format-version: 1.2 data-version: 2011-09-20 date: 20:09:2011 16:17 saved-by: wasiladahdul auto-generated-by: OBO-Edit 2.1-beta16 synonymtypedef: PLURAL "PLURAL" default-namespace: vertebrate_anatomy treat-xrefs-as-equivalent: CL treat-xrefs-as-equivalent: GO [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] [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] 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] 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] 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] 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] is_a: CARO:0000000 ! anatomical entity [Term] id: CARO:0000008 name: anatomical line namespace: caro def: "Non-material anatomical entity of one dimension, which forms a boundary of an anatomical surface or is a modulation of an anatomical surface." [CARO:MAH] 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] 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] 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] 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] 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] is_a: CARO:0000003 ! anatomical structure relationship: part_of CARO:0000013 ! part_of 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 ! part_of 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] 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] 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: portion of tissue namespace: caro def: "Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships." [CARO:MAH] 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] is_a: CARO:0000043 ! portion of 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] is_a: CARO:0000073 ! unilaminar epithelium [Term] id: CARO:0000068 name: simple columnar epithlium namespace: caro def: "Unilaminar epithelium that consists of a single layer of columnar cells." [CARO:MAH] 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] 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] 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] 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: 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] [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 [Term] id: VAO:0000000 name: cartilaginous element def: "Skeletal element that is composed of cartilage tissue and may be permanent or transient." [VAO:curator] synonym: "chondrogenic element" EXACT [] is_a: VAO:0000128 ! skeletal element intersection_of: VAO:0000128 ! skeletal element intersection_of: OBO_REL:has_part VAO:0000040 ! has_part cartilage tissue relationship: has_quality PATO:0001449 ! has_quality cartilaginous relationship: OBO_REL:has_part VAO:0000040 ! has_part cartilage tissue relationship: develops_from VAO:0000092 ! develops_from chondrogenic condensation [Term] id: VAO: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: VAO:0000002 name: mode of ossification 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] xref: GO:0001503 [Term] id: VAO:0000003 name: permanent cartilage def: "Chondrogenic element that is composed of cartilage that is not replaced." [VAO:curator] comment: TODO: create logical definition with differentia has_quality PATO:permanent (term requested). is_a: VAO:0000000 ! cartilaginous element [Term] id: VAO: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] synonym: "opercles" EXACT [] synonym: "operculum" EXACT [] synonym: " operculare " EXACT [] xref: TAO:0000250 is_a: VAO:0000130 ! dermal bone [Term] id: VAO:0000005 name: basihyal element is_obsolete: true [Term] id: VAO: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)." [VAO:curator] is_a: CARO:0000003 ! anatomical structure [Term] id: VAO:0000007 name: basihyal bone def: "Endochondral bone that is median and is the anterior-most bone of the ventral hyoid arch." [TAO:curator] synonym: "basihyoid" EXACT [] synonym: "glossohyal" EXACT [] xref: TAO:0000316 is_obsolete: true [Term] id: VAO: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." [VAO:curator] xref: CL:0000333 is_a: CARO:0000013 ! cell [Term] id: VAO:0000009 name: notochordal cell def: "Cell of the notochord, often vacuolated or resembles a chondrocyte." [VAO:curator] is_a: CARO:0000013 ! cell relationship: develops_from VAO:0000010 ! develops_from notochordal mesodermal cell [Term] id: VAO:0000010 name: notochordal mesodermal cell is_a: VAO:0000011 ! mesodermal cell [Term] id: VAO:0000011 name: mesodermal cell def: "Cell derived from mesoderm." [VAO:curator] xref: CL:0000222 is_a: CARO:0000013 ! cell [Term] id: VAO: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)." [VAO:curator] is_a: CARO:0000013 ! cell relationship: produces VAO:0000020 ! produces mineralized extracellular matrix relationship: