diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index 73e4dee943..1ed5561468 100644 --- a/docs/odk-workflows/RepositoryFileStructure.md +++ b/docs/odk-workflows/RepositoryFileStructure.md @@ -25,11 +25,11 @@ These are the current imports in UBERON | chebi | http://purl.obolibrary.org/obo/chebi.owl | None | | pato | http://purl.obolibrary.org/obo/pato.owl | None | | bfo | http://purl.obolibrary.org/obo/bfo.owl | None | -| ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon.owl | None | +| ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | None | | nbo | http://purl.obolibrary.org/obo/nbo.owl | None | | ceph | http://purl.obolibrary.org/obo/ceph.owl | None | | cteno | http://purl.obolibrary.org/obo/cteno.owl | None | -| ehdaa2 | http://purl.obolibrary.org/obo/ehdaa2.owl | None | +| ehdaa2 | https://raw.githubusercontent.com/cmungall/human-developmental-anatomy-ontology/uberon/src/ontology/ehdaa2-edit.obo | None | | emapa | http://purl.obolibrary.org/obo/emapa.owl | None | | fbbt | http://purl.obolibrary.org/obo/fbbt.owl | None | | fbdv | http://purl.obolibrary.org/obo/fbdv.owl | None | diff --git a/imports/cl_import.owl b/imports/cl_import.owl index 52d0966ef5..1dee496648 100644 --- a/imports/cl_import.owl +++ b/imports/cl_import.owl @@ -4,20 +4,22 @@ xmlns:cl="http://purl.obolibrary.org/obo/cl#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cl1="http://purl.obolibrary.org/obo/cl#3" - xmlns:cl2="http://purl.obolibrary.org/obo/cl#1" + xmlns:cl2="http://purl.obolibrary.org/obo/cl#2" + xmlns:cl3="http://purl.obolibrary.org/obo/cl#1" xmlns:obo="http://purl.obolibrary.org/obo/" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:terms="http://purl.org/dc/terms/" xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + - 2021-11-25 + 2022-02-16 Alexander Diehl Ceri van Slyke Chris Mungall @@ -76,7 +78,6 @@ - IAO:0000116 uberon editor_note @@ -117,12 +118,6 @@ - - - - - - @@ -154,8 +149,8 @@ Chris Mungall - ?X DisjointWith RO_0002162 some ?Y Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y) + Class: ?X DisjointWith: RO_0002162 some ?Y RO:0002161 uberon never_in_taxon @@ -205,19 +200,6 @@ - - - - depicted:by - uberon - depicted_by - true - depicted_by - depicted by - - - - @@ -647,15 +629,6 @@ - - - - - - - - - @@ -728,6 +701,15 @@ + + + + + + + + + @@ -804,6 +786,12 @@ + + + + + + @@ -937,24 +925,12 @@ - - - - - - - - - - - - @@ -979,7 +955,6 @@ http://www.w3.org/2000/01/rdf-schema#seeAlso - seeAlso uberon seeAlso true @@ -995,6 +970,19 @@ + + + + http://xmlns.com/foaf/0.1/depicted_by + uberon + depicted_by + true + depicted_by + depicted by + + + + - - A meso-epithelial cell that lies between the cartilaginous fibers in the synovial membrane of a joint and produces hyaluronic acid. - BTO:0003652 + A cell located in the synovial joint. CALOHA:TS-0995 - FMA:66786 synoviocyte - hyaluronic acid secreting cell cell CL:0000214 synovial cell @@ -5186,6 +5166,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + cell CL:0000241 @@ -6130,9 +6111,10 @@ Covers cells actively being cultured or stored in a quiescent state for future u A cell secreting tears, the fluid secreted by the lacrimal glands. This fluid moistens the conjunctiva and cornea. + tears secreting cell cell CL:0000315 - tears secreting cell + tear secreting cell @@ -6287,7 +6269,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - cell CL:0000327 @@ -6616,7 +6597,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - cell CL:0000350 @@ -6732,7 +6712,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A smooth muscle cell assocatiated with the vasculature. + A smooth muscle cell associated with the vasculature. VSMC vascular smooth muscle cell cell @@ -6983,9 +6963,10 @@ Covers cells actively being cultured or stored in a quiescent state for future u + support cell (sensu Nematoda and Protostomia) cell CL:0000378 - support cell (sensu Nematoda and Protostomia) + supporting cell (sensu Nematoda and Protostomia) @@ -7773,7 +7754,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A peptide hormone cell that secretes prolactin. cell @@ -9210,7 +9190,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. - BTO:0000938 CALOHA:TS-0683 FBbt:00005106 @@ -9253,6 +9232,18 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + @@ -9351,6 +9342,18 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + @@ -9384,6 +9387,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers. FMA:83505 basophilic normoblast @@ -9401,6 +9410,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + @@ -9437,6 +9452,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + @@ -9609,6 +9630,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + @@ -9633,14 +9660,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + Interneuron of the vertebrate retina. They integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. They lack large axons. BTO:0004044 - FBbt:00005127 FMA:67766 amacrine neuron cell CL:0000561 - Not clear if this term overlaps with retinal bipolar neuron (CL:0000748). amacrine cell @@ -9965,6 +9991,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and neutrophil-specific granules has started. No nucleolus is present. This cell type is CD13-positive, CD16-negative, integrin alpha-M-positive, CD15-positive, CD33-positive, CD24-positive, C/EBP-a-positive, C/EBPe-positive, PU.1-positive, lactotransferrin-positive, myeloperoxidase-positive and NGAL-positive. BTO:0003455 FMA:83540 @@ -9996,6 +10028,18 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + @@ -10569,9 +10613,10 @@ Covers cells actively being cultured or stored in a quiescent state for future u + support cell (sensu Nematoda) cell CL:0000619 - support cell (sensu Nematoda) + supporting cell (sensu Nematoda) @@ -10679,6 +10724,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + Granule cell that is part of the olfactory bulb. cell CL:0000626 @@ -10730,9 +10776,10 @@ Covers cells actively being cultured or stored in a quiescent state for future u A cell whose primary function is to support other cell types. BTO:0002315 + supportive cell cell CL:0000630 - supportive cell + supporting cell @@ -10753,7 +10800,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A cell that is found in the perisinusoidal space of the liver that is capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components that can contribute to liver fibrosis. This activated state has a myofibroblast-like phenotype, though it's not clear in the literature if this is terminally differentiated. This cell type comprises approximately 8-15% of total cells in the liver. BTO:0002741 @@ -12017,11 +12063,13 @@ radial glial cells acting as neural progenitors throughout life. - - A subset of motor neurons that innervates intrafusal muscle fibers and has small diameter axons. + OBSOLETE. A subset of motor neurons that innervates intrafusal muscle fibers and has small diameter axons. + CL:0008037 cell CL:0000717 - fusimotor neuron + Term merged into CL:0008037. Refer to https://github.com/obophenotype/cell-ontology/issues/1364 + obsolete fusimotor neuron + true @@ -12756,7 +12804,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + @@ -12778,6 +12843,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + @@ -12796,7 +12867,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + @@ -12836,7 +12924,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + @@ -12859,6 +12964,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -12876,7 +12993,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + @@ -12921,7 +13055,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + @@ -13114,6 +13265,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + @@ -14159,6 +14316,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -14180,6 +14349,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -14480,9 +14661,10 @@ radial glial cells acting as neural progenitors throughout life. Neuromast support cell is a non-sensory cell of the neuromast that extend between the sensory hair cells from the basement membrane to the apical surface; neuromast support cells are surrounded by neuromast mantle cells. + neuromast support cell cell CL:0000852 - neuromast support cell + neuromast supporting cell @@ -14494,12 +14676,13 @@ radial glial cells acting as neural progenitors throughout life. Olfactory epithelial support cell is a columnar cell that extends from the epithelial free margin to the basement membrane of the olfactory epithelium. This cell type has a large, vertically, elongate, euchromatic nucleus, along with other nuclei, forms a layer superficial to the cell body of the receptor cell; sends long somewhat irregular microvilli into the mucus layer; at the base, with expanded end-feet containing numerous lamellated dense bodies resembling lipofuscin of neurons. FMA:62302 + olfactory epithelial support cell olfactory sustentacular cell supporting cell of olfactory epithelium sustentaculocyte of olfactory epithelium cell CL:0000853 - olfactory epithelial support cell + olfactory epithelial supporting cell @@ -17633,6 +17816,8 @@ radial glial cells acting as neural progenitors throughout life. + + Granule cell that is part of the cerebral cortex. cell CL:0001032 @@ -17645,7 +17830,6 @@ radial glial cells acting as neural progenitors throughout life. - Granule cell that is part of the hippocampus. cell CL:0001033 @@ -18071,6 +18255,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -18379,6 +18564,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -21688,7 +21874,6 @@ radial glial cells acting as neural progenitors throughout life. - A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells. tmeehan @@ -21828,9 +22013,10 @@ radial glial cells acting as neural progenitors throughout life. 2010-08-25T03:41:30Z CL:1000401 FMA:62954 + mucus neck cell of gastric gland cell CL:0002181 - mucus neck cell of gastric gland + mucous neck cell of gastric gland @@ -22147,10 +22333,13 @@ radial glial cells acting as neural progenitors throughout life. - - A renal intercalated cell that secretes base and reabsorbs acid in the coritcal collecting duct to mantain acid/base balance. + + + A renal intercalated cell that secretes base and reabsorbs acid in the distal segments of the kidney tubule to maintain acid/base balance. tmeehan 2010-09-02T01:43:55Z + type B intercalated cell + type B-IC cell CL:0002201 renal beta-intercalated cell @@ -23856,12 +24045,17 @@ radial glial cells acting as neural progenitors throughout life. - A synovial cell type that resembles fibroblasts, has abundant granular endoplasmic reticulum but contains fewer vacuoles and vesicles. This cell type secretes glycoproteins and hyaluronic acid. + + A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles. tmeehan 2010-09-13T03:39:14Z + BTO:0003652 FMA:66788 + fibroblast-like synoviocyte + synovial fibroblast cell CL:0002301 + Type B synovial cells play a key role in the pathogenesis of chronic inflammatory diseases, such as rheumatoid arthritis, and are essential for the maintenance of normal joint functions. Fibroblast-like synoviocytes from different joints have different properties, which may contribute to the characteristic pattern of joint involvement in different types of arthritis. type B synovial cell @@ -23871,6 +24065,7 @@ radial glial cells acting as neural progenitors throughout life. + A synovial cell that is macrophage-like, characterized by surface ruffles or lamellipodia, plasma membrane invaginations and associated micropinocytotic vesicles, Golgi apparatus and little granular endoplasmic reticulum. tmeehan 2010-09-13T03:39:17Z @@ -23878,6 +24073,7 @@ radial glial cells acting as neural progenitors throughout life. type A synoviocyte cell CL:0002302 + Type A cells are usually round and located in the upper part of the synovial intima. type A synovial cell @@ -24157,7 +24353,7 @@ radial glial cells acting as neural progenitors throughout life. FMA:86712 cell CL:0002318 - periperhal blood mesothelial cell + peripheral blood mesothelial cell @@ -24284,6 +24480,8 @@ radial glial cells acting as neural progenitors throughout life. FMA:79866 epithelial cell of lactiferous gland luminal cell of alveolus of lactiferous gland + mammary alveolar epithelial cell + mammary gland alveolar epithelial cell cell CL:0002325 mammary alveolar cell @@ -24757,7 +24955,6 @@ radial glial cells acting as neural progenitors throughout life. - A hematopoietic stem found in the yolk sac. In mice, this cell type is Sca-1-negative, CD45-negative, MHC-negative, HSA-positive, AA4.1-positive, CD44-positive. tmeehan @@ -26057,6 +26254,7 @@ radial glial cells acting as neural progenitors throughout life. tmeehan 2010-10-21T02:29:19Z T.4int8+.Th + T_4int8+_Th cell CL:0002430 CD4-intermediate, CD8-positive double-positive thymocyte @@ -26077,7 +26275,8 @@ radial glial cells acting as neural progenitors throughout life. A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD8 co-receptor. tmeehan 2010-10-21T02:29:23Z - T.4int8+.th + T.4+8int.Th + T_4+8int_Th cell CL:0002431 CD4-positive, CD8-intermediate double-positive thymocyte @@ -26444,18 +26643,23 @@ radial glial cells acting as neural progenitors throughout life. - - The cell type from which oligodendrocytes develop. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons. + A progenitor cell of the central nervous system that can differentiate into oligodendrocytes or type-2 astrocytes. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons. + http://orcid.org/0000-0002-1773-2692 tmeehan 2010-11-10T02:51:34Z + O-2A/OPC + O2A/OPC + oligodendrocyte-type 2 astrocyte (O-2A) progenitor cell + oligodendrocyte/type-2 astrocyte progenitor cell cell CL:0002453 + This cell type can be purified from optic nerves and other regions of the embryonic, postnatal and adult rat CNS and can be differentiated in vitro to oligodendrocytes and type-2 astrocytes. Some references use the terms 'oligodendrocyte precursor cell' and 'oligodendrocyte type-2 astrocyte (O-2A) progenitor' to refer to the same entity (e.g., PMID:10704434), while others describe an oligodendrocyte type-2 astrocyte (O-2A) progenitor cell as the precurosr to oligodendrocyte- and type-2 astrocyte- progenitor cells (e.g, ISBN:9780702028991). oligodendrocyte precursor cell @@ -27159,6 +27363,7 @@ radial glial cells acting as neural progenitors throughout life. A trophoblast cell that arises in the junctional zone (basal plate) of the placenta. tmeehan 2010-12-07T12:56:56Z + spongiotrophoblast cell CL:0002499 spongiotrophoblast cell @@ -28170,6 +28375,8 @@ radial glial cells acting as neural progenitors throughout life. A melanocyte that appears darker due to content or amount of melanin granules. tmeehan 2011-03-01T05:57:11Z + melanotic melanocyte + melanotic melanophore cell CL:0002566 dark melanocyte @@ -28184,6 +28391,8 @@ radial glial cells acting as neural progenitors throughout life. A melanocyte that appears lighter in color. tmeehan 2011-03-01T05:58:23Z + amelanotic melanocyte + amelanotic melanophore cell CL:0002567 light melanocyte @@ -28227,9 +28436,10 @@ radial glial cells acting as neural progenitors throughout life. A mesenchymal stem cell of adipose tissue. tmeehan 2011-03-01T09:57:17Z + mesenchymal stem cell of adipose cell CL:0002570 - mesenchymal stem cell of adipose + mesenchymal stem cell of adipose tissue @@ -28784,9 +28994,10 @@ radial glial cells acting as neural progenitors throughout life. - - - A CNS neuron of the cerebral cortex. + OBSOLETE. A CNS neuron of the cerebral cortex. + + + CL:0010012 tmeehan 2011-03-06T07:37:08Z BTO:0004102 @@ -28794,7 +29005,8 @@ radial glial cells acting as neural progenitors throughout life. cortical neuron cell CL:0002609 - neuron of cerebral cortex + obsolete neuron of cerebral cortex + true @@ -29440,9 +29652,9 @@ radial glial cells acting as neural progenitors throughout life. A venule endothelial cell that is cubodial, expresses leukocyte-specific receptors, and allows for passage of lymphocytes into bloodstream. tmeehan 2011-07-08T03:14:10Z + endothelial cell of postcapillary venule of lymph node FMA:67759 HEV cell - endothelial cell of postcapillary venule of lymph node cell CL:0002652 Markers expressed on HEV include: MAdCAM-1,PNAd (sulfated and glycosylated molecules, i.e. GlyCAM-1, CD34, endomucin, nepmucin), ICAM-1, ICAM-2,Fuc-TVII, beta 3GlcNAcT-3, GlcNAc6ST2,CCL21, CCL19, CXCL13, CXCL12, Autotaxin, DARC, angiomodulin, LRHG. @@ -30080,10 +30292,12 @@ radial glial cells acting as neural progenitors throughout life. A cuboidal epithelial cell of the kidney that regulates acid/base balance. + http://orcid.org/0000-0002-1773-2692 FMA:86560 intercalated cell cell CL:0005010 + Intercalated cells are also called “mitochondria-rich cells”, reflecting the high levels of round mitochondria at their apical pole, or in their cytoplasm, a distribution that is quite different from that of other kidney tubule cells, which accumulated mitochondria around the basolateral membrane. These cells also have numerous irregular apical microvilli compared with the surrounding segment-specific cells. Intercalated cells lack a central cilium, at least in the cortex, which also differentiates them from the adjacent principal cells. renal intercalated cell @@ -30092,10 +30306,15 @@ radial glial cells acting as neural progenitors throughout life. - + + + A cuboidal epithelial cell of the kidney which secretes acid and reabsorbs base to regulate acid/base balance. + type A intercalated cell + type A-IC cell CL:0005011 + Type A intercalated cells are the more abundant type of intercalated cell in the outer stripe of the outer medulla in most mammalian species. renal alpha-intercalated cell @@ -30136,9 +30355,10 @@ radial glial cells acting as neural progenitors throughout life. A non-sensory cell that extends from the basement membrane to the apical surface of the auditory epithelium and provides support for auditory hair cells. + auditory epithelial support cell cell CL:0005014 - auditory epithelial support cell + auditory epithelial supporting cell @@ -30607,10 +30827,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - An epidermal cell with apical microvilli or a single apical projection have synaptic associations with nerve fibres in the epidermis. haendel CL:0007017 @@ -30623,8 +30840,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - + Ciliated cell of the embryonic epidermis and functions in embryonic movements. haendel @@ -30666,6 +30882,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u Secretory cell that produces a chemical mixture that triggers antipredator behavior. The substance is released only upon disruption of the epidermis. [Behavior of teleost fishes, second edition, edited by Pitcher, 1992] haendel + alarm substance secreting cell club cell (zebrafish) club cell CL:0007021 @@ -31175,6 +31392,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u FMA:83660 MESH:D009047 SAO:143800623 + fusimotor neuron CL:0008037 gamma motor neuron @@ -31262,12 +31480,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u A giant pyramidal neuron with a soma in layer Vb of the primary motor cortex that sends its axons down the spinal cord via the corticospinal tract, either synapsing directly with alpha motor neurons, or targeting interneurons in the spinal cord. In humans, Betz cells are the largest known in the central nervous system. - https://en.wikipedia.org/w/index.php?title=Betz_cell&oldid=977472330#/media/File:GolgiStainedPyramidalCell.jpg dos 2020-09-28T09:52:58Z pyramidal cell of Betz CL:0008049 Betz cell + https://en.wikipedia.org/w/index.php?title=Betz_cell&oldid=977472330#/media/File:GolgiStainedPyramidalCell.jpg @@ -31724,7 +31942,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + A mesothelial cell that is located in a vermiform appendix. http://orcid.org/0000-0002-2825-0621 @@ -32523,6 +32741,134 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + An epithelial cell that is part of an endometrial gland. + 2021-11-30T16:13:30Z + http://orcid.org/0000-0002-2825-0621 + EFO:0010710 + endometrial glandular epithelial cell + CL:0009084 + + epithelial cell of endometrial gland + + + + + + + + + An endothelial cell that is part of a respiratory system lymphatic vessel. + 2021-12-03T14:00:44Z + http://orcid.org/0000-0002-2825-0621 + EFO:0010667 + CL:0009086 + + endothelial cell of respiratory system lymphatic vessel + + + + + + + + + An extravillous trophoblast that is polynuclear. + 2021-12-03T14:37:32Z + http://orcid.org/0000-0002-2825-0621 + EFO:0010712 + fused EVT + CL:0009087 + fused extravillous trophoblast + + + + + + + + + A pericyte cell that is part of a lung. + 2021-12-03T17:13:33Z + http://orcid.org/0000-0002-2825-0621 + EFO:0010669 + lung pericyte cell + pulmonary pericyte + CL:0009089 + + lung pericyte + + + + + + + + + + An endothelial cell that is part of a placenta. + 2021-12-13T13:53:01Z + http://orcid.org/0000-0002-2825-0621 + EFO:0010708 + placental endothelial cell + CL:0009092 + + endothelial cell of placenta + + + + + + + + + A smooth muscle cell that is part of a placenta. + 2021-12-13T13:56:42Z + http://orcid.org/0000-0002-2825-0621 + EFO:0010709 + placental smooth muscle cell + CL:0009093 + + smooth muscle cell of placenta + + + + + + + + + An endothelial cell that is part of a hepatic portal vein. + 2021-12-13T14:01:05Z + http://orcid.org/0000-0002-2825-0621 + portal endothelial cell + EFO:0010704 + CL:0009094 + + endothelial cell of hepatic portal vein + + + + + + + + + An endothelial cell that is part of a uterus. + 2021-12-13T14:39:25Z + http://orcid.org/0000-0002-2825-0621 + EFO:0010711 + uterine endothelial cell + CL:0009095 + + endothelial cell of uterus + + + + @@ -32648,6 +32994,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + CL:0010010 cerebellar stellate cell @@ -32658,8 +33005,9 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + + A GABAergic interneuron whose soma is located in the cerebral cortex. CL:0010011 cerebral cortex GABAergic interneuron @@ -32671,9 +33019,17 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A neuron that is part_of a cerebral cortex. + A CNS neuron of the cerebral cortex. + + CL:0002609 + BTO:0004102 + FMA:84104 + cortical neuron + neuron of cerebral cortex + cell CL:0010012 cerebral cortex neuron + https://github.com/obophenotype/cell-ontology/issues/1359 @@ -33170,6 +33526,21 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + Any microvascular endothelial cell that is part of the dermis. + http://orcid.org/0000-0001-5208-3432 + DMEC cell + dermal microvascular endothelium cell + CL:0011030 + dermal microvascular endothelial cell + + + + @@ -33485,6 +33856,137 @@ plexiform layer using GABA. + + + + Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain. + tmeehan + 2010-05-25T01:36:34Z + cell + CL:0017500 + neutrophillic cytoplasm + + + + + + + + Nucleus with two or more lobes connected by a thin filament that contains no internal chromatin. + http://purl.obolibrary.org/obo/GO_0098537 + tmeehan + 2009-12-22T03:54:43Z + cell + CL:0017501 + Obsoleted because duplicate with GO term. + obsolete lobed nucleus + https://github.com/obophenotype/cell-ontology/issues/734 + true + + + + + + + + Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain. + tmeehan + 2009-12-22T04:23:25Z + eosinophilic + cell + CL:0017502 + acidophilic cytoplasm + + + + + + + + Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. + tmeehan + 2009-12-22T04:24:54Z + cell + CL:0017503 + basophilic cytoplasm + + + + + + + + Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. + tmeehan + 2009-12-28T04:25:23Z + cell + CL:0017504 + polychromatophilic cytoplasm + + + + + + + + A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. + tmeehan + 2009-12-23T10:53:24Z + cell + CL:0017505 + increased nucleus size + + + + + + + + A concave nuclear shape where the nucleus is indented to more than half the distance to the farthest nuclear margin, but in no area is the chromatin condensed to a single filament. + tmeehan + 2009-12-23T02:18:43Z + cell + CL:0017506 + banded nucleus + + + + + + + + A concave nucleus shape where the indentation is smaller than half of the distance to the farthest nuclear margin. + tmeehan + 2009-12-23T02:31:25Z + cell + CL:0017507 + reniform nucleus + + + + + + + + Heterochromatin that is arranged in a carthwheel pattern. + tmeehan + 2009-12-28T04:28:35Z + cell + CL:0017508 + cartwheel heterochromatin + + + + + + + + CL:0017509 + alobate nucleus + + + + @@ -33609,7 +34111,9 @@ plexiform layer using GABA. An endothelial cell found in the periportal region hepatic sinusoid, near the portal triad. The fenestrae of these cells are larger but fewer in number compared with those of endothelial cells near the centrilobular region of the hepatic sinusoid. 2020-09-09T13:56:47Z + EFO:0010705 periportal LSEC + periportal hepatic sinusoidal endothelial cell CL:0019021 endothelial cell of periportal hepatic sinusoid @@ -33623,6 +34127,8 @@ plexiform layer using GABA. An endothelial cell found in the centrilobular region hepatic sinusoid, near the central vein. The fenestrae of these cells are smaller but more numerous compared with those of endothelial cells near the periportal region of the hepatic sinusoid. 2020-09-10T12:38:29Z + EFO:0010706 + central venous hepatic sinusoidal endothelial cell pericentral LSEC CL:0019022 endothelial cell of pericentral hepatic sinusoid @@ -33715,6 +34221,7 @@ plexiform layer using GABA. + CL:1000022 mesonephric nephron tubule epithelial cell @@ -33799,6 +34306,7 @@ plexiform layer using GABA. + CL:1000090 pronephric nephron tubule epithelial cell @@ -33809,6 +34317,7 @@ plexiform layer using GABA. + CL:1000123 metanephric nephron tubule epithelial cell @@ -35373,7 +35882,6 @@ plexiform layer using GABA. - A type I vestibular sensory cell that is part of the stato-acoustic epithelium. FMA:263186 @@ -35387,7 +35895,6 @@ plexiform layer using GABA. - A type I vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth. FMA:263188 @@ -35401,7 +35908,6 @@ plexiform layer using GABA. - A type I vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth. FMA:263190 @@ -35415,7 +35921,6 @@ plexiform layer using GABA. - A type I vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth. FMA:263192 @@ -35429,7 +35934,6 @@ plexiform layer using GABA. - A type II vestibular sensory cell that is part of the stato-acoustic epithelium. FMA:263194 @@ -35443,7 +35947,6 @@ plexiform layer using GABA. - A type II vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth. FMA:263196 @@ -35457,7 +35960,6 @@ plexiform layer using GABA. - A type II vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth. FMA:263198 @@ -35471,7 +35973,6 @@ plexiform layer using GABA. - A type II vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth. FMA:263200 @@ -36334,6 +36835,7 @@ plexiform layer using GABA. + An epithelial cell that is part of the collecting duct of renal tubule. FMA:70982 @@ -36823,6 +37325,7 @@ plexiform layer using GABA. + An epithelial cell that is part of a nephron tubule. FMA:86785 @@ -36905,7 +37408,7 @@ plexiform layer using GABA. - + KUPO:0001020 cell CL:1000507 @@ -36968,7 +37471,7 @@ plexiform layer using GABA. - + KUPO:0001063 cell @@ -37069,6 +37572,7 @@ plexiform layer using GABA. + KUPO:0001024 cell @@ -37302,6 +37806,7 @@ plexiform layer using GABA. + KUPO:0001130 @@ -37315,6 +37820,7 @@ plexiform layer using GABA. + KUPO:0001131 @@ -38131,7 +38637,7 @@ plexiform layer using GABA. - + KUPO:0001012 Wikipedia:Kidney_collecting_duct_cell cell @@ -39260,6 +39766,7 @@ plexiform layer using GABA. + Any lung endothelial cell that is part of a microvascular endothelium. TermGenie 2014-06-04T16:00:56Z @@ -39544,9 +40051,10 @@ plexiform layer using GABA. Any neuromast support cell that is part of a anterior lateral line. TermGenie 2014-06-25T03:44:51Z + anterior lateral line neuromast support cell cell CL:2000036 - anterior lateral line neuromast support cell + anterior lateral line neuromast supporting cell @@ -39586,9 +40094,10 @@ plexiform layer using GABA. Any neuromast support cell that is part of a posterior lateral line. TermGenie 2014-06-25T03:45:11Z + posterior lateral line neuromast support cell cell CL:2000039 - posterior lateral line neuromast support cell + posterior lateral line neuromast supporting cell @@ -39930,7 +40439,7 @@ plexiform layer using GABA. - + Any capillary endothelial cell that is part of a placenta. TermGenie 2014-10-07T17:55:56Z @@ -40198,12 +40707,13 @@ plexiform layer using GABA. - Any mesenchymal stem cell of adipose that is part of a abdomen. + Any mesenchymal stem cell of adipose tissue that is part of an abdomen. TermGenie 2014-12-02T19:10:34Z + mesenchymal stem cell of abdominal adipose cell CL:2000080 - mesenchymal stem cell of abdominal adipose + mesenchymal stem cell of abdominal adipose tissue @@ -40343,6 +40853,8 @@ plexiform layer using GABA. + + Any stellate cell that is part of a dentate gyrus of hippocampal formation. TermGenie 2015-02-23T05:48:40Z @@ -40356,6 +40868,7 @@ plexiform layer using GABA. + Any microvascular endothelial cell that is part of a endometrial blood vessel. TermGenie @@ -40428,7 +40941,6 @@ plexiform layer using GABA. - Any fibroblast that is part of a reticular layer of dermis. TermGenie @@ -40647,12 +41159,12 @@ plexiform layer using GABA. - A Vip GABAergic cortical interneuron with bipolar morphology, with a soma found in L2/3. L2/3 bipolar Vip Cells have extending axons across all layers (with preferences for layers II/III and Va) and a dendritic tree that is vertically more restricted than deeper layer VIP cells and extend fewer dendrites into the layers outside their home layer (location of soma). L2/3 Bipolar Vip Cells have great variability in firing patterns, though most are continuous adapting. L2/3 Bipolar Vip Cells are more depolarized in their resting state, had less fast rectification, and had smaller after hyperpolarization than deeper Vip cells. + A vip GABAergic cortical interneuron with bipolar morphology, with a soma found in L2/3. L2/3 bipolar vip cells have extending axons across all layers (with preferences for layers II/III and Va) and a dendritic tree that is vertically more restricted than deeper layer vip cells and extend fewer dendrites into the layers outside their home layer (location of soma). L2/3 bipolar vip cells have great variability in firing patterns, though most are continuous adapting. L2/3 bipolar vip cells are more depolarized in their resting state, had less fast rectification, and had smaller after hyperpolarization than deeper vip cells. L2/3 bipolar Vip (Mus) CL:4023007 - L2/3 bipolar Vip GABAergic cortical interneuron (Mus musculus) + L2/3 bipolar vip GABAergic cortical interneuron (Mus musculus) @@ -40713,7 +41225,7 @@ plexiform layer using GABA. ILX:0770149 CL:4023011 - Lamp5 GABAergic cortical interneuron + lamp5 GABAergic cortical interneuron @@ -40753,12 +41265,12 @@ plexiform layer using GABA. - A Vip GABAergic cortical interneuron with a soma found in L5. L5 Vip cells have mostly local morphology with some deep-projecting axons. They show only moderate resistance, comparable to that of Sst subclass and unlike typical Vip subclass cells that tend to show high input resistance. L5 Vip cells show particularly low resting membrane potential. + A vip GABAergic cortical interneuron with a soma found in L5. L5 vip cells have mostly local morphology with some deep-projecting axons. They show only moderate resistance, comparable to that of sst subclass and unlike typical Vip subclass cells that tend to show high input resistance. L5 vip cells show particularly low resting membrane potential. L5 VIP (Mus) CL:4023014 - L5 Vip cortical GABAergic interneuron (Mus musculus) + L5 vip cortical GABAergic interneuron (Mus musculus) @@ -40786,7 +41298,7 @@ plexiform layer using GABA. ILX:0770151 CL:4023016 - Vip GABAergic cortical interneuron + vip GABAergic cortical interneuron @@ -40823,12 +41335,12 @@ plexiform layer using GABA. - A Vip GABAergic cortical interneuron that expresses CCK. L5/6 CCK cells have soma found mainly in L5 and L6 and have large axonal arborization. + A vip GABAergic cortical interneuron that expresses cck. L5/6 cck cells have soma found mainly in L5 and L6 and have large axonal arborization. L5/6 CCK Vip (Mus) CL:4023019 - L5/6 CCK, Vip cortical GABAergic interneuron (Mus musculus) + L5/6 cck, vip cortical GABAergic interneuron (Mus musculus) @@ -40865,7 +41377,7 @@ plexiform layer using GABA. http://orcid.org/0000-0001-7258-9596 CL:4023022 - canopy Lamp5 GABAergic cortical interneuron (Mus musculus) + canopy lamp5 GABAergic cortical interneuron (Mus musculus) @@ -40875,12 +41387,12 @@ plexiform layer using GABA. - A Lamp 5 GABAergic cortical interneuron with neurogliaform morphology with a soma found in L5,6. L5,6 NGC Lamp5 have deep afterhyperpolarization (AHP) but narrow action potentials (APs). Unlike other deep neurogliaform cells (which are caudal ganglionic eminence (CGE) derived), L5,6 NGC Lamp5 cells are medial ganglionic eminence (MGE)-derived + A lamp 5 GABAergic cortical interneuron with neurogliaform morphology with a soma found in L5,6. L5,6 NGC lamp5 have deep afterhyperpolarization (AHP) but narrow action potentials (APs). Unlike other deep neurogliaform cells (which are caudal ganglionic eminence (CGE) derived), L5,6 NGC lamp5 cells are medial ganglionic eminence (MGE)-derived http://orcid.org/0000-0001-7258-9596 L5,6 NGC Lamp5 (mus) CL:4023023 - L5,6 Neurogliaform Lamp5 GABAergic cortical interneuron (Mus musculus) + L5,6 neurogliaform lamp5 GABAergic cortical interneuron (Mus musculus) @@ -40890,12 +41402,12 @@ plexiform layer using GABA. - A Lamp5 GABAergic cortical interneuron with layer-adapting morphology. NGC Lamp5 cells have a small round soma, short dendrites, and a wide dense axonal arbor that tends to establish a dense axonal mesh with high connection probability both to themselves and L2 pyramidal cells. NGC Lamp5 cells have unique synaptic properties that distinguish them from other GABAergic interneurons, including the release of GABA to the extracellular space via volume transmission, and the ability to produce GABA-B responses in connected postsynaptic targets. + A lamp5 GABAergic cortical interneuron with layer-adapting morphology. NGC lamp5 cells have a small round soma, short dendrites, and a wide dense axonal arbor that tends to establish a dense axonal mesh with high connection probability both to themselves and L2 pyramidal cells. NGC lamp5 cells have unique synaptic properties that distinguish them from other GABAergic interneurons, including the release of GABA to the extracellular space via volume transmission, and the ability to produce GABA-B responses in connected postsynaptic targets. http://orcid.org/0000-0001-7258-9596 NGC Lamp5 (mus) CL:4023024 - Neurogliaform Lamp5 GABAergic cortical interneuron (Mus musculus) + neurogliaform lamp5 GABAergic cortical interneuron (Mus musculus) @@ -40903,13 +41415,13 @@ plexiform layer using GABA. - - A Sst GABAergic cortical interneuron that is both an interneuron and a projecting neuron. They are found in all layers from upper L2/3 down to the bottom of L6. They have long-range projections, some with axons fading into white matter. These cells have low rebound potential, low hyperpolarization sag, and high variability in membrane time constant. + + A sst GABAergic cortical interneuron that is both an interneuron and a projecting neuron. They are found in all layers from upper L2/3 down to the bottom of L6. They have long-range projections, some with axons fading into white matter. These cells have low rebound potential, low hyperpolarization sag, and high variability in membrane time constant. http://orcid.org/0000-0001-7258-9596 LP SST (Mus) CL:4023025 - Long-range projecting Sst GABAergic cortical interneuron (Mus musculus) + long-range projecting sst GABAergic cortical interneuron (Mus musculus) @@ -40919,12 +41431,12 @@ plexiform layer using GABA. - A Sst GABAergic cortical interneuron with a soma found in L5 and possesses 'T-shaped' Martinotti morphologies with local axonal plexus in L5a and translaminar axons restricted to the uppermost part of L1. They show low-threshold spiking patterns with strong rebound firing, and inhibit the L1 apical tuft of nearby pyramidal cells. + A sst GABAergic cortical interneuron with a soma found in L5 and possesses 'T-shaped' Martinotti morphologies with local axonal plexus in L5a and translaminar axons restricted to the uppermost part of L1. They show low-threshold spiking patterns with strong rebound firing, and inhibit the L1 apical tuft of nearby pyramidal cells. http://orcid.org/0000-0001-7258-9596 L5 T Martinotti SST (Mus) CL:4023027 - L5 T-Martinotti Sst GABAergic cortical interneuron (Mus musculus) + L5 T-Martinotti sst GABAergic cortical interneuron (Mus musculus) @@ -40933,12 +41445,12 @@ plexiform layer using GABA. - A Sst GABAergic cortical interneuron with a soma found in lower L5 with mostly local axonal arborization but with some sparse ascending axons. L5 non-Martinotti Sst cells show somatic localization and local axon plexus in L5b and L5b/6 and substantial innervation of L3 and L4, and receive thalamic input from the ventral posteromedial nucleus and specifically target L4 neurons, avoiding L5 pyramidal cells. L5 non-Martinotti Sst cells tend to show a higher input resistance and seem to be less stuttering. + A sst GABAergic cortical interneuron with a soma found in lower L5 with mostly local axonal arborization but with some sparse ascending axons. L5 non-Martinotti sst cells show somatic localization and local axon plexus in L5b and L5b/6 and substantial innervation of L3 and L4, and receive thalamic input from the ventral posteromedial nucleus and specifically target L4 neurons, avoiding L5 pyramidal cells. L5 non-Martinotti sst cells tend to show a higher input resistance and seem to be less stuttering. http://orcid.org/0000-0001-7258-9596 L5 non-Martinotti SST (Mus) CL:4023028 - L5 non-Martinotti Sst GABAergic cortical interneuron (Mus musculus) + L5 non-Martinotti sst GABAergic cortical interneuron (Mus musculus) @@ -40948,13 +41460,13 @@ plexiform layer using GABA. - A Sst GABAergic cortical interneuron that has "fanning-out' Martinotti morphology that is found in layer 2/3/5 of the cerebral cortex. They have local axon arbor and long ascending axons that spreads horizontally and arborizes significantly in L1. + A sst GABAergic cortical interneuron that has "fanning-out' Martinotti morphology that is found in layer 2/3/5 of the cerebral cortex. They have local axon arbor and long ascending axons that spreads horizontally and arborizes significantly in L1. http://orcid.org/0000-0001-7258-9596 L2/3/5 fan Martinotti SST (Mus) CL:4023030 L2/3/5 fan Martionotti SST cells have an adapting firing pattern and non-zero afterdepolarization (ADP). - L2/3/5 fan Martinotti Sst GABAergic cortical interneuron (Mus musculus) + L2/3/5 fan Martinotti sst GABAergic cortical interneuron (Mus musculus) @@ -40964,12 +41476,12 @@ plexiform layer using GABA. - A Sst GABAergic cortical interneuron with a soma found in lower L2/3 and upper 5, L4 Sst cells have Martinotti morphology with ascending axons but denser local axons and sparser ‘fanning-out’ projections to L1. L4 Sst cells have smaller membrane time constant to calb2 (L2/3/5 Fan Martinotti Cell) and non-zero afterdepolarization (ADP). + A sst GABAergic cortical interneuron with a soma found in lower L2/3 and upper 5, L4 Sst cells have Martinotti morphology with ascending axons but denser local axons and sparser ‘fanning-out’ projections to L1. L4 sst cells have smaller membrane time constant to calb2 (L2/3/5 fan Martinotti Cell) and non-zero afterdepolarization (ADP). http://orcid.org/0000-0001-7258-9596 L4 SST (Mus) CL:4023031 - L4 Sst GABAergic cortical interneuron (Mus musculus) + L4 sst GABAergic cortical interneuron (Mus musculus) @@ -40977,13 +41489,14 @@ plexiform layer using GABA. - - A Sst GABAergic cortical interneuron transcriptomically between the Sst and the Pvalb families with a soma found in L2/3. Some L2/3 PV-like SST cells have Martinotti morphology while some have basket cell morphology. L2/3 PV-like SST cells have lower AP width and higher firing rate than typical Sst subclass cells. L2/3 PV-like SST cells have high maximum firing rate variability, with many classified as belonging to the Pvalb subclass on the basis of electrophysiology. + OBSOLETE A sst GABAergic cortical interneuron transcriptomically between the sst and the pvalb families with a soma found in L2/3. Some L2/3 PV-like sst cells have Martinotti morphology while some have basket cell morphology. L2/3 PV-like sst cells have lower AP width and higher firing rate than typical Sst subclass cells. L2/3 PV-like sst cells have high maximum firing rate variability, with many classified as belonging to the pvalb subclass on the basis of electrophysiology. + PCL:1000002 http://orcid.org/0000-0001-7258-9596 L2/3 PV-like SST Mus) CL:4023034 - - L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) + Moved to PCL - see https://github.com/obophenotype/brain_data_standards_ontologies/issues/231. Use PCL:1000002 instead. + obsolete L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) + true @@ -40993,14 +41506,14 @@ plexiform layer using GABA. - A Pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. + A pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. http://orcid.org/0000-0001-7258-9596 ILX:0107356 Chandelier PV CL:4023036 In mice, Chandelier PV cells have soma found in in upper L2/3, with some in deep L5 and exhibit fast-spiking but lower firing rate compared to basket cells, and have practically absent hyperpolarization sag. - Chandelier Pvalb GABAergic cortical interneuron + chandelier pvalb GABAergic cortical interneuron @@ -41334,14 +41847,14 @@ plexiform layer using GABA. - - - A L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) that has Martinotti morphology. + OBSOLETE A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has Martinotti morphology. + PCL:1000004 Martinotti L2/3 PV-like SST (Mus) CL:4023067 - - Martinotti morphology L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) + Moved to PCL - see https://github.com/obophenotype/brain_data_standards_ontologies/issues/231. Use PCL:1000004 instead. + obsolete Martinotti morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) + true @@ -41377,12 +41890,26 @@ plexiform layer using GABA. - A GABAergic cortical interneuron that expresses CCK. L5/6 CCK cells have soma found mainly in L5 and L6 and have large axonal arborization. + A GABAergic cortical interneuron that expresses cck. L5/6 cck cells have soma found mainly in L5 and L6 and have large axonal arborization. L5/6 CCK (Mus) CL:4023071 - L5/6 CCK cortical GABAergic interneuron (Mus musculus) + L5/6 cck cortical GABAergic interneuron (Mus musculus) + + + + + + + + + A sst GABAergic cortical interneuron found in L6 that expresses tyrosine hydroxylase. L6 Th+ SST cells have mostly local axonal arborization within L6. + + L6 Th+ SST (Mus) + CL:4023075 + + L6 tyrosine hydroxylase positive sst expressing GABAergic cortical interneuron (Mus musculus) @@ -41420,14 +41947,14 @@ plexiform layer using GABA. - - - A L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) that has basket morphology. + OBSOLETE A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has basket morphology. + PCL:1000003 basket L2/3 PV-like SST (Mus) CL:4023078 - - basket morphology L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) + Moved to PCL - see https://github.com/obophenotype/brain_data_standards_ontologies/issues/231. Use PCL:1000003 instead. + obsolete basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) + true @@ -41601,7 +42128,6 @@ plexiform layer using GABA. - A mesothelial fibroblast of the arachnoid barrier layer. Arachnoid barrier cells make up the tight-junctioned layer in the leptomeninx that functions as the physiologic barrier between the cerebrospinal fluid in the subarachnoid space and the fenestrated capillaries in the dura. @@ -41929,6 +42455,179 @@ plexiform layer using GABA. + + + + + A sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection. + + long-range GABAergic interneuron + CL:4023121 + sst chodl GABAergic cortical interneuron + + + + + + + + + An interneuron located in the cerebral cortex that expresses the oxytocin receptor. These interneurons also express somatostatin. + + + OxtrINs + CL:4023122 + These cells were first identified in mouse. + oxytocin receptor sst GABAergic cortical interneuron + + + + + + + + + A retinal cell that is immature or undifferentiated. + + + retinal stem cell + CL:4023129 + retinoblast + + + + + + + + + + Any capillary endothelial cell that is part of a lung. + http://orcid.org/0000-0002-3293-5463 + 2021-11-23T02:31:40Z + lung capillary endothelial cell + CL:4028001 + pulmonary capillary endothelial cell + + + + + + + + + + An alveolar capillary endothelial cell that is located distally to alveolar capillary type 2 endothelial cells. + http://orcid.org/0000-0002-3293-5463 + 2021-11-23T03:23:53Z + 'CAP1' + 'capillary 1 cell' + 'gCAP' + 'general capillary cell' + CL:4028002 + alveolar capillary type 1 endothelial cell + + + + + + + + + + An alveolar capillary endothelial cell that is located proximally to alveolar capillary type 1 endothelial cells and in close apposition to alveolar type 1 epithelial cells (also known as type I pneumocytes). + http://orcid.org/0000-0002-3293-5463 + 2021-11-23T03:23:53Z + CD34hi endothelial cells + Car4+ capillary endothelial cell + aCAP + aerocyte + alveolar capillary cell + capillary 2 cell + CL:4028003 + alveolar capillary type 2 endothelial cell + + + + + + + + + + A pulmonary interstitial fibroblast that is part of the alveolus and contains lipid droplets. + https://orcid.org/0000-0001-9610-7627 + https://orcid.org/0000-0002-1425-877X + https://orcid.org/0000-0002-8445-4565 + http://orcid.org/0000-0002-3293-5463 + 2021-12-09T15:34:13Z + AF1 + alveolar fibroblast + alveolar fibroblast 1 + lipid interstitial cell + lipofibroblast + matrix fibroblast 1 + pulmonary lipofibroblast + CL:4028004 + alveolar type 1 fibroblast cell + + + + + + + + + + A pulmonary interstitial fibroblast that is part of the alveolus and localizes to vascular adventitia. + http://orcid.org/0000-0002-3293-5463 + 2021-12-09T15:53:21Z + AF2 + MANC + adventitial fibroblast + alveolar fibroblast + matrix fibroblast 2 + mesenchymal alveolar niche cell + type-2 associated stromal cell + CL:4028006 + alveolar type 2 fibroblast cell + + + + + + + + + A melanocyte located in the vascular uvea and involved in photoprotection, regulation of oxidative damage and immune responses. + http://orcid.org/0000-0002-1773-2692 + 2022-01-20T12:59:06Z + uveal melanocyte + CL:4030000 + Cellular functions and extracellular interactions of choroidal melanocytes are distinct to skin melanocytes. They might have both neuroectodermal as well as mesectodermal origins. + choroidal melanocyte + + + + + + + + + An alpha-beta memory T cell with the phenotype CD45RA-positive. + + 2022-02-01T13:04:46Z + TEMRA + effector memory RA T cell + TEMRA cell + terminally differentiated effector memory CD45RA+ T cells + terminally differentiated effector memory cells re-expressing CD45RA + CL:4030002 + effector memory CD45RA-positive, alpha-beta T cell, terminally differentiated + + + + diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 842192dfa6..c2b871607b 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -280,13 +280,6 @@ $(IMPORTDIR)/chebi_import.owl: $(MIRRORDIR)/chebi.owl $(IMPORTDIR)/chebi_terms_c query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \ annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi -## Module for ontology: ncbitaxon - -$(IMPORTDIR)/ncbitaxon_import.owl: $(MIRRORDIR)/ncbitaxon.owl $(IMPORTDIR)/ncbitaxon_terms_combined.txt - if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) extract -i $< -T $(IMPORTDIR)/ncbitaxon_terms_combined.txt --force true --individuals include --method BOT \ - query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \ - annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi - .PHONY: refresh-imports refresh-imports: make IMP=true MIR=true PAT=false IMP_LARGE=true all_imports -B @@ -374,7 +367,7 @@ mirror-ro: | $(TMPDIR) .PHONY: mirror-bspo .PRECIOUS: $(MIRRORDIR)/bspo.owl mirror-bspo: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/bspo.owl --create-dirs -o $(MIRRORDIR)/bspo.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/bspo.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/bspo/bspo-base.owl --create-dirs -o $(MIRRORDIR)/bspo.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/bspo.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: chebi @@ -402,7 +395,7 @@ mirror-bfo: | $(TMPDIR) .PHONY: mirror-ncbitaxon .PRECIOUS: $(MIRRORDIR)/ncbitaxon.owl mirror-ncbitaxon: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then curl -L $(URIBASE)/ncbitaxon.owl.gz --create-dirs -o $(MIRRORDIR)/ncbitaxon.owl.gz --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/ncbitaxon.owl.gz -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: nbo @@ -430,7 +423,7 @@ mirror-cteno: | $(TMPDIR) .PHONY: mirror-ehdaa2 .PRECIOUS: $(MIRRORDIR)/ehdaa2.owl mirror-ehdaa2: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/ehdaa2.owl --create-dirs -o $(MIRRORDIR)/ehdaa2.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/ehdaa2.