ! skeletal subdivision relationship: part_of VSAO:0000076 ! appendicular skeleton created_by: haendel creation_date: 2012-06-26T09:34:08Z [Term] id: VSAO:0000303 name: appendage girdle region def: "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." [UBERON:cjm] is_a: CARO:0000032 ! organism subdivision created_by: haendel creation_date: 2012-06-26T09:36:49Z [Term] id: VSAO:0000304 name: pelvic girdle region def: "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." [UBERON:cjm] comment: Note that this class describes the central subdivision of the pelvic girdle complex, NOT the skeleton within. is_a: VSAO:0000303 ! appendage girdle region relationship: part_of VSAO:0000215 ! pelvic appendage/girdle complex created_by: haendel creation_date: 2012-06-26T09:40:03Z [Term] id: VSAO:0000305 name: pectoral girdle region def: "An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism." [UBERON:cjm] comment: Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within. is_a: VSAO:0000303 ! appendage girdle region relationship: part_of VSAO:0000213 ! pectoral appendage/girdle complex created_by: haendel creation_date: 2012-06-26T09:40:22Z [Term] id: VSAO:0000306 name: appendicular skeletal system def: "Skeletal system which consists of the appendicular skeleton plus associated joints." [UBERON:cjm] is_a: VSAO:0000027 ! skeletal system created_by: haendel creation_date: 2012-06-26T10:22:36Z [Term] id: VSAO:0000307 name: perichordal bone def: "Bone element that is adjacent to the notochord." [GO_REF:0000034] is_a: VSAO:0000057 ! bone element created_by: haendel creation_date: 2012-07-13T10:45:03Z [Term] id: VSAO:0000308 name: perichondral bone def: "Bone element that is located on the surface of a cartilage element." [GO_REF:0000034] is_a: VSAO:0000023 ! membrane bone intersection_of: VSAO:0000057 ! bone element intersection_of: participates_in GO:0036073 ! perichondral ossification relationship: participates_in GO:0036073 ! perichondral ossification created_by: haendel creation_date: 2012-07-13T10:46:34Z [Term] id: VSAO:0005007 name: stylopodial skeleton def: "Proximal element of the limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively." [VSAO:NI] synonym: "propodium" RELATED [] synonym: "stylopod" RELATED [] is_a: VSAO:0000042 ! skeletal subdivision relationship: part_of VSAO:0000300 ! free limb skeleton created_by: nizaribrahim creation_date: 2012-01-27T02:33:19Z [Term] id: VSAO:0005010 name: zeugopodial skeleton def: "Section of the forelimb skeleton located between the stylopodium and the autopodium." [VSAO:NI] synonym: "epipodium" EXACT [] synonym: "zygopodium" EXACT [] is_a: VSAO:0000042 ! skeletal subdivision relationship: part_of VSAO:0000300 ! free limb skeleton created_by: nizaribrahim creation_date: 2012-01-27T02:50:34Z [Term] id: VSAO:0005019 name: autopodial skeleton def: "Distal section of the limb skeleton, consisting of the anterior autopodium or posterior autopodium." [VSAO:NI] is_a: VSAO:0000042 ! skeletal subdivision relationship: part_of VSAO:0000300 ! free limb skeleton created_by: nizaribrahim creation_date: 2012-01-30T01:38:27Z [Term] id: VSAO:0005022 name: mesopodial skeleton def: "Limb skeleton subdivision consisting of endochondral bones increasing the freedom of movement of the autopodia, and located between zeugopodia and autopodia." [VSAO:NI] synonym: "basipodium" EXACT [] is_a: VSAO:0000042 ! skeletal subdivision relationship: part_of VSAO:0005019 ! autopodial skeleton created_by: nizaribrahim creation_date: 2012-01-30T01:45:41Z [Term] id: VSAO:0005025 name: metapodial skeleton def: "Endochondral bone complex located between the mesopodium and the acropodium and consisting of the metacarpals or metatarsals." [VSAO:NI] is_a: VSAO:0000042 ! skeletal subdivision relationship: part_of VSAO:0005019 ! autopodial skeleton created_by: nizaribrahim creation_date: 2012-01-30T01:58:58Z [Term] id: VSAO:0005028 name: acropodial skeleton def: "Endochondral terminal bones at the distalmost end of the autopodium, consisting of the phalanges." [VSAO:NI] comment: sometimes mistakenly used to include the metapodium xref: UBERON:0002254 is_a: VSAO:0000042 ! skeletal subdivision relationship: part_of VSAO:0005019 ! autopodial skeleton created_by: nizaribrahim creation_date: 2012-01-30T02:09:30Z [Typedef] id: OBO_REL:transformation_of name: transformation_of alt_id: OBO_REL:0000013 def: "Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2." [PMID:15892874] comment: When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes. is_transitive: true [Typedef] id: adjacent_to name: adjacent_to [Typedef] id: capable_of name: capable_of xref: RO:0002215 [Typedef] id: capable_of_producing name: capable_of_producing [Typedef] id: develops_from name: develops from xref: RO:0002202 is_transitive: true [Typedef] id: develops_in name: develops_in xref: RO:0002226 [Typedef] id: has_integral_part name: has_integral_part alt_id: OBO_REL:0000005 is_anti_symmetric: true is_reflexive: true is_transitive: true is_a: has_part ! has part inverse_of: integral_part_of ! integral_part_of [Typedef] id: has_location name: has_location [Typedef] id: has_part name: has part xref: BFO:0000051 is_transitive: true inverse_of: part_of ! part_of [Typedef] id: has_quality name: has_quality namespace: caro [Typedef] id: integral_part_of name: integral_part_of alt_id: OBO_REL:0000004 def: "C integral_part_of C' if and only if: C part_of C' AND C' has_part C" [PMID:15892874] is_anti_symmetric: true is_reflexive: true is_transitive: true is_a: part_of ! part_of [Typedef] id: overlaps name: overlaps xref: RO:0002131 [Typedef] id: part_of name: part_of comment: note that all the uses of part_of in this ontology are for proper part of xref: BFO:0000050 is_transitive: true [Typedef] id: participates_in name: participates in namespace: BFO xref: BFO:0000056 [Typedef] id: produces name: produces xref: RO:0003000