produces VAO:0000013 ! produces mineralized tissue [Term] id: VAO:0000013 name: mineralized tissue is_a: VAO:0000015 ! skeletal tissue [Term] id: VAO:0000014 name: basihyal cartilage def: "Pharyngeal arch cartilage that is median and is the anterior-most cartilage of the ventral hyoid arch." [TAO:curator] synonym: "copula 1" EXACT [] xref: TAO:0001510 is_obsolete: true [Term] id: VAO:0000015 name: skeletal tissue def: "Connective tissue that functions in mechanical and structural support." [VAO:curator] is_a: VAO:0000017 ! connective tissue relationship: develops_from VAO:0000012 ! develops_from skeletogenic cell [Term] id: VAO:0000016 name: basihyal condensation is_obsolete: true [Term] id: VAO:0000017 name: connective tissue def: "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance." [VAO:curator] synonym: "portion of connective tissue" EXACT [] is_a: CARO:0000043 ! portion of tissue [Term] id: VAO:0000018 name: ventral hyoid arch synonym: "ventral visceral arch 2" EXACT [] xref: TAO:0001402 is_obsolete: true [Term] id: VAO:0000019 name: chordablast def: "Epithelial cell that is large, vacuolated, and part of the notochord." [VAO:curator] is_a: CARO:0000077 ! epithelial cell relationship: OBO_REL:part_of VAO:0000032 ! part_of notochord [Term] id: VAO:0000020 name: mineralized extracellular matrix def: "Extracellular matrix that is mineralized." [VAO:curator] is_a: VAO:0000021 ! proteinaceous extracellular matrix [Term] id: VAO: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\], VAO:curator] is_a: VAO:0000022 ! extracellular matrix [Term] id: VAO:0000022 name: extracellular matrix def: "Combination of protein fibers, ground substance and tissue fluid; typically has embedded cells." [VAO:curator] synonym: "ECM" EXACT [VAO:curator] is_a: CARO:0000040 ! acellular anatomical structure [Term] id: VAO:0000023 name: membrane bone is_a: VAO:0000128 ! skeletal element relationship: participates_in VAO:0000136 ! participates_in direct ossification relationship: OBO_REL:has_part VAO:0000047 ! has_part bone tissue relationship: has_quality PATO:0001448 ! has_quality ossified [Term] id: VAO: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] synonym: "opisthotic" EXACT [] xref: TAO:0000474 is_obsolete: true [Term] id: VAO:0000025 name: odontogenic papilla def: "Cell condensation that is a well-defined population of densely organized mesenchymal cells that aggregates adjacent to an epithelium." [VAO:curator] synonym: "odontogenic condensation" EXACT [VAO:curator] synonym: "dental papilla" EXACT [VAO:curator] is_a: VAO:0000006 ! cell condensation [Term] id: VAO:0000026 name: skeleton is_a: CARO:0000041 ! anatomical cluster relationship: OBO_REL:part_of VAO:0000027 ! part_of skeletal system [Term] id: VAO:0000027 name: skeletal system def: "Multi-element, multi-tissue anatomical cluster." [VAO:curator] is_a: CARO:0000011 ! anatomical system relationship: OBO_REL:part_of VAO:0000031 ! part_of musculoskeletal system [Term] id: VAO:0000028 name: integumentary papilla def: "Odontogenic papilla that is located in the integument." [VAO:curator] synonym: "scale papilla" EXACT [VAO:curator] is_a: VAO:0000025 ! odontogenic papilla relationship: has_location VAO:0000029 ! has_location integument [Term] id: VAO:0000029 name: integument def: "Surface structure that is the outer protective covering of the body." [VAO:curator] is_a: VAO:0000001 ! surface structure [Term] id: VAO:0000030 name: oropharyngeal papilla def: "Odontogenic papilla located along the jaws or pharyngeal skeleton." [VAO:curator] synonym: "oropharyngeal dental papilla" EXACT [VAO:curator] is_a: VAO:0000025 ! odontogenic papilla relationship: has_location VAO:0000034 ! has_location oropharynx [Term] id: VAO:0000031 name: musculoskeletal system is_a: CARO:0000011 ! anatomical system [Term] id: VAO:0000032 name: notochord def: "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue." [VAO:curator] is_a: CARO:0000055 ! multi-tissue structure [Term] id: VAO:0000033 name: muscular system synonym: "musculature system" EXACT [VAO:curator] is_a: CARO:0000011 ! anatomical system relationship: OBO_REL:part_of VAO:0000031 ! part_of musculoskeletal system [Term] id: VAO:0000034 name: oropharynx is_a: CARO:0000041 ! anatomical cluster [Term] id: VAO:0000035 name: dermal skeleton def: "Skeletal system 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." [VAO:curator] synonym: "dermoskeleton" RELATED [VAO:curator] synonym: "exoskeleton" RELATED [VAO:curator] synonym: "desmoskeleton" RELATED [VAO:curator] synonym: "dermal skeletal system" RELATED [VAO:curator] is_a: CARO:0000041 ! anatomical cluster relationship: OBO_REL:part_of VAO:0000026 ! part_of skeleton [Term] id: VAO:0000036 name: perichondrium def: "Fibrous connective tissue that surrounds cartilage." [VAO:curator] is_a: VAO:0000017 ! connective tissue [Term] id: VAO:0000037 name: endoskeleton def: "Skeletal system that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues." [VAO:curator] synonym: "replacement skeleton" EXACT [VAO:curator] is_a: CARO:0000041 ! anatomical cluster relationship: OBO_REL:part_of VAO:0000026 ! part_of skeleton [Term] id: VAO:0000038 name: preameloblast def: "Skeletogenic cell that has the potential to develop into an ameloblast." [VAO:curator] is_a: VAO:0000012 ! skeletogenic cell relationship: develops_from VAO:0000008 ! develops_from neural crest cell relationship: overlies VAO:0000025 ! overlies odontogenic papilla [Term] id: VAO:0000039 name: chordoblast def: "Skeletogenic cell that is derived from the notochordal mesoderm and produces notochordal tissue (and cartilage tissue in some taxa)." [VAO:curator] is_a: VAO:0000012 ! skeletogenic cell relationship: produces VAO:0000040 ! produces cartilage tissue relationship: develops_from VAO:0000010 ! develops_from notochordal mesodermal cell [Term] id: VAO: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." [VAO:curator] synonym: "chondrogenic tissue" EXACT [VAO:curator] synonym: "cartilage" EXACT [VAO:curator] is_a: VAO:0000015 ! skeletal tissue relationship: OBO_REL:part_of VAO:0000037 ! part_of endoskeleton [Term] id: VAO:0000041 name: preodontoblast def: "Skeletogenic cell that has the potential to form an odontoblast, deposits predentine, and arises from a neural crest cell." [VAO:curator] is_a: VAO:0000012 ! skeletogenic cell relationship: develops_from VAO:0000008 ! develops_from neural crest cell relationship: OBO_REL:part_of VAO:0000025 ! part_of odontogenic papilla relationship: OBO_REL:part_of VAO:0000071 ! part_of pre-dentine relationship: produces VAO:0000071 ! produces pre-dentine [Term] id: VAO:0000043 name: precementoblast def: "Skeletogenic cell that has the potential to develop into a cementoblast." [VAO:curator] is_a: VAO:0000012 ! skeletogenic cell relationship: develops_from VAO:0000008 ! develops_from neural crest cell relationship: OBO_REL:part_of VAO:0000025 ! part_of odontogenic papilla [Term] id: VAO: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." [VAO:curator] is_a: VAO:0000012 ! skeletogenic cell relationship: develops_from VAO:0000011 ! develops_from mesodermal cell relationship: develops_from VAO:0000009 ! develops_from notochordal cell relationship: develops_from VAO:0000008 ! develops_from neural crest cell [Term] id: VAO:0000045 name: preosteoblast def: "Skeletogenic cell that has the potential to transform into an osteoblast, and develops from neural crest or mesodermal cells." [VAO:curator] is_a: VAO:0000012 ! skeletogenic cell relationship: develops_from VAO:0000008 ! develops_from neural crest cell relationship: develops_from VAO:0000011 ! develops_from mesodermal cell relationship: OBO_REL:part_of VAO:0000046 ! part_of osteoid [Term] id: VAO:0000046 name: osteoid def: "Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue." [VAO:curator] synonym: "prebone" EXACT [VAO:curator] synonym: "pre-bone" EXACT [VAO:curator] is_a: VAO:0000021 ! proteinaceous extracellular matrix is_a: VAO:0000047 ! bone tissue [Term] id: VAO: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." [VAO:curator] synonym: "osteogenic tissue" EXACT [VAO:curator] synonym: "bone" EXACT [VAO:curator] is_a: VAO:0000015 ! skeletal tissue relationship: OBO_REL:part_of VAO:0000035 ! part_of dermal skeleton relationship: OBO_REL:part_of VAO:0000037 ! part_of endoskeleton [Term] id: VAO:0000048 name: scale relationship: OBO_REL:part_of VAO:0000026 ! part_of skeleton [Term] id: VAO:0000049 name: cranial skeleton def: "Skeletal system of head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus." [VAO:curator] is_a: CARO:0000041 ! anatomical cluster relationship: OBO_REL:part_of VAO:0000056 ! part_of axial skeleton [Term] id: VAO: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)." [VAO:curator] is_a: VAO:0000017 ! connective tissue [Term] id: VAO:0000051 name: lepidosteoid scale def: "Multi-layer ganoid scale composed of ganoine and cellular bone." [VAO:curator] is_a: VAO:0000052 ! ganoid scale [Term] id: VAO:0000052 name: ganoid scale def: "Thick, rhomboid-shaped integumentary skeletal element composed of multiple tissues including ganoine and bone." [VAO:curator] is_a: VAO:0000048 ! scale [Term] id: VAO:0000053 name: vacuolated notochordal tissue def: "Connective tissue that is matrix-poor with large number of vacuolated cells." [VAO:curator] synonym: "notochord proper" EXACT [VAO:curator] is_a: VAO:0000017 ! connective tissue relationship: OBO_REL:part_of VAO:0000032 ! part_of notochord [Term] id: VAO:0000054 name: perichordal tissue def: "Fibrous connective tissue that surrounds the notochord; includes a layer of elastin." [VAO:curator] comment: Derived from cells surrounding the notochord (possibly the slerotome). Disparate from (not derived from) notochord. synonym: "perichordal sheath" EXACT [VAO:curator] synonym: "perichordal connective tissue" EXACT [VAO:curator] synonym: "perichordal sheath tissue" EXACT [VAO:curator] synonym: "notochord" RELATED [VAO:curator] is_a: VAO:0000017 ! connective tissue relationship: OBO_REL:part_of VAO:0000032 ! part_of notochord [Term] id: VAO:0000055 name: polypteroid scale def: "Multi-tissue structure composed of ganoine, dentine, elasmodine and cellular bone." [VAO:curator] synonym: "polypterid scale" EXACT [VAO:curator] is_a: VAO:0000052 ! ganoid scale [Term] id: VAO:0000056 name: axial skeleton def: "Anatomical cluster of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum." [VAO:curator] synonym: "axial skeletal system" EXACT [VAO:curator] is_a: CARO:0000041 ! anatomical cluster relationship: OBO_REL:part_of VAO:0000026 ! part_of skeleton [Term] id: VAO: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." [VAO:curator] xref: CL:0000058 is_a: VAO:0000012 ! skeletogenic cell relationship: produces VAO:0000059 ! produces avascular GAG-rich matrix relationship: develops_from VAO:0000044 ! develops_from prechondroblast relationship: OBO_REL:part_of VAO:0000040 ! part_of cartilage tissue relationship: produces VAO:0000040 ! produces cartilage tissue [Term] id: VAO:0000059 name: avascular GAG-rich matrix def: "Proteinaceous extracellular matrix that is avascular and consists primarily of glycosaminoglycans." [VAO:curator] synonym: "avascular glycosaminoglycan-rich matrix" EXACT [VAO:curator] synonym: "cartilage matrix" EXACT [VAO:curator] synonym: "cartilage-like matrix" EXACT [VAO:curator] is_a: VAO:0000021 ! proteinaceous extracellular matrix [Term] id: VAO: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." [VAO:curator] xref: CL:0000062 is_a: VAO:0000012 ! skeletogenic cell relationship: produces VAO:0000046 ! produces osteoid relationship: OBO_REL:transformation_of VAO:0000045 ! transformation_of preosteoblast relationship: capable_of_producing VAO:0000020 ! capable_of_producing mineralized extracellular matrix relationship: OBO_REL:part_of VAO:0000046 ! part_of osteoid [Term] id: VAO:0000061 name: cementoblast def: "Skeletogenic cell that produces cementum (= bone of attachment), is part of the odontogenic papilla, and develops from a precementoblast cell." [VAO:curator] xref: CL:0000061 is_a: VAO:0000012 ! skeletogenic cell relationship: develops_from VAO:0000043 ! develops_from precementoblast relationship: OBO_REL:part_of VAO:0000025 ! part_of odontogenic papilla relationship: produces VAO:0000062 ! produces cementum [Term] id: VAO: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." [VAO:curator] synonym: "bone of attachment" EXACT [VAO:curator] is_a: VAO:0000063 ! odontoid tissue [Term] id: VAO:0000063 name: odontoid tissue def: "Skeletal tissue that is part of the exoskeleton and derived from an odontogenic papilla." [VAO:curator] synonym: "odontogenic tissue" EXACT [VAO:curator] synonym: "dental tissue" RELATED [VAO:curator] is_a: VAO:0000015 ! skeletal tissue relationship: OBO_REL:part_of VAO:0000035 ! part_of dermal skeleton relationship: develops_from VAO:0000025 ! develops_from odontogenic papilla [Term] id: VAO:0000064 name: ameloblast def: "Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell." [VAO:curator] xref: CL:0000059 is_a: VAO:0000012 ! skeletogenic cell relationship: produces VAO:0000065 ! produces enamel relationship: OBO_REL:transformation_of VAO:0000038 ! transformation_of preameloblast relationship: overlies VAO:0000025 ! overlies odontogenic papilla relationship: produces VAO:0000066 ! produces pre-enamel [Term] id: VAO: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." [VAO:curator] synonym: "enamel tissue" EXACT [VAO:curator] is_a: VAO:0000063 ! odontoid tissue relationship: develops_from VAO:0000066 ! develops_from pre-enamel [Term] id: VAO: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." [VAO:curator] synonym: "pre-enamel tissue" EXACT [VAO:curator] synonym: "preenamel tissue" EXACT [VAO:curator] is_a: VAO:0000063 ! odontoid tissue [Term] id: VAO:0000068 name: odontoblast def: "Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell." [VAO:curator] xref: CL:0000060 is_a: VAO:0000012 ! skeletogenic cell relationship: OBO_REL:part_of VAO:0000069 ! part_of dentine relationship: produces VAO:0000071 ! produces pre-dentine relationship: produces VAO:0000069 ! produces dentine relationship: OBO_REL:part_of VAO:0000025 ! part_of odontogenic papilla