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://raw.githubusercontent.com/cmungall/human-developmental-anatomy-ontology/uberon/src/ontology/ehdaa2-edit.obo -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: emapa diff --git a/src/ontology/components/develops-from-chains.owl b/src/ontology/components/develops-from-chains.owl new file mode 100644 index 0000000000..10891b3159 --- /dev/null +++ b/src/ontology/components/develops-from-chains.owl @@ -0,0 +1,13 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +SubObjectPropertyOf(ObjectPropertyChain( ) ) + +) \ No newline at end of file diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 162c426eb8..0c31d17365 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -186,8 +186,8 @@ property_value: doap-GitRepository https://github.com/cmungall/uberon/ xsd:anyUR property_value: doap-mailing-list https://lists.sourceforge.net/lists/listinfo/obo-anatomy xsd:anyURI property_value: doap-SVNRepository https://obo.svn.sourceforge.net/svnroot/obo/uberon/ xsd:anyURI property_value: foaf-homepage http://uberon.org xsd:anyURI -property_value: IAO:0000700 UBERON:0000104 -property_value: IAO:0000700 UBERON:0001062 +property_value: has_ontology_root_term UBERON:0000104 +property_value: has_ontology_root_term UBERON:0001062 treat-xrefs-as-has-subclass: EHDAA treat-xrefs-as-has-subclass: EV treat-xrefs-as-has-subclass: NCIT @@ -45979,6 +45979,7 @@ property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/4/43/C id: UBERON:0002246 name: dorsal thoracic nucleus def: "Two column-shaped nuclear masses formed by large cells. Clarke's nuclei are located in the regions dorsolateral to the central canal in the thoratic and upper lumbar segments." [NLXANAT:20090102] +comment: "Created by Sarah M. Maynard" xsd:string subset: uberon_slim synonym: "Clarke's column" EXACT [] synonym: "Clarke's nuclei" RELATED PLURAL [NLXANAT:20090102] @@ -46002,7 +46003,6 @@ xref: Wikipedia:Clarke's_column is_a: UBERON:0011777 {source="FMA"} ! nucleus of spinal cord relationship: part_of UBERON:0002256 ! dorsal horn of spinal cord property_value: external_definition "Clarke's column (column of Clarke, dorsal nucleus, posterior thoracic nucleus, nucleus dorsalis of Clarke) is a group of interneurons found in the medial part of Lamina VII, also known as the intermediate zone, of the spinal cord. It is mainly located from the T1 to L3-L4 levels and is an important structure for proprioception[Wikipedia:Posterior_thoracic_nucleus]." xsd:string {source="Wikipedia:Posterior_thoracic_nucleus"} -property_value: IAO:0000117 "Sarah M. Maynard" xsd:string [Term] id: UBERON:0002247 @@ -81571,7 +81571,6 @@ xref: NCIT:C32256 xref: SCTID:280605006 xref: UMLS:C0229108 {source="ncithesaurus:Canal_of_Schlemm"} xref: Wikipedia:Schlemm's_canal -xref: ZFA:0005829 is_a: UBERON:0001638 ! vein relationship: part_of UBERON:0003956 ! aqueous drainage system relationship: tributary_of UBERON:0003712 {source="FMA/obol"} ! cavernous sinus @@ -91649,7 +91648,6 @@ xref: UMLS:C0022427 {source="ncithesaurus:Jugular_Vein"} xref: Wikipedia:Jugular_vein is_a: UBERON:0001638 ! vein relationship: drains UBERON:0000033 ! head -relationship: part_of UBERON:0000974 ! neck property_value: depicted_by http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png xsd:anyURI [Term] @@ -191126,127 +191124,127 @@ is_a: UBERON:0005612 ! intercostal artery [Term] id: UBERON:0039838 name: seventh anterior intercostal artery +xref: FMA:10649 is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery relationship: part_of UBERON:0006632 {source="FMA"} ! musculo-phrenic artery -xref: FMA:10649 ! seventh anterior intercostal artery [Term] id: UBERON:0039839 name: eighth anterior intercostal artery +xref: FMA:10650 is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery relationship: part_of UBERON:0006632 {source="FMA"} ! musculo-phrenic artery -xref: FMA:10650 ! eighth anterior intercostal artery [Term] id: UBERON:0039840 name: ninth anterior intercostal artery +xref: FMA:10651 is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery relationship: part_of UBERON:0006632 {source="FMA"} ! musculo-phrenic artery -xref: FMA:10651 ! ninth anterior intercostal artery [Term] id: UBERON:0039841 name: first anterior intercostal artery +synonym: "first intercostal branch of internal thoracic artery" EXACT [FMA:10652] +xref: FMA:10652 is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery relationship: part_of UBERON:0002456 {source="FMA"} ! internal thoracic artery -synonym: "first intercostal branch of internal thoracic artery" EXACT [FMA:10652] -xref: FMA:10652 ! first anterior intercostal artery [Term] id: UBERON:0039842 name: second anterior intercostal artery +synonym: "second intercostal branch of internal thoracic artery" EXACT [FMA:10653] +xref: FMA:10653 is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery relationship: part_of UBERON:0002456 {source="FMA"} ! internal thoracic artery -synonym: "second intercostal branch of internal thoracic artery" EXACT [FMA:10653] -xref: FMA:10653 ! second anterior intercostal artery [Term] id: UBERON:0039843 name: third anterior intercostal artery +synonym: "third intercostal branch of internal thoracic artery" EXACT [FMA:10654] +xref: FMA:10654 is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery relationship: part_of UBERON:0002456 {source="FMA"} ! internal thoracic artery -synonym: "third intercostal branch of internal thoracic artery" EXACT [FMA:10654] -xref: FMA:10654 ! third anterior intercostal artery [Term] id: UBERON:0039844 name: fourth anterior intercostal artery +synonym: "fourth intercostal branch of internal thoracic artery" EXACT [FMA:10655] +xref: FMA:10655 is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery relationship: part_of UBERON:0002456 {source="FMA"} ! internal thoracic artery -synonym: "fourth intercostal branch of internal thoracic artery" EXACT [FMA:10655] -xref: FMA:10655 ! fourth anterior intercostal artery [Term] id: UBERON:0039845 name: fifth anterior intercostal artery +synonym: "fifth intercostal branch of internal thoracic artery" EXACT [FMA:10656] +xref: FMA:10656 is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery relationship: part_of UBERON:0002456 {source="FMA"} ! internal thoracic artery -synonym: "fifth intercostal branch of internal thoracic artery" EXACT [FMA:10656] -xref: FMA:10656 ! fifth anterior intercostal artery [Term] id: UBERON:0039846 name: sixth anterior intercostal artery +synonym: "sixth intercostal branch of internal thoracic artery" EXACT [FMA:10657] +xref: FMA:10657 is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery relationship: part_of UBERON:0002456 {source="FMA"} ! internal thoracic artery -synonym: "sixth intercostal branch of internal thoracic artery" EXACT [FMA:10657] -xref: FMA:10657 ! sixth anterior intercostal artery [Term] id: UBERON:0039847 name: suprascapular artery +synonym: "transverse scapular artery" EXACT [FMA:10663] +xref: FMA:10663 is_a: UBERON:0001637 ! artery relationship: part_of UBERON:0039260 {source="FMA"} ! thyrocervical artery -synonym: "transverse scapular artery" EXACT [FMA:10663] -xref: FMA:10663 ! suprascapular artery [Term] id: UBERON:0039848 name: anterior external vertebral venous plexus +xref: FMA:10787 is_a: UBERON:0039258 {source="FMA"} ! external vertebral venous plexus -xref: FMA:10787 ! anterior external vertebral venous plexus [Term] id: UBERON:0039849 name: posterior external vertebral venous plexus +xref: FMA:12852 is_a: UBERON:0039258 {source="FMA"} ! external vertebral venous plexus -xref: FMA:12852 ! posterior external vertebral venous plexus [Term] id: UBERON:0039850 name: left anterior segmental artery -synonym: "anterior bronchopulmonary segment of left pulmonary artery" EXACT [FMA:13279] -synonym: "anterior segmental artery of left lung" EXACT [FMA:13279] -synonym: "anterior segmental artery of left upper lobe" EXACT [FMA:13279] -xref: FMA:13279 ! left anterior segmental artery +synonym: "anterior bronchopulmonary segment of left pulmonary artery" EXACT [FMA:13279] +synonym: "anterior segmental artery of left lung" EXACT [FMA:13279] +synonym: "anterior segmental artery of left upper lobe" EXACT [FMA:13279] +xref: FMA:13279 [Term] id: UBERON:0039851 name: apicoposterior segmental artery +synonym: "apicoposterior artery of left lung" EXACT [FMA:13281] +synonym: "apicoposterior bronchopulmonary segment of left pulmonary artery" EXACT [FMA:13281] +synonym: "left apicoposterior pulmonary artery" EXACT [FMA:13281] +xref: FMA:13281 is_a: UBERON:0039262 {source="FMA"} ! segmental pulmonary artery -synonym: "apicoposterior artery of left lung" EXACT [FMA:13281] -synonym: "apicoposterior bronchopulmonary segment of left pulmonary artery" EXACT [FMA:13281] -synonym: "left apicoposterior pulmonary artery" EXACT [FMA:13281] -xref: FMA:13281 ! apicoposterior segmental artery [Term] id: UBERON:0039856 name: right ovarian vein def: "Ovarian vein, each instance of which is a tributary of some inferior vena cava that drains the right pampiniform plexus of some broad ligament." [FMA:14342] +xref: FMA:14342 is_a: UBERON:0001145 {source="FMA"} ! ovarian vein intersection_of: UBERON:0001145 ! ovarian vein intersection_of: drains UBERON:0002118 ! right ovary relationship: tributary_of UBERON:0001072 {source="FMA"} ! posterior vena cava -xref: FMA:14342 ! right ovarian vein [Term] id: UBERON:0039857 name: left ovarian vein def: "Ovarian vein, each instance of which is a tributary of some left renal vein that drains the left pampiniform plexus of some broad ligament." [FMA:14347] +xref: FMA:14347 is_a: UBERON:0001145 {source="FMA"} ! ovarian vein intersection_of: UBERON:0001145 ! ovarian vein intersection_of: drains UBERON:0002119 ! left ovary -xref: FMA:14347 ! left ovarian vein [Term] id: UBERON:1000000 @@ -222069,7 +222067,7 @@ def: "The ridge of the trochlea on a humerus lies in the middle of the distal en is_a: UBERON:4200230 ! surface of bone relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:0000144 ! trochlea of humerus -property_value: http://purl.org/dc/elements/1.1/date 2021-05-27T23:57:42Z xsd:dateTime +property_value: dcterms-date 2021-05-27T23:57:42Z xsd:dateTime [Term] id: UBERON:7500062 @@ -222079,7 +222077,7 @@ synonym: "fossa digitalis" EXACT [] intersection_of: UBERON:0005813 ! tubercle intersection_of: part_of UBERON:0008772 ! proximal epiphysis of tibia relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 -property_value: http://purl.org/dc/elements/1.1/date 2021-05-28T00:06:11Z xsd:dateTime +property_value: dcterms-date 2021-05-28T00:06:11Z xsd:dateTime [Term] id: UBERON:7500063 @@ -222090,7 +222088,7 @@ synonym: "trochlea of astragalus" EXACT [] synonym: "trochlea tali" EXACT [] is_a: UBERON:7500081 ! articular surface for the tibia on the talus relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 -property_value: http://purl.org/dc/elements/1.1/date 2021-05-28T00:56:19Z xsd:dateTime +property_value: dcterms-date 2021-05-28T00:56:19Z xsd:dateTime [Term] id: UBERON:7500064 @@ -222100,7 +222098,7 @@ synonym: "trochlear groove of astragalus" EXACT [] is_a: UBERON:4200230 ! surface of bone relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:0002395 ! talus -property_value: http://purl.org/dc/elements/1.1/date 2021-05-28T00:57:49Z xsd:dateTime +property_value: dcterms-date 2021-05-28T00:57:49Z xsd:dateTime [Term] id: UBERON:7500065 @@ -222110,7 +222108,7 @@ synonym: "condyle of astragalus" EXACT [] intersection_of: UBERON:0009979 ! condyle intersection_of: part_of UBERON:0002395 ! talus relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 -property_value: http://purl.org/dc/elements/1.1/date 2021-05-28T00:59:42Z xsd:dateTime +property_value: dcterms-date 2021-05-28T00:59:42Z xsd:dateTime [Term] id: UBERON:7500066 @@ -222120,7 +222118,7 @@ synonym: "medial condyle of astragalus" EXACT [] is_a: UBERON:0009979 ! condyle relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:0002395 ! talus -property_value: http://purl.org/dc/elements/1.1/date 2021-05-28T01:00:50Z xsd:dateTime +property_value: dcterms-date 2021-05-28T01:00:50Z xsd:dateTime [Term] id: UBERON:7500067 @@ -222130,7 +222128,7 @@ synonym: "lateral condyle of astragalus" EXACT [] is_a: UBERON:0009979 ! condyle relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:0002395 ! talus -property_value: http://purl.org/dc/elements/1.1/date 2021-05-28T01:02:26Z xsd:dateTime +property_value: dcterms-date 2021-05-28T01:02:26Z xsd:dateTime [Term] id: UBERON:7500068 @@ -222140,7 +222138,7 @@ synonym: "ridge of medial condyle of astragalus" EXACT [] is_a: UBERON:4200230 ! surface of bone relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:7500066 ! medial condyle of talus -property_value: http://purl.org/dc/elements/1.1/date 2021-05-28T01:03:10Z xsd:dateTime +property_value: dcterms-date 2021-05-28T01:03:10Z xsd:dateTime [Term] id: UBERON:7500069 @@ -222150,7 +222148,7 @@ synonym: "ridge of lateral condyle of astragalus" EXACT [] is_a: UBERON:4200230 ! surface of bone relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:7500067 ! lateral condyle of talus -property_value: http://purl.org/dc/elements/1.1/date 2021-05-28T01:03:51Z xsd:dateTime +property_value: dcterms-date 2021-05-28T01:03:51Z xsd:dateTime [Term] id: UBERON:7500070 @@ -222160,7 +222158,7 @@ synonym: "sulcus for flexor hallucis longus tendon" EXACT [] is_a: UBERON:0000093 ! sulcus relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:0002395 ! talus -property_value: http://purl.org/dc/elements/1.1/date 2021-05-28T01:09:52Z xsd:dateTime +property_value: dcterms-date 2021-05-28T01:09:52Z xsd:dateTime [Term] id: UBERON:7500071 @@ -222174,7 +222172,7 @@ relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: part_of UBERON:0003128 ! cranium relationship: part_of UBERON:0004089 ! midface -property_value: http://purl.org/dc/elements/1.1/date 2021-05-28T06:58:22Z xsd:dateTime +property_value: dcterms-date 2021-05-28T06:58:22Z xsd:dateTime [Term] id: UBERON:7500073 @@ -222183,7 +222181,7 @@ def: "Nasal bone on the left side of an organism when in anatomical position." [ intersection_of: UBERON:0001681 ! nasal bone intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 -property_value: http://purl.org/dc/elements/1.1/date 2021-05-28T19:07:14Z xsd:dateTime +property_value: dcterms-date 2021-05-28T19:07:14Z xsd:dateTime [Term] id: UBERON:7500074 @@ -222192,7 +222190,7 @@ def: "Nasal bone on the right side of an organism when in anatomical position." intersection_of: UBERON:0001681 ! nasal bone intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 -property_value: http://purl.org/dc/elements/1.1/date 2021-05-28T19:08:06Z xsd:dateTime +property_value: dcterms-date 2021-05-28T19:08:06Z xsd:dateTime [Term] id: UBERON:7500075 @@ -222201,7 +222199,7 @@ def: "Zygomatic arch on the left side of an organism when in anatomical position intersection_of: UBERON:0002500 ! zygomatic arch intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 -property_value: http://purl.org/dc/elements/1.1/date 2021-05-28T19:10:56Z xsd:dateTime +property_value: dcterms-date 2021-05-28T19:10:56Z xsd:dateTime [Term] id: UBERON:7500076 @@ -222210,7 +222208,7 @@ def: "Zygomatic arch on the right side of an organism when in anatomical positio intersection_of: UBERON:0002500 ! zygomatic arch intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 -property_value: http://purl.org/dc/elements/1.1/date 2021-05-28T19:11:21Z xsd:dateTime +property_value: dcterms-date 2021-05-28T19:11:21Z xsd:dateTime [Term] id: UBERON:7500077 @@ -222219,7 +222217,7 @@ def: "A trochlea on the distal end of a femur that interacts with the patella." synonym: "patellar surface of femur" EXACT [] is_a: UBERON:4200230 ! surface of bone relationship: part_of UBERON:0004406 ! distal epiphysis of femur -property_value: http://purl.org/dc/elements/1.1/date 2021-06-02T00:19:07Z xsd:dateTime +property_value: dcterms-date 2021-06-02T00:19:07Z xsd:dateTime [Term] id: UBERON:7500078 @@ -222230,7 +222228,7 @@ synonym: "radial styloid process" EXACT [] intersection_of: UBERON:0009979 ! condyle intersection_of: part_of UBERON:0004407 ! distal epiphysis of radius relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 -property_value: http://purl.org/dc/elements/1.1/date 2021-06-03T00:20:10Z xsd:dateTime +property_value: dcterms-date 2021-06-03T00:20:10Z xsd:dateTime [Term] id: UBERON:7500079 @@ -222242,7 +222240,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: in_taxon NCBITaxon:9788 ! Equidae relationship: part_of UBERON:0004407 ! distal epiphysis of radius -property_value: http://purl.org/dc/elements/1.1/date 2021-06-03T00:22:09Z xsd:dateTime +property_value: dcterms-date 2021-06-03T00:22:09Z xsd:dateTime [Term] id: UBERON:7500080 @@ -222252,7 +222250,7 @@ synonym: "distal articular surface of radius" EXACT [] is_a: UBERON:4100003 ! articular surface relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:0004407 ! distal epiphysis of radius -property_value: http://purl.org/dc/elements/1.1/date 2021-06-03T00:23:08Z xsd:dateTime +property_value: dcterms-date 2021-06-03T00:23:08Z xsd:dateTime [Term] id: UBERON:7500081 @@ -222261,7 +222259,7 @@ def: "Contact surface between the tibia and the talus located on the talus." [ht is_a: UBERON:4100003 ! articular surface relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:0002395 ! talus -property_value: http://purl.org/dc/elements/1.1/date 2021-07-27T17:04:35Z xsd:dateTime +property_value: dcterms-date 2021-07-27T17:04:35Z xsd:dateTime [Term] id: UBERON:7500083 @@ -222270,7 +222268,7 @@ def: "A foramen of the skull found at either posterior angle of the hard palate, is_a: UBERON:0013685 ! foramen of skull relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:0001682 ! palatine bone -property_value: http://purl.org/dc/elements/1.1/date 2021-07-28T20:01:21Z xsd:dateTime +property_value: dcterms-date 2021-07-28T20:01:21Z xsd:dateTime [Term] id: UBERON:7500084 @@ -222279,7 +222277,7 @@ def: "A foramen of the skull found at either posterior angle of the hard palate is_a: UBERON:0013685 ! foramen of skull relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:0001682 ! palatine bone -property_value: http://purl.org/dc/elements/1.1/date 2021-07-28T20:07:21Z xsd:dateTime +property_value: dcterms-date 2021-07-28T20:07:21Z xsd:dateTime [Term] id: UBERON:7500085 @@ -222288,17 +222286,17 @@ def: "A pulp-dentin complex or endodont that is part of a calcareous tooth." [ht synonym: "endodont" EXACT [] synonym: "pulp-dentin complex" EXACT [] is_a: UBERON:0010365 ! odontoid tissue +relationship: dc-contributor http://orcid.org/0000-0003-2699-3066 relationship: has_part UBERON:0001751 ! dentine relationship: has_part UBERON:0001754 ! dental pulp relationship: part_of UBERON:0001091 ! calcareous tooth -property_value: http://purl.org/dc/elements/1.1/date 2021-07-28T20:20:53Z xsd:dateTime -property_value: term:editor http://orcid.org/0000-0003-2699-3066 +property_value: dcterms-date 2021-07-28T20:20:53Z xsd:dateTime [Term] id: UBERON:7500088 name: obsolete distal articular surface of radius comment: already made this term -property_value: http://purl.org/dc/elements/1.1/date 2021-08-03T21:28:12Z xsd:dateTime +property_value: dcterms-date 2021-08-03T21:28:12Z xsd:dateTime is_obsolete: true replaced_by: UBERON:7500080 @@ -222310,7 +222308,7 @@ synonym: "proximal facet of calcaneum" EXACT [] is_a: UBERON:4300038 ! facet relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:0001450 ! calcaneus -property_value: http://purl.org/dc/elements/1.1/date 2021-08-04T00:14:22Z xsd:dateTime +property_value: dcterms-date 2021-08-04T00:14:22Z xsd:dateTime [Term] id: UBERON:7500091 @@ -222319,7 +222317,7 @@ def: "Middle facet on the proximal surface of the calcaneus for the articulation is_a: UBERON:4300038 ! facet relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:0001450 ! calcaneus -property_value: http://purl.org/dc/elements/1.1/date 2021-08-04T00:19:10Z xsd:dateTime +property_value: dcterms-date 2021-08-04T00:19:10Z xsd:dateTime [Term] id: UBERON:7500092 @@ -222329,7 +222327,7 @@ synonym: "distal facet of calcaneum" EXACT [] is_a: UBERON:4300038 ! facet relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:0001450 ! calcaneus -property_value: http://purl.org/dc/elements/1.1/date 2021-08-04T00:21:34Z xsd:dateTime +property_value: dcterms-date 2021-08-04T00:21:34Z xsd:dateTime [Term] id: UBERON:7500093 @@ -222339,7 +222337,7 @@ synonym: "corpus calcanei" EXACT [] is_a: UBERON:0005913 ! zone of bone organ relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:0001450 ! calcaneus -property_value: http://purl.org/dc/elements/1.1/date 2021-08-04T00:23:29Z xsd:dateTime +property_value: dcterms-date 2021-08-04T00:23:29Z xsd:dateTime [Term] id: UBERON:7500094 @@ -222350,7 +222348,7 @@ synonym: "trochlear process of calcaneus" EXACT [] intersection_of: UBERON:0005813 ! tubercle intersection_of: part_of UBERON:0001450 ! calcaneus relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 -property_value: http://purl.org/dc/elements/1.1/date 2021-08-04T00:25:01Z xsd:dateTime +property_value: dcterms-date 2021-08-04T00:25:01Z xsd:dateTime [Term] id: UBERON:7500095 @@ -222358,7 +222356,7 @@ name: lateral tubercle of calcaneus def: "A raised projection on the lateral side of a calcaneus." [https://orcid.org/0000-0003-2699-3066] is_a: UBERON:7500094 ! tubercle of calcaneus relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 -property_value: http://purl.org/dc/elements/1.1/date 2021-08-04T00:26:41Z xsd:dateTime +property_value: dcterms-date 2021-08-04T00:26:41Z xsd:dateTime [Term] id: UBERON:7500096 @@ -222366,7 +222364,7 @@ name: medial tubercle of calcaneus def: "A raised projection on the medial side of a calcaneus." [https://orcid.org/0000-0003-2699-3066] is_a: UBERON:7500094 ! tubercle of calcaneus relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 -property_value: http://purl.org/dc/elements/1.1/date 2021-08-04T00:27:56Z xsd:dateTime +property_value: dcterms-date 2021-08-04T00:27:56Z xsd:dateTime [Term] id: UBERON:7500101 @@ -222473,7 +222471,7 @@ relationship: only_in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0014860 ! copepodite stage relationship: part_of UBERON:0018378 ! crustacean larval stage relationship: preceded_by UBERON:0014406 ! nauplius stage -property_value: http://purl.org/dc/elements/1.1/date 2021-07-26T14:57:48Z xsd:dateTime +property_value: dcterms-date 2021-07-26T14:57:48Z xsd:dateTime [Term] id: UBERON:8200003 @@ -222485,7 +222483,7 @@ relationship: only_in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0014860 ! copepodite stage relationship: part_of UBERON:0018378 ! crustacean larval stage relationship: preceded_by UBERON:8200002 ! copepodite stage 1 -property_value: http://purl.org/dc/elements/1.1/date 2021-07-26T15:07:18Z xsd:dateTime +property_value: dcterms-date 2021-07-26T15:07:18Z xsd:dateTime [Term] id: UBERON:8200004 @@ -222497,7 +222495,7 @@ relationship: only_in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0014860 ! copepodite stage relationship: part_of UBERON:0018378 ! crustacean larval stage relationship: preceded_by UBERON:8200003 ! copepodite stage 2 -property_value: http://purl.org/dc/elements/1.1/date 2021-07-26T15:43:37Z xsd:dateTime +property_value: dcterms-date 2021-07-26T15:43:37Z xsd:dateTime [Term] id: UBERON:8200005 @@ -222509,7 +222507,7 @@ relationship: only_in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0014860 ! copepodite stage relationship: part_of UBERON:0018378 ! crustacean larval stage relationship: preceded_by UBERON:8200004 ! copepodite stage 3 -property_value: http://purl.org/dc/elements/1.1/date 2021-07-26T15:45:12Z xsd:dateTime +property_value: dcterms-date 2021-07-26T15:45:12Z xsd:dateTime [Term] id: UBERON:8200006 @@ -222520,7 +222518,7 @@ relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 relationship: only_in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0000113 ! post-juvenile adult stage relationship: preceded_by UBERON:8200005 ! copepodite stage 4 -property_value: http://purl.org/dc/elements/1.1/date 2021-07-26T15:46:40Z xsd:dateTime +property_value: dcterms-date 2021-07-26T15:46:40Z xsd:dateTime [Term] id: UBERON:8200007 @@ -222531,7 +222529,7 @@ relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 relationship: only_in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0000066 ! fully formed stage relationship: preceded_by UBERON:8200006 ! copepodite stage 5 -property_value: http://purl.org/dc/elements/1.1/date 2021-07-26T15:48:54Z xsd:dateTime +property_value: dcterms-date 2021-07-26T15:48:54Z xsd:dateTime [Term] id: UBERON:8300000 @@ -223429,7 +223427,7 @@ synonym: "small intestine capillary" EXACT [] intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0002108 ! small intestine relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/elements/1.1/date 2021-12-21T15:14:31Z xsd:dateTime +property_value: dcterms-date 2021-12-21T15:14:31Z xsd:dateTime [Term] id: UBERON:8410069 @@ -223440,7 +223438,7 @@ synonym: "avian lymphoid nodule" EXACT [] is_a: UBERON:0001744 ! lymphoid tissue relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: in_taxon NCBITaxon:8782 ! Aves -property_value: http://purl.org/dc/elements/1.1/date 2022-01-24T16:47:47Z xsd:dateTime +property_value: dcterms-date 2022-01-24T16:47:47Z xsd:dateTime [Term] id: UBERON:8410070 @@ -223456,30 +223454,34 @@ relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: has_muscle_insertion UBERON:0002228 ! rib relationship: has_muscle_origin UBERON:0001077 ! transverse process of vertebra relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: http://purl.org/dc/elements/1.1/date 2022-01-27T10:41:44Z xsd:dateTime +property_value: dcterms-date 2022-01-27T10:41:44Z xsd:dateTime [Term] id: UBERON:8410071 name: subcapsular sinus ceiling -def: "The upward section of the subcapsular sinus of lymph node. In human, it's characterized by specific protein markers." [PMID:31402260] +def: "The section of the lymph node capsule that faces the subcapsular sinus. In human, it's characterized by specific protein markers." [PMID:31402260] synonym: "ceiling of subcapsular sinus of lymph node" EXACT [] +synonym: "floor of capsule of lymph node" EXACT [] synonym: "subcapsular sinus of lymph node ceiling" EXACT [] is_a: UBERON:0000064 ! organ part +relationship: adjacent_to UBERON:0005463 ! subcapsular sinus of lymph node relationship: dc-contributor http://orcid.org/0000-0002-2825-0621 -relationship: part_of UBERON:0005463 ! subcapsular sinus of lymph node +relationship: part_of UBERON:0002194 ! capsule of lymph node relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: http://purl.org/dc/elements/1.1/date 2022-02-22T17:04:49Z xsd:dateTime +property_value: dcterms-date 2022-02-22T17:04:49Z xsd:dateTime [Term] id: UBERON:8410072 name: subcapsular sinus floor -def: "The downward section of the subcapsular sinus of lymph node. In human, it's characterized by specific protein markers." [PMID:31402260] +def: "The section of the lymph node cortex that faces the subcapsular sinus. In human, it's characterized by specific protein markers." [PMID:31402260] +synonym: "ceiling of cortex of lymph node" EXACT [] synonym: "floor of subcapsular sinus of lymph node" EXACT [] synonym: "subcapsular sinus of lymph node floor" EXACT [] is_a: UBERON:0000064 ! organ part +relationship: adjacent_to UBERON:0005463 ! subcapsular sinus of lymph node relationship: dc-contributor http://orcid.org/0000-0002-2825-0621 -relationship: part_of UBERON:0005463 ! subcapsular sinus of lymph node -property_value: http://purl.org/dc/elements/1.1/date 2022-02-22T17:16:40Z xsd:dateTime +relationship: part_of UBERON:0002006 ! cortex of lymph node +property_value: dcterms-date 2022-02-22T17:16:40Z xsd:dateTime [Term] id: UBERON:8410073 @@ -223491,7 +223493,7 @@ is_a: UBERON:0000064 ! organ part relationship: has_part UBERON:0001284 ! renal column relationship: has_part UBERON:0004200 ! kidney pyramid relationship: part_of UBERON:0002113 ! kidney -property_value: http://purl.org/dc/elements/1.1/date 2022-02-03T14:18:40Z xsd:dateTime +property_value: dcterms-date 2022-02-03T14:18:40Z xsd:dateTime property_value: seeAlso https://github.com/obophenotype/uberon/issues/2126 xsd:string created_by: http://orcid.org/0000-0002-2825-0621 @@ -223507,7 +223509,7 @@ is_a: UBERON:0004111 ! anatomical conduit relationship: dc-contributor http://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410066 ! lymph node paracortex relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: http://purl.org/dc/elements/1.1/date 2022-02-24T11:30:26Z xsd:dateTime +property_value: dcterms-date 2022-02-24T11:30:26Z xsd:dateTime [Term] id: UBERON:8410075 @@ -223518,7 +223520,7 @@ is_a: UBERON:0000353 ! parenchyma relationship: dc-contributor http://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410066 ! lymph node paracortex relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: http://purl.org/dc/elements/1.1/date 2022-02-24T11:40:24Z xsd:dateTime +property_value: dcterms-date 2022-02-24T11:40:24Z xsd:dateTime [Term] id: UBERON:8410076 @@ -223533,7 +223535,7 @@ synonym: "glomus body" EXACT [PMID:30799440] synonym: "Luschka's gland" EXACT [WikipediaVersioned:Coccygeal_glomus&oldid=1019065130] is_a: UBERON:0010000 ! multicellular anatomical structure relationship: dc-contributor http://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/elements/1.1/date 2022-02-24T14:12:33Z xsd:dateTime +property_value: dcterms-date 2022-02-24T14:12:33Z xsd:dateTime [Term] id: UBERON:8410077 @@ -223545,7 +223547,7 @@ xref: EFO:0010666 intersection_of: UBERON:0011148 ! submucosal gland intersection_of: part_of UBERON:0000065 ! respiratory tract relationship: dc-contributor http://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/elements/1.1/date 2022-03-24T14:21:59Z xsd:dateTime +property_value: dcterms-date 2022-03-24T14:21:59Z xsd:dateTime [Term] id: UBERON:8410078 @@ -223557,7 +223559,7 @@ xref: FMA:5832 is_a: UBERON:0001473 ! lymphatic vessel relationship: dc-contributor http://orcid.org/0000-0002-2825-0621 relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: http://purl.org/dc/elements/1.1/date 2022-03-25T10:41:22Z xsd:dateTime +property_value: dcterms-date 2022-03-25T10:41:22Z xsd:dateTime [Term] id: UBERON:8420000 @@ -223873,6 +223875,12 @@ name: title xref: http://purl.org/dc/elements/1.1/title is_metadata_tag: true +[Typedef] +id: dcterms-date +name: date +xref: http://purl.org/dc/terms/date +is_metadata_tag: true + [Typedef] id: dcterms-isReferencedBy name: is referenced by @@ -224272,6 +224280,12 @@ expand_assertion_to: "Class: EquivalentT is_metadata_tag: true is_class_level: true +[Typedef] +id: has_ontology_root_term +name: has ontology root term +xref: IAO:0000700 +is_metadata_tag: true + [Typedef] id: has_part name: has part diff --git a/src/ontology/uberon-odk.yaml b/src/ontology/uberon-odk.yaml index d17438371e..282f5d8fe2 100644 --- a/src/ontology/uberon-odk.yaml +++ b/src/ontology/uberon-odk.yaml @@ -36,19 +36,20 @@ import_group: - id: envo - id: ro - id: bspo + use_base: TRUE - id: chebi is_large: TRUE use_gzipped: TRUE - id: pato - id: bfo - id: ncbitaxon - is_large: TRUE - use_gzipped: TRUE + mirror_from: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl - id: nbo # Pipeline dependencies (not directly imported) - id: ceph - id: cteno - id: ehdaa2 + mirror_from: https://raw.githubusercontent.com/cmungall/human-developmental-anatomy-ontology/uberon/src/ontology/ehdaa2-edit.obo - id: emapa - id: fbbt - id: fbdv diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index 316ebbac29..d0014807cd 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -24,7 +24,7 @@ RELSIM = BFO:0000050 RO:0002202 immediate_transformation_of TAXON_GCI_RELS = RO:0002202 RO:0002496 RO:0002497 BFO:0000051 -all: uberon-qc prepare_release clean +all: uberon-qc echo "make $@ succeeded..." # ---------------------------------------- @@ -82,6 +82,8 @@ checks: $(REPORTDIR)/uberon-edit-xp-check $(REPORTDIR)/uberon-edit-obscheck.txt $(REPORTDIR)/uberon-orphans \ $(REPORTDIR)/uberon-synclash +test: $(REPORTDIR)/uberon-edit-xp-check reports/bfo-check.txt + # ---------------------------------------- # STEP 1: pre-processing and quick validation # ---------------------------------------- @@ -108,8 +110,13 @@ tmp/uberon-merged.owl: $(SRC) $(OWLSRC): tmp/uberon-merged.owl $(COMPONENTSDIR)/disjoint_union_over.ofn $(REPORTDIR)/$(SRC)-gocheck $(REPORTDIR)/$(SRC)-iconv $(SCRIPTSDIR)/expand-dbxref-literals.pl echo "STRONG WARNING: issues/contributor.owl needs to be manually updated." $(OWLTOOLS) --no-logging $< $(COMPONENTSDIR)/disjoint_union_over.ofn issues/contributor.owl --merge-support-ontologies --expand-macros -o $@ && $(SCRIPTSDIR)/expand-dbxref-literals.pl $@ > $@.tmp - $(ROBOT) query -i $@.tmp --update $(SPARQLDIR)/taxon_constraint_never_in_taxon.ru --update $(SPARQLDIR)/remove_axioms.ru -o $@ \ - query --update ../sparql/delete-definition-dot.ru merge -i imports/ro_import.owl -o $@ + # The previous step seems to be necessary because somehow the expand-dbxref-literals script expects the owtools output.. No idea why + $(ROBOT) merge -i $@.tmp \ + query \ + --update $(SPARQLDIR)/taxon_constraint_never_in_taxon.ru \ + --update $(SPARQLDIR)/remove_axioms.ru \ + --update $(SPARQLDIR)/delete-definition-dot.ru \ + merge -i imports/ro_import.owl -o $@ $(TMPDIR)/NORMALIZE.obo: $(SRC) $(ROBOT) convert -i $< -o $@.tmp.obo && mv $@.tmp.obo $@ @@ -174,12 +181,16 @@ $(TMPDIR)/is_ok: $(TMPDIR)/materialized.owl ## **Hacking_Feb_2022** TODO - rewrite as as expansions from annotation axioms using SPARQL. Expanded axioms --> component (as for taxon restrictions). TMP_REFL=$(COMPONENTSDIR)/reflexivity_axioms.owl +DEVELOPS_FROM_CHAIN=$(COMPONENTSDIR)/develops-from-chains.owl +# see https://github.com/obophenotype/uberon/issues/2381 + $(TMPDIR)/materialized.owl: $(TMPDIR)/unreasoned.owl $(TMP_REFL) - $(ROBOT) merge -i $< --collapse-import-closure false \ + $(ROBOT) merge -i $< -i $(DEVELOPS_FROM_CHAIN) --collapse-import-closure false \ relax \ materialize -T $(CONFIGDIR)/basic_properties.txt -r elk \ reason -r elk --exclude-duplicate-axioms true --equivalent-classes-allowed asserted-only \ unmerge -i $(TMP_REFL) \ + unmerge -i $(DEVELOPS_FROM_CHAIN) \ annotate -O $(URIBASE)/uberon/materialized.owl -V $(RELEASE)/materialized.owl -o $@ 2>&1 > $@.LOG .PRECIOUS: $(TMPDIR)/materialized.owl @@ -254,70 +265,30 @@ subsets/cumbo.obo: subsets/cumbo.owl # merge BSPO into RO # get rid of it -mirror/bspo.owl: $(OWLSRC) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) merge -I $(URIBASE)/bspo.owl remove --select "BFO:* RO:*" --select "object-properties" --axioms "annotation" -o $@.tmp.owl && mv $@.tmp.owl $@; fi +mirror/bspo.owl: mirror-bspo | $(MIRRORDIR) + if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) merge -I $(URIBASE)/bspo/bspo-base.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi .PRECIOUS: mirror/bspo.owl # Probably no reason to merge them first # --add-obo-shorthand-to-properties: remove this to add mappings into remove -mirror/ro.owl: $(OWLSRC) mirror/bspo.owl - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(OWLTOOLS_NO_CAT) $(URIBASE)/ro.owl mirror/bspo.owl --merge-support-ontologies --merge-imports-closure --add-obo-shorthand-to-properties -o $@ && touch $@; fi - -# make-subset-by-properties -f BFO:0000050 excludes all properties that are not BFO:0000050, essentially making a basic file. Not super relevant here remove here -mirror/pato.owl: $(OWLSRC) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(OWLTOOLS_NO_CAT) $(URIBASE)/pato.owl --extract-mingraph --make-subset-by-properties -f BFO:0000050 // --set-ontology-id $(URIBASE)/pato.owl -o $@; fi - -mirror/envo.owl: $(OWLSRC) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(OWLTOOLS_NO_CAT) $(URIBASE)/envo.owl --extract-mingraph --set-ontology-id $(URIBASE)/envo.owl -o $@; fi - -mirror/nbo.owl: $(OWLSRC) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(OWLTOOLS_NO_CAT) $(URIBASE)/nbo.owl --extract-mingraph --set-ontology-id $(URIBASE)/nbo.owl -o $@; fi - -mirror/chebi.obo.gz: $(OWLSRC) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then wget --no-check-certificate $(URIBASE)/chebi.obo.gz -O $@.tmp && mv $@.tmp $@ && touch $@; fi - -mirror/chebi.obo: mirror/chebi.obo.gz - if [ $(MIR) = true ] && [ $(IMP) = true ]; then gunzip -c $< > $@; fi - -# Does chebi still have these bad non RO OPs? Double check if relations are RO (partof) -mirror/chebi.owl: mirror/chebi.obo - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(OWLTOOLS_NO_CAT) $< --extract-mingraph --rename-entity $(URIBASE)/chebi#has_part $(URIBASE)/BFO_0000051 --make-subset-by-properties -f BFO:0000051 // --set-ontology-id -v $(RELEASE)/chebi.owl $(URIBASE)/chebi.owl -o $@ && touch $@; fi - -# Do not rebuild: PR is now too big -# Why this step? (NICO: to get the branch and remove BFO top level). Dates back to the time when there were bad URIs, maybe we can switch to something normal now. - -#mirror/pr.owl.gz: $(OWLSRC) -# if [ $(MIR) = true ] && [ $(IMP) = true ]; then wget --no-check-certificate $(URIBASE)/pr.owl.gz -O $@.tmp && mv $@.tmp $@ && touch $@; fi -# currently using pro_obo_slim +mirror/ro.owl: mirror/bspo.owl mirror-ro | $(MIRRORDIR) + if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(OWLTOOLS_NO_CAT) $(URIBASE)/ro.owl $< --merge-support-ontologies --merge-imports-closure --add-obo-shorthand-to-properties -o $@ && touch $@; fi -#mirror/pr-gunzip.owl: mirror/pr.owl.gz -# if [ $(MIR) = true ] && [ $(IMP) = true ]; then gunzip -c $< > $@; fi -# currently using pro_obo_slim +imports/envo_import.owl: + echo "ERROR $@ IMPORT CURRENTLY BLOCKED BECAUSE BROKEN UPSTREAM." -#mirror/aminoacid.owl: mirror/pr-gunzip.owl -# if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(OWLTOOLS_NO_CAT) $< --reasoner-query -r elk PR_000018263 --reasoner-dispose --make-ontology-from-results $(URIBASE)/uberon/aminoacid.owl -o $@; fi -# currently using pro_obo_slim +############ -#mirror/pr.owl: mirror/aminoacid.owl -# if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(OWLTOOLS_NO_CAT) mirror/aminoacid.owl --extract-mingraph --rename-entity $(URIBASE)/pr#has_part $(URIBASE)/BFO_0000051 --rename-entity $(URIBASE)/pr#part_of $(URIBASE)/BFO_0000050 --make-subset-by-properties -f BFO:0000050 BFO:0000051 // --split-ontology -d components -l snap --remove-imports-declarations --remove-dangling --set-ontology-id $(URIBASE)/pr.owl -o $@ && touch $@; fi -# currently using pro_obo_slim - -mirror/ncbitaxon.obo: - if [ $(MIR) = true ] && [ $(IMP) = true ]; then wget $(URIBASE)/ncbitaxon.obo -O $@; fi - -mirror/fbbt.obo: - if [ $(MIR) = true ] && [ $(IMP) = true ]; then wget $(URIBASE)/fbbt.obo -O $@; fi - - -$(TMPDIR)/mirror-%: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then wget --no-check-certificate $(URIBASE)/$* -O $@ && touch $@; fi -.PRECIOUS: $(TMPDIR)/mirror-% +# This goal here is needed as a new _intermediate_ for mirrors that need to be fixed +# by hacking into their OBO format representations. +$(TMPDIR)/mirror-%.obo: mirror-% | $(TMPDIR) + if [ $(IMP) = true ] && [ $(MIR) = true ]; then $(ROBOT) convert --input $(TMPDIR)/mirror-$*.owl --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo; fi # Filter only EMAPA classes # EMAPA using a list flat ids for stages, these are mapped to MmusDv ids by fix-emapa-stages.pl # It would be useful to make a combined stage ontology, but than make it filterable by species (subsets) -$(TMPDIR)/fixed-emapa.obo: $(TMPDIR)/mirror-emapa.obo | $(TMPDIR) - $(SCRIPTSDIR)/obo-grep.pl -r 'id: EMAPA' $< | $(SCRIPTSDIR)/fix-emapa-stages.pl > $@ +$(TMPDIR)/fixed-emapa.obo: $(TMPDIR)/mirror-emapa.obo + if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(SCRIPTSDIR)/obo-grep.pl -r 'id: EMAPA' $< | $(SCRIPTSDIR)/fix-emapa-stages.pl > $@; fi # stages must be mapped to MmusDv # We should add releate targets to stage ontology repo makefile. @@ -342,14 +313,14 @@ mirror/zfa.owl: $(TMPDIR)/fixed-zfa.obo $(TMPDIR)/fixed-ehdaa2.obo: $(TMPDIR)/mirror-ehdaa2.obo | $(SCRIPTSDIR)/obo-grep.pl $(SCRIPTSDIR)/fix-ehdaa2-stages.pl if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(SCRIPTSDIR)/obo-grep.pl -r 'id: (EHDAA2|AEO)' $< | $(SCRIPTSDIR)/fix-ehdaa2-stages.pl | grep -v ^alt_id > $@; fi -mirror/ehdaa2.obo: mirror/ehdaa2.owl +mirror/%.obo: mirror/%.owl if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(MAKEOBO); fi # https://raw.githubusercontent.com/cmungall/human-developmental-anatomy-ontology/uberon/src/ontology/ehdaa2-edit.obo # There was a period when Jonathan sent OBO files to Chris # Jonathan has "essentially" seeded the ownership? Double check -mirror/ehdaa2.owl: - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(OWLTOOLS_NO_CAT) https://raw.githubusercontent.com/cmungall/human-developmental-anatomy-ontology/uberon/src/ontology/ehdaa2-edit.obo -o -f ofn $@; fi +#mirror/ehdaa2.owl: +# if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(OWLTOOLS_NO_CAT) https://raw.githubusercontent.com/cmungall/human-developmental-anatomy-ontology/uberon/src/ontology/ehdaa2-edit.obo -o -f ofn $@; fi #CMUNGALL_OBO_SCRIPTS=https://raw.githubusercontent.com/cmungall/obo-scripts/master/ #$(SCRIPTSDIR)/%.pl: @@ -376,8 +347,6 @@ mirror/ehdaa2.owl: # wget http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl -O cached-$@.owl && perl -pi -ne 's@http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#@$(URIBASE)/NIF_GrossAnatomy_@g' cached-$@.owl && owltools cached-$@.owl -o -f obo $@ - - #################################### ### Local Ontology dependencies #### #################################### @@ -394,6 +363,9 @@ imports/local-ceph.owl: # NON-ORTHOGONAL ONTOLOGY MIRRORING +## Devloper notes: Local files are used for a bunch of quality checks, and the composite file +## Not anywhere in normal uberon. + ## Map legacy OBO-format ObjectProperties to their BFO/RO intended equivalent ## a mirror is just a mirror, and local-mirror is a file with all that wrangling needed to message it into the right form. local- files are needed in composite file generation. ## @@ -443,13 +415,6 @@ imports/pato_import.owl: mirror/pato.owl imports/pato_terms_combined.txt query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \ annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi -# TODO - logical definitions go->ubr,cl -imports/go_import.owl: mirror/go.owl $(TMPDIR)/seed.owl - if [ $(IMP) = true ]; then $(OWLTOOLS) --map-ontology-iri $(ONTBASE)/$@ $< $(TMPDIR)/seed.owl --extract-module -s $(URIBASE)/go.owl -c --extract-mingraph --set-ontology-id -v $(RELEASE)/$@ $(ONTBASE)/$@ -o $@; fi - -imports/envo_import.owl: mirror/envo.owl $(TMPDIR)/seed.owl - if [ $(IMP) = true ]; then $(OWLTOOLS) --map-ontology-iri $(ONTBASE)/$@ $< $(TMPDIR)/seed.owl --extract-module -s $(URIBASE)/envo.owl -c --make-subset-by-properties --force --extract-mingraph --set-ontology-id -v $(RELEASE)/$@ $(ONTBASE)/$@ -o $@; fi - imports/nbo_import.owl: mirror/nbo.owl imports/nbo_terms_combined.txt if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ extract -T imports/nbo_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \ @@ -457,13 +422,6 @@ imports/nbo_import.owl: mirror/nbo.owl imports/nbo_terms_combined.txt remove --select "" \ query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \ annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi - -imports/chebi_import.owl: mirror/chebi.owl $(TMPDIR)/seed.owl - if [ $(IMP) = true ]; then $(OWLTOOLS) --map-ontology-iri $(ONTBASE)/$@ $< $(TMPDIR)/seed.owl --extract-module -s $(URIBASE)/chebi.owl -c --extract-mingraph --set-ontology-id -v $(RELEASE)/$@ $(ONTBASE)/$@ -o $@; fi - -#imports/pr_import.owl: mirror/pr.owl $(TMPDIR)/seed.owl -# if [ $(IMP) = true ]; then $(OWLTOOLS) --map-ontology-iri $(ONTBASE)/$@ $< $(TMPDIR)/seed.owl --extract-module -s $(URIBASE)/pr.owl -c --extract-mingraph --set-ontology-id -v $(RELEASE)/$@ $(ONTBASE)/$@ -o $@; fi -# Currently using pro_obo_slim imports/fbbt_import.owl: mirror/fbbt.owl imports/fbbt_terms_combined.txt if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ @@ -471,25 +429,6 @@ imports/fbbt_import.owl: mirror/fbbt.owl imports/fbbt_terms_combined.txt query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru --update $(SPARQLDIR)/remove_axioms.ru \ annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi -imports/cl_import.owl: mirror/cl.owl imports/cl_terms_combined.txt - if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ - extract -T imports/cl_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \ - remove --select "" --axioms annotation --signature true \ - remove --select "" --axioms annotation --signature true \ - query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \ - annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi - -.PRECIOUS: imports/%_import.owl - -# TODO - use full taxonomy -#ncbitaxon.owl: -# OWLTOOLS_MEMORY=14G owltools $(URIBASE)/ncbitaxon.owl -o $@ && touch $@ -## owltools $(URIBASE)/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl --merge-import-closure --make-subset-by-properties -f RO:0002162 // --split-ontology -d null -l cl go caro --remove-imports-declarations --set-ontology-id $(URIBASE)/$@ -o $@ - - -imports/ncbitaxon_import.owl: mirror/ncbitaxon.obo $(TMPDIR)/seed.owl $(TMPDIR)/composite-stages.obo - if [ $(IMP) = true ]; then $(OWLTOOLS) --map-ontology-iri $(ONTBASE)/$@ $< $(TMPDIR)/seed.owl $(TMPDIR)/composite-stages.obo --merge-support-ontologies --extract-module -s $(URIBASE)/ncbitaxon.owl -c --extract-mingraph --remove-dangling-annotations --create-taxon-disjoint-over-in-taxon -s -r NCBITaxon:2759 -m --set-ontology-id -v $(RELEASE)/$@ $(ONTBASE)/$@ -o $@; fi - # CL - take **everything** imports/cl_import.owl: $(TMPDIR)/cl-core.obo $(OWLSRC) if [ $(IMP) = true ]; then $(OWLTOOLS) $< --set-ontology-id -v $(RELEASE)/$@ $(ONTBASE)/$@ -o $@; fi @@ -497,9 +436,6 @@ imports/cl_import.owl: $(TMPDIR)/cl-core.obo $(OWLSRC) %_import.obo: %_import.owl if [ $(IMP) = true ]; then $(OWLTOOLS_NO_CAT) $< --add-obo-shorthand-to-properties -o -f obo --no-check $@; fi -imports: imports/pato_import.obo imports/chebi_import.obo imports/pr_import.obo imports/ncbitaxon_import.obo imports/cl_import.obo imports/go_import.obo imports/ro_import.obo - echo "STRONG WARNING: THIS GOAL HARDBAKES THE FOLLOWING IMPORTS AND COULD BE INCOMPLETE: $^" && touch $@ - # ---------------------------------------- # MARKDOWN EXPORT # ---------------------------------------- @@ -734,9 +670,8 @@ extra-full-bridge-checks: $(patsubst %,$(REPORTDIR)/extra-full-bridge-check-%.tx ##$(REPORTDIR)/bfo-check.txt: $(TMPDIR)/uberon-edit-plus-tax-equivs.owl # TODO @cmungall: worth fixing! # TODO @matentzn: use ROBOT merge instead and dump debug modules.. -$(REPORTDIR)/bfo-check.txt: $(OWLSRC) $(CATALOG_DYNAMIC) - echo "STRONG WARNING: check $@ FAIL currently!" - $(OWLTOOLS_CAT_DYNAMIC) $(URIBASE)/bfo.owl $(URIBASE)/ro.owl $< $(BRIDGEDIR)/uberon-bridge-to-bfo.owl --merge-support-ontologies -o $(REPORTDIR)/bfo-check.owl $(QELK) --run-reasoner -r elk -u > $@.tmp +$(REPORTDIR)/bfo-check.txt: $(OWLSRC) mirror/ro.owl mirror/bfo.owl + $(ROBOT) merge -i $(OWLSRC) -I $(URIBASE)/bfo.owl -I $(URIBASE)/ro.owl -i $(BRIDGEDIR)/uberon-bridge-to-bfo.owl reason --reasoner ELK --equivalent-classes-allowed asserted-only bfo-basic-check.txt: basic.owl $(CATALOG_DYNAMIC) $(OWLTOOLS_CAT_DYNAMIC) $(URIBASE)/bfo.owl $< $(BRIDGEDIR)/uberon-bridge-to-bfo.owl --merge-support-ontologies $(QELK) --run-reasoner -r elk -u > $@.tmp && mv $@.tmp $@ @@ -804,6 +739,10 @@ $(TMPDIR)/ext-merged-%.owl: ext.owl $(BRIDGEDIR)/bridges $(TMPDIR)/external-disj # check for dangling classes # TODO: add to Oort + +merged.obo: tmp/merged.owl + $(ROBOT) convert -i $< --check false -o $@.tmp.obo && mv $@.tmp.obo $@ + $(REPORTDIR)/%-orphans: %.obo $(SCRIPTSDIR)/obo-grep.pl --neg -r "(is_a|intersection_of|is_obsolete):" $< | $(SCRIPTSDIR)/obo-grep.pl -r Term - | $(SCRIPTSDIR)/obo-grep.pl --neg -r "id: UBERON:(0001062|0000000)" - | $(SCRIPTSDIR)/obo-grep.pl -r Term - > $@.tmp && (egrep '^(id|name):' $@.tmp > $@ || echo ok) @@ -1311,6 +1250,7 @@ ext-xref-conflict2.obo: echo "STRONG WARNING: $@ skipped, because there is no more blip." && touch $@ #blip-findall -r pext -r ZFA -i pe/tao-obsoletions.obo "entity_xref(Z,T),entity_replaced_by(T,U),\+id_idspace(Z,'UBERON'),id_idspace(U,'UBERON'),entity_xref(Ux,Z),id_idspace(Ux,'UBERON'),Ux\=U" -select "x(U,Z,Ux)" -label > $@ +.PHONY: release-diff release-diff: cd diffs && make all @@ -1320,18 +1260,29 @@ release-diff: #RELDIR=../.. +DEPLOY_GH=true -prepare_release: release-diff -# TODO @matentzn. Verify removal of following -# cp composite-brain.{obo,owl} $(RELDIR) ;\ +.PHONY: uberon +uberon: + $(MAKE) prepare_release IMP=false PAT=false BRI=true CLEANFILES=tmp/merged-uberon-edit.obo + $(MAKE) copy_additional_files # Probably not needed anymore now that we put everything on GitHub + $(MAKE) release-diff + if [ $(DEPLOY_GH) = true ]; then $(MAKE) deploy_release GHVERSION="v$(TODAY)" --generate-notes; fi -prepare_release: copy_additional_files +.PHONY: copy_additional_files copy_additional_files: rm -rf ../../bridge mkdir -p ../../bridge cp $(TMPDIR)/external-disjoints.owl ../../bridge/ ;\ cp $(COMPONENTSDIR)/external-disjoints.obo ../../bridge/ + # TODO @matentzn. Verify removal of following + # cp composite-brain.{obo,owl} $(RELDIR) ;\ + +deploy_release: + @test $(GHVERSION) + ls -alt $(ASSETS) + gh release create $(GHVERSION) --notes "TBD." --title "$(GHVERSION)" --draft $(ASSETS) #S3CMD = s3cmd -c ~/.s3cfg.go-push --acl-public --reduced-redundancy @@ -1771,9 +1722,6 @@ $(TMPDIR)/external-disjoints.owl: components/external-disjoints.obo $(ROBOT) convert -i $< -f owl -o $@ .PRECIOUS: $(TMPDIR)/external-disjoints.owl -$(BRIDGEDIR)/uberon-bridge-to-nifstd.obo: - echo "STRONG WARNING make $@ failed, because xref-to-equiv.pl script is missing!" && touch $@ - TEMPLATESDIR=templates TEMPLATES=$(patsubst %.tsv, $(TEMPLATESDIR)/%.owl, $(notdir $(wildcard $(TEMPLATESDIR)/*.tsv))) @@ -1813,10 +1761,6 @@ feature_diff: reports/robot_main_diff.md ######################## #### Utility commands ## -.PHONY: bless-mirrors -bless-mirrors: - touch go.owl chebi.owl mirror/ncbitaxon.obo - .PHONY: quick-qc quick-qc: tmp/core.owl $(REPORTDIR)/uberon-edit-obscheck.txt cat $(REPORTDIR)/uberon-edit-obscheck.txt @@ -1830,7 +1774,7 @@ normalize: $(TMPDIR)/NORMALIZE.obo mv $< $(SRC) echo "WARNING: $(SRC) has been overwritten! Please carefully check your diff before you commit!" -clean: +clean_uberon: rm -rf ./*.tmp rm -rf ./*.tmp1 rm -rf ./*.tmp2 @@ -1841,6 +1785,7 @@ clean: rm -f uberon.owl uberon.obo tmp/core.owl BUILDLOGUBERON.txt unsat_all_explanation.md rm -f ext.owl +clean: clean_uberon explain: $(ROBOT) explain --input $(TMPDIR)/unreasoned-composite-metazoan.owl --reasoner ELK \ @@ -1867,9 +1812,6 @@ cl_mondo_merged.owl: reports/composite-metazoan-dv.txt: echo "ERROR ERROR WARNING ERROR: $@ currently fails!" && touch $@ -subsets/life-stages-composite.obo: - echo "ERROR ERROR WARNING ERROR: $@ currently fails!" && touch $@ - OLDLOCATION=http://svn.code.sf.net/p/obo/svn/uberon/releases/2020-09-16 diffr-%: $(ROBOT) diff --left-iri $(OLDLOCATION)/$* --right ../../$* -o diff_$(shell echo $* | tr -cd '[:alnum:]._-').txt @@ -1956,9 +1898,6 @@ test_obsolete: test: test_obsolete -update_docs: - mkdocs build --config-file ../../mkdocs.yaml - .PHONY: test_owlaxioms test_owlaxioms: ! grep "owl-axioms: " uberon-edit.obo diff --git a/uberon.obo b/uberon.obo index 4c18a44d32..9a09c3343d 100644 --- a/uberon.obo +++ b/uberon.obo @@ -1,6 +1,7 @@ format-version: 1.2 -data-version: releases/2022-02-21 +data-version: releases/2022-04-05 subsetdef: 1_STAR "" +subsetdef: 2_STAR "" subsetdef: 3_STAR "" subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" @@ -68,7 +69,6 @@ subsetdef: pheno_slim "" subsetdef: pheno_slim "Phenotype slim" subsetdef: phenotype_rcn "" subsetdef: phenotype_rcn "A subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMA" -subsetdef: relational_slim "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" subsetdef: scalar_slim "" @@ -2320,6 +2320,8 @@ id: CL:0000034 name: stem cell namespace: cell def: "A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." [] +comment: This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’. +synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 is_a: CL:0011115 ! precursor cell @@ -2338,6 +2340,7 @@ is_a: CL:0000723 ! somatic stem cell id: CL:0000036 name: epithelial fate stem cell namespace: cell +synonym: "epithelial stem cell" EXACT [] is_a: CL:0000035 ! single fate stem cell [Term] @@ -2402,6 +2405,7 @@ xref: FMA:83553 is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 ! monopoietic cell relationship: develops_from CL:0002009 ! macrophage dendritic cell progenitor +relationship: has_part CL:0017503 ! basophilic cytoplasm [Term] id: CL:0000041 @@ -3008,6 +3012,7 @@ synonym: "polynuclear neutrophilic leukocyte" EXACT [] xref: BTO:0003473 is_a: CL:0000234 ! phagocyte is_a: CL:0000775 ! neutrophil +relationship: has_part CL:0017500 ! neutrophillic cytoplasm [Term] id: CL:0000097 @@ -3090,7 +3095,7 @@ is_a: CL:0000099 ! interneuron id: CL:0000104 name: multipolar neuron namespace: cell -def: "Neuron with an axon and two or more dendrites." [] +def: "A neuron with three or more neurites, usually an axon and multiple dendrites." [] subset: BDS_subset xref: FMA:67287 is_a: CL:0000540 ! neuron @@ -3958,7 +3963,7 @@ relationship: develops_from CL:0000857 ! slow muscle myoblast id: CL:0000190 name: fast muscle cell namespace: cell -def: "A muscle cell that can develop high tension rapidly. It is usually innervated by a single alpha neuron ." [] +def: "A muscle cell that can develop high tension rapidly. It is usually innervated by a single alpha neuron." [] synonym: "glycolytic muscle fiber" EXACT [] is_a: CL:0008046 ! extrafusal muscle fiber relationship: develops_from CL:0000858 ! fast muscle myoblast @@ -3970,7 +3975,7 @@ namespace: cell alt_id: CL:0000191 def: "A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast)." [] synonym: "myocytes, smooth muscle" EXACT [] -synonym: "non-striated muscle cell" NARROW [] +synonym: "non-striated muscle cell" BROAD [] synonym: "SMCs" EXACT [] synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 @@ -4151,12 +4156,9 @@ is_a: CL:0000215 ! barrier cell id: CL:0000214 name: synovial cell namespace: cell -def: "A meso-epithelial cell that lies between the cartilaginous fibers in the synovial membrane of a joint and produces hyaluronic acid." [] -synonym: "hyaluronic acid secreting cell" NARROW [] +def: "A cell located in the synovial joint." [] synonym: "synoviocyte" EXACT [] -xref: BTO:0003652 xref: CALOHA:TS-0995 -xref: FMA:66786 is_a: CL:0000153 ! glycosaminoglycan secreting cell is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell @@ -4428,6 +4430,7 @@ is_a: CL:0000079 ! stratified epithelial cell id: CL:0000241 name: stratified cuboidal epithelial cell namespace: cell +is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0000079 ! stratified epithelial cell [Term] @@ -4988,9 +4991,10 @@ is_a: CL:0000151 ! secretory cell [Term] id: CL:0000315 -name: tears secreting cell +name: tear secreting cell namespace: cell def: "A cell secreting tears, the fluid secreted by the lacrimal glands. This fluid moistens the conjunctiva and cornea." [] +synonym: "tears secreting cell" EXACT [] is_a: CL:0000152 ! exocrine cell [Term] @@ -5269,7 +5273,6 @@ is_a: CL:0002371 ! somatic cell id: CL:0000350 name: amnioserosal cell namespace: cell -is_a: CL:0000066 ! epithelial cell is_a: CL:0000349 ! extraembryonic cell [Term] @@ -5339,7 +5342,7 @@ is_a: CL:0000192 ! smooth muscle cell id: CL:0000359 name: vascular associated smooth muscle cell namespace: cell -def: "A smooth muscle cell assocatiated with the vasculature." [] +def: "A smooth muscle cell associated with the vasculature." [] synonym: "vascular smooth muscle cell" EXACT [] synonym: "VSMC" EXACT [] is_a: CL:0000192 ! smooth muscle cell @@ -5414,7 +5417,7 @@ id: CL:0000367 name: sheath cell (sensu Nematoda) namespace: cell synonym: "glial cell (sensu Nematoda)" RELATED [] -is_a: CL:0000619 ! support cell (sensu Nematoda) +is_a: CL:0000619 ! supporting cell (sensu Nematoda) [Term] id: CL:0000368 @@ -5488,8 +5491,9 @@ is_a: CL:0000069 ! branched duct epithelial cell [Term] id: CL:0000378 -name: support cell (sensu Nematoda and Protostomia) +name: supporting cell (sensu Nematoda and Protostomia) namespace: cell +synonym: "support cell (sensu Nematoda and Protostomia)" EXACT [] is_a: CL:0000630 ! supporting cell [Term] @@ -5504,7 +5508,7 @@ name: thecogen cell namespace: cell def: "The support cell that makes the thecogen dendritic cap - a cuticle-like matrix around the tip of the eo-dendrite and which encloses the soma of the eo-neuron." [] synonym: "fly sheath cell" EXACT [] -is_a: CL:0000378 ! support cell (sensu Nematoda and Protostomia) +is_a: CL:0000378 ! supporting cell (sensu Nematoda and Protostomia) [Term] id: CL:0000381 @@ -5519,7 +5523,7 @@ id: CL:0000382 name: scolopale cell namespace: cell xref: FBbt:00005219 -is_a: CL:0000378 ! support cell (sensu Nematoda and Protostomia) +is_a: CL:0000378 ! supporting cell (sensu Nematoda and Protostomia) [Term] id: CL:0000383 @@ -5572,7 +5576,7 @@ is_a: CL:0000386 ! attachment cell id: CL:0000389 name: socket cell (sensu Nematoda) namespace: cell -is_a: CL:0000619 ! support cell (sensu Nematoda) +is_a: CL:0000619 ! supporting cell (sensu Nematoda) is_a: CL:0000658 ! cuticle secreting cell [Term] @@ -5949,7 +5953,6 @@ id: CL:0000439 name: prolactin secreting cell namespace: cell def: "A peptide hormone cell that secretes prolactin." [] -is_a: CL:0000154 ! protein secreting cell is_a: CL:0000167 ! peptide hormone secreting cell [Term] @@ -6827,6 +6830,8 @@ xref: VHOG:0001535 is_a: CL:0000842 ! mononuclear cell disjoint_from: CL:0000766 ! myeloid leukocyte relationship: develops_from CL:0000051 ! common lymphoid progenitor +relationship: has_part CL:0017500 ! neutrophillic cytoplasm +relationship: has_part CL:0017505 ! increased nucleus size [Term] id: CL:0000543 @@ -6892,6 +6897,8 @@ xref: FMA:83518 is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell relationship: develops_from CL:0000038 ! erythroid progenitor cell +relationship: has_part CL:0017503 ! basophilic cytoplasm +relationship: has_part CL:0017505 ! increased nucleus size [Term] id: CL:0000548 @@ -6911,6 +6918,7 @@ synonym: "early normoblast" EXACT [] synonym: "prorubricyte" EXACT [] xref: FMA:83505 is_a: CL:0000765 ! erythroblast +relationship: has_part CL:0017503 ! basophilic cytoplasm [Term] id: CL:0000550 @@ -6926,6 +6934,7 @@ synonym: "rubricyte" EXACT [] xref: FMA:83506 is_a: CL:0000765 ! erythroblast relationship: develops_from CL:0000549 ! basophilic erythroblast +relationship: has_part CL:0017504 ! polychromatophilic cytoplasm [Term] id: CL:0000551 @@ -6946,6 +6955,7 @@ synonym: "pyknotic eto enrythroblast" EXACT [] xref: FMA:84646 is_a: CL:0000765 ! erythroblast relationship: develops_from CL:0000550 ! polychromatophilic erythroblast +relationship: has_part CL:0017502 ! acidophilic cytoplasm [Term] id: CL:0000553 @@ -7053,18 +7063,18 @@ synonym: "rod neutrophil" EXACT [] synonym: "stab cell" BROAD [] is_a: CL:0000096 ! mature neutrophil relationship: develops_from CL:0000582 ! neutrophilic metamyelocyte +relationship: has_part CL:0017506 ! banded nucleus [Term] id: CL:0000561 name: amacrine cell namespace: cell def: "Interneuron of the vertebrate retina. They integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. They lack large axons." [] -comment: Not clear if this term overlaps with retinal bipolar neuron (CL:0000748). synonym: "amacrine neuron" EXACT [] xref: BTO:0004044 -xref: FBbt:00005127 xref: FMA:67766 is_a: CL:0000099 ! interneuron +is_a: CL:0009004 ! retinal cell [Term] id: CL:0000562 @@ -7258,6 +7268,7 @@ xref: FMA:83540 is_a: CL:0000776 ! immature neutrophil is_a: CL:0002087 ! nongranular leukocyte is_a: CL:0002193 ! myelocyte +relationship: has_part CL:0017502 ! acidophilic cytoplasm [Term] id: CL:0000581 @@ -7280,6 +7291,8 @@ xref: FMA:84197 is_a: CL:0000776 ! immature neutrophil is_a: CL:0002192 ! metamyelocyte relationship: develops_from CL:0000580 ! neutrophilic myelocyte +relationship: has_part CL:0017502 ! acidophilic cytoplasm +relationship: has_part CL:0017507 ! reniform nucleus [Term] id: CL:0000583 @@ -7626,9 +7639,10 @@ is_a: CL:0000075 ! columnar/cuboidal epithelial cell [Term] id: CL:0000619 -name: support cell (sensu Nematoda) +name: supporting cell (sensu Nematoda) namespace: cell -is_a: CL:0000378 ! support cell (sensu Nematoda and Protostomia) +synonym: "support cell (sensu Nematoda)" EXACT [] +is_a: CL:0000378 ! supporting cell (sensu Nematoda and Protostomia) [Term] id: CL:0000620 @@ -7700,6 +7714,7 @@ name: olfactory granule cell namespace: cell def: "Granule cell that is part of the olfactory bulb." [] is_a: CL:0000120 ! granule cell +is_a: CL:0012001 ! neuron of the forebrain [Term] id: CL:0000627 @@ -7726,9 +7741,9 @@ is_a: CL:0000325 ! stuff accumulating cell [Term] id: CL:0000630 name: supporting cell -name: supportive cell namespace: cell def: "A cell whose primary function is to support other cell types." [] +synonym: "supportive cell" EXACT [] xref: BTO:0002315 is_a: CL:0000003 ! native cell @@ -7755,7 +7770,6 @@ xref: BTO:0002741 xref: CALOHA:TS-0452 xref: FMA:67763 is_a: CL:0000057 ! fibroblast -is_a: CL:0000152 ! exocrine cell is_a: CL:0000327 ! extracellular matrix secreting cell [Term] @@ -8169,7 +8183,7 @@ id: CL:0000676 name: cap cell namespace: cell xref: BTO:0001033 -is_a: CL:0000378 ! support cell (sensu Nematoda and Protostomia) +is_a: CL:0000378 ! supporting cell (sensu Nematoda and Protostomia) [Term] id: CL:0000677 @@ -8509,10 +8523,12 @@ is_a: CL:0000735 ! lymph gland hemocyte [Term] id: CL:0000717 -name: fusimotor neuron +name: obsolete fusimotor neuron namespace: cell -def: "A subset of motor neurons that innervates intrafusal muscle fibers and has small diameter axons." [] -is_a: CL:0008039 ! lower motor neuron +def: "OBSOLETE. A subset of motor neurons that innervates intrafusal muscle fibers and has small diameter axons." [] +comment: Term merged into CL:0008037. Refer to https://github.com/obophenotype/cell-ontology/issues/1364 +is_obsolete: true +replaced_by: CL:0008037 [Term] id: CL:0000718 @@ -8950,7 +8966,10 @@ def: "Any of the immature forms of a basophil, in which basophilic specific gran synonym: "immature basophilic leucocyte" EXACT [] synonym: "immature basophilic leukocyte" EXACT [] is_a: CL:0000767 ! basophil +intersection_of: CL:0000767 ! basophil +intersection_of: has_part CL:0017509 ! alobate nucleus relationship: develops_from CL:0000830 ! basophilic promyelocyte +relationship: has_part CL:0017509 ! alobate nucleus [Term] id: CL:0000769 @@ -8961,6 +8980,7 @@ xref: FMA:84198 is_a: CL:0000768 ! immature basophil is_a: CL:0002192 ! metamyelocyte relationship: develops_from CL:0000614 ! basophilic myelocyte +relationship: has_part CL:0017507 ! reniform nucleus [Term] id: CL:0000770 @@ -8968,7 +8988,10 @@ name: band form basophil namespace: cell def: "A late basophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature basophil." [] is_a: CL:0000768 ! immature basophil +intersection_of: CL:0000768 ! immature basophil +intersection_of: has_part CL:0017506 ! banded nucleus relationship: develops_from CL:0000769 ! basophilic metamyelocyte +relationship: has_part CL:0017506 ! banded nucleus [Term] id: CL:0000771 @@ -8996,7 +9019,10 @@ synonym: "immature eosinocyte" EXACT [] synonym: "immature eosinophilic leucocyte" EXACT [] synonym: "immature eosinophilic leukocyte" EXACT [] is_a: CL:0000771 ! eosinophil +intersection_of: CL:0000771 ! eosinophil +intersection_of: has_part CL:0017509 ! alobate nucleus relationship: develops_from CL:0000833 ! eosinophilic promyelocyte +relationship: has_part CL:0017509 ! alobate nucleus [Term] id: CL:0000773 @@ -9006,6 +9032,8 @@ def: "A eosinophil precursor in the granulocytic series, being a cell intermedia is_a: CL:0000772 ! immature eosinophil is_a: CL:0002192 ! metamyelocyte relationship: develops_from CL:0000612 ! eosinophilic myelocyte +relationship: has_part CL:0017502 ! acidophilic cytoplasm +relationship: has_part CL:0017507 ! reniform nucleus [Term] id: CL:0000774 @@ -9013,7 +9041,10 @@ name: band form eosinophil namespace: cell def: "A late eosinophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature eosinophil." [] is_a: CL:0000772 ! immature eosinophil +intersection_of: CL:0000772 ! immature eosinophil +intersection_of: has_part CL:0017506 ! banded nucleus relationship: develops_from CL:0000773 ! eosinophilic metamyelocyte +relationship: has_part CL:0017506 ! banded nucleus [Term] id: CL:0000775 @@ -9048,7 +9079,10 @@ synonym: "immature neutrophil leucocyte" EXACT [] synonym: "immature neutrophil leukocyte" EXACT [] synonym: "immature neutrophilic leucocyte" EXACT [] is_a: CL:0000775 ! neutrophil +intersection_of: CL:0000775 ! neutrophil +intersection_of: has_part CL:0017509 ! alobate nucleus relationship: develops_from CL:0000564 ! neutrophilic promyelocyte +relationship: has_part CL:0017509 ! alobate nucleus [Term] id: CL:0000777 @@ -9170,6 +9204,7 @@ xref: BTO:0000392 xref: FMA:70574 is_a: CL:0000946 ! antibody secreting cell relationship: develops_from CL:0000980 ! plasmablast +relationship: has_part CL:0017508 ! cartwheel heterochromatin [Term] id: CL:0000787 @@ -9813,6 +9848,8 @@ xref: FMA:83524 is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 ! granulocytopoietic cell relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell +relationship: has_part CL:0017503 ! basophilic cytoplasm +relationship: has_part CL:0017505 ! increased nucleus size [Term] id: CL:0000836 @@ -9824,6 +9861,8 @@ xref: FMA:83530 is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 ! granulocytopoietic cell relationship: develops_from CL:0000835 ! myeloblast +relationship: has_part CL:0017503 ! basophilic cytoplasm +relationship: has_part CL:0017505 ! increased nucleus size [Term] id: CL:0000837 @@ -10011,17 +10050,19 @@ disjoint_from: CL:0000855 ! sensory hair cell [Term] id: CL:0000852 -name: neuromast support cell +name: neuromast supporting cell namespace: cell def: "Neuromast support cell is a non-sensory cell of the neuromast that extend between the sensory hair cells from the basement membrane to the apical surface; neuromast support cells are surrounded by neuromast mantle cells." [] +synonym: "neuromast support cell" EXACT [] is_a: CL:0000630 ! supporting cell disjoint_from: CL:0000855 ! sensory hair cell [Term] id: CL:0000853 -name: olfactory epithelial support cell +name: olfactory epithelial supporting cell namespace: cell def: "Olfactory epithelial support cell is a columnar cell that extends from the epithelial free margin to the basement membrane of the olfactory epithelium. This cell type has a large, vertically, elongate, euchromatic nucleus, along with other nuclei, forms a layer superficial to the cell body of the receptor cell; sends long somewhat irregular microvilli into the mucus layer; at the base, with expanded end-feet containing numerous lamellated dense bodies resembling lipofuscin of neurons." [] +synonym: "olfactory epithelial support cell" EXACT [] synonym: "olfactory sustentacular cell" EXACT [] synonym: "supporting cell of olfactory epithelium" EXACT [] synonym: "sustentaculocyte of olfactory epithelium" EXACT [] @@ -11921,6 +11962,8 @@ name: cortical granule cell namespace: cell def: "Granule cell that is part of the cerebral cortex." [] is_a: CL:0000120 ! granule cell +is_a: CL:0010012 ! cerebral cortex neuron +is_a: CL:0012001 ! neuron of the forebrain [Term] id: CL:0001033 @@ -11928,7 +11971,6 @@ name: hippocampal granule cell namespace: cell def: "Granule cell that is part of the hippocampus." [] is_a: CL:0001032 ! cortical granule cell -is_a: CL:0002608 ! hippocampal neuron [Term] id: CL:0001034 @@ -12228,6 +12270,7 @@ synonym: "CD8+ TEMRA" EXACT [] synonym: "CD8-positive TEMRA" EXACT [] synonym: "TEMRA" BROAD [] is_a: CL:0000909 ! CD8-positive, alpha-beta memory T cell +is_a: CL:4030002 ! effector memory CD45RA-positive, alpha-beta T cell, terminally differentiated relationship: develops_from CL:0000913 ! effector memory CD8-positive, alpha-beta T cell [Term] @@ -12414,6 +12457,7 @@ synonym: "CD4+ TEMRA" EXACT [] synonym: "CD4-positive TEMRA" EXACT [] synonym: "TEMRA" BROAD [] is_a: CL:0000897 ! CD4-positive, alpha-beta memory T cell +is_a: CL:4030002 ! effector memory CD45RA-positive, alpha-beta T cell, terminally differentiated property_value: dc-creator http://orcid.org/0000-0001-9990-8331 relationship: develops_from CL:0000905 ! effector memory CD4-positive, alpha-beta T cell @@ -14493,7 +14537,6 @@ xref: KUPO:0001033 is_a: CL:0000650 ! mesangial cell is_a: CL:1000500 ! kidney interstitial cell is_a: CL:1000618 ! juxtaglomerular complex cell -is_a: CL:1000746 ! glomerular cell is_a: CL:1001318 ! renal interstitial pericyte created_by: tmeehan creation_date: 2010-08-25T02:20:55Z @@ -14577,10 +14620,11 @@ creation_date: 2010-08-25T03:38:51Z [Term] id: CL:0002181 -name: mucus neck cell of gastric gland +name: mucous neck cell of gastric gland namespace: cell alt_id: CL:1000401 def: "A neck cell that secretes mucus within the stomach. Its products are distinct histochemically from those of the surface mucous cells of stomach." [] +synonym: "mucus neck cell of gastric gland" EXACT [] xref: FMA:62954 is_a: CL:0000152 ! exocrine cell is_a: CL:0000651 ! mucous neck cell @@ -14786,8 +14830,11 @@ creation_date: 2010-09-02T11:33:26Z id: CL:0002201 name: renal beta-intercalated cell namespace: cell -def: "A renal intercalated cell that secretes base and reabsorbs acid in the coritcal collecting duct to mantain acid/base balance." [] -is_a: CL:0005010 ! renal intercalated cell +def: "A renal intercalated cell that secretes base and reabsorbs acid in the distal segments of the kidney tubule to maintain acid/base balance." [] +synonym: "type B intercalated cell" EXACT [] +synonym: "type B-IC" EXACT [] +is_a: CL:1000507 ! kidney tubule cell +is_a: CL:1001432 ! kidney collecting duct intercalated cell created_by: tmeehan creation_date: 2010-09-02T01:43:55Z @@ -15971,7 +16018,11 @@ creation_date: 2010-09-13T03:23:25Z id: CL:0002301 name: type B synovial cell namespace: cell -def: "A synovial cell type that resembles fibroblasts, has abundant granular endoplasmic reticulum but contains fewer vacuoles and vesicles. This cell type secretes glycoproteins and hyaluronic acid." [] +def: "A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles." [] +comment: Type B synovial cells play a key role in the pathogenesis of chronic inflammatory diseases, such as rheumatoid arthritis, and are essential for the maintenance of normal joint functions. Fibroblast-like synoviocytes from different joints have different properties, which may contribute to the characteristic pattern of joint involvement in different types of arthritis. +synonym: "fibroblast-like synoviocyte" EXACT [] +synonym: "synovial fibroblast" EXACT [] +xref: BTO:0003652 xref: FMA:66788 is_a: CL:0000214 ! synovial cell created_by: tmeehan @@ -15982,9 +16033,11 @@ id: CL:0002302 name: type A synovial cell namespace: cell def: "A synovial cell that is macrophage-like, characterized by surface ruffles or lamellipodia, plasma membrane invaginations and associated micropinocytotic vesicles, Golgi apparatus and little granular endoplasmic reticulum." [] +comment: Type A cells are usually round and located in the upper part of the synovial intima. synonym: "type A synoviocyte" EXACT [] xref: FMA:66787 is_a: CL:0000214 ! synovial cell +is_a: CL:0000234 ! phagocyte created_by: tmeehan creation_date: 2010-09-13T03:39:17Z @@ -16147,7 +16200,7 @@ namespace: cell def: "An epithelial supporting cell located in the cochlea." [] xref: FMA:79796 is_a: CL:0001035 ! bone cell -is_a: CL:0005014 ! auditory epithelial support cell +is_a: CL:0005014 ! auditory epithelial supporting cell created_by: tmeehan creation_date: 2010-09-14T03:31:38Z @@ -16157,7 +16210,7 @@ name: supporting cell of vestibular epithelium namespace: cell def: "A supporting cell of the vestibular epithelium." [] xref: FMA:75607 -is_a: CL:0005014 ! auditory epithelial support cell +is_a: CL:0005014 ! auditory epithelial supporting cell created_by: tmeehan creation_date: 2010-09-14T03:31:44Z @@ -16173,7 +16226,7 @@ creation_date: 2010-09-14T03:33:50Z [Term] id: CL:0002318 -name: periperhal blood mesothelial cell +name: peripheral blood mesothelial cell namespace: cell def: "A mesothelial cell capable of circulating in the blood by first losing its squamous character. This cell can incorporate into the regenerating mesothelium." [] xref: FMA:86712 @@ -16271,6 +16324,8 @@ alt_id: CL:1000476 def: "The milk-producing cell of the alveolar unit that emerges during pregnancy." [] synonym: "epithelial cell of lactiferous gland" EXACT [] synonym: "luminal cell of alveolus of lactiferous gland" EXACT [] +synonym: "mammary alveolar epithelial cell" EXACT [] +synonym: "mammary gland alveolar epithelial cell" EXACT [] xref: FMA:74506 xref: FMA:79866 is_a: CL:0000314 ! milk secreting cell @@ -16565,7 +16620,6 @@ name: yolk sac hematopoietic stem cell namespace: cell def: "A hematopoietic stem found in the yolk sac. In mice, this cell type is Sca-1-negative, CD45-negative, MHC-negative, HSA-positive, AA4.1-positive, CD44-positive." [] synonym: "hemangioblast precursor" EXACT [] -is_a: CL:0000066 ! epithelial cell is_a: CL:0002352 ! gestational hematopoietic stem cell created_by: tmeehan creation_date: 2010-09-22T09:08:34Z @@ -17370,6 +17424,7 @@ name: CD4-intermediate, CD8-positive double-positive thymocyte namespace: cell def: "A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD4 co-receptor." [] synonym: "T.4int8+.Th" EXACT [] +synonym: "T_4int8+_Th" EXACT [] is_a: CL:0000809 ! double-positive, alpha-beta thymocyte relationship: develops_from CL:0002429 ! CD69-positive double-positive thymocyte created_by: tmeehan @@ -17380,7 +17435,8 @@ id: CL:0002431 name: CD4-positive, CD8-intermediate double-positive thymocyte namespace: cell def: "A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD8 co-receptor." [] -synonym: "T.4int8+.th" EXACT [] +synonym: "T.4+8int.Th" EXACT [] +synonym: "T_4+8int_Th" EXACT [] is_a: CL:0000809 ! double-positive, alpha-beta thymocyte relationship: develops_from CL:0002429 ! CD69-positive double-positive thymocyte created_by: tmeehan @@ -17606,7 +17662,12 @@ creation_date: 2010-11-10T01:46:51Z id: CL:0002453 name: oligodendrocyte precursor cell namespace: cell -def: "The cell type from which oligodendrocytes develop. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons." [] +def: "A progenitor cell of the central nervous system that can differentiate into oligodendrocytes or type-2 astrocytes. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons." [] +comment: This cell type can be purified from optic nerves and other regions of the embryonic, postnatal and adult rat CNS and can be differentiated in vitro to oligodendrocytes and type-2 astrocytes. Some references use the terms 'oligodendrocyte precursor cell' and 'oligodendrocyte type-2 astrocyte (O-2A) progenitor' to refer to the same entity (e.g., PMID:10704434), while others describe an oligodendrocyte type-2 astrocyte (O-2A) progenitor cell as the precurosr to oligodendrocyte- and type-2 astrocyte- progenitor cells (e.g, ISBN:9780702028991). +synonym: "O-2A/OPC" BROAD [] +synonym: "O2A/OPC" BROAD [] +synonym: "oligodendrocyte-type 2 astrocyte (O-2A) progenitor cell" BROAD [] +synonym: "oligodendrocyte/type-2 astrocyte progenitor cell" BROAD [] is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) relationship: develops_from CL:0000339 ! glioblast (sensu Vertebrata) created_by: tmeehan @@ -18074,6 +18135,7 @@ id: CL:0002499 name: spongiotrophoblast cell namespace: cell def: "A trophoblast cell that arises in the junctional zone (basal plate) of the placenta." [] +synonym: "spongiotrophoblast" EXACT [] is_a: CL:0000351 ! trophoblast cell created_by: tmeehan creation_date: 2010-12-07T12:56:56Z @@ -18730,6 +18792,8 @@ id: CL:0002566 name: dark melanocyte namespace: cell def: "A melanocyte that appears darker due to content or amount of melanin granules." [] +synonym: "melanotic melanocyte" EXACT [] +synonym: "melanotic melanophore" EXACT [] is_a: CL:0000148 ! melanocyte created_by: tmeehan creation_date: 2011-03-01T05:57:11Z @@ -18739,6 +18803,8 @@ id: CL:0002567 name: light melanocyte namespace: cell def: "A melanocyte that appears lighter in color." [] +synonym: "amelanotic melanocyte" EXACT [] +synonym: "amelanotic melanophore" EXACT [] is_a: CL:0000148 ! melanocyte created_by: tmeehan creation_date: 2011-03-01T05:58:23Z @@ -18764,10 +18830,10 @@ creation_date: 2011-03-01T09:55:12Z [Term] id: CL:0002570 -name: mesenchymal stem cell of adipose name: mesenchymal stem cell of adipose tissue namespace: cell def: "A mesenchymal stem cell of adipose tissue." [] +synonym: "mesenchymal stem cell of adipose" EXACT [] is_a: CL:0000134 ! mesenchymal stem cell created_by: tmeehan creation_date: 2011-03-01T09:57:17Z @@ -19124,19 +19190,6 @@ is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) created_by: tmeehan creation_date: 2011-03-06T07:31:49Z -[Term] -id: CL:0002609 -name: neuron of cerebral cortex -namespace: cell -def: "A CNS neuron of the cerebral cortex." [] -synonym: "cortical neuron" EXACT [] -xref: BTO:0004102 -xref: FMA:84104 -is_a: CL:0010012 ! cerebral cortex neuron -is_a: CL:0012001 ! neuron of the forebrain -created_by: tmeehan -creation_date: 2011-03-06T07:37:08Z - [Term] id: CL:0002610 name: raphe nuclei neuron @@ -19566,7 +19619,7 @@ name: endothelial cell of high endothelial venule namespace: cell def: "A venule endothelial cell that is cubodial, expresses leukocyte-specific receptors, and allows for passage of lymphocytes into bloodstream." [] comment: Markers expressed on HEV include: MAdCAM-1,PNAd (sulfated and glycosylated molecules, i.e. GlyCAM-1, CD34, endomucin, nepmucin), ICAM-1, ICAM-2,Fuc-TVII, beta 3GlcNAcT-3, GlcNAc6ST2,CCL21, CCL19, CXCL13, CXCL12, Autotaxin, DARC, angiomodulin, LRHG. -synonym: "endothelial cell of postcapillary venule of lymph node" EXACT [] +synonym: "endothelial cell of postcapillary venule of lymph node" BROAD [] synonym: "HEV cell" EXACT [] xref: FMA:67759 is_a: CL:0000075 ! columnar/cuboidal epithelial cell @@ -19972,6 +20025,7 @@ id: CL:0005010 name: renal intercalated cell namespace: cell def: "A cuboidal epithelial cell of the kidney that regulates acid/base balance." [] +comment: Intercalated cells are also called “mitochondria-rich cells”, reflecting the high levels of round mitochondria at their apical pole, or in their cytoplasm, a distribution that is quite different from that of other kidney tubule cells, which accumulated mitochondria around the basolateral membrane. These cells also have numerous irregular apical microvilli compared with the surrounding segment-specific cells. Intercalated cells lack a central cilium, at least in the cortex, which also differentiates them from the adjacent principal cells. synonym: "intercalated cell" EXACT [] xref: FMA:86560 is_a: CL:0000075 ! columnar/cuboidal epithelial cell @@ -19983,7 +20037,12 @@ id: CL:0005011 name: renal alpha-intercalated cell namespace: cell def: "A cuboidal epithelial cell of the kidney which secretes acid and reabsorbs base to regulate acid/base balance." [] -is_a: CL:0005010 ! renal intercalated cell +comment: Type A intercalated cells are the more abundant type of intercalated cell in the outer stripe of the outer medulla in most mammalian species. +synonym: "type A intercalated cell" EXACT [] +synonym: "type A-IC" EXACT [] +is_a: CL:1000768 ! kidney connecting tubule epithelial cell +is_a: CL:1000849 ! kidney distal convoluted tubule epithelial cell +is_a: CL:1001432 ! kidney collecting duct intercalated cell [Term] id: CL:0005012 @@ -20005,9 +20064,10 @@ is_a: CL:0000067 ! ciliated epithelial cell [Term] id: CL:0005014 -name: auditory epithelial support cell +name: auditory epithelial supporting cell namespace: cell def: "A non-sensory cell that extends from the basement membrane to the apical surface of the auditory epithelium and provides support for auditory hair cells." [] +synonym: "auditory epithelial support cell" EXACT [] is_a: CL:0000630 ! supporting cell is_a: CL:0000710 ! neurecto-epithelial cell is_a: CL:0002491 ! auditory epithelial cell @@ -20297,10 +20357,7 @@ id: CL:0007017 name: Stiftchenzellen def: "An epidermal cell with apical microvilli or a single apical projection have synaptic associations with nerve fibres in the epidermis." [] comment: Taxon specificity not yet fully known, but are known in anuran larvae but not in adults. -is_a: CL:0000006 ! neuronal receptor cell -is_a: CL:0000098 ! sensory epithelial cell is_a: CL:0000206 ! chemoreceptor cell -is_a: CL:0000362 ! epidermal cell created_by: haendel [Term] @@ -20308,8 +20365,7 @@ id: CL:0007018 name: epidermal ciliary cell def: "Ciliated cell of the embryonic epidermis and functions in embryonic movements." [] comment: Taxon specificity not clear -present in embryonic anurans. -is_a: CL:0000067 ! ciliated epithelial cell -is_a: CL:0000362 ! epidermal cell +is_a: CL:0000064 ! ciliated cell is_a: CL:0002321 ! embryonic cell (metazoa) created_by: haendel @@ -20331,6 +20387,7 @@ created_by: haendel id: CL:0007021 name: alarm substance cell def: "Secretory cell that produces a chemical mixture that triggers antipredator behavior. The substance is released only upon disruption of the epidermis. [Behavior of teleost fishes, second edition, edited by Pitcher, 1992]" [] +synonym: "alarm substance secreting cell" EXACT [] synonym: "club cell" RELATED [] synonym: "club cell (zebrafish)" EXACT [] is_a: CL:0000151 ! secretory cell @@ -20463,7 +20520,6 @@ name: inhibitory motor neuron def: "A motor neuron that is capable of directly inhibiting muscle contraction." [] comment: In vertebrates, all motor neurons are excitatory, but various types of inhibitory motor neurons exist in invertebrates. is_a: CL:0000100 ! motor neuron -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: CL:0008016 @@ -20629,6 +20685,7 @@ creation_date: 2020-03-02T08:45:06Z id: CL:0008037 name: gamma motor neuron def: "A lower motor neuron that innervates only intrafusal muscle fibers. Unlike the alpha motor neurons, gamma motor neurons do not directly adjust the lengthening or shortening of muscles but function in adjusting the sensitivity of muscle spindles and in keeping muscle spindles taut, thereby allowing the continued firing of alpha neurons." [] +synonym: "fusimotor neuron" EXACT [] xref: FMA:83660 xref: MESH:D009047 xref: SAO:143800623 @@ -20998,7 +21055,7 @@ subset: location_grouping synonym: "appendix mesothelial cell" EXACT [] synonym: "mesothelial cell of appendix vermiformis" EXACT [] synonym: "mesothelial cell of vermiform appendix" EXACT [] -is_a: CL:0009025 ! mesothelial cell of colon +is_a: CL:0000077 ! mesothelial cell is_a: CL:1000405 ! epithelial cell of appendix created_by: http://orcid.org/0000-0002-2825-0621 @@ -21499,6 +21556,86 @@ comment: There is growing evidence that molecular markers characterizing double is_a: CL:0002489 ! double negative thymocyte created_by: http://orcid.org/0000-0002-2825-0621 +[Term] +id: CL:0009084 +name: epithelial cell of endometrial gland +def: "An epithelial cell that is part of an endometrial gland." [] +subset: location_grouping +synonym: "endometrial glandular epithelial cell" EXACT [] +xref: EFO:0010710 +is_a: CL:0000066 ! epithelial cell +created_by: http://orcid.org/0000-0002-2825-0621 + +[Term] +id: CL:0009086 +name: endothelial cell of respiratory system lymphatic vessel +def: "An endothelial cell that is part of a respiratory system lymphatic vessel." [] +subset: location_grouping +xref: EFO:0010667 +is_a: CL:0000115 ! endothelial cell +created_by: http://orcid.org/0000-0002-2825-0621 + +[Term] +id: CL:0009087 +name: fused extravillous trophoblast +def: "An extravillous trophoblast that is polynuclear." [] +synonym: "fused EVT" EXACT [] +xref: EFO:0010712 +is_a: CL:0008036 ! extravillous trophoblast +created_by: http://orcid.org/0000-0002-2825-0621 + +[Term] +id: CL:0009089 +name: lung pericyte +def: "A pericyte cell that is part of a lung." [] +subset: location_grouping +synonym: "lung pericyte cell" EXACT [] +synonym: "pulmonary pericyte" EXACT [] +xref: EFO:0010669 +is_a: CL:0000669 ! pericyte cell +created_by: http://orcid.org/0000-0002-2825-0621 + +[Term] +id: CL:0009092 +name: endothelial cell of placenta +def: "An endothelial cell that is part of a placenta." [] +subset: location_grouping +synonym: "placental endothelial cell" EXACT [] +xref: EFO:0010708 +is_a: CL:0000115 ! endothelial cell +is_a: CL:0002577 ! placental epithelial cell +created_by: http://orcid.org/0000-0002-2825-0621 + +[Term] +id: CL:0009093 +name: smooth muscle cell of placenta +def: "A smooth muscle cell that is part of a placenta." [] +subset: location_grouping +synonym: "placental smooth muscle cell" EXACT [] +xref: EFO:0010709 +is_a: CL:0000192 ! smooth muscle cell +created_by: http://orcid.org/0000-0002-2825-0621 + +[Term] +id: CL:0009094 +name: endothelial cell of hepatic portal vein +def: "An endothelial cell that is part of a hepatic portal vein." [] +subset: location_grouping +synonym: "portal endothelial cell" BROAD [] +xref: EFO:0010704 +is_a: CL:0000115 ! endothelial cell +created_by: http://orcid.org/0000-0002-2825-0621 + +[Term] +id: CL:0009095 +name: endothelial cell of uterus +def: "An endothelial cell that is part of a uterus." [] +subset: location_grouping +synonym: "uterine endothelial cell" EXACT [] +xref: EFO:0010711 +is_a: CL:0000115 ! endothelial cell +created_by: http://orcid.org/0000-0002-2825-0621 + [Term] id: CL:0010000 name: keratinized cell of hair follicle @@ -21575,20 +21712,29 @@ is_a: CL:0000287 ! eye photoreceptor cell id: CL:0010010 name: cerebellar stellate cell is_a: CL:0000122 ! stellate neuron +is_a: CL:1001611 ! cerebellar neuron [Term] id: CL:0010011 name: cerebral cortex GABAergic interneuron def: "A GABAergic interneuron whose soma is located in the cerebral cortex." [] is_a: CL:0000402 ! CNS interneuron -is_a: CL:0002609 ! neuron of cerebral cortex +is_a: CL:0010012 ! cerebral cortex neuron is_a: CL:0011005 ! GABAergic interneuron +is_a: CL:0012001 ! neuron of the forebrain [Term] id: CL:0010012 name: cerebral cortex neuron -def: "A neuron that is part_of a cerebral cortex." [] +namespace: cell +alt_id: CL:0002609 +def: "A CNS neuron of the cerebral cortex." [] +synonym: "cortical neuron" EXACT [] +synonym: "neuron of cerebral cortex" EXACT [] +xref: BTO:0004102 +xref: FMA:84104 is_a: CL:2000029 ! central nervous system neuron +property_value: dc-creator http://orcid.org/0000-0001-7258-9596 [Term] id: CL:0010013 @@ -21881,8 +22027,12 @@ created_by: http://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011030 name: dermal microvascular endothelial cell +def: "Any microvascular endothelial cell that is part of the dermis." [] +synonym: "dermal microvascular endothelium cell" EXACT [] +synonym: "DMEC cell" EXACT [] is_a: CL:2000008 ! microvascular endothelial cell is_a: CL:2000010 ! dermis blood vessel endothelial cell +created_by: http://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011031 @@ -22069,6 +22219,86 @@ def: "A mesodermal cell that is part of the splanchnic layer of lateral plate me is_a: CL:0011010 ! lateral mesodermal cell property_value: dc-creator https://orcid.org/0000-0003-2473-2313 +[Term] +id: CL:0017500 +name: neutrophillic cytoplasm +namespace: cell +def: "Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain." [] +created_by: tmeehan +creation_date: 2010-05-25T01:36:34Z + +[Term] +id: CL:0017501 +name: obsolete lobed nucleus +namespace: cell +def: "Nucleus with two or more lobes connected by a thin filament that contains no internal chromatin." [] +comment: Obsoleted because duplicate with GO term. +is_obsolete: true +replaced_by: http://purl.obolibrary.org/obo/GO_0098537 +created_by: tmeehan +creation_date: 2009-12-22T03:54:43Z + +[Term] +id: CL:0017502 +name: acidophilic cytoplasm +namespace: cell +def: "Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain." [] +synonym: "eosinophilic" NARROW [] +created_by: tmeehan +creation_date: 2009-12-22T04:23:25Z + +[Term] +id: CL:0017503 +name: basophilic cytoplasm +namespace: cell +def: "Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions." [] +created_by: tmeehan +creation_date: 2009-12-22T04:24:54Z + +[Term] +id: CL:0017504 +name: polychromatophilic cytoplasm +namespace: cell +def: "Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions." [] +created_by: tmeehan +creation_date: 2009-12-28T04:25:23Z + +[Term] +id: CL:0017505 +name: increased nucleus size +namespace: cell +def: "A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell." [] +created_by: tmeehan +creation_date: 2009-12-23T10:53:24Z + +[Term] +id: CL:0017506 +name: banded nucleus +namespace: cell +def: "A concave nuclear shape where the nucleus is indented to more than half the distance to the farthest nuclear margin, but in no area is the chromatin condensed to a single filament." [] +created_by: tmeehan +creation_date: 2009-12-23T02:18:43Z + +[Term] +id: CL:0017507 +name: reniform nucleus +namespace: cell +def: "A concave nucleus shape where the indentation is smaller than half of the distance to the farthest nuclear margin." [] +created_by: tmeehan +creation_date: 2009-12-23T02:31:25Z + +[Term] +id: CL:0017508 +name: cartwheel heterochromatin +namespace: cell +def: "Heterochromatin that is arranged in a carthwheel pattern." [] +created_by: tmeehan +creation_date: 2009-12-28T04:28:35Z + +[Term] +id: CL:0017509 +name: alobate nucleus + [Term] id: CL:0019001 name: tracheobronchial serous cell @@ -22142,7 +22372,9 @@ property_value: dc-creator http://orcid.org/0000-0003-2034-601X id: CL:0019021 name: endothelial cell of periportal hepatic sinusoid def: "An endothelial cell found in the periportal region hepatic sinusoid, near the portal triad. The fenestrae of these cells are larger but fewer in number compared with those of endothelial cells near the centrilobular region of the hepatic sinusoid." [] +synonym: "periportal hepatic sinusoidal endothelial cell" EXACT [] synonym: "periportal LSEC" EXACT [] +xref: EFO:0010705 is_a: CL:1000398 ! endothelial cell of hepatic sinusoid property_value: dc-creator http://orcid.org/0000-0003-2034-601X @@ -22150,7 +22382,9 @@ property_value: dc-creator http://orcid.org/0000-0003-2034-601X id: CL:0019022 name: endothelial cell of pericentral hepatic sinusoid def: "An endothelial cell found in the centrilobular region hepatic sinusoid, near the central vein. The fenestrae of these cells are smaller but more numerous compared with those of endothelial cells near the periportal region of the hepatic sinusoid." [] +synonym: "central venous hepatic sinusoidal endothelial cell" EXACT [] synonym: "pericentral LSEC" EXACT [] +xref: EFO:0010706 is_a: CL:1000398 ! endothelial cell of hepatic sinusoid property_value: dc-creator http://orcid.org/0000-0003-2034-601X @@ -22204,6 +22438,7 @@ is_a: CL:2000029 ! central nervous system neuron [Term] id: CL:1000022 name: mesonephric nephron tubule epithelial cell +is_a: CL:1000449 ! epithelial cell of nephron is_a: CL:1000507 ! kidney tubule cell [Term] @@ -22243,11 +22478,13 @@ is_a: CL:0000357 ! stratified epithelial stem cell [Term] id: CL:1000090 name: pronephric nephron tubule epithelial cell +is_a: CL:1000449 ! epithelial cell of nephron is_a: CL:1000507 ! kidney tubule cell [Term] id: CL:1000123 name: metanephric nephron tubule epithelial cell +is_a: CL:1000449 ! epithelial cell of nephron is_a: CL:1000507 ! kidney tubule cell [Term] @@ -23196,7 +23433,6 @@ name: type 1 vestibular sensory cell of stato-acoustic epithelium namespace: cell def: "A type I vestibular sensory cell that is part of the stato-acoustic epithelium." [] xref: FMA:263186 -is_a: CL:0000098 ! sensory epithelial cell is_a: CL:0002070 ! type I vestibular sensory cell [Term] @@ -23205,7 +23441,6 @@ name: type 1 vestibular sensory cell of epithelium of macula of utricle of membr namespace: cell def: "A type I vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth." [] xref: FMA:263188 -is_a: CL:0000098 ! sensory epithelial cell is_a: CL:0002070 ! type I vestibular sensory cell [Term] @@ -23214,7 +23449,6 @@ name: type 1 vestibular sensory cell of epithelium of macula of saccule of membr namespace: cell def: "A type I vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth." [] xref: FMA:263190 -is_a: CL:0000098 ! sensory epithelial cell is_a: CL:0002070 ! type I vestibular sensory cell [Term] @@ -23223,7 +23457,6 @@ name: type 1 vestibular sensory cell of epithelium of crista of ampulla of semic namespace: cell def: "A type I vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth." [] xref: FMA:263192 -is_a: CL:0000098 ! sensory epithelial cell is_a: CL:0002070 ! type I vestibular sensory cell [Term] @@ -23232,7 +23465,6 @@ name: type 2 vestibular sensory cell of stato-acoustic epithelium namespace: cell def: "A type II vestibular sensory cell that is part of the stato-acoustic epithelium." [] xref: FMA:263194 -is_a: CL:0000098 ! sensory epithelial cell is_a: CL:0002069 ! type II vestibular sensory cell [Term] @@ -23241,7 +23473,6 @@ name: type 2 vestibular sensory cell of epithelium of macula of utricle of membr namespace: cell def: "A type II vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth." [] xref: FMA:263196 -is_a: CL:0000098 ! sensory epithelial cell is_a: CL:0002069 ! type II vestibular sensory cell [Term] @@ -23250,7 +23481,6 @@ name: type 2 vestibular sensory cell of epithelium of macula of saccule of membr namespace: cell def: "A type II vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth." [] xref: FMA:263198 -is_a: CL:0000098 ! sensory epithelial cell is_a: CL:0002069 ! type II vestibular sensory cell [Term] @@ -23259,7 +23489,6 @@ name: type 2 vestibular sensory cell of epithelium of crista of ampulla of semic namespace: cell def: "A type II vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth." [] xref: FMA:263200 -is_a: CL:0000098 ! sensory epithelial cell is_a: CL:0002069 ! type II vestibular sensory cell [Term] @@ -23654,6 +23883,7 @@ synonym: "epithelial cell of renal collecting tubule" EXACT [] xref: FMA:70982 xref: KUPO:0001059 is_a: CL:0000072 ! non-branched duct epithelial cell +is_a: CL:1000449 ! epithelial cell of nephron is_a: CL:1001225 ! kidney collecting duct cell [Term] @@ -23915,6 +24145,7 @@ comment: This needs to be further defined as a juxtamedullary nephron. Will requ synonym: "kidney tubule epithelial cell" EXACT [] xref: FMA:86785 xref: KUPO:0001022 +is_a: CL:1000449 ! epithelial cell of nephron is_a: CL:1000507 ! kidney tubule cell [Term] @@ -23963,7 +24194,7 @@ id: CL:1000507 name: kidney tubule cell namespace: cell xref: KUPO:0001020 -is_a: CL:1000449 ! epithelial cell of nephron +is_a: CL:1000497 ! kidney cell [Term] id: CL:1000510 @@ -24001,7 +24232,7 @@ id: CL:1000549 name: kidney cortex collecting duct epithelial cell namespace: cell xref: KUPO:0001063 -is_a: CL:0002584 ! renal cortical epithelial cell +is_a: CL:0002681 ! kidney cortical cell is_a: CL:1001225 ! kidney collecting duct cell [Term] @@ -24062,6 +24293,7 @@ name: kidney cortex tubule cell namespace: cell xref: KUPO:0001024 is_a: CL:0002584 ! renal cortical epithelial cell +is_a: CL:1000449 ! epithelial cell of nephron is_a: CL:1000507 ! kidney tubule cell [Term] @@ -24205,6 +24437,7 @@ id: CL:1000714 name: kidney cortex collecting duct principal cell namespace: cell xref: KUPO:0001130 +is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000549 ! kidney cortex collecting duct epithelial cell is_a: CL:1001431 ! kidney collecting duct principal cell @@ -24213,6 +24446,7 @@ id: CL:1000715 name: kidney cortex collecting duct intercalated cell namespace: cell xref: KUPO:0001131 +is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000549 ! kidney cortex collecting duct epithelial cell is_a: CL:1001432 ! kidney collecting duct intercalated cell @@ -24710,7 +24944,7 @@ name: kidney collecting duct cell namespace: cell xref: http://en.wikipedia.org/wiki/Kidney_collecting_duct_cell xref: KUPO:0001012 -is_a: CL:1000449 ! epithelial cell of nephron +is_a: CL:1000497 ! kidney cell [Term] id: CL:1001285 @@ -25617,10 +25851,11 @@ creation_date: 2014-06-25T03:44:44Z [Term] id: CL:2000036 -name: anterior lateral line neuromast support cell +name: anterior lateral line neuromast supporting cell namespace: cell def: "Any neuromast support cell that is part of a anterior lateral line." [] -is_a: CL:0000852 ! neuromast support cell +synonym: "anterior lateral line neuromast support cell" EXACT [] +is_a: CL:0000852 ! neuromast supporting cell created_by: TermGenie creation_date: 2014-06-25T03:44:51Z @@ -25644,10 +25879,11 @@ creation_date: 2014-06-25T03:45:04Z [Term] id: CL:2000039 -name: posterior lateral line neuromast support cell +name: posterior lateral line neuromast supporting cell namespace: cell def: "Any neuromast support cell that is part of a posterior lateral line." [] -is_a: CL:0000852 ! neuromast support cell +synonym: "posterior lateral line neuromast support cell" EXACT [] +is_a: CL:0000852 ! neuromast supporting cell created_by: TermGenie creation_date: 2014-06-25T03:45:11Z @@ -25880,7 +26116,7 @@ namespace: cell def: "Any capillary endothelial cell that is part of a placenta." [] comment: http://www.ncbi.nlm.nih.gov/books/NBK53245/ is_a: CL:0002144 ! capillary endothelial cell -is_a: CL:0002577 ! placental epithelial cell +is_a: CL:0009092 ! endothelial cell of placenta created_by: TermGenie creation_date: 2014-10-07T17:55:56Z @@ -26053,11 +26289,11 @@ creation_date: 2014-12-02T19:07:31Z [Term] id: CL:2000080 -name: mesenchymal stem cell of abdominal adipose name: mesenchymal stem cell of abdominal adipose tissue namespace: cell -def: "Any mesenchymal stem cell of adipose that is part of a abdomen." [] -is_a: CL:0002570 ! mesenchymal stem cell of adipose +def: "Any mesenchymal stem cell of adipose tissue that is part of an abdomen." [] +synonym: "mesenchymal stem cell of abdominal adipose" EXACT [] +is_a: CL:0002570 ! mesenchymal stem cell of adipose tissue created_by: TermGenie creation_date: 2014-12-02T19:10:34Z @@ -26153,6 +26389,8 @@ name: dentate gyrus of hippocampal formation stellate cell namespace: cell def: "Any stellate cell that is part of a dentate gyrus of hippocampal formation." [] is_a: CL:0000122 ! stellate neuron +is_a: CL:0010012 ! cerebral cortex neuron +is_a: CL:0012001 ! neuron of the forebrain created_by: TermGenie creation_date: 2015-02-23T05:48:40Z @@ -26161,6 +26399,7 @@ id: CL:2000091 name: endometrial microvascular endothelial cells namespace: cell def: "Any microvascular endothelial cell that is part of a endometrial blood vessel." [] +is_a: CL:0009095 ! endothelial cell of uterus is_a: CL:2000008 ! microvascular endothelial cell created_by: TermGenie creation_date: 2015-03-31T21:02:36Z @@ -26208,7 +26447,6 @@ id: CL:2000096 name: fibroblast of the reticular layer of dermis namespace: cell def: "Any fibroblast that is part of a reticular layer of dermis." [] -is_a: CL:0000066 ! epithelial cell is_a: CL:0002551 ! fibroblast of dermis created_by: TermGenie creation_date: 2015-08-11T16:28:16Z @@ -26340,12 +26578,12 @@ created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023007 -name: L2/3 bipolar Vip GABAergic cortical interneuron (Mus musculus) -def: "A Vip GABAergic cortical interneuron with bipolar morphology, with a soma found in L2/3. L2/3 bipolar Vip Cells have extending axons across all layers (with preferences for layers II/III and Va) and a dendritic tree that is vertically more restricted than deeper layer VIP cells and extend fewer dendrites into the layers outside their home layer (location of soma). L2/3 Bipolar Vip Cells have great variability in firing patterns, though most are continuous adapting. L2/3 Bipolar Vip Cells are more depolarized in their resting state, had less fast rectification, and had smaller after hyperpolarization than deeper Vip cells." [] +name: L2/3 bipolar vip GABAergic cortical interneuron (Mus musculus) +def: "A vip GABAergic cortical interneuron with bipolar morphology, with a soma found in L2/3. L2/3 bipolar vip cells have extending axons across all layers (with preferences for layers II/III and Va) and a dendritic tree that is vertically more restricted than deeper layer vip cells and extend fewer dendrites into the layers outside their home layer (location of soma). L2/3 bipolar vip cells have great variability in firing patterns, though most are continuous adapting. L2/3 bipolar vip cells are more depolarized in their resting state, had less fast rectification, and had smaller after hyperpolarization than deeper vip cells." [] subset: BDS_subset synonym: "L2/3 bipolar Vip (Mus)" EXACT [] is_a: CL:0000103 ! bipolar neuron -is_a: CL:4023016 ! Vip GABAergic cortical interneuron +is_a: CL:4023016 ! vip GABAergic cortical interneuron property_value: dc-creator http://orcid.org/0000-0001-7258-9596 [Term] @@ -26382,7 +26620,7 @@ created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023011 -name: Lamp5 GABAergic cortical interneuron +name: lamp5 GABAergic cortical interneuron def: "A GABAergic neuron located in the cerebral cortex that expresses Lamp5" [] subset: BDS_subset xref: ILX:0770149 @@ -26412,11 +26650,11 @@ property_value: dc-creator http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023014 -name: L5 Vip cortical GABAergic interneuron (Mus musculus) -def: "A Vip GABAergic cortical interneuron with a soma found in L5. L5 Vip cells have mostly local morphology with some deep-projecting axons. They show only moderate resistance, comparable to that of Sst subclass and unlike typical Vip subclass cells that tend to show high input resistance. L5 Vip cells show particularly low resting membrane potential." [] +name: L5 vip cortical GABAergic interneuron (Mus musculus) +def: "A vip GABAergic cortical interneuron with a soma found in L5. L5 vip cells have mostly local morphology with some deep-projecting axons. They show only moderate resistance, comparable to that of sst subclass and unlike typical Vip subclass cells that tend to show high input resistance. L5 vip cells show particularly low resting membrane potential." [] subset: BDS_subset synonym: "L5 VIP (Mus)" EXACT [] -is_a: CL:4023016 ! Vip GABAergic cortical interneuron +is_a: CL:4023016 ! vip GABAergic cortical interneuron property_value: dc-creator http://orcid.org/0000-0001-7258-9596 [Term] @@ -26430,7 +26668,7 @@ created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023016 -name: Vip GABAergic cortical interneuron +name: vip GABAergic cortical interneuron def: "A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide" [] subset: BDS_subset xref: ILX:0770151 @@ -26457,11 +26695,11 @@ created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023019 -name: L5/6 CCK, Vip cortical GABAergic interneuron (Mus musculus) -def: "A Vip GABAergic cortical interneuron that expresses CCK. L5/6 CCK cells have soma found mainly in L5 and L6 and have large axonal arborization." [] +name: L5/6 cck, vip cortical GABAergic interneuron (Mus musculus) +def: "A vip GABAergic cortical interneuron that expresses cck. L5/6 cck cells have soma found mainly in L5 and L6 and have large axonal arborization." [] subset: BDS_subset synonym: "L5/6 CCK Vip (Mus)" EXACT [] -is_a: CL:4023071 ! L5/6 CCK cortical GABAergic interneuron (Mus musculus) +is_a: CL:4023071 ! L5/6 cck cortical GABAergic interneuron (Mus musculus) property_value: dc-creator http://orcid.org/0000-0001-7258-9596 [Term] @@ -26480,45 +26718,45 @@ created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023022 -name: canopy Lamp5 GABAergic cortical interneuron (Mus musculus) +name: canopy lamp5 GABAergic cortical interneuron (Mus musculus) def: "A Lamp5 GABAergic cortical interneuron that has extended axons in the surface of L1. Canopy Lamp5 cells resemble neurogliaform cells in having elongated horizontal axonal arbors largely confined to L1; but the dendritic arbors are wider and have fewer branches, while the axon is less tortuous and extends further from the soma" [] subset: BDS_subset -is_a: CL:4023011 ! Lamp5 GABAergic cortical interneuron +is_a: CL:4023011 ! lamp5 GABAergic cortical interneuron created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023023 -name: L5,6 Neurogliaform Lamp5 GABAergic cortical interneuron (Mus musculus) -def: "A Lamp 5 GABAergic cortical interneuron with neurogliaform morphology with a soma found in L5,6. L5,6 NGC Lamp5 have deep afterhyperpolarization (AHP) but narrow action potentials (APs). Unlike other deep neurogliaform cells (which are caudal ganglionic eminence (CGE) derived), L5,6 NGC Lamp5 cells are medial ganglionic eminence (MGE)-derived" [] +name: L5,6 neurogliaform lamp5 GABAergic cortical interneuron (Mus musculus) +def: "A lamp 5 GABAergic cortical interneuron with neurogliaform morphology with a soma found in L5,6. L5,6 NGC lamp5 have deep afterhyperpolarization (AHP) but narrow action potentials (APs). Unlike other deep neurogliaform cells (which are caudal ganglionic eminence (CGE) derived), L5,6 NGC lamp5 cells are medial ganglionic eminence (MGE)-derived" [] subset: BDS_subset synonym: "L5,6 NGC Lamp5 (mus)" EXACT [] is_a: CL:0000693 ! neurogliaform cell -is_a: CL:4023011 ! Lamp5 GABAergic cortical interneuron +is_a: CL:4023011 ! lamp5 GABAergic cortical interneuron created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023024 -name: Neurogliaform Lamp5 GABAergic cortical interneuron (Mus musculus) -def: "A Lamp5 GABAergic cortical interneuron with layer-adapting morphology. NGC Lamp5 cells have a small round soma, short dendrites, and a wide dense axonal arbor that tends to establish a dense axonal mesh with high connection probability both to themselves and L2 pyramidal cells. NGC Lamp5 cells have unique synaptic properties that distinguish them from other GABAergic interneurons, including the release of GABA to the extracellular space via volume transmission, and the ability to produce GABA-B responses in connected postsynaptic targets." [] +name: neurogliaform lamp5 GABAergic cortical interneuron (Mus musculus) +def: "A lamp5 GABAergic cortical interneuron with layer-adapting morphology. NGC lamp5 cells have a small round soma, short dendrites, and a wide dense axonal arbor that tends to establish a dense axonal mesh with high connection probability both to themselves and L2 pyramidal cells. NGC lamp5 cells have unique synaptic properties that distinguish them from other GABAergic interneurons, including the release of GABA to the extracellular space via volume transmission, and the ability to produce GABA-B responses in connected postsynaptic targets." [] subset: BDS_subset synonym: "NGC Lamp5 (mus)" EXACT [] is_a: CL:0000693 ! neurogliaform cell -is_a: CL:4023011 ! Lamp5 GABAergic cortical interneuron +is_a: CL:4023011 ! lamp5 GABAergic cortical interneuron created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023025 -name: Long-range projecting Sst GABAergic cortical interneuron (Mus musculus) -def: "A Sst GABAergic cortical interneuron that is both an interneuron and a projecting neuron. They are found in all layers from upper L2/3 down to the bottom of L6. They have long-range projections, some with axons fading into white matter. These cells have low rebound potential, low hyperpolarization sag, and high variability in membrane time constant." [] +name: long-range projecting sst GABAergic cortical interneuron (Mus musculus) +def: "A sst GABAergic cortical interneuron that is both an interneuron and a projecting neuron. They are found in all layers from upper L2/3 down to the bottom of L6. They have long-range projections, some with axons fading into white matter. These cells have low rebound potential, low hyperpolarization sag, and high variability in membrane time constant." [] subset: BDS_subset synonym: "LP SST (Mus)" EXACT [] -is_a: CL:4023017 ! sst GABAergic cortical interneuron +is_a: CL:4023121 ! sst chodl GABAergic cortical interneuron created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023027 -name: L5 T-Martinotti Sst GABAergic cortical interneuron (Mus musculus) -def: "A Sst GABAergic cortical interneuron with a soma found in L5 and possesses 'T-shaped' Martinotti morphologies with local axonal plexus in L5a and translaminar axons restricted to the uppermost part of L1. They show low-threshold spiking patterns with strong rebound firing, and inhibit the L1 apical tuft of nearby pyramidal cells." [] +name: L5 T-Martinotti sst GABAergic cortical interneuron (Mus musculus) +def: "A sst GABAergic cortical interneuron with a soma found in L5 and possesses 'T-shaped' Martinotti morphologies with local axonal plexus in L5a and translaminar axons restricted to the uppermost part of L1. They show low-threshold spiking patterns with strong rebound firing, and inhibit the L1 apical tuft of nearby pyramidal cells." [] subset: BDS_subset synonym: "L5 T Martinotti SST (Mus)" EXACT [] is_a: CL:4023017 ! sst GABAergic cortical interneuron @@ -26527,8 +26765,8 @@ created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023028 -name: L5 non-Martinotti Sst GABAergic cortical interneuron (Mus musculus) -def: "A Sst GABAergic cortical interneuron with a soma found in lower L5 with mostly local axonal arborization but with some sparse ascending axons. L5 non-Martinotti Sst cells show somatic localization and local axon plexus in L5b and L5b/6 and substantial innervation of L3 and L4, and receive thalamic input from the ventral posteromedial nucleus and specifically target L4 neurons, avoiding L5 pyramidal cells. L5 non-Martinotti Sst cells tend to show a higher input resistance and seem to be less stuttering." [] +name: L5 non-Martinotti sst GABAergic cortical interneuron (Mus musculus) +def: "A sst GABAergic cortical interneuron with a soma found in lower L5 with mostly local axonal arborization but with some sparse ascending axons. L5 non-Martinotti sst cells show somatic localization and local axon plexus in L5b and L5b/6 and substantial innervation of L3 and L4, and receive thalamic input from the ventral posteromedial nucleus and specifically target L4 neurons, avoiding L5 pyramidal cells. L5 non-Martinotti sst cells tend to show a higher input resistance and seem to be less stuttering." [] subset: BDS_subset synonym: "L5 non-Martinotti SST (Mus)" EXACT [] is_a: CL:4023017 ! sst GABAergic cortical interneuron @@ -26536,8 +26774,8 @@ created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023030 -name: L2/3/5 fan Martinotti Sst GABAergic cortical interneuron (Mus musculus) -def: "A Sst GABAergic cortical interneuron that has \"fanning-out' Martinotti morphology that is found in layer 2/3/5 of the cerebral cortex. They have local axon arbor and long ascending axons that spreads horizontally and arborizes significantly in L1." [] +name: L2/3/5 fan Martinotti sst GABAergic cortical interneuron (Mus musculus) +def: "A sst GABAergic cortical interneuron that has \"fanning-out' Martinotti morphology that is found in layer 2/3/5 of the cerebral cortex. They have local axon arbor and long ascending axons that spreads horizontally and arborizes significantly in L1." [] comment: L2/3/5 fan Martionotti SST cells have an adapting firing pattern and non-zero afterdepolarization (ADP). subset: BDS_subset synonym: "L2/3/5 fan Martinotti SST (Mus)" EXACT [] @@ -26547,8 +26785,8 @@ created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023031 -name: L4 Sst GABAergic cortical interneuron (Mus musculus) -def: "A Sst GABAergic cortical interneuron with a soma found in lower L2/3 and upper 5, L4 Sst cells have Martinotti morphology with ascending axons but denser local axons and sparser ‘fanning-out’ projections to L1. L4 Sst cells have smaller membrane time constant to calb2 (L2/3/5 Fan Martinotti Cell) and non-zero afterdepolarization (ADP)." [] +name: L4 sst GABAergic cortical interneuron (Mus musculus) +def: "A sst GABAergic cortical interneuron with a soma found in lower L2/3 and upper 5, L4 Sst cells have Martinotti morphology with ascending axons but denser local axons and sparser ‘fanning-out’ projections to L1. L4 sst cells have smaller membrane time constant to calb2 (L2/3/5 fan Martinotti Cell) and non-zero afterdepolarization (ADP)." [] subset: BDS_subset synonym: "L4 SST (Mus)" EXACT [] is_a: CL:4023017 ! sst GABAergic cortical interneuron @@ -26557,17 +26795,18 @@ created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023034 -name: L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) -def: "A Sst GABAergic cortical interneuron transcriptomically between the Sst and the Pvalb families with a soma found in L2/3. Some L2/3 PV-like SST cells have Martinotti morphology while some have basket cell morphology. L2/3 PV-like SST cells have lower AP width and higher firing rate than typical Sst subclass cells. L2/3 PV-like SST cells have high maximum firing rate variability, with many classified as belonging to the Pvalb subclass on the basis of electrophysiology." [] -subset: BDS_subset +name: obsolete L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) +def: "OBSOLETE A sst GABAergic cortical interneuron transcriptomically between the sst and the pvalb families with a soma found in L2/3. Some L2/3 PV-like sst cells have Martinotti morphology while some have basket cell morphology. L2/3 PV-like sst cells have lower AP width and higher firing rate than typical Sst subclass cells. L2/3 PV-like sst cells have high maximum firing rate variability, with many classified as belonging to the pvalb subclass on the basis of electrophysiology." [] +comment: Moved to PCL - see https://github.com/obophenotype/brain_data_standards_ontologies/issues/231. Use PCL:1000002 instead. synonym: "L2/3 PV-like SST Mus)" EXACT [] -is_a: CL:4023017 ! sst GABAergic cortical interneuron +is_obsolete: true +replaced_by: PCL:1000002 created_by: http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023036 -name: Chandelier Pvalb GABAergic cortical interneuron -def: "A Pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner." [] +name: chandelier pvalb GABAergic cortical interneuron +def: "A pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner." [] comment: In mice, Chandelier PV cells have soma found in in upper L2/3, with some in deep L5 and exhibit fast-spiking but lower firing rate compared to basket cells, and have practically absent hyperpolarization sag. subset: BDS_subset synonym: "Chandelier PV" EXACT [] @@ -26789,13 +27028,13 @@ property_value: dc-creator http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023067 -name: Martinotti morphology L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) -def: "A L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) that has Martinotti morphology." [] -subset: BDS_subset +name: obsolete Martinotti morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) +def: "OBSOLETE A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has Martinotti morphology." [] +comment: Moved to PCL - see https://github.com/obophenotype/brain_data_standards_ontologies/issues/231. Use PCL:1000004 instead. synonym: "Martinotti L2/3 PV-like SST (Mus)" EXACT [] -is_a: CL:4023034 ! L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) -is_a: CL:4023076 ! Martinotti neuron property_value: dc-creator http://orcid.org/0000-0001-7258-9596 +is_obsolete: true +replaced_by: PCL:1000004 [Term] id: CL:4023069 @@ -26815,14 +27054,23 @@ property_value: dc-creator http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023071 -name: L5/6 CCK cortical GABAergic interneuron (Mus musculus) -def: "A GABAergic cortical interneuron that expresses CCK. L5/6 CCK cells have soma found mainly in L5 and L6 and have large axonal arborization." [] +name: L5/6 cck cortical GABAergic interneuron (Mus musculus) +def: "A GABAergic cortical interneuron that expresses cck. L5/6 cck cells have soma found mainly in L5 and L6 and have large axonal arborization." [] subset: BDS_subset synonym: "L5/6 CCK (Mus)" EXACT [] is_a: CL:0000402 ! CNS interneuron is_a: CL:0011005 ! GABAergic interneuron property_value: dc-creator http://orcid.org/0000-0001-7258-9596 +[Term] +id: CL:4023075 +name: L6 tyrosine hydroxylase positive sst expressing GABAergic cortical interneuron (Mus musculus) +def: "A sst GABAergic cortical interneuron found in L6 that expresses tyrosine hydroxylase. L6 Th+ SST cells have mostly local axonal arborization within L6." [] +subset: BDS_subset +synonym: "L6 Th+ SST (Mus)" EXACT [] +is_a: CL:4023017 ! sst GABAergic cortical interneuron +property_value: dc-creator http://orcid.org/0000-0001-7258-9596 + [Term] id: CL:4023076 name: Martinotti neuron @@ -26845,13 +27093,13 @@ property_value: dc-creator http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023078 -name: basket morphology L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) -def: "A L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) that has basket morphology." [] -subset: BDS_subset +name: obsolete basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) +def: "OBSOLETE A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has basket morphology." [] +comment: Moved to PCL - see https://github.com/obophenotype/brain_data_standards_ontologies/issues/231. Use PCL:1000003 instead. synonym: "basket L2/3 PV-like SST (Mus)" EXACT [] -is_a: CL:0000118 ! basket cell -is_a: CL:4023034 ! L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) property_value: dc-creator http://orcid.org/0000-0001-7258-9596 +is_obsolete: true +replaced_by: PCL:1000003 [Term] id: CL:4023080 @@ -26965,7 +27213,6 @@ name: arachnoid barrier cell def: "A mesothelial fibroblast of the arachnoid barrier layer. Arachnoid barrier cells make up the tight-junctioned layer in the leptomeninx that functions as the physiologic barrier between the cerebrospinal fluid in the subarachnoid space and the fenestrated capillaries in the dura." [] synonym: "AB cell" EXACT [] synonym: "ABC" EXACT [] -is_a: CL:0002078 ! meso-epithelial cell is_a: CL:4023058 ! mesothelial fibroblast of the leptomeninx property_value: dc-creator http://orcid.org/0000-0001-7258-9596 @@ -27175,11 +27422,124 @@ is_a: CL:0000202 ! auditory hair cell is_a: CL:0002374 ! ear hair cell property_value: dc-creator http://orcid.org/0000-0001-7258-9596 +[Term] +id: CL:4023121 +name: sst chodl GABAergic cortical interneuron +def: "A sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection." [] +synonym: "long-range GABAergic interneuron" BROAD [] +is_a: CL:4023017 ! sst GABAergic cortical interneuron +property_value: dc-creator http://orcid.org/0000-0001-7258-9596 + +[Term] +id: CL:4023122 +name: oxytocin receptor sst GABAergic cortical interneuron +def: "An interneuron located in the cerebral cortex that expresses the oxytocin receptor. These interneurons also express somatostatin." [] +comment: These cells were first identified in mouse. +synonym: "OxtrINs" BROAD [] +is_a: CL:4023017 ! sst GABAergic cortical interneuron +property_value: dc-creator http://orcid.org/0000-0001-7258-9596 +relationship: present_in_taxon NCBITaxon:10090 ! Mus musculus + +[Term] +id: CL:4023129 +name: retinoblast +def: "A retinal cell that is immature or undifferentiated." [] +synonym: "retinal stem cell" EXACT [] +is_a: CL:0009004 ! retinal cell +property_value: dc-contributor http://orcid.org/0000-0001-7258-9596 +property_value: dc-contributor http://orcid.org/0000-0002-0819-0473 + [Term] id: CL:4028001 name: pulmonary capillary endothelial cell +def: "Any capillary endothelial cell that is part of a lung." [] +synonym: "lung capillary endothelial cell" EXACT [] is_a: CL:0002144 ! capillary endothelial cell is_a: CL:2000016 ! lung microvascular endothelial cell +created_by: http://orcid.org/0000-0002-3293-5463 +creation_date: 2021-11-23T02:31:40Z + +[Term] +id: CL:4028002 +name: alveolar capillary type 1 endothelial cell +def: "An alveolar capillary endothelial cell that is located distally to alveolar capillary type 2 endothelial cells." [] +synonym: "'CAP1'" BROAD [] +synonym: "'capillary 1 cell'" BROAD [] +synonym: "'gCAP'" BROAD [] +synonym: "'general capillary cell'" BROAD [] +is_a: CL:0010003 ! epithelial cell of alveolus of lung +is_a: CL:4028001 ! pulmonary capillary endothelial cell +created_by: http://orcid.org/0000-0002-3293-5463 +creation_date: 2021-11-23T03:23:53Z + +[Term] +id: CL:4028003 +name: alveolar capillary type 2 endothelial cell +def: "An alveolar capillary endothelial cell that is located proximally to alveolar capillary type 1 endothelial cells and in close apposition to alveolar type 1 epithelial cells (also known as type I pneumocytes)." [] +synonym: "aCAP" BROAD [] +synonym: "aerocyte" BROAD [] +synonym: "alveolar capillary cell" BROAD [] +synonym: "capillary 2 cell" BROAD [] +synonym: "Car4+ capillary endothelial cell" BROAD [] +synonym: "CD34hi endothelial cells" BROAD [] +is_a: CL:0010003 ! epithelial cell of alveolus of lung +is_a: CL:4028001 ! pulmonary capillary endothelial cell +created_by: http://orcid.org/0000-0002-3293-5463 +creation_date: 2021-11-23T03:23:53Z + +[Term] +id: CL:4028004 +name: alveolar type 1 fibroblast cell +def: "A pulmonary interstitial fibroblast that is part of the alveolus and contains lipid droplets." [] +synonym: "AF1" BROAD [] +synonym: "alveolar fibroblast" BROAD [] +synonym: "alveolar fibroblast 1" BROAD [] +synonym: "lipid interstitial cell" BROAD [] +synonym: "lipofibroblast" BROAD [] +synonym: "matrix fibroblast 1" BROAD [] +synonym: "pulmonary lipofibroblast" BROAD [] +is_a: CL:0002241 ! pulmonary interstitial fibroblast +is_a: CL:0002553 ! fibroblast of lung +created_by: http://orcid.org/0000-0002-3293-5463 +creation_date: 2021-12-09T15:34:13Z + +[Term] +id: CL:4028006 +name: alveolar type 2 fibroblast cell +def: "A pulmonary interstitial fibroblast that is part of the alveolus and localizes to vascular adventitia." [] +synonym: "adventitial fibroblast" BROAD [] +synonym: "AF2" BROAD [] +synonym: "alveolar fibroblast" BROAD [] +synonym: "MANC" BROAD [] +synonym: "matrix fibroblast 2" BROAD [] +synonym: "mesenchymal alveolar niche cell" BROAD [] +synonym: "type-2 associated stromal cell" BROAD [] +is_a: CL:0002241 ! pulmonary interstitial fibroblast +is_a: CL:0002553 ! fibroblast of lung +created_by: http://orcid.org/0000-0002-3293-5463 +creation_date: 2021-12-09T15:53:21Z + +[Term] +id: CL:4030000 +name: choroidal melanocyte +def: "A melanocyte located in the vascular uvea and involved in photoprotection, regulation of oxidative damage and immune responses." [] +comment: Cellular functions and extracellular interactions of choroidal melanocytes are distinct to skin melanocytes. They might have both neuroectodermal as well as mesectodermal origins. +synonym: "uveal melanocyte" EXACT [] +is_a: CL:0000148 ! melanocyte +creation_date: 2022-01-20T12:59:06Z + +[Term] +id: CL:4030002 +name: effector memory CD45RA-positive, alpha-beta T cell, terminally differentiated +def: "An alpha-beta memory T cell with the phenotype CD45RA-positive." [] +synonym: "effector memory RA T cell" BROAD [] +synonym: "TEMRA" BROAD [] +synonym: "TEMRA cell" EXACT [] +synonym: "terminally differentiated effector memory CD45RA+ T cells" EXACT [] +synonym: "terminally differentiated effector memory cells re-expressing CD45RA" EXACT [] +is_a: CL:0000791 ! mature alpha-beta T cell +property_value: dc-contributor http://orcid.org/0000-0002-1773-2692 +creation_date: 2022-02-01T13:04:46Z [Term] id: ENVO:00000000 @@ -43156,6 +43516,11 @@ is_a: UBERON:0003296 ! gland of diencephalon is_a: UBERON:0010133 ! neuroendocrine gland relationship: capable_of_part_of GO:0007276 ! gamete generation relationship: contributes_to_morphology_of UBERON:0001894 ! diencephalon +relationship: develops_from UBERON:0000033 ! head +relationship: develops_from UBERON:0000153 ! anterior region of body +relationship: develops_from UBERON:0007811 ! craniocervical region +relationship: develops_from UBERON:0013701 ! main body axis +relationship: develops_from UBERON:0013702 ! body proper relationship: develops_from UBERON:0034875 ! future pituitary gland relationship: has_part CL:0000440 {source="ZFA"} ! melanocyte stimulating hormone secreting cell relationship: has_part CL:0000642 {source="ZFA"} ! folliculostellate cell @@ -43608,7 +43973,6 @@ is_a: UBERON:0000021 ! cutaneous appendage is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0001003 ! skin epidermis relationship: has_part GO:0045095 ! keratin filament -relationship: never_in_taxon NCBITaxon:314146 ! Euarchontoglires relationship: only_in_taxon NCBITaxon:436491 ! Theropoda [Term] @@ -43631,18 +43995,6 @@ intersection_of: UBERON:0000026 ! appendage intersection_of: has_quality PATO:0002236 ! aliform relationship: capable_of_part_of GO:0060361 ! flight relationship: has_quality PATO:0002236 ! aliform -relationship: never_in_taxon NCBITaxon:118072 {source="bgee"} ! Coelacanthimorpha -relationship: never_in_taxon NCBITaxon:186634 {seeAlso="Wikipedia:Flying_fish", source="bgee"} ! Otomorpha -relationship: never_in_taxon NCBITaxon:314147 {source="bgee"} ! Glires -relationship: never_in_taxon NCBITaxon:6231 {source="bgee"} ! Nematoda -relationship: never_in_taxon NCBITaxon:7878 {source="bgee"} ! Dipnomorpha -relationship: never_in_taxon NCBITaxon:8292 {notes="we do not consider flying frogs to have wings", source="bgee"} ! Amphibia -relationship: never_in_taxon NCBITaxon:8457 {source="bgee"} ! Sauropsida -relationship: never_in_taxon NCBITaxon:91561 {source="bgee"} ! Artiodactyla -relationship: never_in_taxon NCBITaxon:9254 {source="bgee"} ! Prototheria -relationship: never_in_taxon NCBITaxon:9263 {source="bgee"} ! Metatheria -relationship: never_in_taxon NCBITaxon:9443 {source="bgee"} ! Primates -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: only_in_taxon NCBITaxon:33213 ! Bilateria [Term] @@ -43998,7 +44350,6 @@ is_a: UBERON:0005057 ! immune organ is_a: UBERON:0005178 ! thoracic cavity element relationship: composed_primarily_of CL:0000738 {source="Honma1983"} ! leukocyte relationship: located_in UBERON:0001096 ! wall of esophagus -relationship: never_in_taxon NCBITaxon:7863 {source="Wikipedia"} ! Holocephali relationship: only_in_taxon NCBITaxon:7778 {source="Wikipedia"} ! Elasmobranchii relationship: part_of UBERON:0002390 ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system @@ -44132,7 +44483,7 @@ xref: VHOG:0000222 xref: XAO:0000210 xref: ZFA:0000200 is_a: UBERON:0001800 {source="MA"} ! sensory ganglion -is_a: UBERON:0010313 ! neural crest-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000045 ! ganglion intersection_of: extends_fibers_into UBERON:0001780 ! spinal nerve intersection_of: extends_fibers_into UBERON:0002261 ! dorsal root of spinal cord @@ -44164,7 +44515,6 @@ xref: EHDAA:5621 xref: EHDAA:918 xref: EMAPA:32846 xref: EV:0100372 -xref: FBbt:00005137 xref: FMA:5884 xref: http://en.wikipedia.org/wiki/Ganglion xref: http://linkedlifedata.com/resource/umls/id/C0017067 @@ -44200,7 +44550,6 @@ subset: uberon_slim synonym: "pit eye" EXACT [http://en.wikipedia.org/wiki/Eye#Pit_eyes] xref: http://en.wikipedia.org/wiki/Stemma is_a: UBERON:0000047 ! simple eye -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: UBERON:0000047 @@ -44238,7 +44587,6 @@ subset: uberon_slim xref: Multiple_lenses is_a: UBERON:0000047 ! simple eye relationship: has_component UBERON:0005389 {min_cardinality="2"} ! transparent eye structure -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata [Term] id: UBERON:0000051 @@ -44350,7 +44698,6 @@ xref: TAO:0000386 xref: ZFA:0000386 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part GO:0070451 ! cell hair relationship: part_of UBERON:0001846 ! internal ear @@ -44588,7 +44935,6 @@ disjoint_from: UBERON:0034921 ! multi organ part structure relationship: capable_of GO:0008150 ! biological_process relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage relationship: has_boundary UBERON:0006984 ! anatomical surface -relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} ! Xenoturbella relationship: part_of UBERON:0000467 ! anatomical system [Term] @@ -44742,7 +45088,6 @@ xref: OGES:000008 xref: ZFS:0000048 is_a: UBERON:0000105 ! life cycle stage relationship: immediately_preceded_by UBERON:0000068 ! embryo stage -relationship: never_in_taxon NCBITaxon:32524 ! Amniota relationship: part_of GO:0002164 ! larval development relationship: part_of UBERON:0000092 ! post-embryonic stage relationship: simultaneous_with GO:0002164 ! larval development @@ -47244,6 +47589,9 @@ synonym: "spatium leptomeningeum" RELATED LATIN [BTO:0000230] synonym: "spatium subarachnoideum" RELATED LATIN [BTO:0000230] synonym: "spatium subarachnoideum" RELATED LATIN [http://en.wikipedia.org/wiki/Subarachnoid_space] synonym: "subarachnoid cavity" RELATED [BTO:0000230] +synonym: "subarachnoid space of central nervous system" EXACT [] +synonym: "subarachnoid space of CNS" EXACT [] +synonym: "subarachnoid space of neuraxis" EXACT [FMA:322060] xref: BTO:0000230 xref: EMAPA:32666 xref: FMA:83716 @@ -47260,7 +47608,7 @@ relationship: adjacent_to UBERON:0002361 ! pia mater relationship: adjacent_to UBERON:0002362 ! arachnoid mater relationship: contains UBERON:0001359 ! cerebrospinal fluid relationship: contains UBERON:0001981 {source="ISBN:0471888893"} ! blood vessel -relationship: part_of UBERON:0000955 ! brain +relationship: part_of UBERON:0010743 ! meningeal cluster [Term] id: UBERON:0000316 @@ -47730,7 +48078,6 @@ is_a: UBERON:0005174 ! dorsal region element is_a: UBERON:0008846 ! skeletal ligament relationship: attaches_to UBERON:0001676 ! occipital bone relationship: attaches_to UBERON:0002413 {notes="C7 in humans"} ! cervical vertebra -relationship: never_in_taxon NCBITaxon:9596 ! Pan relationship: part_of UBERON:0012477 {source="BTO"} ! dorsal part of neck relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: present_in_taxon NCBITaxon:9608 ! Canidae @@ -47841,7 +48188,6 @@ xref: UMLS:C1947929 {source="ncithesaurus:Prepucial_Gland_MMHCC"} is_a: UBERON:0003937 ! reproductive gland is_a: UBERON:0015251 {source="ISBN:0123813611", source="MA"} ! modified sebaceous gland relationship: fma_set_term FMA:71652 -relationship: never_in_taxon NCBITaxon:9606 {source="ISBN:0123813611", source="MP:0013329"} ! Homo sapiens relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0000990 ! reproductive system @@ -48377,7 +48723,6 @@ xref: UMLS:C0930083 {source="ncithesaurus:Apocrine_Sweat_Gland"} is_a: UBERON:0001820 {source="FMA"} ! sweat gland is_a: UBERON:0010243 {notes="The term apocrine sweat gland is a misnomer. While it was once thought that apocrine sweat glands were true apocrine glands, it is now known that they use merocrine excretion. However, they have retained the original name", source="Wikipedia"} ! merocrine gland disjoint_from: UBERON:0000423 ! eccrine sweat gland -relationship: never_in_taxon NCBITaxon:9822 {source="http://www.nal.usda.gov/awic/pubs/swine/swine.htm"} ! Sus relationship: part_of UBERON:0001003 {source="FMA"} ! skin epidermis [Term] @@ -48413,7 +48758,6 @@ intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: composed_primarily_of UBERON:0001015 ! musculature relationship: capable_of GO:0003012 ! muscle system process relationship: composed_primarily_of UBERON:0001015 ! musculature -relationship: never_in_taxon NCBITaxon:6040 ! Porifera relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa [Term] @@ -48468,7 +48812,6 @@ is_a: UBERON:0013522 ! subdivision of tube relationship: develops_from UBERON:0003115 {source="EHDAA2"} ! pharyngeal arch 4 relationship: has_component UBERON:0001742 ! epiglottic cartilage relationship: has_component UBERON:0004982 ! mucosa of epiglottis -relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0001051 ! hypopharynx [Term] @@ -48483,7 +48826,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/280626006 xref: MESH:A09.371.509.225 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000479 ! tissue intersection_of: surrounds UBERON:0000390 ! lens nucleus relationship: develops_from UBERON:0005614 ! lens anterior epithelium @@ -48500,7 +48842,6 @@ xref: FMA:58971 xref: http://www.snomedbrowser.com/Codes/Details/280628007 xref: MESH:A09.371.509.670 is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0034944 ! zone of organ intersection_of: UBERON:0034944 ! zone of organ intersection_of: surrounded_by UBERON:0000389 ! lens cortex @@ -49107,7 +49448,7 @@ xref: EMAPA:35446 xref: FMA:77597 xref: MA:0001147 is_a: UBERON:0001816 ! autonomic nerve plexus -is_a: UBERON:0010313 ! neural crest-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001810 ! nerve plexus intersection_of: part_of UBERON:0002005 ! enteric nervous system relationship: part_of UBERON:0002005 ! enteric nervous system @@ -49273,6 +49614,7 @@ name: trabecula def: "A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP]." [GO:0060343, http://en.wikipedia.org/wiki/Trabecula] subset: grouping_class subset: pheno_slim +synonym: "trabeculae" EXACT PLURAL [] xref: BTO:0002501 xref: FMA:85273 xref: http://en.wikipedia.org/wiki/Trabecula @@ -49347,8 +49689,8 @@ name: habenular trigone def: "The habenular trigone is a small depressed triangular area situated in front of the superior colliculus and on the lateral aspect of the posterior part of the taenia thalami. It contains a group of nerve cells termed the ganglion habenulC&. Fibers enter it from the stalk of the pineal body, and others, forming what is termed the habenular commissure, pass across the middle line to the corresponding ganglion of the opposite side. Most of its fibers are, however, directed downward and form a bundle, the fasciculus retroflexus of Meynert, which passes medial to the red nucleus, and, after decussating with the corresponding fasciculus of the opposite side, ends in the interpeduncular ganglion." [http://en.wikipedia.org/wiki/Habenular_trigone] comment: superclass in BTO is thalamic nucleus, not present in most ontologies synonym: "trigone of habenulae" RELATED [BTO:0002700] -synonym: "trigonum habenulae" RELATED [BTO:0002700] synonym: "trigonum habenulae" RELATED LATIN [http://en.wikipedia.org/wiki/Habenular_trigone] +synonym: "trigonum habenulae" RELATED [BTO:0002700] xref: BAMS:hbt xref: BTO:0002700 xref: FMA:74868 @@ -50154,7 +50496,6 @@ xref: AEO:0000054 xref: BILA:0000054 xref: CARO:0000054 xref: EHDAA2:0003054 -xref: FBbt:00007276 xref: HAO:0000054 xref: TAO:0001512 xref: TGMA:0001846 @@ -50878,6 +51219,7 @@ xref: VHOG:0000153 xref: XAO:0000001 xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer +relationship: develops_from UBERON:0000307 ! blastula relationship: develops_from UBERON:0006601 ! presumptive ectoderm relationship: has_part CL:0000221 ! ectodermal cell relationship: immediate_transformation_of UBERON:0006601 {source="Bgee:AN"} ! presumptive ectoderm @@ -50915,6 +51257,7 @@ xref: VHOG:0000154 xref: XAO:0000090 xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer +relationship: develops_from UBERON:0000307 ! blastula relationship: develops_from UBERON:0006595 ! presumptive endoderm relationship: has_part CL:0000223 ! endodermal cell relationship: immediate_transformation_of UBERON:0006595 {source="Bgee:AN"} ! presumptive endoderm @@ -50958,10 +51301,10 @@ xref: VHOG:0000152 xref: XAO:0000050 xref: ZFA:0000041 is_a: UBERON:0000923 {notes="sometimes not considered primary"} ! germ layer +relationship: develops_from UBERON:0000307 ! blastula relationship: develops_from UBERON:0006603 ! presumptive mesoderm relationship: has_part CL:0000222 ! mesodermal cell relationship: immediate_transformation_of UBERON:0006603 {source="Bgee:AN"} ! presumptive mesoderm -relationship: never_in_taxon NCBITaxon:6040 ! Porifera relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa [Term] @@ -51135,7 +51478,7 @@ subset: uberon_slim synonym: "ventral cord" EXACT [GO:0007419] xref: BTO:0002328 xref: EFO:0000896 -xref: FBbt:00001102 +xref: FBbt:00005097 xref: http://en.wikipedia.org/wiki/Ventral_nerve_cord xref: MAT:0000339 xref: MIAA:0000339 @@ -51145,7 +51488,6 @@ is_a: UBERON:0005053 ! primary nerve cord intersection_of: UBERON:0005053 ! primary nerve cord intersection_of: intersects_midsagittal_plane_of UBERON:0013235 ! ventrum relationship: intersects_midsagittal_plane_of UBERON:0013235 ! ventrum -relationship: never_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0013235 ! ventrum [Term] @@ -51399,10 +51741,6 @@ is_a: UBERON:0004921 {source="cjm"} ! subdivision of digestive tract is_a: UBERON:0010039 {source="cjm"} ! food storage organ relationship: capable_of GO:0001696 {evidence="ISBN:0486692132"} ! gastric acid secretion relationship: contributes_to_morphology_of UBERON:0001007 ! digestive system -relationship: never_in_taxon NCBITaxon:7864 {source="Wikipedia"} ! Chimaeriformes -relationship: never_in_taxon NCBITaxon:7878 {source="Wikipedia"} ! Dipnomorpha -relationship: never_in_taxon NCBITaxon:7955 {source="ZFA"} ! Danio rerio -relationship: never_in_taxon NCBITaxon:9259 {source="Wikipedia"} ! Tachyglossidae relationship: only_in_taxon NCBITaxon:7742 {source="Wikipedia"} ! Vertebrata relationship: only_in_taxon NCBITaxon:7776 {notes="absent in lampreys and hagfishes", source="ISBN:0073040584"} ! Gnathostomata relationship: part_of UBERON:0001041 ! foregut @@ -51538,8 +51876,6 @@ relationship: contributes_to_morphology_of UBERON:0004535 ! cardiovascular syste relationship: develops_from UBERON:0004141 ! heart tube relationship: has_developmental_contribution_from UBERON:0002342 {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neural crest relationship: has_part UBERON:0004151 ! cardiac chamber -relationship: never_in_taxon NCBITaxon:6239 ! Caenorhabditis elegans -relationship: never_in_taxon NCBITaxon:7227 ! Drosophila melanogaster relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium @@ -51732,6 +52068,7 @@ relationship: composed_primarily_of CL:0002319 ! neural cell relationship: contributes_to_morphology_of UBERON:0001016 ! nervous system property_value: dc-contributor https://github.com/cmungall relationship: develops_from UBERON:0001049 {gci_relation="part_of", gci_filler="NCBITaxon:7711"} ! neural tube +relationship: develops_from UBERON:0002346 ! neurectoderm relationship: develops_from UBERON:0006238 ! future brain relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: immediate_transformation_of UBERON:0006238 {source="Bgee:AN"} ! future brain @@ -52096,7 +52433,6 @@ relationship: develops_from UBERON:0003072 {source="EHDAA2"} ! optic cup relationship: has_part CL:0000573 {source="FMA"} ! retinal cone cell relationship: has_part CL:0000604 {source="FMA"} ! retinal rod cell relationship: has_part CL:0000740 {source="FMA"} ! retinal ganglion cell -relationship: never_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0001802 ! posterior segment of eyeball relationship: part_of UBERON:0019207 ! chorioretinal region @@ -52198,7 +52534,6 @@ is_a: UBERON:0000026 {source="FBbt"} ! appendage is_a: UBERON:0015212 ! lateral structure relationship: has_quality PATO:0000402 {gci_relation="part_of", gci_filler="NCBITaxon:6657", source="Wikipedia"} ! branched relationship: in_lateral_side_of UBERON:0000033 ! head -relationship: never_in_taxon NCBITaxon:6843 ! Chelicerata relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0000033 ! head @@ -52280,7 +52615,6 @@ relationship: connected_to UBERON:0008256 {gci_relation="part_of", gci_filler="N relationship: contributes_to_morphology_of UBERON:0003252 ! thoracic rib cage property_value: dc-contributor https://github.com/alex-dececchi property_value: dc-contributor https://github.com/cmungall -relationship: never_in_taxon NCBITaxon:8570 {source="Wikipedia"} ! Serpentes relationship: only_in_taxon NCBITaxon:32523 {source="ISBN:0073040584"} ! Tetrapoda relationship: part_of RO:0002577 ! system relationship: part_of UBERON:0000915 ! thoracic segment of trunk @@ -53006,6 +53340,7 @@ xref: UMLS:C0042149 {source="ncithesaurus:Uterus"} xref: VHOG:0001137 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0013515 {source="cjm"} ! subdivision of oviduct +relationship: develops_from UBERON:0000922 ! embryo relationship: develops_from UBERON:0005795 ! embryonic uterus relationship: immediate_transformation_of UBERON:0005795 ! embryonic uterus relationship: only_in_taxon NCBITaxon:32525 ! Theria @@ -53353,7 +53688,6 @@ disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003016 ! respiratory system process relationship: capable_of GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:147099 {source="http://en.wikipedia.org/wiki/Acoelomorpha"} ! Acoelomorpha relationship: only_in_taxon NCBITaxon:33213 ! Bilateria [Term] @@ -53506,8 +53840,6 @@ disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0007588 ! excretion relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} ! Xenoturbella -relationship: never_in_taxon NCBITaxon:147099 {source="http://en.wikipedia.org/wiki/Acoelomorpha"} ! Acoelomorpha relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa [Term] @@ -53519,7 +53851,6 @@ synonym: "systema cardiovasculare" RELATED LATIN [http://en.wikipedia.org/wiki/C xref: AAO:0000959 xref: CALOHA:TS-2103 xref: Circulatory:system -xref: FBbt:00005057 xref: OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA xref: VHOG:0001248 is_a: UBERON:0000467 ! anatomical system @@ -53537,9 +53868,6 @@ disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003013 ! circulatory system process relationship: dubious_for_taxon NCBITaxon:6231 {notes="WBbt coelomocyte currently classified as circulating cell"} ! Nematoda relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:147099 {source="http://en.wikipedia.org/wiki/Acoelomorpha"} ! Acoelomorpha -relationship: never_in_taxon NCBITaxon:6073 ! Cnidaria -relationship: never_in_taxon NCBITaxon:6157 ! Platyhelminthes relationship: only_in_taxon NCBITaxon:33213 ! Bilateria [Term] @@ -53577,7 +53905,6 @@ xref: MESH:D006458 xref: MIAA:0000054 xref: TGMA:0000000 is_a: UBERON:0000463 ! organism substance -relationship: never_in_taxon NCBITaxon:33511 ! Deuterostomia relationship: part_of UBERON:0001009 ! circulatory system [Term] @@ -53744,11 +54071,11 @@ disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0050877 ! nervous system process relationship: composed_primarily_of CL:0002319 ! neural cell +relationship: develops_from UBERON:0000922 ! embryo relationship: develops_from UBERON:0016880 ! future nervous system relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part CL:0000540 ! neuron relationship: immediate_transformation_of UBERON:0016880 {source="Bgee:AN"} ! future nervous system -relationship: never_in_taxon NCBITaxon:6040 ! Porifera relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa [Term] @@ -53799,7 +54126,6 @@ is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision relationship: develops_from UBERON:0001049 {gci_relation="part_of", gci_filler="NCBITaxon:7742", evidence="definitional"} ! neural tube relationship: develops_from UBERON:0016879 ! future central nervous system relationship: immediate_transformation_of UBERON:0016879 {source="Bgee:AN"} ! future central nervous system -relationship: never_in_taxon NCBITaxon:147099 {source="http://en.wikipedia.org/wiki/Acoelomorpha"} ! Acoelomorpha relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001016 ! nervous system @@ -53858,7 +54184,6 @@ synonym: "commissure" BROAD [] synonym: "commissure of neuraxis" EXACT [FMA:83906] synonym: "neuraxis commissure" EXACT [FMA:83906] synonym: "white matter commissure" NARROW [CUMBO:CUMBO] -xref: FBbt:00005103 xref: FMA:83906 xref: http://en.wikipedia.org/wiki/Commissure xref: http://linkedlifedata.com/resource/umls/id/C1185742 @@ -54772,7 +55097,6 @@ is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000477 ! anatomical cluster relationship: capable_of_part_of GO:0007613 {source="Wikipedia"} ! memory relationship: capable_of_part_of GO:0008355 {source="Wikipedia"} ! olfactory learning -relationship: never_in_taxon NCBITaxon:6217 ! Nemertea relationship: only_in_taxon NCBITaxon:33317 {notes="annelids and arthropods"} ! Protostomia relationship: part_of UBERON:0000955 ! brain relationship: present_in_taxon NCBITaxon:6340 ! Annelida @@ -55600,7 +55924,6 @@ xref: VHOG:0001733 xref: XAO:0000431 xref: ZFA:0000694 is_a: UBERON:0003913 ! tooth-like structure -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0008281 ! tooth bud relationship: has_developmental_contribution_from UBERON:0000930 {source="XAO-modified"} ! stomodeum @@ -55609,10 +55932,6 @@ relationship: has_part UBERON:0001751 ! dentine relationship: has_part UBERON:0001752 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! enamel relationship: immediate_transformation_of UBERON:0008281 {source="cjm"} ! tooth bud relationship: in_lateral_side_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! jaw region -relationship: never_in_taxon NCBITaxon:189497 {source="Wikipedia"} ! Echidna -relationship: never_in_taxon NCBITaxon:8782 ! Aves -relationship: never_in_taxon NCBITaxon:9257 {source="http://www.ncbi.nlm.nih.gov/pubmed/10210685"} ! Ornithorhynchus -relationship: never_in_taxon NCBITaxon:9761 ! Mysticeti relationship: part_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! jaw region [Term] @@ -55956,7 +56275,6 @@ relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue relationship: develops_from UBERON:0010084 ! future diaphragm relationship: immediate_transformation_of UBERON:0010084 {evidence="definitional"} ! future diaphragm relationship: innervated_by UBERON:0001884 ! phrenic nerve -relationship: never_in_taxon NCBITaxon:8782 {source="Comparative_anatomy_and_evolution"} ! Aves relationship: only_in_taxon NCBITaxon:40674 {source="http://www.ncbi.nlm.nih.gov/pubmed/23586979"} ! Mammalia relationship: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0001004 ! respiratory system @@ -56701,7 +57019,6 @@ intersection_of: UBERON:0000075 ! subdivision of skeletal system intersection_of: composed_primarily_of UBERON:0010913 ! vertebral element disjoint_from: UBERON:0008260 ! spine appendage relationship: composed_primarily_of UBERON:0010913 ! vertebral element -relationship: never_in_taxon NCBITaxon:7762 ! Myxinidae relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0011138 {source="cjm"} ! postcranial axial skeletal system relationship: protects UBERON:0002240 ! spinal cord @@ -56881,7 +57198,6 @@ xref: EFO:0000889 xref: EHDAA2:0003141 xref: EMAPA:32717 xref: EV:0100378 -xref: FBbt:00003525 xref: FMA:14070 xref: GAID:167 xref: galen:SmoothMuscle @@ -57384,7 +57700,6 @@ is_a: UBERON:0009854 ! digestive tract diverticulum relationship: continuous_with UBERON:0001156 {source="Wikipedia"} ! ascending colon relationship: contributes_to_morphology_of UBERON:0000059 ! large intestine relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut -relationship: never_in_taxon NCBITaxon:32443 {source="Wikipedia"} ! Teleostei relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0000059 {source="MA"} ! large intestine relationship: part_of UBERON:0001155 {source="EHDAA2"} ! colon @@ -57987,6 +58302,10 @@ relationship: channel_for UBERON:0001970 ! bile relationship: channels_into UBERON:0001174 ! common bile duct relationship: continuous_with UBERON:0001176 {source="Wikipedia"} ! right hepatic duct relationship: continuous_with UBERON:0001177 {source="Wikipedia"} ! left hepatic duct +relationship: develops_from UBERON:0001007 ! digestive system +relationship: develops_from UBERON:0001173 ! biliary tree +relationship: develops_from UBERON:0002294 ! biliary system +relationship: develops_from UBERON:0002423 ! hepatobiliary system relationship: develops_from UBERON:0010081 ! future common hepatic duct relationship: immediate_transformation_of UBERON:0010081 {evidence="definitional"} ! future common hepatic duct relationship: part_of UBERON:0005604 {source="MA"} ! extrahepatic part of hepatic duct @@ -58724,7 +59043,6 @@ intersection_of: part_of UBERON:0001166 ! pylorus relationship: adjacent_to UBERON:0002114 ! duodenum relationship: continuous_with UBERON:0008858 ! pyloric canal relationship: contributes_to_morphology_of UBERON:0001166 ! pylorus -relationship: never_in_taxon NCBITaxon:8355 ! Xenopus laevis relationship: part_of UBERON:0001166 ! pylorus [Term] @@ -58963,7 +59281,6 @@ xref: NCIT:C12771 xref: Peyer's:patch xref: UMLS:C0031272 {source="ncithesaurus:Peyer_s_Patch"} is_a: UBERON:0001962 {source="FMA", source="MA"} ! gut-associated lymphoid tissue -relationship: never_in_taxon NCBITaxon:8459 {source="http://www.ncbi.nlm.nih.gov/pubmed/PMID:20181529"} ! Testudines relationship: only_in_taxon NCBITaxon:32524 {source="http://www.ncbi.nlm.nih.gov/pubmed/PMID:20181529"} ! Amniota relationship: part_of UBERON:0000030 {editor_note="check this"} ! lamina propria relationship: part_of UBERON:0001242 ! intestinal mucosa @@ -59339,10 +59656,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/1106008 xref: MA:0001644 xref: Major:calyx is_a: UBERON:0006517 ! kidney calyx -is_a: UBERON:0013126 ! vein of abdomen -is_a: UBERON:0014401 ! renal venous blood vessel -relationship: drains UBERON:0001227 ! minor calyx -relationship: part_of RO:0002577 ! system [Term] id: UBERON:0001227 @@ -59359,10 +59672,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/26293004 xref: MA:0001645 xref: Minor:calyx is_a: UBERON:0006517 ! kidney calyx -is_a: UBERON:0013126 ! vein of abdomen -is_a: UBERON:0014401 ! renal venous blood vessel -relationship: drains UBERON:0001228 ! renal papilla -relationship: part_of RO:0002577 ! system [Term] id: UBERON:0001228 @@ -59920,7 +60229,7 @@ synonym: "proctodeum" RELATED [] xref: BTO:0001680 xref: CALOHA:TS-2005 xref: EV:0100082 -xref: FBbt:00003148 +xref: FBbt:00047153 xref: FMA:15711 xref: GAID:312 xref: galen:Anus @@ -60205,7 +60514,6 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0018707 {source="BTO"} ! bladder organ relationship: develops_from UBERON:0000164 {notes="upper part of UG sinus"} ! primitive urogenital sinus relationship: located_in UBERON:0002323 ! coelemic cavity lumen -relationship: never_in_taxon NCBITaxon:8782 {editor="BGEE:Ann", id="GOTAX:0010073", source="https://github.com/obophenotype/uberon/issues/454"} ! Aves relationship: part_of UBERON:0001556 {source="FMA"} ! lower urinary tract [Term] @@ -60485,6 +60793,7 @@ name: trabecula of spleen def: "A trabecula that is part of a spleen." [OBOL:automatic] synonym: "spleen trabeculum" EXACT [] synonym: "splenic trabecula" EXACT [] +synonym: "trabeculae of spleen" EXACT PLURAL [] xref: EMAPA:35808 xref: FMA:16027 xref: http://en.wikipedia.org/wiki/Trabeculae_of_spleen @@ -60698,7 +61007,6 @@ property_value: dc-contributor https://github.com/mellybelly relationship: develops_from UBERON:0010714 {source="cjm"} ! iliac cartilage element relationship: dubious_for_taxon NCBITaxon:8570 {source="Wikipedia"} ! Serpentes relationship: in_lateral_side_of UBERON:0007832 ! pelvic girdle skeleton -relationship: never_in_taxon NCBITaxon:32443 {source="Wikipedia"} ! Teleostei relationship: part_of UBERON:0001272 {source="FMA"} ! innominate bone relationship: part_of UBERON:0007832 {source="VSAO"} ! pelvic girdle skeleton @@ -61068,8 +61376,17 @@ xref: ZFA:0005282 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000064 ! organ part relationship: contributes_to_morphology_of UBERON:0002113 ! kidney +relationship: develops_from UBERON:0000468 ! multicellular organism +relationship: develops_from UBERON:0000916 ! abdomen +relationship: develops_from UBERON:0001008 ! renal system +relationship: develops_from UBERON:0002100 ! trunk +relationship: develops_from UBERON:0002113 ! kidney +relationship: develops_from UBERON:0002417 ! abdominal segment of trunk relationship: develops_from UBERON:0004208 {evidence="definitional"} ! nephrogenic mesenchyme relationship: develops_from UBERON:0010532 ! primitive nephron +relationship: develops_from UBERON:0011143 ! upper urinary tract +relationship: develops_from UBERON:0013701 ! main body axis +relationship: develops_from UBERON:0013702 ! body proper relationship: immediate_transformation_of UBERON:0010532 {source="Bgee:AN"} ! primitive nephron relationship: part_of UBERON:0007684 {source="FMA"} ! uriniferous tubule @@ -61484,6 +61801,10 @@ is_a: UBERON:0035651 ! glans intersection_of: UBERON:0035651 ! glans intersection_of: part_of UBERON:0000989 ! penis relationship: contributes_to_morphology_of UBERON:0000989 ! penis +relationship: develops_from UBERON:0000079 ! male reproductive system +relationship: develops_from UBERON:0003101 ! male organism +relationship: develops_from UBERON:0004053 ! external male genitalia +relationship: develops_from UBERON:0006261 ! male genital tubercle relationship: develops_from UBERON:0013239 ! future glans penis relationship: immediate_transformation_of UBERON:0013239 {source="Bgee:AN"} ! future glans penis relationship: part_of UBERON:0000989 ! penis @@ -62737,7 +63058,6 @@ xref: MA:0001298 xref: NCIT:C32909 xref: UMLS:C0229289 {source="ncithesaurus:Lacrimal_Sac"} is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0034944 ! zone of organ relationship: part_of UBERON:0002392 ! nasolacrimal duct @@ -62772,7 +63092,6 @@ xref: UMLS:C0013444 {source="ncithesaurus:External_Acoustic_Meatus"} xref: VHOG:0000977 is_a: UBERON:0004111 ! anatomical conduit is_a: UBERON:0004119 ! endoderm-derived structure -is_a: UBERON:0004121 ! ectoderm-derived structure relationship: capable_of_part_of GO:0055127 ! vibrational conductance of sound to the inner ear relationship: develops_from UBERON:0005872 {source="http://www.ncbi.nlm.nih.gov/pubmed/11237469"} ! 