relationship: develops_from VAO:0000041 ! develops_from preodontoblast [Term] id: VAO: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." [VAO:curator] synonym: "dental tissue" EXACT [VAO:curator] is_a: VAO:0000063 ! odontoid tissue relationship: develops_from VAO:0000071 ! develops_from pre-dentine [Term] id: VAO:0000070 name: elasmoid scale def: "Multi-tissue integumentary element composed dentine, elasmodine, and hypermineralized tissue." [VAO:curator] is_a: VAO:0000048 ! scale relationship: OBO_REL:has_part VAO:0000069 ! has_part dentine [Term] id: VAO: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." [VAO:curator] synonym: "predentine tissue" EXACT [VAO:curator] synonym: "pre-dentine tissue" EXACT [VAO:curator] is_a: VAO:0000063 ! odontoid tissue [Term] id: VAO:0000072 name: ligament def: "Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ." [VAO:curator] is_a: VAO:0000050 ! dense regular connective tissue [Term] id: VAO:0000073 name: tendon def: "Dense regular connective tissue that connects muscle to bone." [VAO:curator] is_a: VAO:0000050 ! dense regular connective tissue [Term] id: VAO:0000074 name: palaeoniscoid scale def: "Multi-tissue structure composed of ganoine, dentine and bone; not known in extant taxa." [VAO:curator] synonym: "Palaeoniscus-type scale" EXACT [VAO:curator] is_a: VAO:0000052 ! ganoid scale [Term] id: VAO:0000075 name: appendage is_a: CARO:0000041 ! anatomical cluster [Term] id: VAO:0000076 name: appendicular skeleton def: "Anatomical cluster consisting of the paired fin or limb skeletal appendages." [VAO:curator] synonym: "Appendicular skeletal system" EXACT [VAO:curator] is_a: CARO:0000041 ! anatomical cluster relationship: OBO_REL:part_of VAO:0000026 ! part_of skeleton relationship: has_location VAO:0000075 ! has_location appendage [Term] id: VAO:0000077 name: non-mineralized chondroid tissue is_a: VAO:0000015 ! skeletal tissue [Term] id: VAO: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." [TAO:curator] synonym: "chondroid bone tissue" EXACT [VAO:curator] is_a: VAO:0000015 ! skeletal tissue relationship: develops_from VAO:0000077 ! develops_from non-mineralized chondroid tissue [Term] id: VAO: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." [VAO:curator] synonym: "placoid scale" EXACT [VAO:curator] is_a: VAO:0000048 ! scale [Term] id: VAO:0000080 name: keratin-based scale def: "Fold or elevation of the epidermis rich in keratin proteins; possibly calcified but does not contain skeletal elements." [VAO:curator] is_a: VAO:0000048 ! scale [Term] id: VAO:0000081 name: cosmoid scale def: "Multi-tissue integumentary element composed of enamel or enameloid, dentine and lamellar bone, and characterized by pore-canal system." [VAO:curator] is_a: VAO:0000048 ! scale [Term] id: VAO:0000082 name: craniofacial skeleton def: "Cranial skeleton derived from neural crest cells." [VAO:curator] synonym: "Cranio-facial skeleton" EXACT [VAO:curator] is_a: VAO:0000049 ! cranial skeleton relationship: has_location VAO:0000083 ! has_location craniofacial region [Term] id: VAO:0000083 name: craniofacial region is_a: CARO:0000041 ! anatomical cluster [Term] id: VAO:0000084 name: cementocyte def: "Skeletogenic cell that produces cementum, is part of the odontogenic papilla, and is a transformation of a cementoblast cell." [VAO:curator] xref: CL:0000141 is_a: VAO:0000012 ! skeletogenic cell relationship: OBO_REL:part_of VAO:0000025 ! part_of odontogenic papilla relationship: OBO_REL:transformation_of VAO:0000061 ! transformation_of cementoblast [Term] id: VAO: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." [VAO:curator] xref: CL:0000138 is_a: VAO:0000012 ! skeletogenic cell relationship: develops_from VAO:0000058 ! develops_from chondroblast relationship: produces VAO:0000059 ! produces avascular GAG-rich matrix relationship: OBO_REL:part_of VAO:0000078 ! part_of chondroid tissue relationship: OBO_REL:part_of VAO:0000040 ! part_of cartilage tissue [Term] id: VAO:0000086 name: secondary cartilage tissue def: "Cartilage tissue that is part of the exoskeleton, deposited adjacent to bone after bone formation." [VAO:curator] is_a: VAO:0000040 ! cartilage tissue relationship: OBO_REL:part_of VAO:0000035 ! part_of dermal skeleton [Term] id: VAO:0000087 name: cosmine synonym: "cosmoid scale tissue" EXACT [VAO:curator] is_a: VAO:0000063 ! odontoid tissue [Term] id: VAO:0000088 name: mineralized cartilage tissue def: "Cartilage tissue that is mineralized." [VAO:curator] is_a: VAO:0000040 ! cartilage tissue [Term] id: VAO:0000089 name: non-mineralized cartilage tissue def: "Cartilage tissue that is not mineralized." [VAO:curator] is_a: VAO:0000040 ! cartilage tissue [Term] id: VAO:0000090 name: integumentary skeleton def: "Part