1st arch pharyngeal cleft relationship: part_of UBERON:0001691 {source="FMA"} ! external ear @@ -63729,7 +64048,6 @@ relationship: has_muscle_antagonist UBERON:0001385 {source="dbpedia"} ! tibialis relationship: has_muscle_insertion UBERON:0003701 {source="dbpedia"} ! calcaneal tendon relationship: has_muscle_origin UBERON:0001446 {notes="fibula medial border of tibia", source="dbpedia"} ! fibula relationship: innervated_by UBERON:0001323 {notes="tibial nerve specifically nerve roots ", source="dbpedia"} ! tibial nerve -relationship: never_in_taxon NCBITaxon:9611 {source="http://en.wikipedia.org/wiki/Soleus"} ! Canis relationship: part_of UBERON:0001665 {source="FMA"} ! triceps surae [Term] @@ -65618,7 +65936,6 @@ xref: MA:0001233 xref: NCIT:C49481 xref: UMLS:C0222110 {source="ncithesaurus:Ear_Skin"} is_a: UBERON:0001084 ! skin of head -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001691 ! external ear relationship: part_of UBERON:0001691 ! external ear @@ -68062,10 +68379,9 @@ xref: ZFA:0000112 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000025 ! tube relationship: connects UBERON:0000165 ! mouth +relationship: develops_from UBERON:0000922 ! embryo relationship: develops_from UBERON:0007026 ! presumptive gut relationship: immediate_transformation_of UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut -relationship: never_in_taxon NCBITaxon:147099 {source="http://en.wikipedia.org/wiki/Acoelomorpha"} ! Acoelomorpha -relationship: never_in_taxon NCBITaxon:41324 {source="https://doi.org/10.1371/journal.pone.0016309"} ! Siboglinidae relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001007 ! digestive system @@ -69043,7 +69359,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/244757006 xref: MA:0001229 is_a: CARO:0000003 is_a: UBERON:0001630 ! muscle organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: attaches_to UBERON:0001848 ! auricular cartilage relationship: part_of RO:0002577 ! system relationship: part_of UBERON:0001757 {source="MA"} ! pinna @@ -69639,7 +69954,26 @@ is_a: UBERON:0010314 ! structure with developmental contribution from neural cre intersection_of: UBERON:0001637 ! artery intersection_of: directly_develops_from UBERON:0003118 ! pharyngeal arch artery 1 relationship: connected_to UBERON:0001070 {subset="human_reference_atlas"} ! external carotid artery +relationship: develops_from NCBITaxon:6072 ! Eumetazoa +relationship: develops_from UBERON:0000062 ! organ +relationship: develops_from UBERON:0000153 ! anterior region of body +relationship: develops_from UBERON:0001004 ! respiratory system +relationship: develops_from UBERON:0001007 ! digestive system +relationship: develops_from UBERON:0001009 ! circulatory system +relationship: develops_from UBERON:0001041 ! foregut +relationship: develops_from UBERON:0001042 ! chordate pharynx +relationship: develops_from UBERON:0001555 ! digestive tract relationship: develops_from UBERON:0003118 ! pharyngeal arch artery 1 +relationship: develops_from UBERON:0004362 ! pharyngeal arch 1 +relationship: develops_from UBERON:0004535 ! cardiovascular system +relationship: develops_from UBERON:0004572 ! arterial system +relationship: develops_from UBERON:0007303 ! pharyngeal vasculature +relationship: develops_from UBERON:0007811 ! craniocervical region +relationship: develops_from UBERON:0008814 ! pharyngeal arch system +relationship: develops_from UBERON:0008816 ! embryonic head +relationship: develops_from UBERON:0011362 ! cranial blood vasculature +relationship: develops_from UBERON:0013701 ! main body axis +relationship: develops_from UBERON:0013702 ! body proper relationship: directly_develops_from UBERON:0003118 ! pharyngeal arch artery 1 relationship: part_of RO:0002577 ! system @@ -70340,7 +70674,6 @@ xref: MA:0001868 xref: ncithesaurus:Transverse_Sinus xref: OpenCyc:Mx4rwDb62ZwpEbGdrcN5Y29ycA xref: Transverse:sinuses -is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0017635 ! paired venous dural sinus intersection_of: UBERON:0017635 ! paired venous dural sinus intersection_of: tributary_of UBERON:0005475 ! sigmoid sinus @@ -70363,7 +70696,6 @@ xref: MA:0001867 xref: NCIT:C12515 xref: OpenCyc:Mx4rv9naEJwpEbGdrcN5Y29ycA xref: UMLS:C0226859 {source="ncithesaurus:Superior_Sagittal_Sinus"} -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0015704 ! sagittal sinus relationship: develops_from UBERON:0009968 {source="cjm"} ! primitive superior sagittal sinus @@ -70923,7 +71255,6 @@ xref: NCIT:C32579 xref: OpenCyc:Mx4rvziz3JwpEbGdrcN5Y29ycA xref: UMLS:C0226532 {source="ncithesaurus:Facial_Vein"} is_a: UBERON:0003496 ! head blood vessel -is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0009141 ! craniocervical region vein relationship: part_of UBERON:0001456 ! face relationship: part_of UBERON:0001586 ! internal jugular vein @@ -70960,9 +71291,7 @@ xref: MA:0002223 xref: NCIT:C53128 xref: UMLS:C0226541 {source="ncithesaurus:Submental_Vein"} is_a: UBERON:0003496 ! head blood vessel -is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0009141 ! craniocervical region vein -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001653 ! facial vein relationship: part_of UBERON:0008199 ! chin relationship: tributary_of UBERON:0001653 {source="FMA/obol"} ! facial vein @@ -71006,7 +71335,6 @@ xref: NCIT:C52700 xref: OpenCyc:Mx4rvmANWZwpEbGdrcN5Y29ycA xref: UMLS:C0226521 {source="ncithesaurus:Superficial_Temporal_Vein"} is_a: UBERON:0001671 ! temporal vein -is_a: UBERON:0003502 ! neck blood vessel relationship: part_of UBERON:0001656 ! retromandibular vein relationship: tributary_of UBERON:0001656 {source="FMA", source="Wikipedia"} ! retromandibular vein @@ -71019,7 +71347,6 @@ xref: FMA:50935 xref: http://www.snomedbrowser.com/Codes/Details/151400007 xref: MA:0002241 is_a: UBERON:0001671 ! temporal vein -is_a: UBERON:0003502 ! neck blood vessel relationship: drains UBERON:0004088 ! orbital region relationship: part_of UBERON:0001656 ! retromandibular vein relationship: tributary_of UBERON:0001656 {source="FMA", source="TFD"} ! retromandibular vein @@ -71034,7 +71361,6 @@ xref: FMA:50938 xref: http://www.snomedbrowser.com/Codes/Details/151501009 xref: MA:0002247 is_a: UBERON:0003496 ! head blood vessel -is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0009141 ! craniocervical region vein intersection_of: UBERON:0001638 ! vein intersection_of: anastomoses_with UBERON:0001653 ! facial vein @@ -71059,7 +71385,6 @@ xref: NCIT:C32855 xref: OpenCyc:Mx4rvlDSc5wpEbGdrcN5Y29ycA xref: UMLS:C0226524 {source="ncithesaurus:Internal_Maxillary_Vein"} is_a: UBERON:0003496 ! head blood vessel -is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0009141 ! craniocervical region vein relationship: part_of UBERON:0001656 ! retromandibular vein relationship: tributary_of UBERON:0001656 {source="FMA"} ! retromandibular vein @@ -71639,7 +71964,6 @@ relationship: develops_from UBERON:0000924 ! ectoderm relationship: develops_from UBERON:0002342 ! neural crest relationship: in_lateral_side_of UBERON:0011156 {source="FMA-abduced-lr"} ! facial skeleton relationship: in_lateral_side_of UBERON:0012072 {source="ISBN:0073040584"} ! palatal part of dermatocranium -relationship: never_in_taxon NCBITaxon:32519 {source="TAO"} ! Ostariophysi relationship: part_of RO:0002577 ! system relationship: part_of UBERON:0011085 ! palatoquadrate arch relationship: part_of UBERON:0011156 ! facial skeleton @@ -71826,6 +72150,7 @@ xref: VHOG:0000688 is_a: UBERON:0001686 ! auditory ossicle bone is_a: UBERON:0002513 ! endochondral bone is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0015016 ! stapes endochondral element intersection_of: UBERON:0015016 ! stapes endochondral element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue @@ -71886,6 +72211,7 @@ xref: UMLS:C0024631 {source="ncithesaurus:Malleus"} xref: VHOG:0000690 is_a: UBERON:0001686 ! auditory ossicle bone is_a: UBERON:0002513 ! endochondral bone +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0015018 ! malleus endochondral element intersection_of: UBERON:0015018 ! malleus endochondral element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue @@ -71982,7 +72308,6 @@ disjoint_from: UBERON:0006618 ! atrium auricular region relationship: contributes_to_morphology_of UBERON:0000033 ! head relationship: contributes_to_morphology_of UBERON:0001690 ! ear relationship: in_lateral_side_of UBERON:0000033 ! head -relationship: never_in_taxon NCBITaxon:9709 {source="Wikipedia"} ! Phocidae relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda relationship: part_of UBERON:0001690 ! ear @@ -72009,7 +72334,6 @@ xref: TAO:0000472 xref: VHOG:0001152 xref: ZFA:0000472 is_a: UBERON:0002513 ! endochondral bone -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011164 ! neurocranium bone is_a: UBERON:0015048 ! basioccipital endochondral element intersection_of: UBERON:0015048 ! basioccipital endochondral element @@ -72044,7 +72368,6 @@ xref: TAO:0000661 xref: VHOG:0001151 xref: ZFA:0000661 is_a: UBERON:0002513 {source="ZFA"} ! endochondral bone -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011164 ! neurocranium bone is_a: UBERON:0015051 ! exoccipital endochondral element intersection_of: UBERON:0015051 ! exoccipital endochondral element @@ -73037,8 +73360,16 @@ is_a: UBERON:0010314 ! structure with developmental contribution from neural cre is_a: UBERON:0013765 ! digestive system element relationship: adjacent_to UBERON:0000166 ! oral opening relationship: contributes_to_morphology_of UBERON:0001007 ! digestive system +relationship: develops_from UBERON:0000033 ! head +relationship: develops_from UBERON:0000153 ! anterior region of body +relationship: develops_from UBERON:0000165 ! mouth +relationship: develops_from UBERON:0001007 ! digestive system +relationship: develops_from UBERON:0001555 ! digestive tract +relationship: develops_from UBERON:0007811 ! craniocervical region relationship: develops_from UBERON:0008814 ! pharyngeal arch system relationship: develops_from UBERON:0010056 ! future tongue +relationship: develops_from UBERON:0013701 ! main body axis +relationship: develops_from UBERON:0013702 ! body proper relationship: has_developmental_contribution_from UBERON:0006260 {notes="anterior 2/3"} ! lingual swellings relationship: has_developmental_contribution_from UBERON:0006756 {source="Wikipedia"} ! median lingual swelling relationship: has_developmental_contribution_from UBERON:0006757 {source="Wikipedia"} ! lateral lingual swelling @@ -73311,7 +73642,6 @@ xref: Soft:palate xref: UMLS:C0030219 {source="ncithesaurus:Soft_Palate"} is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster -relationship: never_in_taxon NCBITaxon:8782 {source="GOC:fmc"} ! Aves relationship: part_of UBERON:0000165 {source="FMA"} ! mouth relationship: part_of UBERON:0001716 {source="MA"} ! secondary palate @@ -73813,8 +74143,6 @@ is_a: UBERON:4000013 ! mineralized skeletal tissue relationship: composed_primarily_of CHEBI:52255 {proportion="85", source="http://en.wikipedia.org/wiki/ENAM"} ! hydroxylapatite relationship: develops_from UBERON:0011588 {source="VSAO"} ! pre-enamel relationship: has_quality PATO:0002444 ! mineralized -relationship: never_in_taxon NCBITaxon:9359 {source="http://www.ncbi.nlm.nih.gov/pubmed/19730686"} ! Dasypodidae -relationship: never_in_taxon NCBITaxon:9816 {source="http://www.ncbi.nlm.nih.gov/pubmed/19730686"} ! Orycteropodidae relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata [Term] @@ -73953,7 +74281,6 @@ xref: Pinna:(anatomy) xref: UMLS:C0928075 {source="ncithesaurus:Auricle"} xref: VHOG:0000460 is_a: UBERON:0001444 ! subdivision of head -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: continuous_with UBERON:0001352 ! external acoustic meatus relationship: develops_from UBERON:0006208 ! auditory hillocks relationship: has_quality PATO:0001297 ! reflectivity @@ -74108,7 +74435,6 @@ xref: OpenCyc:Mx4rv07bVJwpEbGdrcN5Y29ycA xref: UMLS:C1266928 {source="ncithesaurus:Nasal_Turbinate"} is_a: UBERON:0002513 ! endochondral bone is_a: UBERON:0005913 ! zone of bone organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011164 ! neurocranium bone is_a: UBERON:0035612 ! nasal turbinal intersection_of: UBERON:0035612 ! nasal turbinal @@ -74116,7 +74442,6 @@ intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue disjoint_from: UBERON:0006203 ! conchal part of pinna relationship: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:0035007 ! nasal concha cartilage -relationship: never_in_taxon NCBITaxon:436486 {notes="disputed", source="http://palaeos.com/vertebrates/bones/braincase/ethmoid.html"} ! Dinosauria relationship: only_in_taxon NCBITaxon:32524 ! Amniota relationship: transformation_of UBERON:0035007 ! nasal concha cartilage @@ -74180,7 +74505,6 @@ xref: UMLS:C0024957 {source="ncithesaurus:Maxillary_Sinus"} is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0001825 ! paranasal sinus relationship: in_lateral_side_of UBERON:0000033 ! head -relationship: never_in_taxon NCBITaxon:33554 ! Carnivora relationship: part_of UBERON:0002397 ! maxilla [Term] @@ -74781,6 +75105,7 @@ intersection_of: UBERON:0001781 ! layer of retina intersection_of: immediate_transformation_of UBERON:0005424 ! presumptive retinal pigmented epithelium relationship: adjacent_to UBERON:0001787 {source="Wikipedia"} ! photoreceptor layer of retina relationship: adjacent_to UBERON:0003902 ! retinal neural layer +relationship: develops_from NCBITaxon:6072 ! Eumetazoa relationship: develops_from UBERON:0005424 ! presumptive retinal pigmented epithelium relationship: has_part GO:0048770 ! pigment granule relationship: immediate_transformation_of UBERON:0005424 ! presumptive retinal pigmented epithelium @@ -75480,7 +75805,6 @@ xref: VHOG:0000550 xref: ZFA:0005574 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005764 ! acellular membrane -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: bounding_layer_of UBERON:0000965 ! lens of camera-type eye relationship: bounding_layer_of UBERON:0000965 ! lens of camera-type eye @@ -75545,7 +75869,7 @@ xref: NCIT:C12467 xref: Sympathetic:ganglion xref: UMLS:C0017071 {source="ncithesaurus:Sympathetic_Ganglion"} is_a: UBERON:0001805 ! autonomic ganglion -is_a: UBERON:0010313 ! neural crest-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000045 ! ganglion intersection_of: part_of UBERON:0000013 ! sympathetic nervous system relationship: contributes_to_morphology_of UBERON:0000013 ! sympathetic nervous system @@ -75758,8 +76082,6 @@ xref: UMLS:C0006090 {source="ncithesaurus:Brachial_Plexus"} xref: VHOG:0000372 is_a: CARO:0001001 is_a: UBERON:0001813 ! spinal nerve plexus -intersection_of: UBERON:0001813 ! spinal nerve plexus -intersection_of: innervates UBERON:0002102 ! forelimb relationship: innervates UBERON:0002102 ! forelimb [Term] @@ -75787,8 +76109,6 @@ xref: UMLS:C0024093 {source="ncithesaurus:Lumbosacral_Plexus"} xref: VHOG:0000926 is_a: CARO:0001001 is_a: UBERON:0001813 ! spinal nerve plexus -intersection_of: UBERON:0001813 ! spinal nerve plexus -intersection_of: innervates UBERON:0002103 ! hindlimb relationship: innervates UBERON:0002103 ! hindlimb [Term] @@ -75840,14 +76160,12 @@ xref: VHOG:0001476 is_a: UBERON:0002365 ! exocrine gland is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004859 ! eye gland -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0015154 ! lateral gland of orbital region intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0001750 ! lacrimal apparatus disjoint_from: UBERON:0004187 ! Harderian gland relationship: contributes_to_morphology_of UBERON:0001750 ! lacrimal apparatus relationship: develops_from UBERON:0022284 ! lacrimal gland bud -relationship: never_in_taxon NCBITaxon:8570 {source="http://www.ncbi.nlm.nih.gov/pubmed/7559104"} ! Serpentes relationship: part_of UBERON:0001750 ! lacrimal apparatus relationship: part_of UBERON:0002330 ! exocrine system @@ -76228,7 +76546,6 @@ xref: UMLS:C0030580 {source="ncithesaurus:Parotid_Gland"} xref: VHOG:0000308 is_a: UBERON:0000409 ! serous gland is_a: UBERON:0001829 ! major salivary gland -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0012102 ! buccal salivary gland disjoint_from: UBERON:0013219 ! parotoid gland relationship: develops_from UBERON:0008801 ! parotid gland primordium @@ -76293,10 +76610,10 @@ xref: TAO:0007006 xref: UMLS:C0023759 {source="ncithesaurus:Lip"} xref: VHOG:0000677 xref: ZFA:0007006 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0003102 {source="ZFA"} ! surface structure disjoint_from: UBERON:0004084 ! genital labium relationship: contributes_to_morphology_of UBERON:0000165 ! mouth -relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0000165 {source="BTO", source="FMA-implicit", source="VHOG", source="ZFA"} ! mouth relationship: surrounds UBERON:0000166 {source="cjm"} ! oral opening @@ -76323,7 +76640,20 @@ is_a: UBERON:0001833 ! lip is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0001833 ! lip intersection_of: part_of UBERON:0001709 ! upper jaw region +relationship: develops_from UBERON:0000033 ! head +relationship: develops_from UBERON:0000062 ! organ +relationship: develops_from UBERON:0000153 ! anterior region of body +relationship: develops_from UBERON:0000165 ! mouth +relationship: develops_from UBERON:0001007 ! digestive system +relationship: develops_from UBERON:0001456 ! face +relationship: develops_from UBERON:0001555 ! digestive tract +relationship: develops_from UBERON:0001709 ! upper jaw region +relationship: develops_from UBERON:0004089 ! midface +relationship: develops_from UBERON:0007811 ! craniocervical region relationship: develops_from UBERON:0011592 ! future upper lip +relationship: develops_from UBERON:0011595 ! jaw region +relationship: develops_from UBERON:0013701 ! main body axis +relationship: develops_from UBERON:0013702 ! body proper relationship: immediate_transformation_of UBERON:0011592 ! future upper lip relationship: part_of UBERON:0001709 ! upper jaw region @@ -76456,7 +76786,6 @@ xref: UMLS:C0458699 {source="ncithesaurus:Osseous_Labyrinth"} xref: VHOG:0001219 xref: XAO:0000193 is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0001694 {source="FMA", source="MA"} ! petrous part of temporal bone relationship: part_of UBERON:0001846 {source="FMA"} ! internal ear @@ -76494,7 +76823,6 @@ xref: XAO:0000198 xref: ZFA:0000431 is_a: UBERON:0000025 {source="GO"} ! tube is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0003051 ! ear vesicle relationship: part_of UBERON:0001846 {source="MA"} ! internal ear relationship: part_of UBERON:0001849 {source="OG"} ! membranous labyrinth @@ -76615,7 +76943,6 @@ xref: VHOG:0000691 xref: XAO:0000197 xref: ZFA:0000374 is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0034921 ! multi organ part structure relationship: contributes_to_morphology_of UBERON:0001846 ! internal ear relationship: has_quality PATO:0000404 {gci_relation="part_of", gci_filler="NCBITaxon:32525", source="Wikipedia"} ! coiled @@ -76690,7 +77017,6 @@ xref: VHOG:0000284 xref: XAO:0000192 xref: ZFA:0000217 is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0034921 ! multi organ part structure relationship: develops_from UBERON:0003051 {evidence="definitional"} ! ear vesicle relationship: part_of UBERON:0001690 ! ear @@ -76717,7 +77043,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/362544006 xref: MA:0002468 xref: NCIT:C32999 xref: UMLS:C0229315 {source="ncithesaurus:Lobule_of_the_Auricle"} -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0034929 ! external soft tissue zone relationship: contributes_to_morphology_of UBERON:0001691 ! external ear relationship: has_part UBERON:0001013 ! adipose tissue @@ -76735,7 +77060,7 @@ xref: EMAPA:35158 xref: FMA:61013 xref: http://www.snomedbrowser.com/Codes/Details/279627003 xref: MA:0001227 -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0034944 ! zone of organ intersection_of: UBERON:0034944 ! zone of organ intersection_of: part_of UBERON:0001757 ! pinna @@ -76768,7 +77093,6 @@ xref: VHOG:0000729 xref: XAO:0000194 is_a: UBERON:0000062 ! organ is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0003051 ! ear vesicle relationship: located_in UBERON:0004637 ! otic capsule relationship: part_of UBERON:0001846 {source="FMA", source="MA"} ! internal ear @@ -76791,7 +77115,6 @@ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: channel_for UBERON:0001827 ! secretion of lacrimal gland relationship: connects UBERON:0001707 ! nasal cavity relationship: connects UBERON:0010284 ! lacrimal punctum -relationship: never_in_taxon NCBITaxon:8459 {source="http://www.ncbi.nlm.nih.gov/pubmed/7559104"} ! Testudines relationship: only_in_taxon NCBITaxon:32523 {source="ISBN:9780674021839"} ! Tetrapoda relationship: part_of UBERON:0001750 {source="FMA"} ! lacrimal apparatus @@ -76944,7 +77267,6 @@ xref: UMLS:C1323110 {source="BIRNLEX:2562"} xref: VHOG:0000507 is_a: UBERON:0000025 ! tube is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0002499 {source="FMA", source="MA"} ! cochlear labyrinth [Term] @@ -76963,7 +77285,6 @@ xref: UMLS:C1323109 {source="ncithesaurus:Semicircular_Duct"} xref: VHOG:0000238 is_a: UBERON:0000025 ! tube is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001840 {source="MA"} ! semicircular canal relationship: part_of UBERON:0001862 {source="FMA", source="MA"} ! vestibular labyrinth @@ -77035,7 +77356,6 @@ xref: TAO:0002194 xref: ZFA:0001705 is_a: UBERON:0000025 ! tube is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001849 ! membranous labyrinth [Term] @@ -77054,7 +77374,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/279805009 xref: MA:0000244 is_a: UBERON:0000025 ! tube is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: connects UBERON:0001854 {source="Wikipedia"} ! saccule of membranous labyrinth relationship: connects UBERON:0001855 {source="Wikipedia"} ! cochlear duct of membranous labyrinth relationship: part_of UBERON:0001862 {source="EMAPA"} ! vestibular labyrinth @@ -77084,7 +77403,6 @@ xref: UMLS:C0042606 {source="ncithesaurus:Vestibular_Labyrinth"} xref: XAO:0004145 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001849 ! membranous labyrinth [Term] @@ -77135,7 +77453,6 @@ xref: FMA:61289 xref: MA:0001234 is_a: UBERON:0000025 ! tube is_a: UBERON:0004119 ! endoderm-derived structure -is_a: UBERON:0004121 ! ectoderm-derived structure relationship: composed_primarily_of UBERON:0002418 ! cartilage tissue relationship: part_of UBERON:0001352 ! external acoustic meatus @@ -78039,6 +78356,7 @@ xref: VHOG:0000383 xref: XAO:0000011 xref: ZFA:0000109 is_a: UBERON:0002616 ! regional part of brain +disjoint_from: UBERON:0002298 ! brainstem relationship: contributes_to_morphology_of UBERON:0000955 ! brain relationship: develops_from UBERON:0003080 ! anterior neural tube relationship: develops_from UBERON:0006240 ! future forebrain @@ -78278,6 +78596,11 @@ xref: VHOG:0000741 is_a: UBERON:0004733 ! segmental subdivision of hindbrain relationship: contributes_to_morphology_of UBERON:0002028 ! hindbrain property_value: dc-contributor https://github.com/cmungall +relationship: develops_from NCBITaxon:6072 ! Eumetazoa +relationship: develops_from UBERON:0000955 ! brain +relationship: develops_from UBERON:0001016 ! nervous system +relationship: develops_from UBERON:0001017 ! central nervous system +relationship: develops_from UBERON:0002028 ! hindbrain relationship: develops_from UBERON:0010092 ! future metencephalon relationship: dubious_for_taxon NCBITaxon:7955 ! Danio rerio relationship: immediate_transformation_of UBERON:0010092 {evidence="definitional"} ! future metencephalon @@ -81715,9 +82038,15 @@ intersection_of: part_of UBERON:0005386 ! olfactory segment of nasal mucosa relationship: capable_of_part_of GO:0050911 ! detection of chemical stimulus involved in sensory perception of smell relationship: contributes_to_morphology_of UBERON:0000004 ! nose relationship: contributes_to_morphology_of UBERON:0005725 ! olfactory system +relationship: develops_from UBERON:0000033 ! head +relationship: develops_from UBERON:0000076 ! external ectoderm +relationship: develops_from UBERON:0000153 ! anterior region of body +relationship: develops_from UBERON:0007811 ! craniocervical region +relationship: develops_from UBERON:0013701 ! main body axis +relationship: develops_from UBERON:0013702 ! body proper relationship: develops_from UBERON:2001431 ! primitive olfactory epithelium relationship: has_part CL:0000207 {source="NBK26868"} ! olfactory receptor cell -relationship: has_part CL:0000853 {source="NBK26868"} ! olfactory epithelial support cell +relationship: has_part CL:0000853 {source="NBK26868"} ! olfactory epithelial supporting cell relationship: has_part CL:0002169 {source="NBK26868"} ! basal cell of olfactory epithelium relationship: immediate_transformation_of UBERON:2001431 ! primitive olfactory epithelium relationship: part_of UBERON:0000012 {source="NIFSTD"} ! somatic nervous system @@ -81899,7 +82228,7 @@ xref: MIAA:0000102 xref: TAO:0001155 xref: UMLS:C0206111 {source="BIRNLEX:1166"} xref: ZFA:0001155 -is_a: UBERON:0010313 ! neural crest-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: contributes_to_morphology_of UBERON:0002410 ! autonomic nervous system relationship: develops_from UBERON:0005428 {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest", source="Wikipedia", source="ZFA"} ! vagal neural crest @@ -82959,7 +83288,6 @@ relationship: capable_of NBO:0000347 ! gross motor coordination relationship: contributes_to_morphology_of UBERON:0001895 ! metencephalon relationship: develops_from UBERON:0006215 {evidence="definitional"} ! rhombic lip relationship: dubious_for_taxon NCBITaxon:117569 {source="http://icb.oxfordjournals.org/content/42/4/743.full"} ! Hyperoartia -relationship: never_in_taxon NCBITaxon:117565 {source="ISBN:0471888893"} ! Myxini relationship: only_in_taxon NCBITaxon:7742 {source="ISBN:0471888893"} ! Vertebrata relationship: part_of UBERON:0001895 {source="FMA", source="MA"} ! metencephalon relationship: part_of UBERON:0002028 {source="NIF", source="ZFA"} ! hindbrain @@ -83159,8 +83487,8 @@ xref: DMBA:16629 xref: EMAPA:35597 xref: FMA:68464 xref: HBA:9047 -xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=514 {source="BIRNLEX:896"} xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=514 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=514 {source="BIRNLEX:896"} xref: http://linkedlifedata.com/resource/umls/id/C0262291 xref: http://www.snomedbrowser.com/Codes/Details/369250001 xref: MA:0001072 @@ -83328,8 +83656,6 @@ relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system relationship: develops_from UBERON:0000118 ! lung bud relationship: in_lateral_side_of UBERON:0000170 ! pair of lungs relationship: located_in UBERON:0002224 ! thoracic cavity -relationship: never_in_taxon NCBITaxon:32443 {editor="BGEE:fb", source="https://github.com/obophenotype/uberon/issues/701"} ! Teleostei -relationship: never_in_taxon NCBITaxon:7777 {editor="BGEE:fb", source="https://github.com/obophenotype/uberon/issues/701"} ! Chondrichthyes relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0000170 {note="some species only have a single lung"} ! pair of lungs relationship: surrounded_by UBERON:0009778 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! pleural sac @@ -83863,6 +84189,8 @@ is_a: UBERON:0010314 ! structure with developmental contribution from neural cre is_a: UBERON:0013754 ! integumentary system layer relationship: composed_primarily_of UBERON:0002384 ! connective tissue relationship: deep_to UBERON:0001003 ! skin epidermis +relationship: develops_from UBERON:0002199 ! integument +relationship: develops_from UBERON:0002416 ! integumental system relationship: develops_from UBERON:0010083 ! future dermis relationship: has_developmental_contribution_from UBERON:0002342 {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neural crest relationship: has_part GO:0071953 ! elastic fiber @@ -85159,7 +85487,6 @@ intersection_of: UBERON:0034925 ! anatomical collection intersection_of: has_member UBERON:0000003 {minCardinality="2", maxCardinality="2"} ! naris relationship: has_member UBERON:0000003 ! naris relationship: has_part UBERON:0000003 ! naris -relationship: never_in_taxon NCBITaxon:7745 {source="http://webs.lander.edu/rsfox/invertebrates/ammocoetes.html"} ! Petromyzontiformes relationship: part_of UBERON:0000004 ! nose [Term] @@ -85208,9 +85535,6 @@ relationship: contributes_to_morphology_of UBERON:0001173 ! biliary tree relationship: develops_from UBERON:0004912 ! biliary bud relationship: develops_from UBERON:0006242 {evidence="definitional"} ! gall bladder primordium relationship: located_in UBERON:0002323 ! coelemic cavity lumen -relationship: never_in_taxon NCBITaxon:10114 {source="ISBN:9780120749034"} ! Rattus -relationship: never_in_taxon NCBITaxon:8801 {source="GOC:mr", source="ISBN:9781840761122"} ! Struthio camelus -relationship: never_in_taxon NCBITaxon:8930 {source="GOC:mr", source="ISBN:9781840761122"} ! Columbidae relationship: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0002423 {source="MA", source="ZFA", source="cjm"} ! hepatobiliary system @@ -85355,7 +85679,6 @@ xref: XAO:0000236 is_a: UBERON:0004921 {order="3", source="cjm"} ! subdivision of digestive tract relationship: continuous_with UBERON:0001166 ! pylorus relationship: contributes_to_morphology_of UBERON:0002108 ! small intestine -relationship: never_in_taxon NCBITaxon:7955 {source="ZFA:0000348"} ! Danio rerio relationship: part_of UBERON:0002108 ! small intestine relationship: proximalmost_part_of UBERON:0002108 ! small intestine @@ -85771,7 +86094,6 @@ xref: MESH:D002529 xref: UMLS:C0007763 {source="BIRNLEX:1568"} is_a: UBERON:0007245 ! nuclear complex of neuraxis is_a: UBERON:0019263 ! gray matter of hindbrain -relationship: never_in_taxon NCBITaxon:32443 {contributor="michaelerice", source="http://www.ncbi.nlm.nih.gov/pubmed/17134989", source="http://www.ncbi.nlm.nih.gov/pubmed/2040726"} ! Teleostei relationship: part_of UBERON:0002037 ! cerebellum [Term] @@ -87451,7 +87773,6 @@ xref: VHOG:0000262 xref: XAO:0000121 is_a: UBERON:0000117 ! respiratory tube relationship: located_in UBERON:0002224 ! thoracic cavity -relationship: never_in_taxon NCBITaxon:8507 {source="Wikipedia"} ! Sphenodon relationship: part_of UBERON:0007196 ! tracheobronchial tree [Term] @@ -88426,7 +88747,7 @@ relationship: part_of UBERON:0002663 {source="MA-modified"} ! septal nuclear com [Term] id: UBERON:0002221 name: fontanelle -def: "Anatomical structure that is a membranous gap between bones of the skull[TAO]. In humans: Fontanelles are soft spots on a baby's head which, during birth, enable the bony plates of the skull to flex, allowing the child's head to pass through the birth canal. The ossification of the bones of the skull cause the fontanelles to close over by a child's second birthday. The closures eventually form the sutures of the neurocranium. Although there are the two anterior and posterior fontanelles, there are two more fontanelles of interest, the mastoid fontanelle, and the sphenoidal fontanelle[WP]." [http://en.wikipedia.org/wiki/Fontanelle] +def: "Anatomical structure that is a membranous gap between bones of the skull[TAO]. In humans: Fontanelles are soft spots on a baby's head which, during birth, enable the bony plates of the skull to flex, allowing the child's head to pass through the birth canal. The ossification of the bones of the skull cause the fontanelles to close over by a child's second birthday. The closures eventually form the sutures of the neurocranium. Although there are the two anterior and posterior fontanelles, there are two more fontanelles of interest, the mastoid fontanelle, and the sphenoidal fontanelle[WP]." [http://en.wikipedia.org/wiki/Fontanelle, https://orcid.org/0000-0002-2825-0621] subset: pheno_slim subset: uberon_slim subset: vertebrate_core @@ -88444,7 +88765,8 @@ xref: TAO:0001738 xref: UMLS:C0224548 {source="ncithesaurus:Fontanelle"} xref: ZFA:0005536 is_a: CARO:0000000 ! anatomical entity -is_a: UBERON:0007651 {source="FMA"} ! anatomical junction +is_a: UBERON:0002209 {source="FMA"} ! fibrous joint +is_a: UBERON:0003685 ! cranial suture relationship: adjacent_to UBERON:0003685 ! cranial suture relationship: part_of UBERON:0001703 {source="MA", source="ZFA"} ! neurocranium @@ -88578,7 +88900,6 @@ xref: UMLS:C0004816 {source="BIRNLEX:2521"} xref: UMLS:C0004816 {source="ncithesaurus:Basilar_Membrane"} is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005764 {source="Wikipedia"} ! acellular membrane -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: adjacent_to UBERON:0001864 ! scala tympani relationship: adjacent_to UBERON:0002295 ! scala media relationship: part_of UBERON:0001855 ! cochlear duct of membranous labyrinth @@ -88619,7 +88940,6 @@ xref: UMLS:C0029207 {source="BIRNLEX:2526"} xref: VHOG:0001567 is_a: UBERON:0000020 ! sense organ is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: capable_of GO:0050910 ! detection of mechanical stimulus involved in sensory perception of sound relationship: dubious_for_taxon NCBITaxon:8292 ! Amphibia relationship: dubious_for_taxon NCBITaxon:8457 ! Sauropsida @@ -88778,7 +89098,6 @@ xref: UMLS:C1184928 {source="BIRNLEX:2531"} is_a: CARO:0000003 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005764 {source="Wikipedia"} ! acellular membrane -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: attaches_to UBERON:0002276 {notes="limbal zone"} ! lamina of spiral limbus relationship: part_of RO:0002577 ! system relationship: part_of UBERON:0001855 ! cochlear duct of membranous labyrinth @@ -88969,6 +89288,8 @@ is_a: UBERON:0000489 ! cavitated compound organ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005174 ! dorsal region element is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: develops_from UBERON:0001016 ! nervous system +relationship: develops_from UBERON:0001017 ! central nervous system relationship: develops_from UBERON:0003076 ! posterior neural tube relationship: develops_from UBERON:0006241 ! future spinal cord relationship: has_developmental_contribution_from UBERON:0003853 {evidence="definitional"} ! spinal cord neural crest @@ -89066,9 +89387,31 @@ xref: ZFA:0000567 is_a: UBERON:0002514 ! intramembranous bone is_a: UBERON:0008907 ! dermal bone is_a: UBERON:0011597 ! bone of upper jaw +relationship: develops_from UBERON:0000033 ! head +relationship: develops_from UBERON:0000153 ! anterior region of body +relationship: develops_from UBERON:0000165 ! mouth +relationship: develops_from UBERON:0001007 ! digestive system +relationship: develops_from UBERON:0001434 ! skeletal system +relationship: develops_from UBERON:0001456 ! face +relationship: develops_from UBERON:0001555 ! digestive tract +relationship: develops_from UBERON:0001708 ! jaw skeleton +relationship: develops_from UBERON:0001709 ! upper jaw region +relationship: develops_from UBERON:0002204 ! musculoskeletal system +relationship: develops_from UBERON:0003113 ! dermatocranium +relationship: develops_from UBERON:0003129 ! skull +relationship: develops_from UBERON:0003277 ! skeleton of upper jaw +relationship: develops_from UBERON:0004089 ! midface +relationship: develops_from UBERON:0004288 ! skeleton +relationship: develops_from UBERON:0007811 ! craniocervical region +relationship: develops_from UBERON:0010323 ! cranial skeletal system +relationship: develops_from UBERON:0010364 ! dermal skeleton +relationship: develops_from UBERON:0011137 ! axial skeletal system +relationship: develops_from UBERON:0011156 ! facial skeleton +relationship: develops_from UBERON:0011595 ! jaw region relationship: develops_from UBERON:0011628 ! early premaxilla +relationship: develops_from UBERON:0013701 ! main body axis +relationship: develops_from UBERON:0013702 ! body proper relationship: immediate_transformation_of UBERON:0011628 {source="Bgee:AN"} ! early premaxilla -relationship: never_in_taxon NCBITaxon:7901 {source="Wikipedia"} ! Acipenser relationship: part_of UBERON:0003113 {source="ISBN:0073040584"} ! dermatocranium relationship: part_of UBERON:0003277 {source="VHOG"} ! skeleton of upper jaw relationship: part_of UBERON:0011156 ! facial skeleton @@ -89112,6 +89455,7 @@ relationship: part_of UBERON:0002129 ! cerebellar cortex id: UBERON:0002246 name: dorsal thoracic nucleus def: "Two column-shaped nuclear masses formed by large cells. Clarke's nuclei are located in the regions dorsolateral to the central canal in the thoratic and upper lumbar segments." [NLXANAT:20090102] +comment: "Created by Sarah M. Maynard" xsd:string subset: uberon_slim synonym: "Clarke's column" EXACT [] synonym: "Clarke's nuclei" RELATED PLURAL [NLXANAT:20090102] @@ -89918,7 +90262,6 @@ xref: http://en.wikipedia.org/wiki/Limbus_laminae_spiralis xref: MA:0001191 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001855 {source="MA"} ! cochlear duct of membranous labyrinth [Term] @@ -89965,7 +90308,6 @@ xref: MA:0001186 xref: MESH:D014723 xref: Vestibular:aqueduct is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0013685 ! foramen of skull intersection_of: UBERON:0013685 ! foramen of skull intersection_of: conduit_for UBERON:0036074 ! vein of vestibular aqueduct @@ -90001,7 +90343,6 @@ xref: UMLS:C0029894 {source="ncithesaurus:Otolith"} xref: ZFA:0001617 is_a: UBERON:0000476 ! acellular anatomical structure is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: capable_of_part_of GO:0009590 ! detection of gravity relationship: composed_primarily_of CHEBI:3311 ! calcium carbonate relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata @@ -90030,7 +90371,6 @@ xref: NCIT:C33083 xref: Reissner's:membrane is_a: UBERON:0000094 ! membrane organ is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: adjacent_to UBERON:0001863 ! scala vestibuli relationship: adjacent_to UBERON:0002295 ! scala media relationship: part_of UBERON:0001855 ! cochlear duct of membranous labyrinth @@ -90327,7 +90667,6 @@ xref: UMLS:C0007769 {source="ncithesaurus:Aqueduct_of_Sylvius"} xref: VHOG:0000832 xref: ZFA:0000159 is_a: UBERON:0004086 ! brain ventricle -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0013148 {source="EHDAA2"} ! early midbrain vesicle relationship: part_of UBERON:0001891 ! midbrain @@ -91377,7 +91716,6 @@ is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle relationship: develops_from UBERON:0003059 {source="ZFA"} ! presomitic mesoderm -relationship: never_in_taxon NCBITaxon:7712 {source="http://www.ncbi.nlm.nih.gov/pubmed/17237766"} ! Tunicata relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata [Term] @@ -91555,7 +91893,6 @@ xref: VHOG:0001608 is_a: UBERON:0002473 {source="FMA-part_of", source="MA"} ! intercerebral commissure is_a: UBERON:0005340 {source="MP"} ! dorsal telencephalic commissure relationship: contributes_to_morphology_of UBERON:0001893 ! telencephalon -relationship: never_in_taxon NCBITaxon:9255 {source="Wikipedia"} ! Monotremata relationship: only_in_taxon NCBITaxon:9347 {source="Wikipedia"} ! Eutheria [Term] @@ -91789,7 +92126,7 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001061 +xref: FBbt:00001057 xref: FMA:87657 xref: http://en.wikipedia.org/wiki/Neuroectoderm xref: http://linkedlifedata.com/resource/umls/id/C1518271 @@ -92279,7 +92616,10 @@ is_a: UBERON:0000094 {source="FMA"} ! membrane organ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: composed_primarily_of UBERON:0002384 ! connective tissue +relationship: develops_from UBERON:0001016 ! nervous system +relationship: develops_from UBERON:0001017 ! central nervous system relationship: develops_from UBERON:0007645 ! future meninx +relationship: develops_from UBERON:0010743 ! meningeal cluster relationship: fma_set_term FMA:76821 relationship: immediate_transformation_of UBERON:0007645 {source="Bgee:AN"} ! future meninx relationship: part_of UBERON:0010743 ! meningeal cluster @@ -92386,7 +92726,6 @@ relationship: composed_primarily_of UBERON:0011823 ! dense connective tissue relationship: continuous_with UBERON:0001773 {source="http://www.ncbi.nlm.nih.gov/pubmed/16496288"} ! sclera relationship: develops_from UBERON:0007647 ! ectomeninx relationship: immediate_transformation_of UBERON:0007647 {evidence="definitional"} ! ectomeninx -relationship: never_in_taxon NCBITaxon:32443 {source="ISBN:0073040584"} ! Teleostei [Term] id: UBERON:0002364 @@ -92416,15 +92755,14 @@ xref: Tympanic:membrane xref: UMLS:C0041445 {source="ncithesaurus:Tympanic_Membrane"} xref: VHOG:0001146 xref: XAO:0000212 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000094 {source="FMA"} ! membrane organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: adjacent_to UBERON:0004114 {source="cjm"} ! tympanic cavity relationship: contributes_to_morphology_of UBERON:0001756 ! middle ear relationship: develops_from UBERON:0009213 {source="Wikipedia"} ! pharyngeal membrane of 1st arch relationship: has_part UBERON:0005042 ! inner epithelial layer of tympanic membrane relationship: has_part UBERON:0010069 ! outer epithelial layer of tympanic membrane relationship: has_part UBERON:0010070 ! intermediate layer of tympanic membrane -relationship: never_in_taxon NCBITaxon:8459 {source="Wikipedia"} ! Testudines relationship: part_of UBERON:0001756 {source="MA"} ! middle ear [Term] @@ -93397,7 +93735,6 @@ xref: VHOG:0000664 is_a: UBERON:0000025 ! tube is_a: UBERON:0000058 ! duct is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: channel_for UBERON:0001827 ! secretion of lacrimal gland relationship: connects UBERON:0001351 ! lacrimal sac relationship: connects UBERON:0001707 ! nasal cavity @@ -93435,8 +93772,8 @@ xref: NCIT:C12500 xref: UMLS:C0015183 {source="ncithesaurus:Eustachian_Tube"} xref: VHOG:0001145 xref: XAO:0000213 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000062 {source="FMA"} ! organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_developmental_contribution_from UBERON:0010020 {source="UBERON:0010062"} ! tubotympanic recess epithelium relationship: has_part UBERON:0010062 ! pharyngotympanic tube epithelium relationship: part_of UBERON:0001756 ! middle ear @@ -94041,7 +94378,6 @@ intersection_of: UBERON:0010913 ! vertebral element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:0011094 ! vertebra cartilage element -relationship: never_in_taxon NCBITaxon:7901 {source="Wikipedia"} ! Acipenser relationship: part_of UBERON:0001130 ! vertebral column [Term] @@ -94122,7 +94458,6 @@ xref: MIAA:0000094 xref: OpenCyc:Mx4rvVjiC5wpEbGdrcN5Y29ycA xref: WBbt:0005741 is_a: UBERON:0011676 ! subdivision of organism along main body axis -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0000154 ! posterior region of body @@ -94644,7 +94979,6 @@ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: adjacent_to UBERON:0002198 ! neurohypophysis relationship: adjacent_to UBERON:0006377 ! remnant of Rathke's pouch relationship: contributes_to_morphology_of UBERON:0000007 ! pituitary gland -relationship: never_in_taxon NCBITaxon:8782 {source="ISBN:0471888893"} ! Aves relationship: part_of UBERON:0002196 {source="FMA", source="ZFA"} ! adenohypophysis relationship: present_in_taxon NCBITaxon:117569 {source="Ariens, p. 1192"} ! Hyperoartia @@ -94671,7 +95005,6 @@ xref: TAO:0001196 xref: VHOG:0001114 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: never_in_taxon NCBITaxon:7955 {source="ZFA:0001196"} ! Danio rerio relationship: part_of UBERON:0002196 ! adenohypophysis [Term] @@ -94918,8 +95251,8 @@ xref: DMBA:17007 xref: EMAPA:35914 xref: FMA:72435 xref: HBA:9069 -xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=518 xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=518 {source="BIRNLEX:1421"} +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=518 xref: http://linkedlifedata.com/resource/umls/id/C0175394 xref: http://www.snomedbrowser.com/Codes/Details/369244006 xref: MA:0001031 @@ -96558,7 +96891,6 @@ xref: NCIT:C32336 xref: UMLS:C0931689 {source="ncithesaurus:Cochlear_Labyrinth"} is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: located_in UBERON:0001844 ! cochlea relationship: part_of UBERON:0001849 {source="FMA"} ! membranous labyrinth @@ -96685,7 +97017,6 @@ xref: MA:0002824 is_a: UBERON:0001637 ! artery is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: branching_part_of UBERON:0018231 ! labyrinthine artery relationship: located_in UBERON:0006723 ! cochlear modiolus relationship: part_of UBERON:0001846 ! internal ear @@ -97000,7 +97331,6 @@ xref: VHOG:0001676 xref: ZFA:0000559 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0006585 ! vestibular organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: capable_of_part_of GO:0060007 ! linear vestibuloocular reflex relationship: develops_from UBERON:0003051 ! ear vesicle relationship: part_of UBERON:0001862 ! vestibular labyrinth @@ -97023,7 +97353,6 @@ xref: MESH:D010037 xref: Otolithic:membrane is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005764 ! acellular membrane -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0005764 ! acellular membrane intersection_of: composed_primarily_of UBERON:0002280 ! otolith intersection_of: part_of UBERON:0016567 ! statoconial membrane @@ -97363,7 +97692,6 @@ intersection_of: UBERON:0004708 ! paired limb/fin intersection_of: has_skeleton UBERON:0010713 ! paired fin skeleton relationship: develops_from UBERON:0002531 {source="PHENOSCAPE:wd", source="ZFA"} ! paired fin bud relationship: has_skeleton UBERON:0010713 ! paired fin skeleton -relationship: never_in_taxon NCBITaxon:32523 ! Tetrapoda [Term] id: UBERON:0002535 @@ -97376,7 +97704,6 @@ xref: http://en.wikipedia.org/wiki/Gill xref: MESH:D005880 is_a: UBERON:0000062 ! organ relationship: confers_advantage_in ENVO:00002030 ! aquatic biome -relationship: never_in_taxon NCBITaxon:32524 ! Amniota relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001004 ! respiratory system @@ -97509,7 +97836,6 @@ xref: XAO:0000095 xref: ZFA:0000034 is_a: UBERON:0001032 ! sensory system relationship: has_part UBERON:0010202 ! lateral line -relationship: never_in_taxon NCBITaxon:32524 {source="http://tolweb.org/Amniota"} ! Amniota relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata [Term] @@ -97547,15 +97873,6 @@ xref: MIAA:0000257 xref: OpenCyc:Mx4rvVi9M5wpEbGdrcN5Y29ycA xref: Scale:(zoology) is_a: UBERON:0003102 ! surface structure -relationship: never_in_taxon NCBITaxon:311790 ! Afrotheria -relationship: never_in_taxon NCBITaxon:314146 ! Euarchontoglires -relationship: never_in_taxon NCBITaxon:33554 ! Carnivora -relationship: never_in_taxon NCBITaxon:7745 ! Petromyzontiformes -relationship: never_in_taxon NCBITaxon:91561 ! Artiodactyla -relationship: never_in_taxon NCBITaxon:9348 ! Xenarthra -relationship: never_in_taxon NCBITaxon:9362 ! Eulipotyphla -relationship: never_in_taxon NCBITaxon:9397 ! Chiroptera -relationship: never_in_taxon NCBITaxon:9787 ! Perissodactyla relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0002416 ! integumental system relationship: present_in_taxon NCBITaxon:9972 @@ -104521,7 +104838,6 @@ xref: UMLS:C0458765 {source="BIRNLEX:2555"} xref: UMLS:C1184827 {source="BIRNLEX:2523"} is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005913 ! zone of bone organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: capable_of_part_of GO:0019230 {source="Wikipedia"} ! proprioception relationship: part_of UBERON:0006106 ! cochlear canal @@ -109745,7 +110061,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/369083001 xref: UMLS:C0228271 {source="BIRNLEX:983"} xref: Uncinate:fasciculus is_a: UBERON:0005838 {source="FMA"} ! fasciculus of brain -relationship: part_of UBERON:0003023 {source="NIFSTD"} ! pontine tegmentum [Term] id: UBERON:0003045 @@ -109893,7 +110208,6 @@ xref: ZFA:0000051 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0007499 ! epithelial sac -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0007499 ! epithelial sac intersection_of: has_potential_to_develop_into UBERON:0001846 ! internal ear @@ -109932,6 +110246,7 @@ xref: ZFA:0000042 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0007651 {inconsistent_with="ZFA", source="https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/"} ! anatomical junction is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: develops_from UBERON:0003075 ! neural plate relationship: develops_from UBERON:0009615 ! midbrain hindbrain boundary neural plate relationship: immediate_transformation_of UBERON:0009615 {source="ZFA"} ! midbrain hindbrain boundary neural plate relationship: part_of UBERON:0000955 {source="ZFA"} ! brain @@ -110068,6 +110383,7 @@ xref: XAO:0000056 xref: ZFA:0000031 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000479 ! tissue +relationship: develops_from UBERON:0000922 ! embryo relationship: develops_from UBERON:0006599 ! presumptive hypochord relationship: immediate_transformation_of UBERON:0006599 {source="Bgee:AN"} ! presumptive hypochord relationship: only_in_taxon NCBITaxon:7711 ! Chordata @@ -110580,7 +110896,9 @@ is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system disjoint_from: UBERON:0011669 ! neural plate of carapace relationship: developmentally_induced_by UBERON:0002328 {source="Wikipedia"} ! notochord +relationship: develops_from UBERON:0004734 ! gastrula relationship: develops_from UBERON:0007284 ! presumptive neural plate +relationship: develops_from UBERON:0016880 ! future nervous system relationship: immediate_transformation_of UBERON:0007284 {source="Bgee:AN"} ! presumptive neural plate relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata @@ -110625,6 +110943,7 @@ xref: ZFA:0000255 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure +relationship: develops_from UBERON:0000307 ! blastula relationship: develops_from UBERON:0007285 ! presumptive paraxial mesoderm relationship: existence_starts_during UBERON:0000109 ! gastrula stage relationship: immediate_transformation_of UBERON:0007285 {source="Bgee:AN"} ! presumptive paraxial mesoderm @@ -111200,12 +111519,10 @@ xref: TAO:0000292 xref: VSAO:0000001 xref: XAO:0003028 xref: ZFA:0000292 -is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000061 ! anatomical structure relationship: adjacent_to UBERON:0013514 ! space surrounding organism property_value: dc-contributor https://github.com/cmungall property_value: dc-contributor https://github.com/wdahdul -relationship: part_of UBERON:0002416 ! integumental system [Term] id: UBERON:0003103 @@ -111343,7 +111660,6 @@ xref: XAO:0003086 xref: ZFA:0000444 is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010912 ! subdivision of skeleton -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0008895 {source="ZFA"} ! splanchnocranium [Term] @@ -111427,7 +111743,6 @@ xref: VHOG:0001665 xref: XAO:0003169 xref: ZFA:0000863 is_a: UBERON:0011159 ! primary subdivision of cranial skeletal system -relationship: never_in_taxon NCBITaxon:7777 {source="ISBN:0073040584"} ! Chondrichthyes relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0010323 {source="ZFA"} ! cranial skeletal system relationship: part_of UBERON:0010364 ! dermal skeleton @@ -111825,7 +112140,6 @@ def: "A respiratory airway that is part of an open tracheal system." [http://orc subset: uberon_slim synonym: "invertebrate trachea" EXACT [] synonym: "trachea" BROAD SENSU [FBbt:00005043] -xref: FBbt:00005043 xref: Invertebrate:trachea xref: SPD:0000434 xref: TADS:0000315 @@ -112819,7 +113133,6 @@ xref: UMLS:C0447640 {source="BIRNLEX:941"} xref: VHOG:0001180 is_a: UBERON:0002616 ! regional part of brain is_a: UBERON:0004120 ! mesoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0006250 {source="MP-def"} ! infundibular recess of 3rd ventricle relationship: part_of UBERON:0002198 ! neurohypophysis @@ -113016,7 +113329,8 @@ xref: EHDAA:5155 xref: EHDAA:6180 xref: EMAPA:17491 xref: VHOG:0000779 -is_a: UBERON:0010371 ! ecto-epithelium +is_a: CARO:0000000 ! anatomical entity +is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001464 ! hip relationship: develops_from UBERON:0003371 {source="EHDAA2"} ! pelvic appendage bud ectoderm @@ -113034,7 +113348,8 @@ xref: EHDAA:5161 xref: EHDAA:6186 xref: EMAPA:17494 xref: VHOG:0000810 -is_a: UBERON:0010371 ! ecto-epithelium +is_a: CARO:0000000 ! anatomical entity +is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001465 ! knee relationship: develops_from UBERON:0003371 {source="EHDAA2"} ! pelvic appendage bud ectoderm @@ -114015,6 +114330,9 @@ xref: VHOG:0000011 is_a: UBERON:0003547 ! brain meninx intersection_of: UBERON:0002360 ! meninx intersection_of: part_of UBERON:0002028 ! hindbrain +relationship: develops_from NCBITaxon:6072 ! Eumetazoa +relationship: develops_from UBERON:0000955 ! brain +relationship: develops_from UBERON:0002028 ! hindbrain relationship: develops_from UBERON:0010091 ! future hindbrain meninx relationship: immediate_transformation_of UBERON:0010091 {evidence="definitional"} ! future hindbrain meninx relationship: part_of UBERON:0002028 ! hindbrain @@ -114645,7 +114963,6 @@ xref: EHDAA:8031 xref: EMAPA:17929 xref: VHOG:0001099 is_a: UBERON:0009891 ! facial mesenchyme -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0034995 ! jaw mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0001709 ! upper jaw region @@ -114691,8 +115008,8 @@ xref: EHDAA2:0001469 xref: EHDAA:8981 xref: EMAPA:17591 xref: VHOG:0000747 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005253 ! head mesenchyme -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0001757 ! pinna relationship: part_of UBERON:0001757 ! pinna @@ -115171,8 +115488,8 @@ synonym: "incisor tooth epithelial tissue" EXACT [OBOL:automatic] synonym: "incisor tooth epithelium" EXACT [OBOL:automatic] xref: EMAPA:32890 xref: MA:0003223 +is_a: UBERON:0000483 ! epithelium is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001098 ! incisor tooth relationship: part_of UBERON:0001098 ! incisor tooth @@ -115383,7 +115700,6 @@ xref: FMA:301283 xref: MA:0001328 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005911 ! endo-epithelium -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0019306 ! nose epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002255 ! vomeronasal organ @@ -115434,9 +115750,9 @@ synonym: "pelvic fin bud ectoderm" NARROW SENSU [] xref: EHDAA2:0001034 xref: EMAPA:16780 xref: VHOG:0001048 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue -is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: bounding_layer_of UBERON:0005420 ! pelvic appendage bud relationship: bounding_layer_of UBERON:0005420 ! pelvic appendage bud @@ -121345,7 +121661,6 @@ intersection_of: has_quality PATO:0005021 ! unicuspidate disjoint_from: UBERON:0007120 ! premolar tooth relationship: has_part UBERON:0006844 {count="1", editor_note="cardinality not allowed with transitivity in OWL"} ! cusp of tooth relationship: has_quality PATO:0005021 ! unicuspidate -relationship: never_in_taxon NCBITaxon:337687 {notes="Although there are a few exceptions, the dental formula for the great majority of cricetids is 1.0.0.3", source="http://en.wikipedia.org/wiki/Cricetidae"} ! Muroidea relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia [Term] @@ -121365,7 +121680,6 @@ xref: MESH:A14.254.900.710 xref: NCIT:C32375 xref: UMLS:C0226993 {source="ncithesaurus:Corona_Dentis"} is_a: UBERON:0000063 ! organ subunit -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001091 ! calcareous tooth @@ -121406,7 +121720,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/245728004 xref: MESH:A14.254.900.750 is_a: CARO:0000003 is_a: UBERON:0000063 ! organ subunit -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: attaches_to UBERON:0001091 ! calcareous tooth relationship: part_of RO:0002577 ! system @@ -121988,7 +122301,7 @@ xref: MESH:D013704 xref: NCIT:C32888 xref: Temporomandibular:joint xref: UMLS:C0039493 {source="ncithesaurus:Jaw_Joint"} -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0011171 ! joint connecting upper and lower jaws is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0000982 ! skeletal joint @@ -122166,7 +122479,6 @@ xref: NCIT:C33557 xref: UMLS:C0503361 {source="ncithesaurus:Sinus_of_Valsava"} is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: contributes_to_morphology_of UBERON:0010172 ! bulb of aorta relationship: part_of UBERON:0010172 {source="FMA", source="MP"} ! bulb of aorta @@ -122563,8 +122875,6 @@ xref: MESH:D002572 xref: OpenCyc:Mx4rvkEE3JwpEbGdrcN5Y29ycA is_a: CARO:0001001 is_a: UBERON:0001813 ! spinal nerve plexus -intersection_of: UBERON:0001813 ! spinal nerve plexus -intersection_of: innervates UBERON:0007811 ! craniocervical region relationship: innervates UBERON:0007811 ! craniocervical region [Term] @@ -124317,6 +124627,7 @@ is_a: UBERON:0001781 ! layer of retina intersection_of: UBERON:0001781 ! layer of retina intersection_of: immediate_transformation_of UBERON:0005425 ! presumptive neural retina relationship: developmentally_induced_by UBERON:0005426 ! lens vesicle +relationship: develops_from NCBITaxon:6072 ! Eumetazoa relationship: develops_from UBERON:0005425 ! presumptive neural retina relationship: has_part CL:0000210 ! photoreceptor cell relationship: has_part CL:0000540 ! neuron @@ -124454,9 +124765,6 @@ is_a: UBERON:0003909 ! sinusoid intersection_of: UBERON:0003909 ! sinusoid intersection_of: part_of UBERON:0001250 ! red pulp of spleen relationship: connected_to UBERON:0010400 {subset="human_reference_atlas"} ! spleen trabecular vein -relationship: never_in_taxon NCBITaxon:10088 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} ! Mus -relationship: never_in_taxon NCBITaxon:9681 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} ! Felidae -relationship: never_in_taxon NCBITaxon:9822 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} ! Sus relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of RO:0002577 ! system relationship: part_of UBERON:0001250 ! red pulp of spleen @@ -125029,7 +125337,6 @@ synonym: "placental labyrinth" EXACT [] is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure relationship: contributes_to_morphology_of UBERON:0001987 ! placenta -relationship: never_in_taxon NCBITaxon:9606 {source="http://placentation.ucsd.edu"} ! Homo sapiens relationship: part_of UBERON:0001987 ! placenta [Term] @@ -125321,6 +125628,11 @@ xref: FMA:6965 xref: http://www.snomedbrowser.com/Codes/Details/280364004 xref: Pterygopalatine:ganglion is_a: UBERON:0001808 ! parasympathetic ganglion +relationship: develops_from RO:0002577 ! system +relationship: develops_from UBERON:0000010 ! peripheral nervous system +relationship: develops_from UBERON:0000011 ! parasympathetic nervous system +relationship: develops_from UBERON:0001016 ! nervous system +relationship: develops_from UBERON:0002410 ! autonomic nervous system relationship: develops_from UBERON:0010128 ! future pterygopalatine ganglion relationship: immediate_transformation_of UBERON:0010128 {evidence="definitional"} ! future pterygopalatine ganglion @@ -125519,7 +125831,6 @@ xref: FMA:77825 xref: http://www.snomedbrowser.com/Codes/Details/279829002 is_a: UBERON:0000025 ! tube is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: connects UBERON:0001854 ! saccule of membranous labyrinth relationship: connects UBERON:0001860 ! endolymphatic duct relationship: part_of UBERON:0011774 ! utriculosaccular duct @@ -125536,7 +125847,6 @@ xref: FMA:77824 xref: http://www.snomedbrowser.com/Codes/Details/279819009 is_a: UBERON:0000025 ! tube is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: connects UBERON:0001853 ! utricle of membranous labyrinth relationship: connects UBERON:0001860 ! endolymphatic duct relationship: part_of UBERON:0011774 ! utriculosaccular duct @@ -125562,7 +125872,6 @@ def: "The utriculo-endolymphatic (UE) valve which is located in the antero-infer subset: pheno_slim is_a: UBERON:0003978 ! valve is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: contributes_to_morphology_of UBERON:0001853 ! utricle of membranous labyrinth relationship: part_of UBERON:0001853 ! utricle of membranous labyrinth @@ -126401,7 +126710,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/280605006 xref: NCIT:C32256 xref: Schlemm's:canal xref: UMLS:C0229108 {source="ncithesaurus:Canal_of_Schlemm"} -xref: ZFA:0005829 is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0009141 ! craniocervical region vein @@ -126570,7 +126878,6 @@ xref: MA:0002770 xref: Osseous:ampullae is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010000 ! multicellular anatomical structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001840 ! semicircular canal relationship: part_of UBERON:0001856 {source="MA"} ! semicircular duct @@ -126836,6 +127143,8 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034706 {source="NCBIBook:NBK10047"} ! proliferating neuroepithelium relationship: adjacent_to UBERON:0003842 ! neural tube lumen +relationship: develops_from UBERON:0001016 ! nervous system +relationship: develops_from UBERON:0001049 ! neural tube relationship: develops_from UBERON:0004022 ! germinal neuroepithelium relationship: immediate_transformation_of UBERON:0004022 {source="NCBIBook:NBK10047"} ! germinal neuroepithelium relationship: part_of UBERON:0001049 ! neural tube @@ -127050,7 +127359,6 @@ xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1243 xref: Interposed:nucleus xref: NLXANAT:20081242 is_a: UBERON:0008995 ! nucleus of cerebellar nuclear complex -relationship: never_in_taxon NCBITaxon:8570 {source="ISBN:0471888893"} ! Serpentes relationship: only_in_taxon NCBITaxon:32524 {source="ISBN:0471888893"} ! Amniota relationship: part_of UBERON:0002130 {source="NIFSTD"} ! cerebellar nuclear complex @@ -128217,6 +128525,7 @@ xref: ZFA:0000360 is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0012275 ! meso-epithelium +relationship: develops_from NCBITaxon:6072 ! Eumetazoa relationship: develops_from UBERON:0005498 ! primitive heart tube relationship: immediate_transformation_of UBERON:0005498 {source="ZFA-modified"} ! primitive heart tube relationship: part_of UBERON:0000922 ! embryo @@ -128465,7 +128774,6 @@ xref: XAO:0004325 is_a: CARO:0000003 is_a: UBERON:0001630 ! muscle organ is_a: UBERON:0004120 ! mesoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue relationship: develops_from UBERON:0010360 {source="http://www.ncbi.nlm.nih.gov/pubmed/21610022"} ! pharyngeal arch mesenchyme from head mesenchyme relationship: innervated_by UBERON:0001785 {source="ISBN:0073040584"} ! cranial nerve @@ -128819,9 +129127,6 @@ intersection_of: UBERON:0015153 ! medial gland of ocular region intersection_of: produces UBERON:0022282 ! secretion of Harderian gland relationship: connected_to UBERON:0010207 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! nictitating membrane relationship: innervated_by UBERON:0015161 ! inferior branch of oculomotor nerve -relationship: never_in_taxon NCBITaxon:9443 {source="http://www.ncbi.nlm.nih.gov/pubmed/7559104"} ! Primates -relationship: never_in_taxon NCBITaxon:9606 {notes="may be transient in embryos", source="http://www.ncbi.nlm.nih.gov/pubmed/7559104"} ! Homo sapiens -relationship: never_in_taxon NCBITaxon:9787 {source="http://www.ncbi.nlm.nih.gov/pubmed/7559104"} ! Perissodactyla relationship: only_in_taxon NCBITaxon:32523 {source="http://www.ncbi.nlm.nih.gov/pubmed/7559104"} ! Tetrapoda relationship: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0002330 {notes="some evidence suggests also endocrine", source="http://www.ncbi.nlm.nih.gov/pubmed/7559104"} ! exocrine system @@ -131786,7 +132091,6 @@ is_a: UBERON:0005172 ! abdomen element is_a: UBERON:0008845 {source="MP"} ! nonskeletal ligament relationship: attaches_to UBERON:0000991 ! gonad relationship: develops_from UBERON:0003064 {source="Wikipedia"} ! intermediate mesoderm -relationship: never_in_taxon NCBITaxon:9721 {notes="primordium does not develop", source="ISBN:0123971756"} ! Cetacea relationship: part_of RO:0002577 ! system relationship: part_of UBERON:0000323 {source="BTO"} ! late embryo relationship: part_of UBERON:0000990 ! reproductive system @@ -135767,7 +136071,6 @@ xref: AAO:0010143 xref: http://www.snomedbrowser.com/Codes/Details/361515007 xref: VHOG:0000854 is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010363 ! endochondral element relationship: part_of UBERON:0001703 ! neurocranium relationship: part_of UBERON:0001846 ! internal ear @@ -136331,8 +136634,8 @@ xref: http://www.snomedbrowser.com/Codes/Details/278228007 xref: MA:0002939 xref: VHOG:0000927 is_a: UBERON:0000158 ! membranous layer +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005983 ! heart layer -is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0000158 ! membranous layer intersection_of: part_of UBERON:0002094 ! interventricular septum relationship: contributes_to_morphology_of UBERON:0002094 ! interventricular septum @@ -137254,10 +137557,9 @@ xref: MA:0002154 xref: MESH:D007601 xref: NCIT:C12738 xref: UMLS:C0022427 {source="ncithesaurus:Jugular_Vein"} -is_a: UBERON:0003502 ! neck blood vessel -is_a: UBERON:0009141 ! craniocervical region vein +is_a: UBERON:0001638 ! vein relationship: drains UBERON:0000033 ! head -relationship: part_of UBERON:0000974 ! neck +relationship: part_of RO:0002577 ! system [Term] id: UBERON:0004713 @@ -137503,7 +137805,6 @@ xref: NCIT:C32063 xref: UMLS:C0229465 {source="ncithesaurus:Ampullary_Crest"} is_a: UBERON:0000020 ! sense organ is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: contributes_to_morphology_of UBERON:0004043 ! semicircular canal ampulla relationship: part_of UBERON:0004043 {source="MA"} ! semicircular canal ampulla @@ -137739,7 +138040,6 @@ name: segmental subdivision of nervous system def: "Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres." [FBbt:00005140, http://orcid.org/0000-0002-6601-2165] subset: non_informative synonym: "neuromere" RELATED [FBbt:00005140] -xref: FBbt:00005140 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000063 ! organ subunit intersection_of: UBERON:0000063 ! organ subunit @@ -137912,7 +138212,6 @@ xref: ZFA:0000184 is_a: UBERON:0007829 ! pectoral girdle bone is_a: UBERON:0008907 {source="ZFA", source="ZFIN:ZDB-PUB-060210-7"} ! dermal bone relationship: connected_to UBERON:0003113 {gci_relation="part_of", gci_filler="NCBITaxon:32443"} ! dermatocranium -relationship: never_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: part_of UBERON:0007831 {source="ZFA"} ! pectoral girdle skeleton [Term] @@ -137962,7 +138261,6 @@ is_a: UBERON:0002513 {source="VSAO"} ! endochondral bone is_a: UBERON:0007829 ! pectoral girdle bone disjoint_from: UBERON:0006633 ! coracoid process of scapula relationship: develops_from UBERON:0004753 ! scapulocoracoid -relationship: never_in_taxon NCBITaxon:32525 {reference="ISBN:0-03-910284-X"} ! Theria relationship: part_of UBERON:0007831 {source="VSAO"} ! pectoral girdle skeleton [Term] @@ -138024,7 +138322,6 @@ xref: TAO:0000575 xref: ZFA:0000575 is_a: UBERON:0002513 ! endochondral bone is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011164 ! neurocranium bone relationship: develops_from UBERON:0004637 ! otic capsule relationship: develops_from UBERON:0005410 ! cartilaginous otic capsule @@ -138047,7 +138344,6 @@ xref: TAO:0000595 xref: VHOG:0001150 xref: ZFA:0000595 is_a: UBERON:0002513 ! endochondral bone -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011164 ! neurocranium bone is_a: UBERON:0015015 ! supraoccipital endochondral element intersection_of: UBERON:0015015 ! supraoccipital endochondral element @@ -138232,7 +138528,6 @@ intersection_of: capable_of GO:0055078 ! sodium ion homeostasis intersection_of: part_of UBERON:0001052 ! rectum relationship: capable_of GO:0055078 ! sodium ion homeostasis relationship: confers_advantage_in ENVO:01000048 ! ocean biome -relationship: never_in_taxon NCBITaxon:32523 ! Tetrapoda relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0001052 ! rectum relationship: present_in_taxon NCBITaxon:118072 ! Coelacanthimorpha @@ -138253,7 +138548,6 @@ intersection_of: UBERON:0002530 ! gland intersection_of: capable_of GO:0055078 ! sodium ion homeostasis relationship: capable_of GO:0055078 ! sodium ion homeostasis relationship: confers_advantage_in ENVO:00000447 ! marine biome -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata [Term] @@ -138897,6 +139191,7 @@ def: "The thymic connective tissue which extends into the parenchyma." [ISBN:0-3 subset: pheno_slim synonym: "thymic trabecula" EXACT [OBOL:automatic] synonym: "thymus gland trabecula" EXACT [OBOL:automatic] +synonym: "thymus trabeculae" EXACT PLURAL [] synonym: "trabecula of thymus" EXACT [OBOL:automatic] synonym: "trabecula of thymus gland" EXACT [OBOL:automatic] xref: http://linkedlifedata.com/resource/umls/id/C1515431 @@ -139448,7 +139743,6 @@ synonym: "epithelium of lacrimal gland" EXACT [OBOL:automatic] synonym: "lacrimal gland epithelial tissue" EXACT [OBOL:automatic] xref: EMAPA:36515 xref: MA:0001297 -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001817 ! lacrimal gland @@ -139989,7 +140283,6 @@ is_a: UBERON:0002203 ! vasculature of eye is_a: UBERON:0036302 ! vasculature of central nervous system plus retina intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000966 ! retina -relationship: never_in_taxon NCBITaxon:8782 {source="http://www.ncbi.nlm.nih.gov/pubmed/21622558", source="http://www.ncbi.nlm.nih.gov/pubmed/2772405", submitter="michaelerice"} ! Aves relationship: part_of UBERON:0000966 ! retina [Term] @@ -140068,8 +140361,6 @@ is_a: UBERON:0003103 {source="cjm"} ! compound organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part UBERON:0005388 {gci_filler="NCBITaxon:8508", gci_relation="part_of", source="Wikipedia"} ! photoreceptor array relationship: has_part UBERON:0005389 {gci_filler="NCBITaxon:8508", gci_relation="part_of", source="Wikipedia"} ! transparent eye structure -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia -relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0015238 {source="cjm"} ! pineal complex [Term] @@ -140657,7 +140948,6 @@ synonym: "gonadal epithelium" EXACT [OBOL:automatic] synonym: "gonadal sheath" RELATED [FBbt:00004859] xref: EHDAA:4032 xref: EHDAA:5931 -xref: FBbt:00004859 xref: http://linkedlifedata.com/resource/umls/id/C1517534 xref: NCIT:C32676 xref: UMLS:C1517534 {source="ncithesaurus:Germinal_Epithelium"} @@ -140676,7 +140966,6 @@ synonym: "testis epithelium" EXACT [OBOL:automatic] synonym: "testis sheath" NARROW SENSU [FBbt:00004955] xref: BTO:0001364 xref: EMAPA:17973 -xref: FBbt:00004955 is_a: UBERON:0004909 ! epithelium of gonad intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000473 ! testis @@ -140690,7 +140979,6 @@ synonym: "ovarian epithelium" EXACT [OBOL:automatic] synonym: "ovarian sheath" NARROW SENSU [FBbt:00004896] synonym: "ovary epithelium" EXACT [OBOL:automatic] xref: BTO:0003661 -xref: FBbt:00004896 is_a: UBERON:0004909 ! epithelium of gonad intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000992 ! ovary @@ -142118,7 +142406,6 @@ synonym: "mucous membrane of major calyx" EXACT [OBOL:automatic] synonym: "organ mucosa of major calix" EXACT [OBOL:automatic] synonym: "organ mucosa of major calyx" EXACT [OBOL:automatic] xref: FMA:17934 -is_a: UBERON:0004797 ! blood vessel layer is_a: UBERON:0005006 ! mucosa of renal pelvis intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001226 ! major calyx @@ -142144,7 +142431,6 @@ synonym: "mucous membrane of minor calyx" EXACT [OBOL:automatic] synonym: "organ mucosa of minor calix" EXACT [OBOL:automatic] synonym: "organ mucosa of minor calyx" EXACT [OBOL:automatic] xref: FMA:17937 -is_a: UBERON:0004797 ! blood vessel layer is_a: UBERON:0005006 ! mucosa of renal pelvis intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001227 ! minor calyx @@ -143088,7 +143374,6 @@ synonym: "organ mucosa of nasolacrimal duct" EXACT [OBOL:automatic] xref: FMA:59664 is_a: UBERON:0000344 ! mucosa is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0002392 ! nasolacrimal duct relationship: part_of UBERON:0002392 ! nasolacrimal duct @@ -143631,7 +143916,6 @@ xref: WBbt:0005843 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000476 ! acellular anatomical structure relationship: bounding_layer_of UBERON:0007379 ! shelled egg -relationship: never_in_taxon NCBITaxon:32525 ! Theria relationship: part_of UBERON:0007379 ! shelled egg [Term] @@ -143751,7 +144035,6 @@ synonym: "muscle" RELATED [] synonym: "muscle element" RELATED [] synonym: "musculus" EXACT [FMA:30316] xref: EMAPA:32715 -xref: FBbt:00005073 xref: FMA:30316 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000061 ! anatomical structure @@ -143975,8 +144258,10 @@ is_a: UBERON:0001285 ! nephron is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001285 ! nephron intersection_of: part_of UBERON:0000081 ! metanephros +relationship: develops_from UBERON:0000081 ! metanephros relationship: develops_from UBERON:0003220 {source="http://en.wikipedia.org/wiki/Nephron"} ! metanephric mesenchyme relationship: develops_from UBERON:0003220 {source="Wikipedia"} ! metanephric mesenchyme +relationship: develops_from UBERON:0005113 ! metanephric cortex mesenchyme relationship: develops_from UBERON:0010535 ! primitive metanephric nephron relationship: immediate_transformation_of UBERON:0010535 {source="Bgee:AN"} ! primitive metanephric nephron relationship: part_of UBERON:0000081 ! metanephros @@ -144693,7 +144978,6 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0034922 ! cell cluster relationship: develops_from UBERON:0000924 ! ectoderm -relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0008281 ! tooth bud [Term] @@ -145006,9 +145290,7 @@ xref: EMAPA:36574 xref: FMA:7473 xref: http://www.snomedbrowser.com/Codes/Details/197423006 xref: MA:0002937 -is_a: UBERON:0004119 ! endoderm-derived structure -is_a: UBERON:0011148 ! submucosal gland -is_a: UBERON:0036225 ! respiratory system gland +is_a: UBERON:8410077 ! airway submucosal gland intersection_of: UBERON:0011148 ! submucosal gland intersection_of: has_part CL:0000159 ! seromucus secreting cell intersection_of: part_of UBERON:0002202 ! submucosa of trachea @@ -145205,7 +145487,7 @@ synonym: "subarachnoid space mesencephalon" RELATED [VHOG:0001304] synonym: "subarachnoid space midbrain" EXACT [VHOG:0001304] xref: EMAPA:19055 xref: VHOG:0001304 -is_a: UBERON:0000315 ! subarachnoid space +is_a: UBERON:0039175 ! subarachnoid space of brain intersection_of: UBERON:0000315 ! subarachnoid space intersection_of: part_of UBERON:0001891 ! midbrain relationship: part_of UBERON:0001891 ! midbrain @@ -145217,7 +145499,7 @@ def: "A subarachnoid space that is part of a diencephalon [Automatically generat synonym: "subarachnoid space diencephalon" EXACT [VHOG:0001302] xref: EMAPA:19053 xref: VHOG:0001302 -is_a: UBERON:0000315 ! subarachnoid space +is_a: UBERON:0039175 ! subarachnoid space of brain intersection_of: UBERON:0000315 ! subarachnoid space intersection_of: part_of UBERON:0001894 ! diencephalon relationship: part_of UBERON:0001894 ! diencephalon @@ -145230,7 +145512,7 @@ synonym: "subarachnoid space hindbrain" EXACT [VHOG:0001303] synonym: "subarachnoid space rhombencephalon" RELATED [VHOG:0001303] xref: EMAPA:18211 xref: VHOG:0001303 -is_a: UBERON:0000315 ! subarachnoid space +is_a: UBERON:0039175 ! subarachnoid space of brain intersection_of: UBERON:0000315 ! subarachnoid space intersection_of: part_of UBERON:0002028 ! hindbrain relationship: part_of UBERON:0002028 ! hindbrain @@ -145307,7 +145589,8 @@ def: "An epithelium that is part of a hindlimb stylopod [Automatically generated xref: EHDAA2:0002131 xref: EMAPA:17500 xref: VHOG:0001041 -is_a: UBERON:0010371 ! ecto-epithelium +is_a: CARO:0000000 ! anatomical entity +is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000376 ! hindlimb stylopod relationship: develops_from UBERON:0003371 {source="EHDAA2"} ! pelvic appendage bud ectoderm @@ -145366,7 +145649,8 @@ def: "An epithelium that is part of a lower leg [Automatically generated definit xref: EHDAA2:0001031 xref: EMAPA:17497 xref: VHOG:0001050 -is_a: UBERON:0010371 ! ecto-epithelium +is_a: CARO:0000000 ! anatomical entity +is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0003823 ! hindlimb zeugopod relationship: develops_from UBERON:0003371 {source="EHDAA2"} ! pelvic appendage bud ectoderm @@ -145438,7 +145722,6 @@ xref: VHOG:0001220 xref: XAO:0000199 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: contributes_to_morphology_of UBERON:0001846 ! internal ear relationship: part_of UBERON:0001839 ! bony labyrinth @@ -146025,7 +146308,6 @@ xref: TAO:0005157 xref: ZFA:0005157 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005283 ! tela choroidea -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0005283 ! tela choroidea intersection_of: part_of UBERON:0002289 ! midbrain cerebral aqueduct relationship: part_of UBERON:0002289 ! midbrain cerebral aqueduct @@ -146123,6 +146405,11 @@ xref: http://en.wikipedia.org/wiki/Myelencephalon xref: MA:0000205 xref: VHOG:0000456 is_a: UBERON:0004733 ! segmental subdivision of hindbrain +relationship: develops_from NCBITaxon:6072 ! Eumetazoa +relationship: develops_from UBERON:0000955 ! brain +relationship: develops_from UBERON:0001016 ! nervous system +relationship: develops_from UBERON:0001017 ! central nervous system +relationship: develops_from UBERON:0002028 ! hindbrain relationship: develops_from UBERON:0010096 ! future myelencephalon relationship: dubious_for_taxon NCBITaxon:7955 ! Danio rerio relationship: immediate_transformation_of UBERON:0010096 {evidence="definitional"} ! future myelencephalon @@ -146274,6 +146561,8 @@ is_a: UBERON:0004910 ! epithelium of male gonad is_a: UBERON:0005295 ! sex cord intersection_of: UBERON:0005295 ! sex cord intersection_of: part_of UBERON:0000473 ! testis +relationship: develops_from UBERON:0000990 ! reproductive system +relationship: develops_from UBERON:0009196 ! indifferent external genitalia relationship: develops_from UBERON:0010141 ! primitive sex cord of indifferent gonad relationship: immediate_transformation_of UBERON:0010141 {source="Bgee:AN"} ! primitive sex cord of indifferent gonad relationship: part_of UBERON:0000473 ! testis @@ -146345,7 +146634,6 @@ intersection_of: UBERON:0000359 ! preputial gland intersection_of: part_of UBERON:0003101 ! male organism disjoint_from: UBERON:0012327 ! pearly penile papule relationship: capable_of GO:0071834 ! mating pheromone secretion -relationship: never_in_taxon NCBITaxon:9606 {source="ISBN:0123813611"} ! Homo sapiens relationship: part_of UBERON:0000079 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! male reproductive system relationship: part_of UBERON:0001332 ! prepuce of penis relationship: part_of UBERON:0003101 ! male organism @@ -146367,7 +146655,6 @@ is_a: UBERON:0000359 ! preputial gland is_a: UBERON:0005398 ! female reproductive gland intersection_of: UBERON:0000359 ! preputial gland intersection_of: part_of UBERON:0003100 ! female organism -relationship: never_in_taxon NCBITaxon:9606 {source="ISBN:0123813611"} ! Homo sapiens relationship: part_of UBERON:0000474 ! female reproductive system relationship: part_of UBERON:0003100 ! female organism @@ -146963,7 +147250,6 @@ xref: EMAPA:37400 {source="MA:th"} xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1894 xref: MBA:1033 is_a: UBERON:0004003 ! cerebellum hemisphere lobule -relationship: never_in_taxon NCBITaxon:9606 {source="MP"} ! Homo sapiens relationship: only_in_taxon NCBITaxon:9989 ! Rodentia [Term] @@ -147109,7 +147395,6 @@ subset: pheno_slim is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010000 ! multicellular anatomical structure relationship: contributes_to_morphology_of UBERON:0002106 ! spleen -relationship: never_in_taxon NCBITaxon:9989 {source="MP:0002363"} ! Rodentia relationship: part_of UBERON:0002106 ! spleen relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens @@ -148568,7 +148853,6 @@ intersection_of: has_potential_to_develop_into UBERON:0004709 ! pelvic appendage intersection_of: part_of UBERON:0000154 ! posterior region of body relationship: has_developmental_contribution_from UBERON:0005730 ! pelvic appendage field relationship: has_potential_to_develop_into UBERON:0004709 ! pelvic appendage -relationship: never_in_taxon NCBITaxon:31033 {source="http://www.ncbi.nlm.nih.gov/pubmed/15893975"} ! Takifugu rubripes relationship: part_of UBERON:0000154 ! posterior region of body [Term] @@ -149694,7 +149978,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/279264003 xref: ncithesaurus:Sigmoid_Sinus xref: Sigmoid:sinus xref: VHOG:0001337 -is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0017635 {source="FMA"} ! paired venous dural sinus relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0001586 ! internal jugular vein @@ -150941,7 +151224,6 @@ xref: MA:0001210 xref: VHOG:0001344 is_a: UBERON:0000025 ! tube is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001856 ! semicircular duct [Term] @@ -152828,7 +153110,6 @@ xref: EHDAA:5707 xref: http://www.snomedbrowser.com/Codes/Details/343518007 is_a: UBERON:0000476 {inconsistent_with="MP-def", source="EHDAA2"} ! acellular anatomical structure is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0003902 {source="EHDAA2"} ! retinal neural layer relationship: located_in UBERON:0005606 {source="EHDAA2"} ! hyaloid cavity relationship: part_of UBERON:0008816 {source="cjm"} ! embryonic head @@ -154313,7 +154594,6 @@ xref: http://en.wikipedia.org/wiki/Labrum_(arthropod_mouthpart) xref: TADS:0000039 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000064 ! organ part -relationship: never_in_taxon NCBITaxon:57294 ! Pycnogonida relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0000165 ! mouth @@ -154867,7 +155147,6 @@ name: blood-inner ear barrier def: "The function of the group of barriers and transport systems which regulate the transport of various substances from blood to inner ear tissue and maintain the microhomeostasis and functional integrity of the inner ear; the endothelial cells of the inner ear blood capillaries, linked to each other by tight junctions, represent the main component of the blood-inner ear barrier." [MP:0004999] is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001846 ! internal ear [Term] @@ -154900,6 +155179,7 @@ synonym: "bulge of hair follicle" EXACT [FMA:70735] xref: BTO:0004904 xref: EMAPA:37876 {source="MA:th"} xref: FMA:70735 +is_a: UBERON:0010188 ! protuberance is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0019204 ! skin epithelium relationship: part_of UBERON:0002073 ! hair follicle @@ -155990,7 +156270,6 @@ xref: TAO:0000519 xref: ZFA:0000519 is_a: UBERON:0005174 ! dorsal region element is_a: UBERON:0010358 ! arch of centrum of vertebra -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: part_of UBERON:0001095 ! caudal vertebra [Term] @@ -156788,7 +157067,6 @@ xref: UMLS:C0009198 {source="BIRNLEX:2553"} xref: UMLS:C0458767 {source="BIRNLEX:2553"} is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005913 ! zone of bone organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001844 ! cochlea [Term] @@ -157161,8 +157439,6 @@ intersection_of: UBERON:0006134 ! nerve fiber intersection_of: has_part GO:0043209 ! myelin sheath disjoint_from: UBERON:0006136 ! unmyelinated nerve fiber relationship: has_part GO:0043209 ! myelin sheath -relationship: never_in_taxon NCBITaxon:117569 ! Hyperoartia -relationship: never_in_taxon NCBITaxon:7762 ! Myxinidae relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: present_in_taxon NCBITaxon:7776 ! Gnathostomata @@ -157517,7 +157793,6 @@ xref: MA:0003054 xref: NCIT:C77673 xref: UMLS:C2698201 {source="ncithesaurus:Auricular_Vein"} is_a: UBERON:0003496 ! head blood vessel -is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0009141 ! craniocervical region vein relationship: drains UBERON:0001691 ! external ear relationship: part_of UBERON:0000033 ! head @@ -157663,8 +157938,8 @@ xref: EHDAA2:0000136 xref: EHDAA:2592 xref: EMAPA:16827 xref: VHOG:0000502 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004142 ! outflow tract septum -is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0002099 ! cardiac septum intersection_of: adjacent_to UBERON:0002333 ! pulmonary trunk intersection_of: adjacent_to UBERON:0005805 ! dorsal aorta @@ -157703,7 +157978,6 @@ xref: VHOG:0001124 is_a: UBERON:0003932 ! cartilage element of chondrocranium is_a: UBERON:0005253 ! head mesenchyme is_a: UBERON:0005863 ! cartilaginous condensation -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0015048 ! basioccipital endochondral element intersection_of: UBERON:0015048 ! basioccipital endochondral element intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue @@ -158356,7 +158630,6 @@ xref: Infundibular:recess is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0012275 ! meso-epithelium relationship: develops_from UBERON:0003309 {source="EHDAA2"} ! floor plate of diencephalon @@ -158539,6 +158812,7 @@ xref: EHDAA2:0001055 xref: EHDAA:9026 xref: EMAPA:17826 xref: VHOG:0000958 +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0015018 ! malleus endochondral element is_a: UBERON:0035132 ! auditory ossicle pre-cartilage element intersection_of: UBERON:0015018 ! malleus endochondral element @@ -158610,7 +158884,6 @@ xref: UMLS:C1513875 {source="ncithesaurus:Nasolacrimal_Groove"} xref: VHOG:0001307 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0019306 ! nose epithelium relationship: adjacent_to UBERON:0004067 ! lateral nasal prominence relationship: adjacent_to UBERON:0005868 ! maxillary prominence @@ -159992,7 +160265,6 @@ intersection_of: UBERON:0001037 ! strand of hair intersection_of: part_of UBERON:0011933 ! vibrissa unit disjoint_from: UBERON:0011931 ! nasal hair relationship: capable_of_part_of GO:0050975 ! sensory perception of touch -relationship: never_in_taxon NCBITaxon:9606 {source="Skinbase"} ! Homo sapiens relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: part_of UBERON:0011933 ! vibrissa unit @@ -160072,7 +160344,6 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0007719 ! bone of reproductive organ intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0000989 ! penis -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: part_of UBERON:0000989 ! penis @@ -160114,7 +160385,6 @@ intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0002411 ! clitoris relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system relationship: contributes_to_morphology_of UBERON:0002411 ! clitoris -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: part_of UBERON:0002411 ! clitoris relationship: sexually_homologous_to UBERON:0006435 ! os penis @@ -160743,7 +161013,9 @@ relationship: part_of UBERON:0000956 ! cerebral cortex [Term] id: UBERON:0006479 name: Brodmann (1909) area 38 -def: "Brodmann area 38, also BA38 or temporopolar area 38 (H), is part of the temporal cortex in the human brain. BA 38 is at the anterior end of the temporal lobe, known as the temporal pole. BA38 is a subdivision of the cytoarchitecturally defined temporal region of cerebral cortex. It is located primarily in the most rostral portions of the superior temporal gyrus and the middle temporal gyrus. Cytoarchitecturally it is bounded caudally by the inferior temporal area 20, the middle temporal area 21, the superior temporal area 22 and the ectorhinal area 36 (Brodmann-1909). Cytoarchitectonic and chemoarchitectonic studies find that it contains at least seven subareas, one of which, TG, is unique to humans. 'The functional significance of this area TG is not known, but it may bind complex, highly processed perceptual inputs to visceral emotional responses.' This area is among the earliest affected by Alzheimer's disease and the earliest involved at the start of temporal lobe seizures. [." [http://en.wikipedia.org/wiki/Brodmann_area_38] +def: "Brodmann area 38, also BA38 or temporopolar area 38 (H), is part of the temporal cortex in the human brain. BA 38 is at the anterior end of the temporal lobe, known as the temporal pole. BA38 is a subdivision of the cytoarchitecturally defined temporal region of cerebral cortex. It is located primarily in the most rostral portions of the superior temporal gyrus and the middle temporal gyrus. Cytoarchitecturally it is bounded caudally by the inferior temporal area 20, the middle temporal area 21, the superior temporal area 22 and the ectorhinal area 36 (Brodmann-1909). Cytoarchitectonic and chemoarchitectonic studies find that it contains at least seven subareas, one of which, TG, is unique to humans. 'The functional significance of this area TG is not known, but it may bind complex, highly processed perceptual inputs to visceral emotional responses.' This area is among the earliest affected by Alzheimer's disease and the earliest involved at the start of temporal lobe seizures." [http://en.wikipedia.org/wiki/Brodmann_area_38, http://www.ncbi.nlm.nih.gov/pubmed/22421014] +synonym: "anterior end of the temporal lobe" EXACT [WikipediaVersioned:Brodmann_area_38&oldid=984922149] +synonym: "anterior temporal lobe" EXACT [WikipediaVersioned:Brodmann_area_38&oldid=984922149] synonym: "area 38 of Brodmann" EXACT [FMA:68635] synonym: "area 38 of Brodmann-1909" EXACT [BIRNLEX:1771] synonym: "area temporopolaris" EXACT [BIRNLEX:1771] @@ -160753,7 +161025,9 @@ synonym: "BA38" EXACT ABBREVIATION [] synonym: "Brodmann (1909) area 38" EXACT [BIRNLEX:1771] synonym: "Brodmann area 38" EXACT [FMA:68635] synonym: "Brodmann area 38, temporopolar" EXACT [BIRNLEX:1771] +synonym: "temporal pole" EXACT [WikipediaVersioned:Brodmann_area_38&oldid=984922149] synonym: "temporopolar area 38" EXACT [FMA:68635] +synonym: "temporopolar area 38 (H)" EXACT [WikipediaVersioned:Brodmann_area_38&oldid=984922149] xref: BIRNLEX:1771 xref: Brodmann_area:38 xref: FMA:68635 @@ -161059,7 +161333,6 @@ xref: EMAPA:35621 xref: FMA:75666 xref: MA:0001183 is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0013685 ! foramen of skull relationship: part_of UBERON:0007223 {source="MA"} ! osseus cochlea @@ -161074,7 +161347,6 @@ xref: EMAPA:37526 {source="MA:th"} xref: FMA:61290 xref: MA:0001235 is_a: UBERON:0004119 ! endoderm-derived structure -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0001352 ! external acoustic meatus @@ -161739,7 +162011,6 @@ synonym: "calcareous statoliths" NARROW [] is_a: UBERON:0000476 ! acellular anatomical structure relationship: capable_of_part_of GO:0009590 ! detection of gravity relationship: has_quality PATO:0002444 ! mineralized -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0006583 ! statocyst [Term] @@ -161753,7 +162024,6 @@ xref: http://en.wikipedia.org/wiki/Statocyst is_a: UBERON:0000020 ! sense organ relationship: capable_of GO:0050973 ! detection of mechanical stimulus involved in equilibrioception relationship: dubious_for_taxon NCBITaxon:110815 {source="Wikipedia"} ! Xenoturbella -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata relationship: present_in_taxon NCBITaxon:147099 {source="http://en.wikipedia.org/wiki/Acoelomorpha"} ! Acoelomorpha relationship: present_in_taxon NCBITaxon:6073 ! Cnidaria relationship: present_in_taxon NCBITaxon:6544 ! Bivalvia @@ -161866,7 +162136,11 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006590 ! remnant of embryonic structure intersection_of: UBERON:0006590 ! remnant of embryonic structure intersection_of: immediate_transformation_of UBERON:0001637 ! artery +relationship: develops_from UBERON:0001009 ! circulatory system relationship: develops_from UBERON:0001637 ! artery +relationship: develops_from UBERON:0004535 ! cardiovascular system +relationship: develops_from UBERON:0004537 ! blood vasculature +relationship: develops_from UBERON:0004572 ! arterial system relationship: immediate_transformation_of UBERON:0001637 ! artery [Term] @@ -161878,7 +162152,11 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006590 ! remnant of embryonic structure intersection_of: UBERON:0006590 ! remnant of embryonic structure intersection_of: immediate_transformation_of UBERON:0001638 ! vein +relationship: develops_from UBERON:0001009 ! circulatory system relationship: develops_from UBERON:0001638 ! vein +relationship: develops_from UBERON:0004535 ! cardiovascular system +relationship: develops_from UBERON:0004537 ! blood vasculature +relationship: develops_from UBERON:0004582 ! venous system relationship: immediate_transformation_of UBERON:0001638 ! vein [Term] @@ -161954,7 +162232,6 @@ is_a: UBERON:0011597 ! bone of upper jaw is_a: UBERON:0015212 ! lateral structure relationship: develops_from UBERON:0004752 {source="ZFA"} ! palatoquadrate cartilage relationship: in_lateral_side_of UBERON:0003277 ! skeleton of upper jaw -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0003108 {source="AAO"} ! suspensorium relationship: part_of UBERON:0003277 ! skeleton of upper jaw @@ -162083,7 +162360,6 @@ xref: Symphysis:menti xref: TAO:0001851 xref: ZFA:0005488 is_a: UBERON:0002216 {source="FMA"} ! symphysis -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0002213 ! cartilaginous joint intersection_of: connects UBERON:0004742 {minCardinality="2", maxCardinality="2"} ! dentary relationship: connects UBERON:0004742 {notes="connects adjacent mandibles"} ! dentary @@ -162160,7 +162436,6 @@ synonym: "shell" RELATED [BTO:0004659] xref: BTO:0004659 xref: http://en.wikipedia.org/wiki/Exoskeleton is_a: UBERON:0000477 ! anatomical cluster -relationship: never_in_taxon NCBITaxon:314146 ! Euarchontoglires relationship: part_of UBERON:0002416 ! integumental system [Term] @@ -162171,7 +162446,6 @@ subset: grouping_class xref: http://en.wikipedia.org/wiki/Seashell xref: ncithesaurus:Shell is_a: UBERON:0000477 ! anatomical cluster -relationship: never_in_taxon NCBITaxon:32525 ! Theria relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0002416 ! integumental system @@ -162434,7 +162708,14 @@ xref: http://en.wikipedia.org/wiki/Median_umbilical_ligament xref: http://www.snomedbrowser.com/Codes/Details/89583000 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006590 {source="FMA"} ! remnant of embryonic structure +relationship: develops_from NCBITaxon:6072 ! Eumetazoa +relationship: develops_from UBERON:0001008 ! renal system +relationship: develops_from UBERON:0001255 ! urinary bladder +relationship: develops_from UBERON:0001556 ! lower urinary tract relationship: develops_from UBERON:0002068 ! urachus +relationship: develops_from UBERON:0002100 ! trunk +relationship: develops_from UBERON:0013701 ! main body axis +relationship: develops_from UBERON:0013702 ! body proper relationship: immediate_transformation_of UBERON:0002068 ! urachus relationship: part_of UBERON:0000916 ! abdomen @@ -162753,7 +163034,7 @@ relationship: part_of UBERON:0002411 ! clitoris [Term] id: UBERON:0006654 name: perineal body -def: "The perineal body (or central tendon of perineum) is a pyramidal fibromuscular mass in the middle line of the perineum at the junction between the urogenital triangle and the anal triangle . It is found in both males and females. In males, it is found between the bulb of penis and the anus; in females, is found between the vagina and anus, and about 1.25 cm in front of the latter. The perineal body is essential for the integrity of the pelvic floor, particularly in females. Its rupture during delivery leads to widening of the gap between the anterior free borders of levator ani muscle of both sides, thus predisposing the woman to prolapse of the uterus, rectum, or even the urinary bladder." [http://en.wikipedia.org/wiki/Perineal_body] +def: "The perineal body (or central tendon of perineum) is a pyramidal fibromuscular mass in the middle line of the perineum at the junction between the urogenital triangle and the anal triangle. It is found in both males and females. In males, it is found between the bulb of penis and the anus; in females, is found between the vagina and anus, and about 1.25 cm in front of the latter. The perineal body is essential for the integrity of the pelvic floor, particularly in females. Its rupture during delivery leads to widening of the gap between the anterior free borders of levator ani muscle of both sides, thus predisposing the woman to prolapse of the uterus, rectum, or even the urinary bladder." [http://en.wikipedia.org/wiki/Perineal_body, https://orcid.org/0000-0002-2825-0621] synonym: "central tendinous point" RELATED [http://en.wikipedia.org/wiki/Perineal_body] synonym: "central tendinous point of the perineum" RELATED [http://en.wikipedia.org/wiki/Perineal_body] synonym: "central tendon of perineum" EXACT [FMA:20274] @@ -162764,7 +163045,8 @@ xref: EMAPA:17892 xref: FMA:20274 xref: http://www.snomedbrowser.com/Codes/Details/367754000 xref: Perineal:body -is_a: UBERON:0007651 ! anatomical junction +is_a: UBERON:0000043 ! tendon +is_a: UBERON:0003838 ! abdominal segment connective tissue relationship: part_of UBERON:0002356 ! perineum [Term] @@ -163035,8 +163317,8 @@ synonym: "canales alveolares maxillae" RELATED LATIN [http://en.wikipedia.org/wi xref: Alveolar:canals xref: EMAPA:25099 xref: FMA:57743 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0005744 ! bone foramen -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: conduit_for UBERON:0018397 ! posterior superior alveolar artery relationship: conduit_for UBERON:0018401 ! posterior superior alveolar nerve relationship: part_of UBERON:0001710 {source="EMAPA"} ! lower jaw region @@ -163062,6 +163344,7 @@ is_a: UBERON:0000043 ! tendon is_a: UBERON:0003570 ! respiratory system connective tissue is_a: UBERON:0003837 ! thoracic segment connective tissue relationship: attaches_to UBERON:0002359 ! fibrous pericardium +relationship: develops_from UBERON:0002204 ! musculoskeletal system relationship: develops_from UBERON:0006239 ! future central tendon relationship: immediate_transformation_of UBERON:0006239 {evidence="definitional"} ! future central tendon relationship: part_of RO:0002577 ! system @@ -163571,9 +163854,12 @@ xref: http://www.snomedbrowser.com/Codes/Details/368738001 xref: MA:0000725 is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0005160 ! vestigial structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest disjoint_from: UBERON:0006713 ! foramen cecum of frontal bone +relationship: develops_from UBERON:0000949 ! endocrine system +relationship: develops_from UBERON:0001004 ! respiratory system +relationship: develops_from UBERON:0001042 ! chordate pharynx relationship: develops_from UBERON:0001761 ! future foramen cecum +relationship: develops_from UBERON:0003091 ! thyroid primordium relationship: immediate_transformation_of UBERON:0001761 ! future foramen cecum relationship: part_of UBERON:0003357 {source="EHDAA2"} ! epithelium of tongue relationship: part_of UBERON:0009471 ! dorsum of tongue @@ -163828,7 +164114,6 @@ xref: NCIT:C33135 xref: UMLS:C0229503 {source="ncithesaurus:Modiolus"} is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005913 ! zone of bone organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest disjoint_from: UBERON:0011386 ! facial modiolus relationship: contributes_to_morphology_of UBERON:0001844 ! cochlea relationship: part_of UBERON:0007223 {source="MA"} ! osseus cochlea @@ -163852,7 +164137,6 @@ xref: MA:0001184 xref: MESH:D013137 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005913 ! zone of bone organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0006723 {source="FMA"} ! cochlear modiolus relationship: part_of UBERON:0007223 {source="MA"} ! osseus cochlea @@ -163877,7 +164161,6 @@ xref: Spiral:ligament is_a: CARO:0000003 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0008845 ! nonskeletal ligament -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: attaches_to UBERON:0006106 {source="MESH-def"} ! cochlear canal relationship: has_part CL:0002665 ! otic fibrocyte relationship: part_of RO:0002577 ! system @@ -164021,7 +164304,6 @@ is_a: UBERON:0001132 ! parathyroid gland is_a: UBERON:0015212 ! lateral structure relationship: has_developmental_contribution_from UBERON:0010027 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="EHDAA2-modified"} ! dorsal part of pharyngeal pouch 4 relationship: in_lateral_side_of UBERON:0000949 {source="FMA-abduced-lr"} ! endocrine system -relationship: never_in_taxon NCBITaxon:9989 ! Rodentia [Term] id: UBERON:0006755 @@ -164142,7 +164424,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/362524000 xref: ZFA:0005573 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0008841 {source="Obol"} ! suspensory ligament -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: continuous_with UBERON:0000965 ! lens of camera-type eye relationship: continuous_with UBERON:0001775 ! ciliary body relationship: develops_from UBERON:0001797 {source="ZFA"} ! vitreous humor @@ -164195,7 +164476,6 @@ name: left anterior vena cava synonym: "left superior vena cava" EXACT [EMAPA:18418] xref: EMAPA:18418 is_a: UBERON:0001638 ! vein -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: part_of UBERON:0001585 ! anterior vena cava [Term] @@ -164839,7 +165119,6 @@ xref: AAO:0000330 xref: Exoccipital:condyle xref: FMA:52861 is_a: UBERON:0005913 ! zone of bone organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001693 ! exoccipital bone [Term] @@ -165195,7 +165474,6 @@ xref: TAO:0001973 xref: UMLS:C0226994 {source="ncithesaurus:Tooth_Cusp"} xref: ZFA:0005434 is_a: UBERON:0000476 {source="ZFA"} ! acellular anatomical structure -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0003675 {source="FMA"} ! tooth crown @@ -165613,10 +165891,10 @@ xref: ANISEED:1235299 xref: BSA:0000064 xref: BTO:0003173 xref: http://en.wikipedia.org/wiki/Endostyle +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0006846 ! surface groove relationship: capable_of GO:0006590 ! thyroid hormone generation relationship: has_potential_to_develop_into UBERON:0002046 {gci_relation="part_of", gci_filler="NCBITaxon:117569"} ! thyroid gland -relationship: never_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: only_in_taxon NCBITaxon:7711 {source="http://en.wikipedia.org/wiki/Endostyle"} ! Chordata relationship: part_of UBERON:0000949 {source="http://webs.lander.edu/rsfox/invertebrates/ammocoetes.html"} ! endocrine system relationship: part_of UBERON:0006562 ! pharynx @@ -166169,7 +166447,6 @@ def: "The epithelial cell layer containing the sensory hair cells and their asso subset: pheno_slim xref: EMAPA:32883 xref: MA:0001189 -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015807 ! ear epithelium intersection_of: UBERON:0000483 ! epithelium @@ -166184,7 +166461,7 @@ xref: EHDAA2:0001470 xref: EHDAA:8983 xref: EMAPA:17592 xref: VHOG:0000632 -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0015814 ! outer ear epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001757 ! pinna @@ -166529,7 +166806,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/69221006 xref: MESH:D006733 is_a: UBERON:0006969 ! cranial appendage disjoint_from: UBERON:0014448 ! feathered ear tuft -relationship: never_in_taxon NCBITaxon:9606 {source="ISBN:9780716717553"} ! Homo sapiens relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: surrounds UBERON:0001474 ! bone element @@ -166818,7 +167094,6 @@ subset: grouping_class synonym: "adult heart" RELATED [FBbt:00003154] synonym: "dorsal tube" NARROW [http://en.wikipedia.org/wiki/Heart] synonym: "heart" NARROW [GO:0007507] -xref: FBbt:00003154 xref: http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg xref: SPD:0000130 xref: TADS:0000147 @@ -166951,7 +167226,6 @@ xref: BTO:0001439 xref: http://en.wikipedia.org/wiki/Venom xref: MESH:D014688 is_a: UBERON:0000456 ! secretion of exocrine gland -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: present_in_taxon NCBITaxon:264759 {source="Wikipedia"} relationship: present_in_taxon NCBITaxon:6656 ! Arthropoda relationship: present_in_taxon NCBITaxon:7898 ! Actinopterygii @@ -167084,7 +167358,6 @@ xref: NCIT:C32201 xref: UMLS:C1704302 {source="ncithesaurus:Bicuspid_Tooth"} is_a: UBERON:0013164 ! molariform tooth relationship: has_part UBERON:0006844 {editor_note="cardinality not allowed with transitivity in OWL", min_count="2", taxon_notes="some premolars may have 3 cusps"} ! cusp of tooth -relationship: never_in_taxon NCBITaxon:337687 {notes="Although there are a few exceptions, the dental formula for the great majority of cricetids is 1.0.0.3", source="http://en.wikipedia.org/wiki/Cricetidae"} ! Muroidea [Term] id: UBERON:0007121 @@ -168183,8 +168456,8 @@ xref: EHDAA2:0002093 xref: EMAPA:16182 xref: TAO:0000999 xref: ZFA:0000999 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005256 ! trunk mesenchyme -is_a: UBERON:0014387 ! mesenchyme derived from neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0003083 ! trunk neural crest relationship: develops_from UBERON:0003083 ! trunk neural crest @@ -169326,7 +169599,6 @@ synonym: "choroid plexus tectal ventricles" RELATED PLURAL [ZFA:0001445] xref: TAO:0001445 xref: ZFA:0001445 is_a: UBERON:0001886 ! choroid plexus -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0001886 ! choroid plexus intersection_of: part_of UBERON:0002289 ! midbrain cerebral aqueduct relationship: part_of UBERON:0002289 ! midbrain cerebral aqueduct @@ -169652,7 +169924,6 @@ def: "A rhamphotheca that is part of a lower beak." [OBOL:automatic] synonym: "gnathotheca" RELATED [http://en.wikipedia.org/wiki/Beak#Rhamphotheca] synonym: "mandibular beak" RELATED [] is_a: UBERON:0007330 ! rhamphotheca -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0007330 ! rhamphotheca intersection_of: part_of UBERON:0010013 ! lower beak relationship: part_of UBERON:0010013 ! lower beak @@ -170032,7 +170303,6 @@ xref: Egg:(biology) is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: develops_from UBERON:0000474 ! female reproductive system -relationship: never_in_taxon NCBITaxon:32525 ! Theria [Term] id: UBERON:0007380 @@ -170651,7 +170921,6 @@ xref: NCIT:C52917 xref: UMLS:C1707983 {source="ncithesaurus:Extensor_Digitorum_Lateralis"} is_a: UBERON:0011024 {source="Wikipedia"} ! extrinsic extensor muscle of manus relationship: has_muscle_insertion UBERON:0003639 {source="ISBN:9780716717553"} ! manual digit 5 phalanx -relationship: never_in_taxon NCBITaxon:9606 {source="ISBN:9780716717553"} ! Homo sapiens [Term] id: UBERON:0007614 @@ -170680,7 +170949,6 @@ xref: EMAPA:29836 xref: MA:0001740 is_a: UBERON:0001328 {source="MA"} ! lobe of prostate relationship: contributes_to_morphology_of UBERON:0002367 ! prostate gland -relationship: never_in_taxon NCBITaxon:9606 {source="http://www.ncbi.nlm.nih.gov/pubmed/15163300"} ! Homo sapiens [Term] id: UBERON:0007616 @@ -171626,7 +171894,6 @@ is_a: UBERON:0001474 ! bone element is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0003133 ! reproductive organ -relationship: never_in_taxon NCBITaxon:9606 {source="Wikipedia"} ! Homo sapiens relationship: part_of UBERON:0003133 ! reproductive organ [Term] @@ -172405,7 +172672,6 @@ def: "Sclerotic rings are rings of bone found in the eyes of several groups of v synonym: "scleral ring" EXACT [http://en.wikipedia.org/wiki/Sclerotic_ring] xref: Sclerotic:ring is_a: UBERON:0010290 {source="http://www.ncbi.nlm.nih.gov/pubmed/17051547"} ! scleral ossicle -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0001697 ! orbit of skull [Term] @@ -172540,7 +172806,6 @@ intersection_of: UBERON:0002415 ! tail intersection_of: part_of UBERON:0006071 ! caudal region relationship: capable_of_part_of GO:0007626 ! locomotory behavior relationship: develops_from UBERON:0007144 ! embryonic post-anal tail -relationship: never_in_taxon NCBITaxon:314295 ! Hominoidea relationship: only_in_taxon NCBITaxon:7711 {notes="possible exception in hemichordates", source="cjm"} ! Chordata relationship: part_of UBERON:0006071 ! caudal region relationship: transformation_of UBERON:0007144 ! embryonic post-anal tail @@ -172636,7 +172901,6 @@ xref: FMA:77849 xref: MA:0001194 is_a: UBERON:0001967 ! reticular lamina of epithelium is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0001967 ! reticular lamina of epithelium intersection_of: part_of UBERON:0002227 ! spiral organ of cochlea relationship: part_of UBERON:0002227 ! spiral organ of cochlea @@ -172813,7 +173077,6 @@ synonym: "osseous semicircular canal" EXACT [OBOL:automatic] xref: MA:0000250 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005913 {notes="checkme"} ! zone of bone organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001839 {source="MA"} ! bony labyrinth relationship: part_of UBERON:0001840 {source="MA"} ! semicircular canal @@ -172926,7 +173189,6 @@ disjoint_from: UBERON:0010372 ! uncinate process of ethmoid disjoint_from: UBERON:0010373 ! uncinate process of pancreas property_value: dc-contributor https://github.com/alex-dececchi property_value: dc-contributor https://github.com/cmungall -relationship: never_in_taxon NCBITaxon:8827 {source="http://www.ncbi.nlm.nih.gov/pubmed/15755883"} ! Anhimidae relationship: part_of UBERON:0010388 {source="ISBN:0073040584"} ! proximal segment of rib [Term] @@ -173319,7 +173581,6 @@ xref: MESH:D002680 xref: NCIT:C81169 xref: TAO:0002254 is_a: UBERON:0001444 ! subdivision of head -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001456 {source="MESH"} ! face relationship: part_of UBERON:0001710 {source="FMA"} ! lower jaw region @@ -173537,8 +173798,6 @@ synonym: "ampulla" BROAD [BTO:0002124] xref: BTO:0002124 is_a: UBERON:0000062 ! organ disjoint_from: UBERON:0009474 ! ascidian ampulla -relationship: never_in_taxon NCBITaxon:35069 {source="Wikipedia"} ! Crinoidea -relationship: never_in_taxon NCBITaxon:7618 {source="Wikipedia"} ! Ophiuroidea relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata relationship: part_of UBERON:0008247 ! tube foot relationship: part_of UBERON:0008251 {source="BTO"} ! water vascular system @@ -173616,7 +173875,6 @@ synonym: "oral side