of the extra-oral dermal skeletal system that develops and remains invested within the integument, primarily the dermis." [VAO:curator] is_a: CARO:0000041 ! anatomical cluster relationship: OBO_REL:part_of VAO:0000035 ! part_of dermal skeleton relationship: has_location VAO:0000029 ! has_location integument [Term] id: VAO:0000091 name: elastic cartilage tissue def: "Cartilage tissue that is flexible and contains abundant elastic fibers." [VAO:curator] is_a: VAO:0000089 ! non-mineralized cartilage tissue relationship: develops_from VAO:0000092 ! develops_from chondrogenic condensation [Term] id: VAO: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: VAO:0000006 ! cell condensation [Term] id: VAO:0000093 name: postcranial axial skeleton def: "Skeletal system of the central body axis including vertebrae, notochord, ribs, and sternum." [VAO:curator] is_a: CARO:0000041 ! anatomical cluster relationship: OBO_REL:part_of VAO:0000056 ! part_of axial skeleton [Term] id: VAO:0000094 name: hyaline cartilage tissue def: "Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance." [VAO:curator] synonym: "hyaline cartilage" EXACT [VAO:curator] is_a: VAO:0000040 ! cartilage tissue [Term] id: VAO: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." [VAO:curator] is_a: VAO:0000068 ! odontoblast relationship: OBO_REL:transformation_of VAO:0000068 ! transformation_of odontoblast [Term] id: VAO:0000096 name: terminally differentiated odontoblast def: "Odontoblast that is terminally differentiated and derived from an odontogenic papilla and associated with dentine." [VAO:curator] is_a: VAO:0000068 ! odontoblast [Term] id: VAO:0000097 name: orthodentine def: "Odontoid tissue that typically contains tubules and is acellular." [VAO:curator] is_a: VAO:0000063 ! odontoid tissue [Term] id: VAO: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)." [VAO:curator] xref: CL:0000743 is_a: VAO:0000085 ! chondrocyte [Term] id: VAO:0000100 name: periarticular chondrocyte def: "Chondrocyte that is located on a joint surface; part of articular cartilage." [VAO:curator] xref: CL:0000742 is_a: VAO:0000085 ! chondrocyte relationship: has_location VAO:0000101 ! has_location articulation [Term] id: VAO:0000101 name: articulation is_a: CARO:0000041 ! anatomical cluster [Term] id: VAO:0000102 name: osteodentine is_a: VAO:0000063 ! odontoid tissue [Term] id: VAO:0000103 name: fibrocartilage def: "Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns." [VAO:curator] is_a: VAO:0000040 ! cartilage tissue [Term] id: VAO:0000104 name: ganoine def: "Odontogenic tissue that is hypermineralized acellular, noncollagenous, covered by an epidermis and often deposited in multiple layers." [VAO:curator] is_a: VAO:0000063 ! odontoid tissue relationship: OBO_REL:part_of VAO:0000052 ! part_of ganoid scale [Term] id: VAO: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." [VAO:curator] relationship: OBO_REL:part_of VAO:0000070 ! part_of elasmoid scale [Term] id: VAO:0000106 name: vasodentine def: "Dentine tissue that lacks dentine tubules and that is penetrated by blood capillaries." [VAO:curator] synonym: "vascular dentine" EXACT [VAO:curator] is_a: VAO:0000063 ! odontoid tissue [Term] id: VAO:0000107 name: elasmodine def: "Odontogenic tissue that consists of multiple layers of collagen fibers organized in orthogonal or twisted arrangements." [VAO:curator] is_a: VAO:0000063 ! odontoid tissue relationship: OBO_REL:part_of VAO:0000070 ! part_of elasmoid scale [Term] id: VAO:0000108 name: non-mineralized hyaline cartilage tissue def: "Hyaline cartilage tissue that is not mineralized." [VAO:curator] is_a: VAO:0000094 ! hyaline cartilage tissue is_a: VAO:0000089 ! non-mineralized cartilage tissue [Term] id: VAO:0000109 name: mineralized hyaline cartilage tissue def: "Hyaline cartilage tissue that is mineralized." [VAO:curator] is_a: VAO:0000088 ! mineralized cartilage tissue is_a: VAO:0000013 ! mineralized tissue is_a: VAO:0000094 ! hyaline cartilage tissue relationship: develops_from VAO:0000094 ! develops_from hyaline cartilage tissue [Term] id: VAO:0000110 name: columnar chondrocyte def: "Chondrocyte that is linearly arranged with other columnar chondrocytes." [VAO:curator] xref: CL:0000744 is_a: VAO:0000085 ! chondrocyte [Term] id: VAO: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." [VAO:curator] xref: CL:0000140 is_a: VAO:0000012 ! skeletogenic cell relationship: OBO_REL:part_of VAO:0000025 ! part_of odontogenic papilla relationship: produces VAO:0000069 ! produces dentine relationship: OBO_REL:part_of VAO:0000069 ! part_of dentine relationship: OBO_REL:transformation_of VAO:0000095 ! transformation_of non-terminally differentiated odontoblast [Term] id: VAO: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." [VAO:curator] synonym: "vitrodentine" EXACT [VAO:curator] synonym: "enameloid tissue" EXACT [VAO:curator] synonym: "bitypic enamel" EXACT [VAO:curator] synonym: "durodentine" EXACT [VAO:curator] is_a: VAO:0000063 ! odontoid tissue relationship: develops_from VAO:0000114 ! develops_from pre-enameloid [Term] id: VAO: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." [VAO:curator] synonym: "non-mineralized enameloid tissue" EXACT [VAO:curator] is_a: VAO:0000063 ! odontoid tissue [Term] id: VAO:0000115 name: mineralized bone tissue def: "Bone tissue mineralized with hydroxyapatite." [VAO:curator] is_a: VAO:0000047 ! bone tissue is_a: VAO:0000013 ! mineralized tissue relationship: OBO_REL:part_of VAO:0000020 ! part_of mineralized extracellular matrix relationship: develops_from VAO:0000046 ! develops_from osteoid [Term] id: VAO: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." [VAO:curator] is_a: VAO:0000060 ! osteoblast [Term] id: VAO: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." [VAO:curator] is_a: VAO:0000060 ! osteoblast relationship: OBO_REL:integral_part_of VAO:0000118 ! integral_part_of cellular bone tissue [Term] id: VAO:0000118 name: cellular bone tissue def: "Mineralized bone tissue that always includes non-terminally differentiated osteoblasts and osteocytes." [VAO:curator] is_a: VAO:0000115 ! mineralized bone tissue [Term] id: VAO:0000119 name: non-mineralized avascular GAG-rich matrix def: "Avascular GAG-rich matrix that is not mineralized." [VAO:curator] synonym: "non-mineralized cartilage" EXACT [VAO:curator] is_a: VAO:0000059 ! avascular GAG-rich matrix relationship: OBO_REL:part_of VAO:0000089 ! part_of non-mineralized cartilage tissue [Term] id: VAO:0000120 name: mineralized avascular GAG-rich matrix def: "Avascular GAG-rich matrix that is mineralized." [VAO:curator] is_a: VAO:0000020 ! mineralized extracellular matrix is_a: VAO:0000059 ! avascular GAG-rich matrix relationship: OBO_REL:part_of VAO:0000088 ! part_of mineralized cartilage tissue [Term] id: VAO:0000122 name: acellular bone tissue def: "Mineralized bone tissue that has terminally differentiated osteoblasts but lacks osteocytes." [VAO:curator] is_a: VAO:0000115 ! mineralized bone tissue relationship: OBO_REL:has_part VAO:0000116 ! has_part terminally differentiated osteoblast [Term] id: VAO: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." [VAO:curator] synonym: "dental tissue" RELATED [VAO:curator] is_a: VAO:0000063 ! odontoid tissue relationship: develops_from VAO:0000071 ! develops_from pre-dentine [Term] id: VAO: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." [VAO:curator] xref: CL:0000137 is_a: VAO:0000012 ! skeletogenic cell relationship: OBO_REL:transformation_of VAO:0000117 ! transformation_of non-terminally differentiated osteoblast relationship: OBO_REL:integral_part_of VAO:0000118 ! integral_part_of cellular bone tissue [Term] id: VAO:0000127 name: gastralia synonym: "abdominal rib" EXACT [VAO:curator] synonym: "Belly rib" EXACT [VAO:curator] is_a: VAO:0000128 ! skeletal element [Term] id: VAO:0000128 name: skeletal element def: "Organ entity that may have different tissue compositions at different stages and typically involved in mechanical support." [VAO:curator] is_a: CARO:0000074 ! solid compound organ relationship: OBO_REL:part_of VAO:0000026 ! part_of skeleton [Term] id: VAO:0000130 name: dermal bone def: "Skeletal element that forms superficially in the organism, usually in association with the ectoderm." [VAO:curator] synonym: "dermal element" EXACT [VAO:curator] synonym: "membrane bone" EXACT [VAO:curator] is_a: VAO:0000023 ! membrane bone [Term] id: VAO:0000131 name: appendicular ossicle is_a: VAO:0000132 ! ossicle [Term] id: VAO:0000132 name: ossicle def: "Skeletal element that is often isolated, small, and is usually ossified." [VAO:curator] is_a: VAO:0000128 ! skeletal element [Term] id: VAO:0000133 name: axial ossicle is_a: VAO:0000132 ! ossicle [Term] id: VAO:0000134 name: intratendonous ossification synonym: "Ossified tendon" EXACT [VAO:curator] is_a: VAO:0000132 ! ossicle [Term] id: VAO:0000135 name: replacement element def: "Skeletal element that forms as a replacement or substitution of another element or tissue." [VAO:curator] is_a: VAO:0000128 ! skeletal element intersection_of: VAO:0000128 ! skeletal element intersection_of: participates_in VAO:0000140 ! participates_in replacement ossification relationship: participates_in VAO:0000140 ! participates_in replacement ossification [Term] id: VAO:0000136 name: direct ossification def: "Ossification that does not require the replacement of pre-existing tissues, most often a cartilaginous model." [VAO:curator] is_a: VAO:0000002 ! mode of ossification [Term] id: VAO:0000137 name: sesamoid def: "Replacement element; an ossicle; often an endochondral replacement element that has cartilage and bone states that develops in dense regular connective tissue (e.g., tendons and ligaments)." [VAO:curator] is_a: VAO:0000132 ! ossicle relationship: develops_in VAO:0000050 ! develops_in dense regular connective tissue [Term] id: VAO:0000138 name: ligamentous replacement element def: "Replacement element that forms as a replacement a ligament." [VAO:curator] is_a: VAO:0000135 ! replacement element [Term] id: VAO:0000139 name: endochondral element def: "A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification." [VAO:curator] synonym: "endochondral replacement element" EXACT [] is_a: VAO:0000135 ! replacement element intersection_of: VAO:0000128 ! skeletal element intersection_of: participates_in VAO:0000143 ! participates_in endochondral ossification relationship: participates_in VAO:0000143 ! participates_in endochondral ossification [Term] id: VAO:0000140 name: replacement ossification def: "Ossification that requires the replacement of a pre-existing tissue prior to bone tissue formation." [VAO:curator] synonym: "indirect ossification" EXACT [] is_a: VAO:0000002 ! mode of ossification [Term] id: VAO:0000141 name: intramembranous ossification def: "Direct ossification that occurs within mesenchyme with the formation of an osteogenic condensation not associated with a perichondrium." [VAO:curator] xref: GO:0001957 is_a: VAO:0000136 ! direct ossification [Term] id: VAO: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." [VAO:curator] synonym: "metaplasia" EXACT [] is_a: VAO:0000136 ! direct ossification [Term] id: VAO:0000143 name: endochondral ossification def: "Replacement ossification wherein bone tissue replaces cartilage." [VAO:curator] xref: GO:0001958 is_a: VAO:0000140 ! replacement ossification [Term] id: VAO:0000144 name: perichondral ossification def: "Intramembranous ossification on the surface of a cartilage element as the perichondrium becomes a periosteum, without replacement of cartilage." [VAO:curator] is_a: VAO:0000141 ! intramembranous ossification [Term] id: VAO:0000145 name: endochondral bone def: "Replacement bone that forms within cartilage." [TAO:curator] comment: TODO: add relationship has_quality PATO:ossified. synonym: "ossified chondrogenic bone" EXACT [] is_a: VAO:0000139 ! endochondral element intersection_of: VAO:0000139 ! endochondral element intersection_of: OBO_REL:has_part VAO:0000047 ! has_part bone tissue intersection_of: develops_from VAO:0000000 ! develops_from cartilaginous element relationship: OBO_REL:has_part VAO:0000047 ! has_part bone tissue relationship: has_quality PATO:0001448 ! has_quality ossified relationship: develops_from VAO:0000000 ! develops_from cartilaginous element [Term] id: VAO: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." [VAO:curator] comment: TODO: create logical definition with differentia has_quality PATO:transient (term requested). synonym: "endochondral replacement cartilage" EXACT [] is_a: VAO:0000139 ! endochondral element is_a: VAO:0000000 ! cartilaginous element relationship: participates_in VAO:0000143 ! participates_in endochondral ossification [Term] id: VAO:0000149 name: pharyngeal arch relationship: OBO_REL:part_of VAO:0000049 ! part_of cranial skeleton [Typedef] id: OBO_REL:has_integral_part name: has_integral_part alt_id: OBO_REL:0000005 is_anti_symmetric: true is_reflexive: true is_transitive: true is_a: OBO_REL:has_part ! has_part inverse_of: OBO_REL:integral_part_of ! integral_part_of [Typedef] id: OBO_REL:has_part name: has_part alt_id: OBO_REL:0000003 is_anti_symmetric: true is_reflexive: true is_transitive: true [Typedef] id: OBO_REL: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: OBO_REL:part_of ! part_of [Typedef] id: OBO_REL:part_of name: part_of alt_id: OBO_REL:0000002 def: "For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)" [PMID:15892874] comment: Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell. is_anti_symmetric: true is_reflexive: true is_transitive: true inverse_of: OBO_REL:has_part ! has_part [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: capable_of_producing name: capable_of_producing [Typedef] id: deposits name: deposits [Typedef] id: develops_from name: develops_from [Typedef] id: develops_in name: develops_in [Typedef] id: has_location name: has_location [Typedef] id: has_quality name: has_quality namespace: caro [Typedef] id: overlaps name: overlaps namespace: caro [Typedef] id: overlies name: overlies [Typedef] id: part_of name: part_of namespace: caro is_transitive: true [Typedef] id: participates_in name: participates_in [Typedef] id: produces name: produces