of organism" RELATED [] synonym: "oral subdivision" RELATED [] is_a: UBERON:0000475 ! organism subdivision relationship: has_part UBERON:0000166 ! oral opening -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: present_in_taxon NCBITaxon:6073 ! Cnidaria relationship: present_in_taxon NCBITaxon:7588 @@ -173633,7 +173891,6 @@ synonym: "aboral side of organism" RELATED [] synonym: "aboral subdivision" RELATED [] is_a: UBERON:0000475 ! organism subdivision relationship: aboral_to UBERON:0008258 ! oral subdivision of organism -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: present_in_taxon NCBITaxon:6073 ! Cnidaria relationship: present_in_taxon NCBITaxon:7588 @@ -173648,7 +173905,6 @@ synonym: "spiny appendage" RELATED [] xref: Spine:(zoology) is_a: UBERON:0000026 {status="unstable"} ! appendage relationship: has_quality PATO:0001954 ! subulate -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: only_in_taxon NCBITaxon:33213 ! Bilateria [Term] @@ -176459,7 +176715,6 @@ xref: NCIT:C32723 xref: UMLS:C0229512 {source="ncithesaurus:Helicotrema"} is_a: UBERON:0000161 {source="FMA"} ! orifice is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0002499 {source="Wikipedia"} ! cochlear labyrinth [Term] @@ -176496,7 +176751,6 @@ is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0013765 ! digestive system element relationship: capable_of_part_of GO:0007631 ! feeding behavior relationship: develops_from UBERON:0007690 {source="cjm"} ! early pharyngeal endoderm -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata relationship: only_in_taxon NCBITaxon:33511 {source="http://www.ncbi.nlm.nih.gov/pubmed/11961109"} ! Deuterostomia relationship: part_of UBERON:0001042 ! chordate pharynx @@ -177059,7 +177313,6 @@ subset: pheno_slim xref: MA:0001723 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005398 ! female reproductive gland -relationship: never_in_taxon NCBITaxon:9443 {source="MP:0010777"} ! Primates relationship: part_of UBERON:0002450 {source="MP"} ! decidua [Term] @@ -177362,7 +177615,6 @@ xref: FMA:61035 xref: http://www.snomedbrowser.com/Codes/Details/362548009 xref: MA:0001228 is_a: UBERON:0008846 {source="FMA"} ! skeletal ligament -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001757 {source="MA"} ! pinna [Term] @@ -177620,8 +177872,6 @@ intersection_of: UBERON:0000026 ! appendage intersection_of: has_skeleton UBERON:0012353 ! fin skeleton relationship: confers_advantage_in ENVO:00002030 ! aquatic biome relationship: has_skeleton UBERON:0012353 ! fin skeleton -relationship: never_in_taxon NCBITaxon:314146 ! Euarchontoglires -relationship: never_in_taxon NCBITaxon:8782 ! Aves [Term] id: UBERON:0008902 @@ -177764,8 +178014,6 @@ relationship: capable_of GO:0050964 ! detection of electrical stimulus involved relationship: develops_from UBERON:0009128 {gci_relation="part_of", gci_filler="NCBITaxon:32443", source="https://doi.org/10.1038/ncomms1502"} ! lateral line placode relationship: develops_from UBERON:0009128 {gci_filler="NCBITaxon:8295", gci_relation="part_of", source="https://doi.org/10.1038/ncomms1502"} ! lateral line placode relationship: innervated_by UBERON:0008906 ! lateral line nerve -relationship: never_in_taxon NCBITaxon:7915 ! Lepisosteidae -relationship: never_in_taxon NCBITaxon:7922 ! Amiidae relationship: part_of UBERON:0010202 ! lateral line relationship: present_in_taxon NCBITaxon:7746 relationship: present_in_taxon NCBITaxon:7777 ! Chondrichthyes @@ -177784,8 +178032,6 @@ xref: http://en.wikipedia.org/wiki/Ampullae_of_Lorenzini is_a: UBERON:0003103 ! compound organ is_a: UBERON:0035555 ! lateral line sense organ relationship: capable_of GO:0050964 ! detection of electrical stimulus involved in electroception -relationship: never_in_taxon NCBITaxon:32443 {source="Wikipedia"} ! Teleostei -relationship: never_in_taxon NCBITaxon:32523 ! Tetrapoda relationship: part_of UBERON:0002540 ! lateral line system relationship: present_in_taxon NCBITaxon:119203 ! Selachii @@ -178212,7 +178458,6 @@ is_a: UBERON:0008948 {source="FMA"} ! upper lobe of lung is_a: UBERON:0008951 ! left lung lobe intersection_of: UBERON:0008948 ! upper lobe of lung intersection_of: part_of UBERON:0002168 ! left lung -relationship: never_in_taxon NCBITaxon:10088 {source="ISBN:0123813611"} ! Mus relationship: part_of UBERON:0002168 ! left lung [Term] @@ -178237,7 +178482,6 @@ is_a: UBERON:0008949 {source="FMA"} ! lower lobe of lung is_a: UBERON:0008951 ! left lung lobe intersection_of: UBERON:0008949 ! lower lobe of lung intersection_of: part_of UBERON:0002168 ! left lung -relationship: never_in_taxon NCBITaxon:10088 {source="ISBN:0123813611"} ! Mus relationship: part_of UBERON:0002168 ! left lung [Term] @@ -178257,7 +178501,6 @@ xref: NCIT:C40373 xref: UMLS:C0225740 {source="ncithesaurus:Lingula"} is_a: UBERON:0000063 {source="FMA"} ! organ subunit is_a: UBERON:0004119 ! endoderm-derived structure -relationship: never_in_taxon NCBITaxon:10088 {source="ISBN:0123813611"} ! Mus relationship: part_of UBERON:0008952 {source="ISBN:0123813611"} ! upper lobe of left lung [Term] @@ -179238,6 +179481,7 @@ is_a: UBERON:0007633 ! nucleus of trapezoid body id: UBERON:0009054 name: open circulatory system comment: The Open Circulatory System is a system in which fluid (called hemolymph) in a cavity called the hemocoel bathes the organs directly with oxygen and nutrients and there is no distinction between blood and interstitial fluid; this combined fluid is called hemolymph or haemolymph +xref: FBbt:00005057 is_a: UBERON:0001009 {source="GO"} ! circulatory system [Term] @@ -179636,7 +179880,6 @@ is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0010912 ! subdivision of skeleton relationship: develops_from UBERON:0002342 {source="http://www.ncbi.nlm.nih.gov/pubmed/19924811"} ! neural crest relationship: has_part UBERON:0002418 ! cartilage tissue -relationship: never_in_taxon NCBITaxon:117570 ! Teleostomi relationship: part_of UBERON:0001042 ! chordate pharynx [Term] @@ -179763,7 +180006,6 @@ is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005085 ! ectodermal placode intersection_of: has_potential_to_develop_into UBERON:0002540 ! lateral line system relationship: has_potential_to_develop_into UBERON:0002540 ! lateral line system -relationship: never_in_taxon NCBITaxon:32524 {source="http://tolweb.org/Amniota"} ! Amniota relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata [Term] @@ -179782,7 +180024,6 @@ is_a: UBERON:0000487 ! simple squamous epithelium is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0002166 ! endocardium of atrium is_a: UBERON:0005291 ! embryonic tissue -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0002165 ! endocardium intersection_of: part_of UBERON:0002078 ! right cardiac atrium @@ -180719,9 +180960,9 @@ synonym: "mesenchyme of maxillary prominence" EXACT [https://orcid.org/0000-0002 xref: EHDAA2:0001071 xref: EMAPA:17361 xref: FMA:312691 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0005291 ! embryonic tissue -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0005868 ! maxillary prominence relationship: part_of UBERON:0005868 ! maxillary prominence @@ -181517,6 +181758,7 @@ synonym: "midbrain-hindbrain boundary neural plate" EXACT [ZFA:0007044] xref: TAO:0007044 xref: ZFA:0007044 is_a: UBERON:0006598 ! presumptive structure +relationship: develops_from UBERON:0006238 ! future brain relationship: develops_from UBERON:0007281 ! presumptive midbrain hindbrain boundary relationship: immediate_transformation_of UBERON:0007281 {notes="https://github.com/obophenotype/uberon/issues/438", source="Bgee:AN"} ! presumptive midbrain hindbrain boundary relationship: part_of UBERON:0003075 {source="ZFA"} ! neural plate @@ -181890,7 +182132,6 @@ xref: MA:0000400 xref: NCIT:C77955 xref: UMLS:C2698103 {source="ncithesaurus:Ampullary_Gland"} is_a: UBERON:0005399 {source="MA"} ! male reproductive gland -relationship: never_in_taxon NCBITaxon:9606 {source="MP"} ! Homo sapiens relationship: only_in_taxon NCBITaxon:9347 ! Eutheria relationship: part_of UBERON:0001000 ! vas deferens @@ -182216,7 +182457,6 @@ xref: FMA:295942 is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0009671 {notes="posterior portion", source="EHDAA2"} ! nasal fin relationship: part_of UBERON:0000166 {source="EHDAA2"} ! oral opening relationship: part_of UBERON:0005384 {source="EHDAA2"} ! nasal cavity epithelium @@ -182490,7 +182730,6 @@ xref: NCIT:C102343 xref: VHOG:0001235 is_a: CARO:0000003 is_a: UBERON:0001081 ! endocardium of ventricle -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0001081 ! endocardium of ventricle intersection_of: part_of UBERON:0002080 ! heart right ventricle relationship: attaches_to UBERON:0006567 {source="FMA"} ! right ventricle myocardium @@ -183486,6 +183725,7 @@ id: UBERON:0009865 name: Hatschek's pit def: "A deep ciliated fossa on the dorsal midline of the buccal cavity (the region of the gut behind the mouth). Among other things, it secrets mucus which entraps food particles from the water[WP]." [http://en.wikipedia.org/wiki/Hatschek's_pit] xref: Hatschek's:pit +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0006846 ! surface groove relationship: capable_of GO:0070254 ! mucus secretion relationship: develops_from UBERON:0009868 ! Hatschek's left diverticulum @@ -184478,7 +184718,6 @@ is_a: UBERON:0005806 ! portal system relationship: connects UBERON:0001898 ! hypothalamus relationship: connects UBERON:0002196 ! adenohypophysis relationship: connects UBERON:0002197 ! median eminence of neurohypophysis -relationship: never_in_taxon NCBITaxon:32443 {source="ISBN:0471888893"} ! Teleostei relationship: part_of UBERON:0000949 ! endocrine system [Term] @@ -184895,6 +185134,7 @@ name: upper beak synonym: "maxillary beak" RELATED [] synonym: "rostrum maxillare" RELATED [] synonym: "upper mandible" RELATED SENSU [] +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0003102 ! surface structure relationship: part_of UBERON:0001709 ! upper jaw region relationship: part_of UBERON:0005094 ! beak @@ -184905,8 +185145,8 @@ name: lower beak synonym: "lower mandible" RELATED SENSU [] synonym: "mandibular beak" RELATED [] synonym: "rostrum mandibulare" RELATED [] +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0003102 ! surface structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001710 ! lower jaw region relationship: part_of UBERON:0005094 ! beak @@ -184921,7 +185161,6 @@ is_a: UBERON:0015212 ! lateral structure relationship: composed_primarily_of CL:0000738 {source="Honma1983"} ! leukocyte relationship: contains_process GO:0030097 ! hemopoiesis relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism -relationship: never_in_taxon NCBITaxon:7863 {source="Wikipedia"} ! Holocephali relationship: only_in_taxon NCBITaxon:7778 {source="Wikipedia"} ! Elasmobranchii relationship: part_of UBERON:0002390 ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system @@ -184948,7 +185187,6 @@ is_a: UBERON:0035118 ! material entity in digestive tract disjoint_from: UBERON:0010017 ! spiral valve of cystic duct disjoint_from: UBERON:0010018 ! spiral valve of conus arteriosus relationship: located_in UBERON:0006909 ! lumen of digestive tract -relationship: never_in_taxon NCBITaxon:32523 {source="Wikipedia"} ! Tetrapoda relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002108 ! small intestine @@ -184977,7 +185215,6 @@ xref: AAO:0010251 xref: http://cwx.prenhall.com/bookbind/pubbooks/martini10/chapter21/medialib/Kardong_fig_12_29.html is_a: UBERON:0003978 {source="cjm"} ! valve is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: never_in_taxon NCBITaxon:32524 ! Amniota relationship: only_in_taxon NCBITaxon:8287 {evidence="NAS"} ! Sarcopterygii relationship: part_of UBERON:0003983 {source="AAO"} ! conus arteriosus @@ -184991,7 +185228,6 @@ xref: Vertebrates is_a: UBERON:0003102 {source="cjm"} ! surface structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0004362 ! pharyngeal arch 1 -relationship: never_in_taxon NCBITaxon:32523 ! Tetrapoda relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001004 ! respiratory system relationship: present_in_taxon NCBITaxon:119203 ! Selachii @@ -185384,7 +185620,6 @@ name: supralabial gland def: "Oral gland in reptiles situated immediately above the lip." [ISBN:0073040584] xref: Duvernoy's:gland is_a: UBERON:0010047 ! oral gland -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: only_in_taxon NCBITaxon:32524 ! Amniota [Term] @@ -185393,7 +185628,6 @@ name: infralabial gland def: "Oral gland in reptiles situated immediately below the lip." [ISBN:0073040584] xref: Duvernoy's:gland is_a: UBERON:0010047 ! oral gland -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: only_in_taxon NCBITaxon:32524 ! Amniota [Term] @@ -185424,13 +185658,13 @@ is_a: UBERON:0000062 ! organ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of_part_of GO:0050959 ! echolocation relationship: capable_of_part_of GO:0050959 ! echolocation -relationship: never_in_taxon NCBITaxon:314146 ! Euarchontoglires [Term] id: UBERON:0010054 name: malleus cartilage element def: "A malleus endochondral element that is composed primarily of cartilage tissue." [OBOL:automatic] xref: EMAPA:18229 +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0015018 ! malleus endochondral element is_a: UBERON:0035131 ! auditory ossicle cartilage element intersection_of: UBERON:0015018 ! malleus endochondral element @@ -185534,7 +185768,6 @@ xref: FMA:285217 xref: MA:0003142 is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0005911 ! endo-epithelium -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0015813 ! middle ear epithelium relationship: develops_from UBERON:0010020 ! tubotympanic recess epithelium relationship: develops_from_part_of UBERON:0010020 {source="EHDAA2"} ! tubotympanic recess epithelium @@ -185546,7 +185779,6 @@ name: tympanic cavity epithelium xref: EHDAA2:0004116 is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0015813 ! middle ear epithelium relationship: develops_from UBERON:0010020 ! tubotympanic recess epithelium relationship: develops_from_part_of UBERON:0010020 {source="EHDAA2"} ! tubotympanic recess epithelium @@ -185572,7 +185804,6 @@ name: auditory meatus epithelium xref: EHDAA2:0004114 is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0005911 ! endo-epithelium -is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015814 ! outer ear epithelium relationship: develops_from UBERON:0005872 {source="http://www.ncbi.nlm.nih.gov/pubmed/16313389", source="EHDAA2"} ! 1st arch pharyngeal cleft relationship: part_of UBERON:0001691 {source="EHDAA2"} ! external ear @@ -185593,7 +185824,6 @@ xref: FMA:52880 xref: http://en.wikipedia.org/wiki/Tympanic_part_of_the_temporal_bone xref: http://www.snomedbrowser.com/Codes/Details/138773005 is_a: UBERON:0005913 {source="cjm"} ! zone of bone organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0002218 ! tympanic ring relationship: part_of UBERON:0001678 ! temporal bone @@ -185610,7 +185840,6 @@ xref: FMA:56819 xref: http://www.snomedbrowser.com/Codes/Details/39725007 is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0009647 ! tympanic membrane epithelium -is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015814 ! outer ear epithelium intersection_of: UBERON:0009647 ! tympanic membrane epithelium intersection_of: part_of UBERON:0001352 ! external acoustic meatus @@ -185637,8 +185866,8 @@ name: layer of tympanic membrane subset: grouping_class synonym: "tympanic membrane layer" EXACT [FMA:56732] xref: FMA:56732 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000064 ! organ part -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0002364 ! tympanic membrane [Term] @@ -186443,7 +186672,6 @@ xref: FMA:3740 xref: http://www.snomedbrowser.com/Codes/Details/362032000 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: contributes_to_morphology_of UBERON:0001496 ! ascending aorta relationship: part_of UBERON:0001496 {source="FMA"} ! ascending aorta @@ -186456,7 +186684,6 @@ synonym: "sinotubular ridge" EXACT [MP:0011572] xref: EMAPA:37951 {source="MA:th"} is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0007651 ! anatomical junction -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: contributes_to_morphology_of UBERON:0001496 ! ascending aorta relationship: part_of UBERON:0001496 {source="MP"} ! ascending aorta @@ -186524,6 +186751,7 @@ id: UBERON:0010183 name: liver trabecula def: "A trabecula that is part of a liver." [GO:0060344, OBOL:automatic] synonym: "hepatic trabecula" RELATED [] +synonym: "liver trabeculae" EXACT PLURAL [] is_a: UBERON:0000440 ! trabecula is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000440 ! trabecula @@ -186674,7 +186902,6 @@ synonym: "portal system of kidney" EXACT [] synonym: "renal-portal system" EXACT [AAO:0010518] xref: AAO:0010518 is_a: UBERON:0005806 ! portal system -relationship: never_in_taxon NCBITaxon:40674 {source="ISBN:0073040584"} ! Mammalia [Term] id: UBERON:0010197 @@ -186773,8 +187000,6 @@ xref: NCIT:C77657 xref: Nictitating:membrane xref: UMLS:C0028058 {source="ncithesaurus:Nictitating_Membrane"} is_a: UBERON:0001711 ! eyelid -relationship: never_in_taxon NCBITaxon:376913 {source="Wikipedia"} ! Haplorrhini -relationship: never_in_taxon NCBITaxon:8570 ! Serpentes relationship: part_of UBERON:0001811 ! conjunctiva relationship: present_in_taxon NCBITaxon:261739 relationship: present_in_taxon NCBITaxon:8292 ! Amphibia @@ -186992,6 +187217,7 @@ synonym: "reticular groove" BROAD SENSU [] synonym: "ruminant reticular groove" EXACT [] xref: BTO:0004789 xref: http://www.snomedbrowser.com/Codes/Details/86149002 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0004111 ! anatomical conduit is_a: UBERON:0006846 ! surface groove relationship: channel_for UBERON:0001913 ! milk @@ -187115,7 +187341,6 @@ synonym: "torus pyloricus" EXACT [] xref: http://www.snomedbrowser.com/Codes/Details/14214007 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000064 ! organ part -relationship: never_in_taxon NCBITaxon:314146 ! Euarchontoglires relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0001166 ! pylorus @@ -187559,7 +187784,6 @@ xref: AAO:0010122 is_a: CARO:0000003 is_a: UBERON:0001601 {source="cjm"} ! extra-ocular muscle relationship: innervated_by UBERON:0001646 ! abducens nerve -relationship: never_in_taxon NCBITaxon:9606 {source="Wikipedia"} ! Homo sapiens relationship: present_in_taxon NCBITaxon:40674 ! Mammalia [Term] @@ -187721,7 +187945,6 @@ is_a: UBERON:0003932 {source="ZFA"} ! cartilage element of chondrocranium is_a: UBERON:0010296 ! scleral skeletal element relationship: developmentally_induced_by UBERON:0001782 {gci_filler="NCBITaxon:9031", gci_relation="part_of", notes="Gallus gallus", source="http://www.ncbi.nlm.nih.gov/pubmed/17051547"} ! pigmented layer of retina relationship: develops_from UBERON:0002342 {source="PMID:17051547 - ossicles"} ! neural crest -relationship: never_in_taxon NCBITaxon:32525 {source="PMID:17051547 - but present in monotremes"} ! Theria relationship: part_of UBERON:0001773 {source="cjm"} ! sclera [Term] @@ -187733,8 +187956,6 @@ synonym: "sclerotic bone" EXACT [ZFA:0001411] synonym: "sclerotic ossicle" EXACT [] xref: http://www.snomedbrowser.com/Codes/Details/45632000 is_a: UBERON:0010296 ! scleral skeletal element -relationship: never_in_taxon NCBITaxon:7777 {source="PMID:17051547 Walls 1942"} ! Chondrichthyes -relationship: never_in_taxon NCBITaxon:7878 {source="PMID:17051547 Kemp 1999"} ! Dipnomorpha relationship: part_of UBERON:0001697 {source="ZFA"} ! orbit of skull relationship: part_of UBERON:0011156 ! facial skeleton @@ -187817,7 +188038,6 @@ relationship: part_of UBERON:0001773 ! sclera id: UBERON:0010296 name: scleral skeletal element is_a: UBERON:0010321 ! skeletal element of eye region -relationship: never_in_taxon NCBITaxon:40674 {source="http://www.ncbi.nlm.nih.gov/pubmed/17051547"} ! Mammalia relationship: only_in_taxon NCBITaxon:7776 {source="http://www.ncbi.nlm.nih.gov/pubmed/17051547"} ! Gnathostomata relationship: part_of UBERON:0000019 ! camera-type eye @@ -187831,7 +188051,6 @@ is_a: UBERON:0002513 {source="ZFA"} ! endochondral bone is_a: UBERON:0003462 ! facial bone is_a: UBERON:0010290 ! scleral ossicle relationship: develops_from UBERON:0010289 {source="ZFA"} ! scleral cartilage -relationship: never_in_taxon NCBITaxon:32523 ! Tetrapoda relationship: part_of UBERON:0002241 {source="ZFA"} ! chondrocranium [Term] @@ -187844,7 +188063,6 @@ is_a: UBERON:0003462 ! facial bone is_a: UBERON:0010290 ! scleral ossicle relationship: developmentally_induced_by UBERON:0010300 {source="http://www.ncbi.nlm.nih.gov/pubmed/16496288"} ! epithelial scleral papilla layer relationship: develops_in UBERON:0010299 ! scleral mesenchyme -relationship: never_in_taxon NCBITaxon:32443 ! Teleostei [Term] id: UBERON:0010299 @@ -188191,6 +188409,7 @@ xref: EHDAA2:0004602 is_a: UBERON:0003104 {source="EHDAA2"} ! mesenchyme is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0009526 ! maxillary process mesenchyme +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0009526 ! maxillary process mesenchyme @@ -188957,7 +189176,6 @@ xref: MA:0000754 xref: NCIT:C49776 xref: UMLS:C1710157 {source="ncithesaurus:Splenic_Marginal_Sinus"} is_a: UBERON:0001959 ! white pulp of spleen -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens [Term] id: UBERON:0010399 @@ -189405,7 +189623,6 @@ intersection_of: connects UBERON:0001729 ! oropharynx intersection_of: part_of UBERON:0001716 ! secondary palate relationship: connects UBERON:0001707 ! nasal cavity relationship: connects UBERON:0001729 ! oropharynx -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: part_of UBERON:0001716 ! secondary palate [Term] @@ -191645,8 +191862,6 @@ is_a: UBERON:0003462 ! facial bone is_a: UBERON:0008907 {source="ISBN:0073040584"} ! dermal bone relationship: adjacent_to UBERON:0000209 ! tetrapod frontal bone relationship: adjacent_to UBERON:0001680 ! lacrimal bone -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia -relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: only_in_taxon NCBITaxon:8287 {source="Wikipedia"} ! Sarcopterygii relationship: part_of UBERON:0003113 {notes="orbital series", source="ISBN:0073040584"} ! dermatocranium relationship: part_of UBERON:0011156 ! facial skeleton @@ -191674,7 +191889,6 @@ xref: EMAPA:18339 is_a: UBERON:0003932 ! cartilage element of chondrocranium is_a: UBERON:0005253 ! head mesenchyme is_a: UBERON:0005863 ! cartilaginous condensation -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0015051 ! exoccipital endochondral element intersection_of: UBERON:0015051 ! exoccipital endochondral element intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue @@ -192325,11 +192539,10 @@ def: "An endochondral element of the nasal capsule that forms septum between nas synonym: "mesethmoid" RELATED [AAO:0000303] synonym: "ventral nasal capsule" EXACT [http://www.ncbi.nlm.nih.gov/pubmed/21270050] xref: AAO:0000303 -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0010363 {source="TAO"} ! endochondral element relationship: develops_from UBERON:0005945 {source="TAO"} ! neurocranial trabecula relationship: dubious_for_taxon NCBITaxon:8292 {editor_note="check AAO"} ! Amphibia -relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0002241 {source="TAO"} ! chondrocranium relationship: part_of UBERON:0011241 {source="ISBN:0073040584"} ! ethmoid region @@ -192346,7 +192559,6 @@ is_a: UBERON:0005928 ! external naris intersection_of: UBERON:0005928 ! external naris intersection_of: intersects_midsagittal_plane_of UBERON:0000033 ! head relationship: intersects_midsagittal_plane_of UBERON:0000033 ! head -relationship: never_in_taxon NCBITaxon:314146 ! Euarchontoglires relationship: present_in_taxon NCBITaxon:7762 ! Myxinidae [Term] @@ -192400,8 +192612,6 @@ xref: VSAO:0000127 is_a: UBERON:0003828 ! abdominal segment bone is_a: UBERON:0005172 ! abdomen element is_a: UBERON:0008907 {source="VSAO"} ! dermal bone -relationship: never_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia -relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: only_in_taxon NCBITaxon:32524 {source="Wikipedia"} ! Amniota relationship: part_of UBERON:0006635 {source="ISBN:0073040584"} ! anterior abdominal wall relationship: part_of UBERON:0014478 ! rib skeletal system @@ -192518,7 +192728,6 @@ comment: see TAO:0000474 - intercalar "Small membrane bone homologous with a car xref: AAO:0010835 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005913 ! zone of bone organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0004637 {source="AAO"} ! otic capsule [Term] @@ -192866,7 +193075,6 @@ relationship: attaches_to UBERON:0001685 ! hyoid bone relationship: develops_from UBERON:0004362 ! pharyngeal arch 1 relationship: has_muscle_origin UBERON:0001684 ! mandible relationship: innervated_by UBERON:0011322 {notes="mandibular division (V3) of the trigeminal (CN V) via the mylohyoid nerve", source="Wikipedia"} ! mylohyoid nerve -relationship: never_in_taxon NCBITaxon:9599 ! Pongo relationship: superficial_to UBERON:0001564 ! mylohyoid muscle [Term] @@ -193660,7 +193868,6 @@ xref: Perilymphatic:duct xref: ZFA:0005461 is_a: UBERON:0000025 ! tube is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001846 {source="MA"} ! internal ear relationship: surrounds UBERON:0001845 ! perilymph @@ -194103,7 +194310,6 @@ is_a: UBERON:0001485 ! knee joint relationship: connects UBERON:0000979 ! tibia relationship: connects UBERON:0000981 ! femur relationship: connects UBERON:0002446 ! patella -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: part_of UBERON:0000978 ! leg [Term] @@ -194368,8 +194574,8 @@ relationship: produces UBERON:0012245 ! silk id: UBERON:0011147 name: Verson's gland def: "A gland found in the larvae of lepidoptera. Each gland is made of three cells: the secretory cell, the reservoir cell and the canal cell." [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0002365 ! exocrine gland is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0019319 ! exocrine gland of integumental system relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0007376 ! outer epithelium @@ -194581,7 +194787,6 @@ synonym: "supra-occipital cartilage condensation" EXACT [] synonym: "supraoccipital cartilage condensation" EXACT [EMAPA:18341] xref: EMAPA:18341 is_a: UBERON:0003932 ! cartilage element of chondrocranium -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0015015 ! supraoccipital endochondral element intersection_of: UBERON:0015015 ! supraoccipital endochondral element intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue @@ -194711,7 +194916,6 @@ intersection_of: connects UBERON:0004744 ! articular/anguloarticular intersection_of: connects UBERON:0006597 ! quadrate bone relationship: connects UBERON:0004744 ! articular/anguloarticular relationship: connects UBERON:0006597 ! quadrate bone -relationship: never_in_taxon NCBITaxon:32525 {source="http://evolution.berkeley.edu"} ! Theria [Term] id: UBERON:0011171 @@ -195537,7 +195741,6 @@ xref: EFO:0003685 xref: TAO:0001405 xref: ZFA:0001405 is_a: UBERON:0003932 {source="TAO"} ! cartilage element of chondrocranium -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0005945 {source="ISBN:0073040584"} ! neurocranial trabecula relationship: part_of UBERON:0002517 {source="FMA"} ! basicranium relationship: part_of UBERON:0011241 {source="AAO"} ! ethmoid region @@ -195716,8 +195919,6 @@ xref: http://en.wikipedia.org/wiki/Rhinarium is_a: UBERON:0003102 ! surface structure is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: never_in_taxon NCBITaxon:9475 ! Tarsiidae -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0007827 ! external nose relationship: surrounds UBERON:0005928 ! external naris @@ -195787,8 +195988,6 @@ xref: Quadratojugal:bone is_a: UBERON:0002514 {source="AAO-def"} ! intramembranous bone is_a: UBERON:0008907 ! dermal bone is_a: UBERON:0011597 ! bone of upper jaw -relationship: never_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia -relationship: never_in_taxon NCBITaxon:8509 {source="Wikipedia"} ! Squamata relationship: part_of UBERON:0003113 {notes="temporal series", source="ISBN:0073040584"} ! dermatocranium relationship: part_of UBERON:0003277 {source="AAO"} ! skeleton of upper jaw @@ -195801,7 +196000,6 @@ synonym: "under-tongue" RELATED [http://en.wikipedia.org/wiki/Sublingua] xref: http://en.wikipedia.org/wiki/Sublingua is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0013765 ! digestive system element -relationship: never_in_taxon NCBITaxon:9606 {source="Wikipedia"} ! Homo sapiens relationship: only_in_taxon NCBITaxon:9347 {source="Wikipedia"} ! Eutheria relationship: part_of UBERON:0000165 ! mouth @@ -196391,7 +196589,6 @@ xref: http://en.wikipedia.org/wiki/Capsule_of_temporomandibular_joint xref: http://www.snomedbrowser.com/Codes/Details/303404000 xref: MFMO:0000046 is_a: UBERON:0001484 ! articular capsule -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0001484 ! articular capsule intersection_of: part_of UBERON:0003700 ! temporomandibular joint @@ -196418,7 +196615,6 @@ xref: http://en.wikipedia.org/wiki/Articular_disk_of_the_temporomandibular_joint xref: http://www.snomedbrowser.com/Codes/Details/282433007 xref: MESH:D019224 is_a: UBERON:0007844 {source="FMA"} ! cartilage element -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0013765 ! digestive system element relationship: part_of UBERON:0003700 {source="BTO"} ! temporomandibular joint @@ -196430,7 +196626,6 @@ xref: FMA:57070 xref: http://www.snomedbrowser.com/Codes/Details/127861009 xref: Ligaments is_a: UBERON:0008846 ! skeletal ligament -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0008846 ! skeletal ligament intersection_of: part_of UBERON:0003700 ! temporomandibular joint @@ -196663,7 +196858,6 @@ is_a: UBERON:0002368 {source="BTO"} ! endocrine gland is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005174 ! dorsal region element is_a: UBERON:0010133 ! neuroendocrine gland -relationship: never_in_taxon NCBITaxon:32523 {source="ISBN:0471888893"} ! Tetrapoda relationship: part_of UBERON:0002240 {source="BTO"} ! spinal cord [Term] @@ -197617,7 +197811,6 @@ synonym: "upper jaw future lip" EXACT [EHDAA2:0002120] xref: EHDAA2:0002120 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0003235 ! epithelium of upper jaw -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0004068 {notes="fusion"} ! medial nasal prominence relationship: develops_from UBERON:0005868 {notes="fusion"} ! maxillary prominence relationship: part_of UBERON:0001709 {source="EHDAA2"} ! upper jaw region @@ -197717,8 +197910,9 @@ synonym: "processus lenticularis incudis" EXACT LATIN [FMA:52775, FMA:TA] xref: FMA:52775 xref: http://palaeos.com/vertebrates/bones/ear/images/Incus3.gif xref: http://www.snomedbrowser.com/Codes/Details/368928003 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004530 ! bony projection -is_a: UBERON:0010313 ! neural crest-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: develops_from UBERON:0005689 ! 2nd arch mesenchyme relationship: part_of UBERON:0001688 {source="FMA"} ! incus bone @@ -197761,7 +197955,6 @@ xref: http://linkedlifedata.com/resource/umls/id/C0227123 xref: http://www.snomedbrowser.com/Codes/Details/304704007 xref: NCIT:C54204 is_a: UBERON:0001828 ! gingiva -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0001828 ! gingiva intersection_of: part_of UBERON:0001710 ! lower jaw region relationship: part_of UBERON:0001710 ! lower jaw region @@ -198374,7 +198567,6 @@ xref: http://en.wikipedia.org/wiki/Interclavicle xref: VSAO:0000161 is_a: UBERON:0007829 ! pectoral girdle bone is_a: UBERON:0008907 {source="VSAO"} ! dermal bone -relationship: never_in_taxon NCBITaxon:32525 ! Theria relationship: part_of UBERON:0007831 {source="VSAO"} ! pectoral girdle skeleton relationship: part_of UBERON:0007841 {gci_relation="part_of", gci_filler="NCBITaxon:8782"} ! furcula relationship: present_in_taxon NCBITaxon:9257 ! Ornithorhynchus @@ -198996,7 +199188,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/279811007 xref: NCIT:C33845 is_a: UBERON:0000025 ! tube is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000025 ! tube intersection_of: connects UBERON:0001853 ! utricle of membranous labyrinth intersection_of: connects UBERON:0001854 ! saccule of membranous labyrinth @@ -199241,7 +199432,6 @@ name: dermal pulp of feather shaft def: "A tissue that is part of a cavity of feather shaft." [OBOL:automatic] is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000479 ! tissue intersection_of: part_of UBERON:0011784 ! feather shaft relationship: develops_from UBERON:0011803 ! feather bud, dermal component @@ -199280,7 +199470,6 @@ synonym: "dermal papilla of feather bud" EXACT [] synonym: "dermal papilla of feather papilla" EXACT [] is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0011802 ! feather bud relationship: develops_from UBERON:0011801 ! dermal condensation of feather follicle @@ -199617,7 +199806,6 @@ synonym: "parotid gland acinus" EXACT [FMA:59863] xref: EMAPA:37933 {source="MA:th"} xref: FMA:59863 xref: http://www.snomedbrowser.com/Codes/Details/46926004 -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011850 ! acinus of salivary gland is_a: UBERON:0013232 ! serous acinus intersection_of: UBERON:0009842 ! glandular acinus @@ -199668,7 +199856,6 @@ def: "An acinus that is part of a lacrimal gland." [OBOL:automatic] synonym: "lacrimal gland acinus" EXACT [FMA:85250] xref: FMA:85250 is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011858 ! acinus of exocrine gland intersection_of: UBERON:0009842 ! glandular acinus intersection_of: part_of UBERON:0001817 ! lacrimal gland @@ -199703,7 +199890,6 @@ xref: NCIT:C95443 xref: UMLS:C0149591 {source="ncithesaurus:Internal_Auditory_Canal_of_Ear"} is_a: UBERON:0004111 ! anatomical conduit is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: conduit_for UBERON:0001647 ! facial nerve relationship: conduit_for UBERON:0001648 ! vestibulocochlear nerve relationship: contributes_to_morphology_of UBERON:0001846 ! internal ear @@ -200278,7 +200464,6 @@ synonym: "cochlea basement membrane" EXACT [] xref: EMAPA:37830 {source="MA:th"} is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005769 ! basement membrane of epithelium -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: part_of UBERON:0002499 ! cochlear labyrinth relationship: part_of UBERON:0002499 ! cochlear labyrinth @@ -200426,7 +200611,7 @@ relationship: part_of UBERON:0006003 {source="ISBN:0123813611"} ! integumentary [Term] id: UBERON:0011933 name: vibrissa unit -def: "A pilosebaceuous unit that contains a strand of virbissa hair (a specialized tactile hair) with the follicle incorporating a blood sinus, heavily innervated by sensory nerves." [http://orcid.org/0000-0002-6601-2165] +def: "A pilosebaceous unit that contains a strand of vibrissa hair (a specialized tactile hair) with the follicle incorporating a blood sinus, heavily innervated by sensory nerves." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim synonym: "vibrissa" RELATED [MA:0000163] xref: EMAPA:17529 @@ -201135,7 +201320,6 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: http://en.wikipedia.org/wiki/Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: never_in_taxon NCBITaxon:147099 {source="http://en.wikipedia.org/wiki/Acoelomorpha"} ! Acoelomorpha relationship: only_in_taxon NCBITaxon:33213 ! Bilateria [Term] @@ -201379,7 +201563,6 @@ xref: FMA:43700 xref: http://en.wikipedia.org/wiki/Fovea_of_head_of_femur is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005055 ! zone of long bone -relationship: never_in_taxon NCBITaxon:9709 ! Phocidae relationship: part_of UBERON:0004412 ! proximal epiphysis of femur [Term] @@ -201773,7 +201956,6 @@ def: "A respiratory pump found in basal craniates." [http://en.wikipedia.org/wik synonym: "velum" BROAD [] is_a: UBERON:0000171 ! respiration organ disjoint_from: UBERON:0035960 ! velum feeding organ -relationship: never_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: only_in_taxon NCBITaxon:89593 ! Craniata relationship: present_in_taxon NCBITaxon:7762 ! Myxinidae @@ -202322,7 +202504,6 @@ xref: NCIT:C33680 xref: UMLS:C1515066 {source="ncithesaurus:Superior_Intercostal_Vein"} is_a: UBERON:0012197 ! intercostal vein relationship: connected_to UBERON:0001594 {subset="human_reference_atlas"} ! azygos vein -relationship: part_of RO:0002577 ! system [Term] id: UBERON:0012195 @@ -202330,6 +202511,10 @@ name: left superior intercostal vein xref: FMA:4797 xref: http://www.snomedbrowser.com/Codes/Details/27297006 is_a: UBERON:0012194 ! superior intercostal vein +is_a: UBERON:0015212 ! lateral structure +intersection_of: UBERON:0012194 ! superior intercostal vein +intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism +relationship: in_left_side_of UBERON:0000468 ! multicellular organism [Term] id: UBERON:0012196 @@ -202337,7 +202522,11 @@ name: right superior intercostal vein xref: FMA:4877 xref: http://www.snomedbrowser.com/Codes/Details/80721005 is_a: UBERON:0012194 ! superior intercostal vein +is_a: UBERON:0015212 ! lateral structure +intersection_of: UBERON:0012194 ! superior intercostal vein +intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism relationship: connected_to UBERON:0001594 {subset="human_reference_atlas"} ! azygos vein +relationship: in_right_side_of UBERON:0000468 ! multicellular organism [Term] id: UBERON:0012197 @@ -202349,8 +202538,9 @@ xref: Intercostal:veins xref: MA:0003166 is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: located_in UBERON:0012198 ! intercostal space -relationship: located_in UBERON:0012198 ! intercostal space +intersection_of: drains UBERON:0012198 ! intercostal space +relationship: drains UBERON:0012198 ! intercostal space +relationship: part_of RO:0002577 ! system [Term] id: UBERON:0012198 @@ -202375,7 +202565,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/89209000 is_a: UBERON:0012197 ! intercostal vein disjoint_from: UBERON:0012200 {source="lexical"} ! anterior intercostal vein relationship: connected_to UBERON:0001594 {subset="human_reference_atlas"} ! azygos vein -relationship: part_of RO:0002577 ! system [Term] id: UBERON:0012200 @@ -202386,7 +202575,6 @@ xref: http://en.wikipedia.org/wiki/Anterior_intercostal_veins xref: http://www.snomedbrowser.com/Codes/Details/15546000 is_a: UBERON:0012197 ! intercostal vein relationship: connected_to UBERON:0001589 {subset="human_reference_atlas"} ! internal thoracic vein -relationship: part_of RO:0002577 ! system [Term] id: UBERON:0012236 @@ -202996,7 +203184,6 @@ is_a: UBERON:0016852 ! skin scent gland intersection_of: UBERON:0001821 ! sebaceous gland intersection_of: part_of UBERON:0011932 ! pilosebaceous unit intersection_of: part_of UBERON:0012336 ! perianal skin -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: part_of UBERON:0011932 ! pilosebaceous unit relationship: part_of UBERON:0012336 ! perianal skin @@ -203428,9 +203615,9 @@ name: maxillary process ectoderm xref: EHDAA2:0004599 xref: EMAPA:17637 xref: FMA:312685 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0005868 {source="EHDAA2"} ! maxillary prominence [Term] @@ -203441,7 +203628,6 @@ xref: EHDAA2:0000039 xref: EMAPA:16389 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue -is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015833 ! foregut epithelium relationship: develops_from UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0000076 {source="EHDAA2"} ! external ectoderm @@ -203653,7 +203839,6 @@ xref: Penile:spines is_a: UBERON:0000479 ! tissue is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: part_of UBERON:0000989 ! penis relationship: present_in_taxon NCBITaxon:40674 ! Mammalia @@ -204505,7 +204690,6 @@ relationship: part_of UBERON:0001179 ! peritoneal cavity id: UBERON:0012443 name: row of scales synonym: "set of scales" RELATED [] -is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0034926 ! anatomical row intersection_of: UBERON:0034926 ! anatomical row intersection_of: has_member UBERON:0002542 ! scale @@ -204834,7 +205018,6 @@ synonym: "oral tentacle" EXACT [] xref: BTO:0001357 is_a: UBERON:0000062 ! organ relationship: adjacent_to UBERON:0000165 ! mouth -relationship: never_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: present_in_taxon NCBITaxon:7568 relationship: present_in_taxon NCBITaxon:7737 ! Branchiostoma @@ -205025,7 +205208,6 @@ is_a: UBERON:0004590 ! sphincter muscle is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0004590 ! sphincter muscle intersection_of: part_of UBERON:0000996 ! vagina -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: part_of UBERON:0000996 ! vagina relationship: present_in_taxon NCBITaxon:8509 ! Squamata @@ -205189,7 +205371,6 @@ synonym: "epitrochlearis" EXACT [BTO:0000423] synonym: "wing epitrochlearis muscle" NARROW SENSU [NCBITaxon:8782, OBOL:automatic] xref: BTO:0000423 is_a: UBERON:0003662 {source="BTO"} ! forelimb muscle -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens [Term] id: UBERON:0012615 @@ -205746,7 +205927,6 @@ synonym: "lip vein" EXACT [OBOL:automatic] synonym: "vena labialis" EXACT LATIN [] xref: http://www.snomedbrowser.com/Codes/Details/367664002 is_a: UBERON:0003496 ! head blood vessel -is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0009141 ! craniocervical region vein intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0001833 ! lip @@ -206029,7 +206209,6 @@ xref: EHDAA2:0000032 xref: EMAPA:16383 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue -is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015833 ! foregut epithelium relationship: develops_from UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0000076 {source="EHDAA2"} ! external ectoderm @@ -206285,7 +206464,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/368942006 xref: NCIT:C32117 xref: UMLS:C1510916 {source="ncithesaurus:Anterior_Wall_of_the_Tympanum"} is_a: UBERON:0005913 ! zone of bone organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0010066 ! tympanic plate [Term] @@ -206476,7 +206654,6 @@ synonym: "wool" RELATED [MESH:A13.970] xref: http://www.snomedbrowser.com/Codes/Details/90080004 xref: MESH:D014935 is_a: UBERON:0010509 ! strand of pelage hair -relationship: never_in_taxon NCBITaxon:9606 {source="https://github.com/obophenotype/uberon/issues/703"} ! Homo sapiens relationship: only_in_taxon NCBITaxon:9963 {source="cjm"} ! Caprinae [Term] @@ -206487,7 +206664,6 @@ comment: analagous to a puparium in other insects is_a: UBERON:0018657 ! pupal case disjoint_from: UBERON:0016927 ! mucus cocoon relationship: composed_primarily_of UBERON:0012245 ! silk -relationship: never_in_taxon NCBITaxon:37572 ! Papilionoidea relationship: only_in_taxon NCBITaxon:33392 ! Endopterygota relationship: surrounds UBERON:0003143 ! pupa @@ -206548,7 +206724,6 @@ xref: Epipubic:bone is_a: UBERON:0007830 {source="cjm"} ! pelvic girdle bone/zone is_a: UBERON:0015212 ! lateral structure relationship: in_lateral_side_of UBERON:0001271 ! pelvic girdle region -relationship: never_in_taxon NCBITaxon:314146 ! Euarchontoglires relationship: only_in_taxon NCBITaxon:40674 ! Mammalia [Term] @@ -206572,12 +206747,6 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005744 ! bone foramen relationship: conduit_for UBERON:0001148 ! median nerve relationship: conduit_for UBERON:0001398 ! brachial artery -relationship: never_in_taxon NCBITaxon:91561 ! Artiodactyla -relationship: never_in_taxon NCBITaxon:9365 ! Erinaceus europaeus -relationship: never_in_taxon NCBITaxon:9397 ! Chiroptera -relationship: never_in_taxon NCBITaxon:9604 ! Hominidae -relationship: never_in_taxon NCBITaxon:9721 ! Cetacea -relationship: never_in_taxon NCBITaxon:9975 ! Lagomorpha relationship: only_in_taxon NCBITaxon:32524 ! Amniota relationship: part_of UBERON:0004404 ! distal epiphysis of humerus relationship: present_in_taxon NCBITaxon:376911 @@ -206729,7 +206898,6 @@ is_a: CARO:0000003 is_a: UBERON:0003663 ! hindlimb muscle relationship: has_muscle_insertion UBERON:0003464 ! hindlimb bone relationship: has_muscle_origin UBERON:0035102 ! transverse process of caudal vertebra -relationship: never_in_taxon NCBITaxon:9606 {source="https://doi.org/10.1002/ar.22919"} ! Homo sapiens relationship: part_of UBERON:0002103 ! hindlimb relationship: present_in_taxon NCBITaxon:399537 {source="https://doi.org/10.1002/ar.22919"} relationship: present_in_taxon NCBITaxon:8492 {source="Wikipedia"} ! Archosauria @@ -206742,7 +206910,6 @@ name: otic notch def: "Otic notches are invagination in the posterior margin of the skull roof, one behind each orbit. Such notches are found in labyrinthodonts and some of their immediate ancestors, but not their reptilian descendants. The presence or absence of the otic notches is one of the traits used to separate the amniotes from the amphibian grade tetrapods." [http://en.wikipedia.org/wiki/Otic_notch] xref: Otic:notch is_a: UBERON:0005913 ! zone of bone organ -relationship: never_in_taxon NCBITaxon:32524 ! Amniota relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda relationship: part_of UBERON:0003113 ! dermatocranium @@ -206843,7 +207010,6 @@ is_a: UBERON:0013229 ! eyelid gland is_a: UBERON:0015153 ! medial gland of ocular region intersection_of: UBERON:0015153 ! medial gland of ocular region intersection_of: produces UBERON:0022286 ! secretion of nictitans gland -relationship: never_in_taxon NCBITaxon:39107 {source="ISBN:1118473523"} ! Murinae relationship: part_of UBERON:0010207 ! nictitating membrane relationship: present_in_taxon NCBITaxon:10047 {source="ISBN:1118473523"} relationship: produces UBERON:0022286 ! secretion of nictitans gland @@ -207373,7 +207539,6 @@ def: "A bony buttress on the inner surface of the foremost part of the ape mandi xref: Simian:shelf is_a: UBERON:0005913 ! zone of bone organ is_a: UBERON:0010313 ! neural crest-derived structure -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: only_in_taxon NCBITaxon:314295 ! Hominoidea relationship: part_of UBERON:0001684 ! mandible @@ -207990,7 +208155,6 @@ is_a: CARO:0000003 is_a: UBERON:0003663 ! hindlimb muscle relationship: has_muscle_insertion UBERON:0000979 ! tibia relationship: has_muscle_origin UBERON:0001273 ! ilium -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: only_in_taxon NCBITaxon:32524 ! Amniota relationship: part_of UBERON:0002103 ! hindlimb @@ -208371,8 +208535,8 @@ xref: BIRNLEX:1741 xref: Brodmann_area:10 xref: DHBA:146034836 xref: FMA:68607 -xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=76 {source="BIRNLEX:1741"} xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=76 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=76 {source="BIRNLEX:1741"} xref: http://linkedlifedata.com/resource/umls/id/C1272532 xref: UMLS:C1272532 {source="BIRNLEX:1741"} is_a: UBERON:0013529 {source="NIFSTD"} ! Brodmann area @@ -209399,7 +209563,7 @@ relationship: part_of UBERON:0002114 ! duodenum id: UBERON:0013645 name: gular gland def: "A gland that is part of the gular region (throat)." [http://orcid.org/0000-0002-6601-2165] -is_a: UBERON:0003297 ! gland of integumental system +is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0011154 ! gular region relationship: part_of UBERON:0011154 ! gular region @@ -209484,7 +209648,6 @@ is_a: UBERON:0010314 ! structure with developmental contribution from neural cre is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: skeleton_of UBERON:0012121 ! respiratory velum -relationship: never_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: only_in_taxon NCBITaxon:89593 ! Craniata relationship: part_of UBERON:0008895 {notes="in hagfishes it is difficult to separate neurocranium from visceral skeleton"} ! splanchnocranium relationship: part_of UBERON:0012121 ! respiratory velum @@ -210238,10 +210401,8 @@ xref: VHOG:0001567 xref: XAO:0003145 is_a: UBERON:0000020 ! sense organ is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: capable_of GO:0050910 ! detection of mechanical stimulus involved in sensory perception of sound relationship: has_part CL:0000202 ! auditory hair cell -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0001855 {source="MA-abduced"} ! cochlear duct of membranous labyrinth [Term] @@ -210660,7 +210821,6 @@ xref: TAO:0005411 xref: ZFA:0005411 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010000 ! multicellular anatomical structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001856 ! semicircular duct [Term] @@ -211417,7 +211577,6 @@ synonym: "nymph" RELATED [BTO:0000954] xref: BTO:0000954 xref: Nymph:(biology) is_a: UBERON:0000069 ! larval stage -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata relationship: only_in_taxon NCBITaxon:33213 ! Bilateria [Term] @@ -211797,8 +211956,6 @@ synonym: "temporal fenestrae" RELATED PLURAL [] is_a: UBERON:0004705 ! fenestra intersection_of: UBERON:0004705 ! fenestra intersection_of: part_of UBERON:0001678 ! temporal bone -relationship: never_in_taxon NCBITaxon:32525 {notes="in extant mammals the synapsis temporal fenestra is closed by the sphenoid", source="Wikipedia"} ! Theria -relationship: never_in_taxon NCBITaxon:8459 {source="Wikipedia"} ! Testudines relationship: only_in_taxon NCBITaxon:32524 {notes="not present in earliest amniotes", source="Wikipedia"} ! Amniota relationship: part_of UBERON:0001678 ! temporal bone @@ -211997,7 +212154,6 @@ is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000075 ! subdivision of skeletal system relationship: composed_primarily_of UBERON:0015019 ! rib endochondral element relationship: has_part UBERON:0003252 ! thoracic rib cage -relationship: never_in_taxon NCBITaxon:7778 {source="Wikipedia"} ! Elasmobranchii relationship: part_of UBERON:0011138 ! postcranial axial skeletal system [Term] @@ -213722,7 +213878,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/279799003 xref: UMLS:C0458781 {source="BIRNLEX:2522"} is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005913 ! zone of bone organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0006723 ! cochlear modiolus [Term] @@ -213735,7 +213890,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/279778001 xref: UMLS:C0458766 {source="BIRNLEX:2556"} is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005913 ! zone of bone organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0006106 ! cochlear canal [Term] @@ -213748,7 +213902,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/279772000 xref: UMLS:C0458761 {source="BIRNLEX:2558"} is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005913 ! zone of bone organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0006106 ! cochlear canal [Term] @@ -213761,7 +213914,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/279780007 xref: UMLS:C0458768 {source="BIRNLEX:2559"} is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005913 ! zone of bone organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0006106 ! cochlear canal [Term] @@ -214293,7 +214445,6 @@ xref: Angular:vein xref: FMA:50893 xref: http://www.snomedbrowser.com/Codes/Details/151804007 is_a: UBERON:0003496 ! head blood vessel -is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0009141 ! craniocervical region vein relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0001653 ! facial vein @@ -214470,9 +214621,9 @@ name: frontonasal process epithelium def: "An epithelium that is part of a frontonasal prominence." [OBOL:automatic] xref: EHDAA2:0004108 xref: EMAPA:32918 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue -is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0004066 ! frontonasal prominence relationship: develops_from UBERON:0000076 {source="EHDAA2"} ! external ectoderm @@ -214580,8 +214731,9 @@ relationship: part_of UBERON:0014710 ! carapacial ridge id: UBERON:0014712 name: carapacial ridge ectoderm def: "An epithelium that is part of a carapacial ridge." [OBOL:automatic] +is_a: CARO:0000000 ! anatomical entity +is_a: UBERON:0000483 ! epithelium is_a: UBERON:0005291 ! embryonic tissue -is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0014710 ! carapacial ridge relationship: develops_from UBERON:0000076 {source="cjm"} ! external ectoderm @@ -214748,7 +214900,6 @@ synonym: "dorsal ventricular ridge" EXACT [] synonym: "DVR" RELATED ABBREVIATION [http://www.ncbi.nlm.nih.gov/pubmed/23027930] is_a: UBERON:0002616 ! regional part of brain is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: only_in_taxon NCBITaxon:32524 ! Amniota relationship: part_of UBERON:0000203 ! pallium relationship: present_in_taxon NCBITaxon:8782 ! Aves @@ -215123,7 +215274,6 @@ synonym: "venae palpebrales" RELATED LATIN [] xref: FMA:51997 xref: http://www.snomedbrowser.com/Codes/Details/152208004 is_a: UBERON:0003496 ! head blood vessel -is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0009141 ! craniocervical region vein intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0001711 ! eyelid @@ -216138,12 +216288,10 @@ id: UBERON:0014895 name: somatic muscle def: "A muscle structure of invertebrates whose origin and insertion sites are in basal side of the epidermis or structures derived from it. The simplest somatic muscles consist of a single cell and associated extracellular structures." [GOC:DOS] synonym: "skeletal muscle" RELATED [FBbt:00005073] -xref: FBbt:00005073 xref: HAO:0001922 is_a: CARO:0000003 is_a: UBERON:0005090 ! muscle structure relationship: attaches_to UBERON:0002416 ! integumental system -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of RO:0002577 ! system relationship: part_of UBERON:0007095 ! somatic musculature @@ -217817,6 +217965,7 @@ xref: Lamina:terminalis xref: VHOG:0001547 is_a: UBERON:0014532 {source="FMA"} ! white matter lamina of cerebral hemisphere relationship: develops_from UBERON:0005078 ! lamina terminalis of neural tube +relationship: develops_from UBERON:0006222 ! future diencephalon relationship: immediate_transformation_of UBERON:0005078 ! lamina terminalis of neural tube relationship: part_of UBERON:0002437 {source="FMA"} ! cerebral hemisphere white matter @@ -218312,7 +218461,6 @@ is_a: UBERON:0000970 ! eye intersection_of: UBERON:0000970 ! eye intersection_of: composed_primarily_of UBERON:0000020 ! sense organ relationship: composed_primarily_of UBERON:0000020 ! sense organ -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata relationship: present_in_taxon NCBITaxon:6340 {notes="present on tentacular crown", source="http://www.ncbi.nlm.nih.gov/pubmed/21062451"} ! Annelida relationship: present_in_taxon NCBITaxon:6544 {notes="present on mantle edge in arcacean Bivalvia", source="http://www.ncbi.nlm.nih.gov/pubmed/21062451"} ! Bivalvia relationship: present_in_taxon NCBITaxon:7588 {notes="The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species", source="http://www.ncbi.nlm.nih.gov/pubmed/21062451"} @@ -218328,11 +218476,6 @@ xref: SPD:0000343 is_a: UBERON:0000957 ! lamina relationship: has_quality PATO:0001297 ! reflectivity relationship: has_quality PATO:0002124 ! laminar -relationship: never_in_taxon NCBITaxon:8782 {editor="cjm", source="http://www.ncbi.nlm.nih.gov/pubmed/14738502"} ! Aves -relationship: never_in_taxon NCBITaxon:9321 {editor="cjm", source="http://www.ncbi.nlm.nih.gov/pubmed/14738502"} ! Osphranter rufus -relationship: never_in_taxon NCBITaxon:9443 {editor="cjm", source="http://www.ncbi.nlm.nih.gov/pubmed/14738502"} ! Primates -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: never_in_taxon NCBITaxon:9822 {editor="cjm", source="http://www.ncbi.nlm.nih.gov/pubmed/14738502"} ! Sus relationship: part_of UBERON:0000970 ! eye [Term] @@ -218499,7 +218642,6 @@ xref: FMA:55627 xref: http://www.snomedbrowser.com/Codes/Details/28638008 xref: NCIT:C32346 is_a: UBERON:0001560 ! neck of organ -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0001560 ! neck of organ intersection_of: part_of UBERON:0001091 ! calcareous tooth @@ -218521,7 +218663,6 @@ def: "A circulatory organ that is reponsible for pumping lymph throughout the bo xref: Lymph:heart is_a: UBERON:0015229 ! accessory circulatory organ relationship: capable_of GO:0003017 ! lymph circulation -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: only_in_taxon NCBITaxon:8287 ! Sarcopterygii relationship: present_in_taxon NCBITaxon:8342 ! Anura relationship: present_in_taxon NCBITaxon:8493 ! Crocodylidae @@ -218631,7 +218772,7 @@ is_a: UBERON:0015216 ! nasal meatus [Term] id: UBERON:0015222 name: ventral nasal meatus -def: "The ventral nasal meatus is found between the ventral nasal concha and the dorsal surface of the hard palate.It connects the nasal vestibule with the nasopharynx. Rostrally it is narrow at the nasal vestibule and widens caudally towards the nasopharyngeal meatus. The ventral nasal meatus is the main passage for air. Apart from olfaction, the nasal cavity functions to warm the inhaled air as it passes through the meatuses over the vascular beds of the mucosa. The air is humidified by the vaporization of tears and serous nasal secretion. The air is cleaned throughout the scattered mucous glands. These glands secrete mucous through the nasal cavity and the mucous serves to trap the large particles that come into contact with it. PPP Clinically in the horse the ventral nasal meatus is the main passage through which a stomach tube can be passed to the pharynx and oesophagus and then to the stomach. This kind of a tube is commonly used when drenching a horse for colic, as well as having many other veterinary applications. The tube has to pass through the ventral nasal meatus to the nasopharyngeal meatus and the caudal nares to reach the pharynx and oesophagus. If the tube is accidentally passed into the dorsal or middle nasal meatuses it would pass to the ethmotubinates and cause massive haemorrhage." [MURDOCH:2178] +def: "The ventral nasal meatus is found between the ventral nasal concha and the dorsal surface of the hard palate.It connects the nasal vestibule with the nasopharynx. Rostrally it is narrow at the nasal vestibule and widens caudally towards the nasopharyngeal meatus. The ventral nasal meatus is the main passage for air. Apart from olfaction, the nasal cavity functions to warm the inhaled air as it passes through the meatuses over the vascular beds of the mucosa. The air is humidified by the vaporization of tears and serous nasal secretion. The air is cleaned throughout the scattered mucous glands. These glands secrete mucous through the nasal cavity and the mucous serves to trap the large particles that come into contact with it. Clinically in the horse the ventral nasal meatus is the main passage through which a stomach tube can be passed to the pharynx and oesophagus and then to the stomach. This kind of a tube is commonly used when drenching a horse for colic, as well as having many other veterinary applications. The tube has to pass through the ventral nasal meatus to the nasopharyngeal meatus and the caudal nares to reach the pharynx and oesophagus. If the tube is accidentally passed into the dorsal or middle nasal meatuses it would pass to the ethmotubinates and cause massive haemorrhage." [MURDOCH:2178] is_a: UBERON:0015216 ! nasal meatus [Term] @@ -218724,7 +218865,7 @@ id: UBERON:0015231 name: circulatory system dorsal vessel def: "A tube that runs longitudinally through the thorax and abdomen, along the inside of the dorsal body wall and that forms the major structural component of the open circulatory system of arthropods." [UBERON:cjm] synonym: "dorsal vessel" RELATED SENSU [FBbt:00058291, NCBITaxon:50557] -xref: FBbt:00003152 +xref: FBbt:00058291 is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: develops_from UBERON:0000926 ! mesoderm @@ -218783,7 +218924,6 @@ is_a: UBERON:0003103 {source="ZFA"} ! compound organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: in_lateral_side_of UBERON:0015238 {gci_relation="part_of", gci_filler="NCBITaxon:117569"} ! pineal complex relationship: in_left_side_of UBERON:0015238 {gci_relation="part_of", gci_filler="NCBITaxon:7954"} ! pineal complex -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0015238 {source="ZFA"} ! pineal complex [Term] @@ -219616,7 +219756,6 @@ name: prostate gland dorsal lobe xref: EMAPA:29808 xref: MA:0003124 is_a: UBERON:0001328 ! lobe of prostate -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: part_of UBERON:0008808 ! prostate gland dorsolateral lobe [Term] @@ -220491,7 +220630,6 @@ xref: http://en.wikipedia.org/wiki/Deep_parotid_lymph_nodes xref: http://www.snomedbrowser.com/Codes/Details/279142004 is_a: UBERON:0015857 {source="FMA"} ! parotid lymph node is_a: UBERON:0015918 ! deep lymph node -relationship: never_in_taxon NCBITaxon:10090 {source="http://www.ncbi.nlm.nih.gov/pubmed/16624319"} ! Mus musculus [Term] id: UBERON:0016394 @@ -221953,7 +222091,6 @@ synonym: "otolith membrane" NARROW [] xref: FMA:75570 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005764 {source="FMA"} ! acellular membrane -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: bounding_layer_of UBERON:0002518 {source="Wikipedia"} ! otolith organ relationship: part_of UBERON:0001862 {source="MA-abduced"} ! vestibular labyrinth relationship: part_of UBERON:0002518 ! otolith organ @@ -221964,7 +222101,6 @@ name: gelatinous layer of statoconial membrane xref: FMA:75588 is_a: UBERON:0000476 {source="FMA"} ! acellular anatomical structure is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0016567 {source="FMA"} ! statoconial membrane [Term] @@ -221973,7 +222109,6 @@ name: subcupular meshwork of statoconial membrane def: "An acellular membrane in the inner ear that is part of the statoconial membrane and consists of long branching filaments cross-bridged to one another. The filaments are continuous with those of the otolithic membrane on one side and with the surface of the epithelium on the other." [ISBN:1565939948] is_a: UBERON:0000476 ! acellular anatomical structure is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: adjacent_to UBERON:0000483 ! epithelium intersection_of: adjacent_to UBERON:0002519 ! otolithic part of statoconial membrane @@ -222204,8 +222339,8 @@ relationship: part_of UBERON:0016618 ! baleen feeding system id: UBERON:0016621 name: lunge feeding organ def: "A fibrous capsule located between the jaws of rorqual whales that contains a gelatinous substance and papillae bearing mechanorecaptors." [http://www.ncbi.nlm.nih.gov/pubmed/22622577] +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000020 ! sense organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0013765 ! digestive system element relationship: has_part UBERON:0016630 ! neurovascular bundle relationship: only_in_taxon NCBITaxon:9765 ! Balaenopteridae @@ -222215,7 +222350,7 @@ relationship: part_of UBERON:0016618 ! baleen feeding system [Term] id: UBERON:0016622 name: lunge feeding organ papilla -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:2001995 ! papilla intersection_of: UBERON:2001995 ! papilla intersection_of: part_of UBERON:0016621 ! lunge feeding organ @@ -223069,7 +223204,6 @@ def: "A linear flat evelation on a tooth." [http://en.wikipedia.org/wiki/Dental_ synonym: "crista of tooth" EXACT [] synonym: "tooth ridge" EXACT [] xref: http://www.snomedbrowser.com/Codes/Details/245699009 -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:4100000 ! skeletal element projection relationship: part_of UBERON:0001091 ! calcareous tooth @@ -224506,7 +224640,6 @@ is_a: UBERON:0003458 ! neck bone intersection_of: UBERON:0002228 ! rib intersection_of: connected_to UBERON:0002413 ! cervical vertebra relationship: connected_to UBERON:0002413 ! cervical vertebra -relationship: never_in_taxon NCBITaxon:9606 {source="should be all Theria, see https://github.com/obophenotype/mouse-anatomy-ontology/issues/116"} ! Homo sapiens relationship: part_of UBERON:0005434 ! cervical region [Term] @@ -224517,7 +224650,6 @@ is_a: UBERON:0002228 ! rib intersection_of: UBERON:0002228 ! rib intersection_of: connected_to UBERON:0002414 ! lumbar vertebra relationship: connected_to UBERON:0002414 ! lumbar vertebra -relationship: never_in_taxon NCBITaxon:32525 ! Theria relationship: part_of RO:0002577 ! system [Term] @@ -224546,14 +224678,15 @@ relationship: produced_by UBERON:0009645 ! ampullary gland [Term] id: UBERON:0018149 name: angle of oral opening -comment: Serves as attachment site for zygomaticus major muscle +def: "The lateral limit of each lateral part of the oral fissure." [https://orcid.org/0000-0002-2825-0621, https://www.imaios.com/en/e-Anatomy/Anatomical-Parts/Angle-of-mouth] +comment: Serves as attachment site for zygomaticus major muscle. synonym: "angle of mouth" EXACT [FMA:77269] synonym: "mouth angle" EXACT [FMA:77269] xref: FMA:77269 xref: http://www.snomedbrowser.com/Codes/Details/263940002 xref: MFMO:0000145 is_a: CARO:0000000 ! anatomical entity -is_a: UBERON:0007651 ! anatomical junction +is_a: UBERON:0010000 ! multicellular anatomical structure relationship: part_of UBERON:0000166 {source="MFMO-modified"} ! oral opening [Term] @@ -224595,8 +224728,8 @@ synonym: "Shrapnell's membrane" EXACT [FMA:56721] xref: FMA:56721 xref: http://en.wikipedia.org/wiki/Pars_flaccida_of_tympanic_membrane xref: http://www.snomedbrowser.com/Codes/Details/279594005 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000064 ! organ part -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0002364 {source="FMA"} ! tympanic membrane [Term] @@ -224606,8 +224739,8 @@ synonym: "pars tensa (membrana tympanica)" EXACT [FMA:56722] synonym: "pars tensa membranae tympanicae" EXACT LATIN [FMA:56722, FMA:TA] xref: FMA:56722 xref: http://www.snomedbrowser.com/Codes/Details/362555006 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000064 ! organ part -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0002364 {source="FMA"} ! tympanic membrane [Term] @@ -224781,7 +224914,6 @@ xref: NCIT:C32834 is_a: UBERON:0001637 ! artery is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: branching_part_of UBERON:0001633 {gci_relation="part_of", gci_filler="NCBITaxon:9606", cases="15%", source="WP"} ! basilar artery relationship: branching_part_of UBERON:0009689 {gci_relation="part_of", gci_filler="NCBITaxon:9606", cases="85-100%", source="WP"} ! anterior inferior cerebellar artery relationship: connected_to UBERON:0009689 {subset="human_reference_atlas"} ! anterior inferior cerebellar artery @@ -224797,7 +224929,6 @@ synonym: "sweat gland of axilla" EXACT [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0000382 {source="ISBN:0123813611"} ! apocrine sweat gland intersection_of: UBERON:0001820 ! sweat gland intersection_of: part_of UBERON:0009472 ! axilla -relationship: never_in_taxon NCBITaxon:10088 {source="ISBN:0123813611"} ! Mus relationship: part_of UBERON:0009472 ! axilla [Term] @@ -224908,7 +225039,6 @@ is_a: UBERON:0008876 ! hypodermis skeletal muscle layer relationship: attaches_to UBERON:0000976 {gci_filler="NCBITaxon:9265", gci_relation="part_of", notes="in the opossum the panniculus carnosis attaches to the humerus", source="https://doi.org/10.2307/1373999", source="FEED:rd"} ! humerus relationship: deep_to UBERON:0013488 ! panniculus adiposus relationship: innervated_by UBERON:0001780 {source="FFED:cw"} ! spinal nerve -relationship: never_in_taxon NCBITaxon:9606 {notes="vestigial or barely detectable"} ! Homo sapiens relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: present_in_taxon NCBITaxon:9261 {notes="by contraction of various parts of the panniculus carnosus, the short-beaked echidna can change shape, the most characteristic shape change being achieved by rolling itself into a ball when threatened, so protecting its belly and presenting a defensive array of sharp spines"} @@ -225268,7 +225398,6 @@ is_a: UBERON:0003913 ! tooth-like structure intersection_of: UBERON:0003913 ! tooth-like structure intersection_of: capable_of_part_of GO:0035188 ! hatching relationship: capable_of_part_of GO:0035188 ! hatching -relationship: never_in_taxon NCBITaxon:9347 ! Eutheria [Term] id: UBERON:0018277 @@ -225560,11 +225689,13 @@ relationship: part_of UBERON:0000976 ! humerus [Term] id: UBERON:0018306 -name: bulge -def: "Expanded and swollen region of a surface that is otherwise relatively flat." [PHENOSCAPE:Nizar] +name: obsolete bulge +def: "OBSOLETE expanded and swollen region of a surface that is otherwise relatively flat" [PHENOSCAPE:Nizar] +comment: Term is redundant with UBERON:0010188 'protuberance' . subset: upper_level xref: UBERONTEMP:dfedeba6-f608-4adc-9e69-b1169f6b0fb3 -is_a: UBERON:0003102 ! surface structure +is_obsolete: true +replaced_by: UBERON:0010188 [Term] id: UBERON:0018307 @@ -225710,7 +225841,6 @@ name: fourth phalanx def: "Fourth most proximal phalanx in manual or pedal digits." [PHENOSCAPE:alex] xref: UBERONTEMP:a8b5fbe4-0d00-4464-97ee-81ffd58a44f8 is_a: UBERON:0003221 ! phalanx -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens [Term] id: UBERON:0018323 @@ -225719,7 +225849,6 @@ def: "Area on the otic capsule for the articulation of the hyoid." [PHENOSCAPE:a xref: UBERONTEMP:e1c1764a-61b5-4dce-8a59-7ca5a9de0a0b is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004905 ! articulation -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0004637 ! otic capsule [Term] @@ -225869,7 +225998,6 @@ def: "An embryonic fissure between the otic capsule and the arches which develop xref: UBERONTEMP:41980771-8a82-40d2-877e-3156cc80857b is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0006846 ! surface groove -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0004637 ! otic capsule [Term] @@ -225921,7 +226049,6 @@ relationship: part_of UBERON:0018345 ! stylar shelf id: UBERON:0018345 name: stylar shelf def: "The stylar shelf is an an expansion of the cingulum; it often bears small cusps (each with its own name...)." [http://animaldiversity.ummz.umich.edu/collections/mammal_anatomy/cheek_teeth_structure, PHENOSCAPE:curators] -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:4100000 ! skeletal element projection relationship: part_of UBERON:0013164 ! molariform tooth @@ -226170,7 +226297,6 @@ def: "A unit of the tectoral membrane that is shaped like string of flat, pearls xref: UBERONTEMP:caa10252-5f7e-4a55-a72c-cf7986a89363 is_a: UBERON:0000063 ! organ subunit is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: only_in_taxon NCBITaxon:8504 {source="ISBN:9780387714691"} ! Lepidosauria relationship: part_of UBERON:0002233 ! tectorial membrane of cochlea relationship: present_in_taxon NCBITaxon:35033 {source="ISBN:9780387714691"} @@ -227611,8 +227737,6 @@ def: "An opening of the otic duct within the inner ear. The recessus basilaris c synonym: "basilar papillar recess" EXACT [] is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0001846 ! internal ear [Term] @@ -228416,6 +228540,7 @@ xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1444 xref: NLX:98733 is_a: UBERON:0002616 ! regional part of brain is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: part_of UBERON:0003044 ! uncinate fasciculus relationship: part_of UBERON:0011299 {source="HBA"} ! white matter of telencephalon [Term] @@ -228710,7 +228835,6 @@ xref: http://linkedlifedata.com/resource/umls/id/C1882706 xref: MA:0003109 xref: NCIT:C60574 is_a: UBERON:0001817 {source="MA"} ! lacrimal gland -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens [Term] id: UBERON:0019325 @@ -228725,7 +228849,6 @@ xref: http://linkedlifedata.com/resource/umls/id/C1882664 xref: MA:0003110 xref: NCIT:C60564 is_a: UBERON:0001817 {source="MA"} ! lacrimal gland -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens [Term] id: UBERON:0019326 @@ -233689,7 +233812,6 @@ xref: http://www.snomedbrowser.com/Codes/Details/279843007 xref: MA:0003003 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001855 {source="MA"} ! cochlear duct of membranous labyrinth [Term] @@ -234971,8 +235093,8 @@ relationship: part_of UBERON:2000622 ! barbel id: UBERON:0034719 name: lip taste bud def: "A taste bud that is located on a lip." [http://orcid.org/0000-0002-6601-2165, http://www.ncbi.nlm.nih.gov/pubmed/11921337] +is_a: UBERON:0001727 ! taste bud is_a: UBERON:0013765 ! digestive system element -is_a: UBERON:0034717 ! integumental taste bud intersection_of: UBERON:0001727 ! taste bud intersection_of: part_of UBERON:0001833 ! lip relationship: part_of UBERON:0001833 ! lip @@ -235379,7 +235501,7 @@ relationship: part_of UBERON:0008200 ! forehead [Term] id: UBERON:0034767 name: buccal vestibule -def: "The buccal vestibule is the space external to teeth and gums and internal to lips and cheeks. The proportion of its walls formed by the lips varies according to species depending upon their feeding action. The horse like most herbivores has a relatively small opening. PPP The buccal vestibule opens to the outside rostrally via a U shaped slit the oral fissure. PPP When the mouth is closed the buccal vestibule and the mouth cavity proper connect via spaces between and behind the teeth. These allow free communication between the two sides of the vestibule. PPP Several salivary ducts open into the dorso caudal part of the vestibule: PPP Parotid gland - opens into the cheek on the small parotid papilla, opposite to the caudal part of upper 4 th premolar teeth PPP Zygomatic gland - the main duct opens in the caudal part of the upper 1 st molar tooth on a small papilla near the vestibular fornix PPP Submucous glands - minimal in number, confined to the lower lip and adjacent part of the cheek. Secretion occurs through about 10 openings located near the fornix of the vestibule." [MURDOCH:240] +def: "The buccal vestibule is the space external to teeth and gums and internal to lips and cheeks. The proportion of its walls formed by the lips varies according to species depending upon their feeding action. The horse like most herbivores has a relatively small opening. The buccal vestibule opens to the outside rostrally via a U shaped slit the oral fissure. When the mouth is closed the buccal vestibule and the mouth cavity proper connect via spaces between and behind the teeth. These allow free communication between the two sides of the vestibule. Several salivary ducts open into the dorso caudal part of the vestibule: Parotid gland - opens into the cheek on the small parotid papilla, opposite to the caudal part of upper 4 th premolar teeth. Zygomatic gland - the main duct opens in the caudal part of the upper 1 st molar tooth on a small papilla near the vestibular fornix. Submucous glands - minimal in number, confined to the lower lip and adjacent part of the cheek. Secretion occurs through about 10 openings located near the fornix of the vestibule." [MURDOCH:240] xref: FMA:289320 xref: MURDOCH:240 is_a: CARO:0000000 ! anatomical entity @@ -236413,6 +236535,7 @@ id: UBERON:0034923 name: disconnected anatomical group def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] xref: CARO:0020000 +xref: FBbt:00007276 is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity relationship: composed_primarily_of UBERON:0000061 ! anatomical structure relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure @@ -236582,7 +236705,6 @@ synonym: "gill bar" RELATED [] is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0004765 ! skeletal element is_a: UBERON:0013765 ! digestive system element -relationship: never_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: only_in_taxon NCBITaxon:33511 ! Deuterostomia relationship: part_of UBERON:0001042 ! chordate pharynx relationship: present_in_taxon NCBITaxon:117569 ! Hyperoartia @@ -236660,7 +236782,6 @@ property_value: dc-contributor https://github.com/cerivs property_value: dc-contributor https://github.com/cmungall property_value: dc-contributor https://github.com/michaelerice relationship: has_part CL:0010015 ! coronet cell -relationship: never_in_taxon NCBITaxon:32523 ! Tetrapoda relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0001898 ! hypothalamus relationship: present_in_taxon NCBITaxon:8022 {source="http://www.ncbi.nlm.nih.gov/pubmed/4115676"} @@ -237508,7 +237629,6 @@ id: UBERON:0035045 name: parotid gland intralobular duct def: "Any of the tubular canals of the parotid gland located within the parenchymal (secretory) tissue i.e. within lobules; both intercalated and striated (secretory) ducts are intralobular ducts." [MP:0013746] is_a: UBERON:0001837 ! duct of salivary gland -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0014719 ! intralobular duct intersection_of: UBERON:0014719 ! intralobular duct intersection_of: part_of UBERON:0001831 ! parotid gland @@ -237538,7 +237658,6 @@ relationship: part_of UBERON:0001831 ! parotid gland id: UBERON:0035048 name: parotid gland excretory duct def: "Any of the interlobular excretory ducts of the parotid gland which are found in the connective tissue septa and formed by the union of several intralobular striated (secretory) ducts; ultimately, the excretory ducts of the parotid gland coalesce and form a single main excretory duct (Stensen's duct) that opens into the oral cavity; excretory ducts do not change the secretory product." [MP:0013750] -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0035049 ! excretory duct of salivary gland intersection_of: UBERON:0035050 ! excretory duct intersection_of: part_of UBERON:0001831 ! parotid gland @@ -237761,7 +237880,6 @@ is_a: UBERON:0003897 ! axial muscle is_a: UBERON:0035091 {source="http://www.ncbi.nlm.nih.gov/pubmed/22753107"} ! extrinsic post-anal tail muscle relationship: has_muscle_insertion UBERON:0003861 ! neural arch relationship: has_muscle_origin UBERON:0001076 ! neural spine -relationship: never_in_taxon NCBITaxon:9606 {source="cjm"} ! Homo sapiens relationship: part_of UBERON:0006071 ! caudal region relationship: present_in_taxon NCBITaxon:28376 @@ -238203,7 +238321,8 @@ synonym: "ossicle element" BROAD [EMAPA:17824, http://en.wikipedia.org/wiki/Audi synonym: "ossicle element of ear" RELATED [] synonym: "ossicle element of inner ear" RELATED [] synonym: "ossicular chain element" RELATED PLURAL [] -is_a: UBERON:0010313 ! neural crest-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010363 ! endochondral element relationship: contributes_to_morphology_of UBERON:0001756 ! middle ear relationship: develops_from UBERON:0003099 {source="http://www.ncbi.nlm.nih.gov/pubmed/11237469", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! cranial neural crest @@ -238872,8 +238991,7 @@ xref: http://en.wikipedia.org/wiki/Posterior_external_jugular_vein xref: http://linkedlifedata.com/resource/umls/id/C0226546 xref: http://www.snomedbrowser.com/Codes/Details/59579009 xref: NCIT:C33360 -is_a: UBERON:0003502 ! neck blood vessel -is_a: UBERON:0009141 ! craniocervical region vein +is_a: UBERON:0001638 ! vein relationship: part_of UBERON:0001101 ! external jugular vein relationship: tributary_of UBERON:0001101 ! external jugular vein @@ -240279,8 +240397,6 @@ xref: TAO:0000235 xref: ZFA:0000235 is_a: UBERON:0006569 {source="ZFA"} ! diencephalic nucleus is_a: UBERON:0035568 ! superficial pretectal nucleus -relationship: never_in_taxon NCBITaxon:27686 {source="ISBN:0471888893"} ! Erpetoichthys -relationship: never_in_taxon NCBITaxon:7900 {source="ISBN:0471888893"} ! Acipenseridae relationship: only_in_taxon NCBITaxon:32443 ! Teleostei relationship: part_of UBERON:2000687 {source="ZFA"} ! superficial pretectum @@ -240323,7 +240439,6 @@ xref: ZFA:0000635 is_a: UBERON:0014450 ! pretectal nucleus intersection_of: UBERON:0000125 ! neural nucleus intersection_of: part_of UBERON:2000183 ! central pretectum -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:2000183 ! central pretectum relationship: present_in_taxon NCBITaxon:118040 {source="ISBN:0471888893"} ! Squalomorphii relationship: present_in_taxon NCBITaxon:7898 {source="ISBN:0471888893"} ! Actinopterygii @@ -240348,7 +240463,6 @@ def: "Any nucleus found in the superficial pretectum." [http://orcid.org/0000-00 is_a: UBERON:0014450 ! pretectal nucleus intersection_of: UBERON:0000125 ! neural nucleus intersection_of: part_of UBERON:2000687 ! superficial pretectum -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:2000687 ! superficial pretectum relationship: present_in_taxon NCBITaxon:118040 {src="ISBN:0471888893"} ! Squalomorphii @@ -240364,7 +240478,6 @@ xref: TAO:0000601 xref: ZFA:0000601 is_a: UBERON:0006569 ! diencephalic nucleus is_a: UBERON:0014450 ! pretectal nucleus -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0001944 ! pretectal region relationship: part_of UBERON:2000293 {source="ZFA"} ! synencephalon relationship: present_in_taxon NCBITaxon:118040 {src="ISBN:0471888893"} ! Squalomorphii @@ -240593,6 +240706,11 @@ synonym: "ophthalmic part of trigeminal ganglion" RELATED [] synonym: "profundal ganglion" NARROW SENSU [] is_a: UBERON:0001714 ! cranial ganglion is_a: UBERON:0010313 ! neural crest-derived structure +relationship: develops_from UBERON:0000033 ! head +relationship: develops_from UBERON:0000153 ! anterior region of body +relationship: develops_from UBERON:0007811 ! craniocervical region +relationship: develops_from UBERON:0013701 ! main body axis +relationship: develops_from UBERON:0013702 ! body proper relationship: develops_from UBERON:0035597 ! profundal placode relationship: immediate_transformation_of UBERON:0035597 ! profundal placode relationship: part_of UBERON:0001675 ! trigeminal ganglion @@ -240606,6 +240724,11 @@ synonym: "ophthalmic ganglion" NARROW SENSU [] synonym: "profundal ganglion" NARROW SENSU [] is_a: UBERON:0001714 ! cranial ganglion is_a: UBERON:0010313 ! neural crest-derived structure +relationship: develops_from UBERON:0000033 ! head +relationship: develops_from UBERON:0000153 ! anterior region of body +relationship: develops_from UBERON:0007811 ! craniocervical region +relationship: develops_from UBERON:0013701 ! main body axis +relationship: develops_from UBERON:0013702 ! body proper relationship: develops_from UBERON:0035598 ! maxillomandibular placode relationship: immediate_transformation_of UBERON:0035598 ! maxillomandibular placode relationship: part_of UBERON:0001675 ! trigeminal ganglion @@ -240648,7 +240771,6 @@ synonym: "cartilago meatus acustici" EXACT [FMA:TA] synonym: "external acoustic meatus cartilage" EXACT [FMA:61298] xref: FMA:61298 is_a: UBERON:0004119 ! endoderm-derived structure -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034944 ! zone of organ intersection_of: UBERON:0034944 ! zone of organ intersection_of: part_of UBERON:0001352 ! external acoustic meatus @@ -240665,7 +240787,6 @@ synonym: "dorsal nerve cord" NARROW [WBbt:0006750] xref: WBbt:0006750 is_a: UBERON:0011215 {source="cjm"} ! central nervous system cell part cluster relationship: intersects_midsagittal_plane_of UBERON:0001137 ! dorsum -relationship: never_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001137 ! dorsum [Term] @@ -240985,7 +241106,6 @@ def: "The anterior facial vein receives a branch of considerable size, the deep xref: FMA:50916 xref: http://en.wikipedia.org/wiki/Deep_facial_vein is_a: UBERON:0003496 ! head blood vessel -is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0009141 ! craniocervical region vein relationship: part_of UBERON:0001653 ! facial vein relationship: tributary_of UBERON:0001653 ! facial vein @@ -240997,7 +241117,6 @@ synonym: "anterior parotid vein" EXACT [FMA:50919] synonym: "parotid branch of facial vein" EXACT [FMA:50919] xref: FMA:50919 is_a: UBERON:0003496 ! head blood vessel -is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0009141 ! craniocervical region vein intersection_of: UBERON:0001638 ! vein intersection_of: drains UBERON:0001831 ! parotid gland @@ -241014,7 +241133,6 @@ xref: http://linkedlifedata.com/resource/umls/id/C1711319 xref: MA:0002116 xref: NCIT:C52687 is_a: UBERON:0003496 ! head blood vessel -is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0009141 ! craniocervical region vein relationship: part_of UBERON:0001653 ! facial vein relationship: tributary_of UBERON:0001653 ! facial vein @@ -241435,7 +241553,6 @@ def: "The dark, nonstriated, V-shaped band (ridge) found on the underside of the synonym: "Hensen's stripe" EXACT [MGI:anna] is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005764 {source="cjm"} ! acellular membrane -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: adjacent_to UBERON:0002233 ! tectorial membrane of cochlea relationship: part_of UBERON:0001855 {source="cjm"} ! cochlear duct of membranous labyrinth @@ -241853,7 +241970,6 @@ def: "A ridge of bone connecting left and right orbital margins located beneath synonym: "infra-orbital bridge" EXACT [] is_a: UBERON:0005913 ! zone of bone organ relationship: connects UBERON:0001697 ! orbit of skull -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: part_of UBERON:0003129 ! skull relationship: present_in_taxon NCBITaxon:8499 @@ -242494,7 +242610,6 @@ name: Kimura membrane def: "The thickening of the lower surface of the tectorial membrane into which the hair bundles of the outer hair cells are embedded." [http://www.ncbi.nlm.nih.gov/pubmed/18797289, https://github.com/obophenotype/mammalian-phenotype-ontology/issues/2141, https://github.com/obophenotype/uberon/issues/1200, MGI:smith] is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005764 {source="cjm"} ! acellular membrane -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0002233 ! tectorial membrane of cochlea [Term] @@ -243226,7 +243341,6 @@ synonym: "vena aqueductus vestibuli" EXACT LATIN [FMA:TA] synonym: "vestibular aqueduct vein" EXACT [FMA:52367] xref: FMA:52367 is_a: UBERON:0003496 ! head blood vessel -is_a: UBERON:0003502 ! neck blood vessel is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0009141 ! craniocervical region vein relationship: part_of UBERON:0001641 ! transverse sinus @@ -243297,7 +243411,6 @@ name: orovelar muscle is_a: CARO:0000003 is_a: UBERON:0001630 ! muscle organ relationship: attaches_to UBERON:0013653 {comment="to be checked"} ! velar skeleton -relationship: never_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: only_in_taxon NCBITaxon:89593 ! Craniata relationship: part_of RO:0002577 ! system @@ -243509,8 +243622,8 @@ synonym: "sulcus auriculae anterior" RELATED [http://en.wikipedia.org/wiki/Incis xref: FMA:61175 xref: http://en.wikipedia.org/wiki/Incisura_anterior_auris xref: http://www.snomedbrowser.com/Codes/Details/362542005 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0006846 ! surface groove -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0006846 ! surface groove intersection_of: adjacent_to UBERON:0010887 ! tragus intersection_of: adjacent_to UBERON:0016467 ! antitragus @@ -243621,7 +243734,6 @@ def: "A notochord that has persisted beyond the embryonic stage." [UBERON:cjm] is_a: UBERON:0002328 ! notochord intersection_of: UBERON:0002328 ! notochord intersection_of: part_of UBERON:0009953 ! post-embryonic organism -relationship: never_in_taxon NCBITaxon:32524 ! Amniota relationship: part_of UBERON:0009953 ! post-embryonic organism relationship: present_in_taxon NCBITaxon:118072 ! Coelacanthimorpha relationship: present_in_taxon NCBITaxon:7737 ! Branchiostoma @@ -243731,7 +243843,6 @@ synonym: "zone of organ of corti" RELATED [] xref: http://www.snomedbrowser.com/Codes/Details/361065006 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005764 ! acellular membrane -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0005764 ! acellular membrane intersection_of: part_of UBERON:0002226 ! basilar membrane of cochlea relationship: part_of UBERON:0002226 ! basilar membrane of cochlea @@ -244042,7 +244153,6 @@ def: "A mucosa that is part of a lip region [Automatically generated definition] synonym: "labial mucosa" EXACT [UBERON:cjm] xref: NCIT:C12226 is_a: UBERON:0003729 ! mouth mucosa -is_a: UBERON:0013754 ! integumentary system layer intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001833 ! lip relationship: part_of UBERON:0001833 ! lip @@ -244270,7 +244380,6 @@ id: UBERON:0036655 name: wall of cerebral aqueduct xref: FMA:242774 is_a: UBERON:0005358 {source="FMA"} ! ventricle of nervous system -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0036661 ! wall of ventricular system of brain intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0002289 ! midbrain cerebral aqueduct @@ -244387,7 +244496,6 @@ synonym: "membranous labyrinth wall" EXACT [FMA:79837] xref: FMA:79837 is_a: UBERON:0000060 {source="FMA"} ! anatomical wall is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001849 ! membranous labyrinth relationship: part_of UBERON:0001849 {source="FMA"} ! membranous labyrinth @@ -245674,9 +245782,10 @@ is_a: UBERON:0037531 {source="FMA"} ! intestinal lymph node [Term] id: UBERON:0039169 name: anterior intercostal artery +def: "The anterior intercostal branches of internal thoracic artery supply the upper five or six intercostal spaces." [https://en.wikipedia.org/wiki/Intercostal_arteries] synonym: "intercostal branch of internal thoracic artery" EXACT [FMA:10641] xref: FMA:10641 -is_a: UBERON:0004573 ! systemic artery +is_a: UBERON:0005612 ! intercostal artery relationship: part_of UBERON:0002456 {source="FMA"} ! internal thoracic artery [Term] @@ -245687,6 +245796,24 @@ xref: FMA:10648 is_a: UBERON:0004573 ! systemic artery relationship: part_of UBERON:0002456 {source="FMA"} ! internal thoracic artery +[Term] +id: UBERON:0039175 +name: subarachnoid space of brain +xref: FMA:322073 +is_a: UBERON:0000315 {source="FMA"} ! subarachnoid space +intersection_of: UBERON:0000315 ! subarachnoid space +intersection_of: part_of UBERON:0000955 ! brain +relationship: part_of UBERON:0000955 ! brain + +[Term] +id: UBERON:0039176 +name: subarachnoid space of spinal cord +xref: FMA:322074 +is_a: UBERON:0000315 {source="FMA"} ! subarachnoid space +intersection_of: UBERON:0000315 ! subarachnoid space +intersection_of: part_of UBERON:0002240 ! spinal cord +relationship: part_of UBERON:0002240 ! spinal cord + [Term] id: UBERON:0039185 name: accessory vertebral vein @@ -245711,8 +245838,7 @@ id: UBERON:0039187 name: suprascapular vein def: "The suprascapular vein is a vein running above the scapula. It empties into the external jugular vein." [https://en.wikipedia.org/wiki/Suprascapular_vei] xref: FMA:14319 -is_a: UBERON:0003502 ! neck blood vessel -is_a: UBERON:0009141 ! craniocervical region vein +is_a: UBERON:0001638 ! vein relationship: part_of UBERON:0001101 ! external jugular vein relationship: tributary_of UBERON:0001101 {source="FMA"} ! external jugular vein @@ -245957,13 +246083,145 @@ union_of: UBERON:0006656 ! deep dorsal vein of penis union_of: UBERON:0039421 ! superficial dorsal vein of penis relationship: part_of UBERON:0000989 ! penis +[Term] +id: UBERON:0039835 +name: posterior intercostal artery +is_a: UBERON:0005612 ! intercostal artery + +[Term] +id: UBERON:0039838 +name: seventh anterior intercostal artery +xref: FMA:10649 +is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery +relationship: part_of UBERON:0006632 {source="FMA"} ! musculo-phrenic artery + +[Term] +id: UBERON:0039839 +name: eighth anterior intercostal artery +xref: FMA:10650 +is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery +relationship: part_of UBERON:0006632 {source="FMA"} ! musculo-phrenic artery + +[Term] +id: UBERON:0039840 +name: ninth anterior intercostal artery +xref: FMA:10651 +is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery +relationship: part_of UBERON:0006632 {source="FMA"} ! musculo-phrenic artery + +[Term] +id: UBERON:0039841 +name: first anterior intercostal artery +synonym: "first intercostal branch of internal thoracic artery" EXACT [FMA:10652] +xref: FMA:10652 +is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery +relationship: part_of UBERON:0002456 {source="FMA"} ! internal thoracic artery + +[Term] +id: UBERON:0039842 +name: second anterior intercostal artery +synonym: "second intercostal branch of internal thoracic artery" EXACT [FMA:10653] +xref: FMA:10653 +is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery +relationship: part_of UBERON:0002456 {source="FMA"} ! internal thoracic artery + +[Term] +id: UBERON:0039843 +name: third anterior intercostal artery +synonym: "third intercostal branch of internal thoracic artery" EXACT [FMA:10654] +xref: FMA:10654 +is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery +relationship: part_of UBERON:0002456 {source="FMA"} ! internal thoracic artery + +[Term] +id: UBERON:0039844 +name: fourth anterior intercostal artery +synonym: "fourth intercostal branch of internal thoracic artery" EXACT [FMA:10655] +xref: FMA:10655 +is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery +relationship: part_of UBERON:0002456 {source="FMA"} ! internal thoracic artery + +[Term] +id: UBERON:0039845 +name: fifth anterior intercostal artery +synonym: "fifth intercostal branch of internal thoracic artery" EXACT [FMA:10656] +xref: FMA:10656 +is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery +relationship: part_of UBERON:0002456 {source="FMA"} ! internal thoracic artery + +[Term] +id: UBERON:0039846 +name: sixth anterior intercostal artery +synonym: "sixth intercostal branch of internal thoracic artery" EXACT [FMA:10657] +xref: FMA:10657 +is_a: UBERON:0039169 {source="FMA"} ! anterior intercostal artery +relationship: part_of UBERON:0002456 {source="FMA"} ! internal thoracic artery + +[Term] +id: UBERON:0039847 +name: suprascapular artery +synonym: "transverse scapular artery" EXACT [FMA:10663] +xref: FMA:10663 +is_a: UBERON:0004573 ! systemic artery +relationship: part_of UBERON:0039260 {source="FMA"} ! thyrocervical artery + +[Term] +id: UBERON:0039848 +name: anterior external vertebral venous plexus +xref: FMA:10787 +is_a: UBERON:0039258 {source="FMA"} ! external vertebral venous plexus + +[Term] +id: UBERON:0039849 +name: posterior external vertebral venous plexus +xref: FMA:12852 +is_a: UBERON:0039258 {source="FMA"} ! external vertebral venous plexus + +[Term] +id: UBERON:0039850 +name: left anterior segmental artery +synonym: "anterior bronchopulmonary segment of left pulmonary artery" EXACT [FMA:13279] +synonym: "anterior segmental artery of left lung" EXACT [FMA:13279] +synonym: "anterior segmental artery of left upper lobe" EXACT [FMA:13279] +xref: FMA:13279 + +[Term] +id: UBERON:0039851 +name: apicoposterior segmental artery +synonym: "apicoposterior artery of left lung" EXACT [FMA:13281] +synonym: "apicoposterior bronchopulmonary segment of left pulmonary artery" EXACT [FMA:13281] +synonym: "left apicoposterior pulmonary artery" EXACT [FMA:13281] +xref: FMA:13281 +is_a: UBERON:0039262 {source="FMA"} ! segmental pulmonary artery + +[Term] +id: UBERON:0039856 +name: right ovarian vein +def: "Ovarian vein, each instance of which is a tributary of some inferior vena cava that drains the right pampiniform plexus of some broad ligament." [FMA:14342] +xref: FMA:14342 +is_a: UBERON:0001145 {source="FMA"} ! ovarian vein +intersection_of: UBERON:0001145 ! ovarian vein +intersection_of: drains UBERON:0002118 ! right ovary +relationship: drains UBERON:0002118 ! right ovary +relationship: part_of UBERON:0001072 ! posterior vena cava +relationship: tributary_of UBERON:0001072 {source="FMA"} ! posterior vena cava + +[Term] +id: UBERON:0039857 +name: left ovarian vein +def: "Ovarian vein, each instance of which is a tributary of some left renal vein that drains the left pampiniform plexus of some broad ligament." [FMA:14347] +xref: FMA:14347 +is_a: UBERON:0001145 {source="FMA"} ! ovarian vein +intersection_of: UBERON:0001145 ! ovarian vein +intersection_of: drains UBERON:0002119 ! left ovary +relationship: drains UBERON:0002119 ! left ovary + [Term] id: UBERON:1000000 name: chin ventral margin def: "Subdivision of the head consisting of the area along the lower edge of the chin." [https://github.com/obophenotype/uberon/issues/34, UBERON:EJS] subset: phenotype_rcn is_a: UBERON:0001444 ! subdivision of head -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest property_value: dc-contributor https://github.com/cmungall property_value: dc-contributor https://github.com/seger relationship: part_of UBERON:0008199 ! chin @@ -246020,9 +246278,9 @@ relationship: part_of UBERON:0001691 ! external ear [Term] id: UBERON:1000005 name: external ear margin -def: "Anatomical junction consisting of the area along the edge of the external ear." [https://github.com/obophenotype/uberon/issues/34, UBERON:EJS] +def: "Area along the edge of the external ear." [https://github.com/obophenotype/uberon/issues/34, https://orcid.org/0000-0002-2825-0621, UBERON:EJS] subset: phenotype_rcn -is_a: UBERON:0007651 ! anatomical junction +is_a: UBERON:0010000 ! multicellular anatomical structure property_value: dc-contributor https://github.com/cmungall property_value: dc-contributor https://github.com/seger relationship: part_of UBERON:0001691 ! external ear @@ -246044,7 +246302,7 @@ id: UBERON:1000007 name: forehead protuberance def: "A bulge, knob, or swelling that protrudes from the forehead." [https://github.com/obophenotype/uberon/issues/34, UBERON:EJS] subset: phenotype_rcn -is_a: UBERON:0001444 ! subdivision of head +is_a: UBERON:0010188 ! protuberance property_value: dc-contributor https://github.com/cmungall property_value: dc-contributor https://github.com/seger relationship: part_of UBERON:0008200 ! forehead @@ -246448,7 +246706,6 @@ def: "The anterior round region of the yolk cell present after the yolk extensio synonym: "yolk ball" EXACT [ZFIN:ZDB-PUB-961014-576] xref: ZFA:0000006 is_a: UBERON:0000475 ! organism subdivision -relationship: never_in_taxon NCBITaxon:40674 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Mammalia relationship: part_of UBERON:2000084 ! yolk [Term] @@ -246490,7 +246747,6 @@ synonym: "median fin-fold" RELATED [TAO:0000040] synonym: "median fin-folds" RELATED PLURAL [TAO:0000040] xref: ZFA:0000040 is_a: UBERON:0003102 ! surface structure -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda [Term] id: UBERON:2000043 @@ -246661,7 +246917,6 @@ def: "Region of the median fin fold that develops into the dorsal fin." [ZFIN:cu synonym: "dorsal fin-fold" EXACT [TAO:0000102] xref: ZFA:0000102 is_a: UBERON:0000481 ! multi-tissue structure -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda relationship: part_of UBERON:2000040 ! median fin fold [Term] @@ -246763,7 +247018,6 @@ def: "Brightly refractile stone-like organ within the otic vesicle and positione synonym: "immature otoliths" EXACT PLURAL [TAO:0000139] is_a: UBERON:0003103 ! compound organ is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0003051 ! ear vesicle [Term] @@ -247101,7 +247355,6 @@ synonym: "pleurethmoïde" EXACT [PSPUB:0000134] synonym: "éthmoïde latéral" EXACT [PSPUB:0000164] xref: ZFA:0000226 is_a: UBERON:0002513 ! endochondral bone -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011164 ! neurocranium bone is_a: UBERON:4300111 ! lateral ethmoid element relationship: composed_primarily_of UBERON:0002481 ! bone tissue @@ -247622,7 +247875,6 @@ name: basioccipital posterodorsal region def: "Endochondral bone which is the posterodorsal region of the basioccipital bone." [TAO:wd] xref: ZFA:0001598 is_a: UBERON:0002513 ! endochondral bone -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011164 ! neurocranium bone relationship: part_of UBERON:0001692 ! basioccipital bone relationship: part_of UBERON:2001620 ! lagenar capsule @@ -247666,7 +247918,6 @@ name: exoccipital posteroventral region def: "Endochondral bone which is the posterodorsal region of the exoccipital bone." [TAO:wd] xref: ZFA:0001597 is_a: UBERON:0002513 ! endochondral bone -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011164 ! neurocranium bone relationship: part_of UBERON:0001693 ! exoccipital bone relationship: part_of UBERON:2001620 ! lagenar capsule @@ -247709,7 +247960,6 @@ synonym: "gill-raker" EXACT [TAO:0000356] synonym: "gillraker" EXACT [TAO:0000356] xref: ZFA:0000356 is_a: UBERON:0008907 ! dermal bone -relationship: never_in_taxon NCBITaxon:40674 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Mammalia relationship: part_of UBERON:0005886 ! post-hyoid pharyngeal arch skeleton [Term] @@ -247976,7 +248226,6 @@ synonym: "alisphenoid" EXACT [TAO:0000419] synonym: "pterosphenoids" EXACT PLURAL [TAO:0000419] xref: ZFA:0000419 is_a: UBERON:0002513 ! endochondral bone -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011164 ! neurocranium bone relationship: develops_from UBERON:2001515 ! taenia marginalis posterior relationship: part_of UBERON:0002241 ! chondrocranium @@ -248134,7 +248383,6 @@ synonym: "parurohyal" EXACT [TAO:Arratia_Schultze_1990] synonym: "urohyal" EXACT [PSPUB:0000164] xref: ZFA:0000452 is_a: UBERON:0008907 ! dermal bone -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda relationship: part_of UBERON:0003113 ! dermatocranium relationship: part_of UBERON:0011153 ! ventral hyoid arch skeleton @@ -248752,7 +249000,6 @@ synonym: "autosphenotic" EXACT [TAO:0000587] synonym: "sphenotics" EXACT PLURAL [TAO:0000587] xref: ZFA:0000587 is_a: UBERON:0002513 ! endochondral bone -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011164 ! neurocranium bone relationship: develops_from UBERON:0006605 ! tectum synoticum relationship: develops_from UBERON:2001515 ! taenia marginalis posterior @@ -248954,6 +249201,7 @@ def: "Surface structure which is a tactile structure found in the branchial regi synonym: "barbels" EXACT PLURAL [TAO:0000622] synonym: "barble" EXACT [TAO:0000622] xref: ZFA:0000622 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:3000972 ! head external integument structure relationship: develops_from UBERON:2005119 ! barbel primordium relationship: part_of UBERON:0000033 ! head @@ -249364,6 +249612,7 @@ synonym: "pharyngeal teeth" EXACT [TAO:0000694] xref: ZFA:0000694 is_a: CARO:0000003 is_a: UBERON:0001091 ! calcareous tooth +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001091 ! calcareous tooth intersection_of: attaches_to UBERON:2001239 ! ceratobranchial 5 bone relationship: attaches_to UBERON:2001239 ! ceratobranchial 5 bone @@ -252140,7 +252389,6 @@ comment: Vertebra 1-4, and sometimes vertebra 5 in some catfishes, are part of t xref: ZFA:0001188 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000477 ! anatomical cluster -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda relationship: part_of UBERON:0001130 ! vertebral column [Term] @@ -253124,7 +253372,6 @@ name: post-Weberian supraneural def: "Posterior to the Weberian apparatus, otophysan supraneurals form as median, unpaired, rod- or platelike elements, as in other actinopterygians." [ZFIN:curator] xref: ZFA:0001397 is_a: UBERON:2000442 ! supraneural bone -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda [Term] id: UBERON:2001403 @@ -253142,7 +253389,6 @@ name: preethmoid bone def: "Small rounded to egg-shaped cartilage bone that sits in an anterolateral depression on the prevomer. Articulates with the autopalatine in all cypriniforms." [ZFIN:curator] xref: ZFA:0001404 is_a: UBERON:0002513 ! endochondral bone -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011164 ! neurocranium bone relationship: develops_from UBERON:0011242 ! ethmoid cartilage relationship: part_of UBERON:0002241 ! chondrocranium @@ -253195,7 +253441,6 @@ synonym: "epioccipitals" EXACT PLURAL [TAO:0001412] xref: ZFA:0001412 is_a: UBERON:0002513 ! endochondral bone is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011164 ! neurocranium bone relationship: develops_from UBERON:0005410 ! cartilaginous otic capsule relationship: part_of UBERON:0002241 ! chondrocranium @@ -253359,7 +253604,6 @@ def: "A plate-like chondrogenic condensation within the pectoral fin, which subd synonym: "fin plate cartilage" EXACT [TAO:0001456] xref: ZFA:0001456 is_a: UBERON:0007390 ! pectoral appendage cartilage tissue -relationship: never_in_taxon NCBITaxon:40674 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Mammalia [Term] id: UBERON:2001457 @@ -254119,7 +254363,6 @@ name: lateral ethmoid palatine process def: "Lateral bony projection proximal to lateral ethmoid-palatine joint, and located anterior to orbital region and posterior to olfactory region." [TAO:wd] synonym: "antorbital process" RELATED [TAO:0001604] is_a: UBERON:0004530 ! bony projection -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:2000226 ! lateral ethmoid bone [Term] @@ -254227,7 +254470,7 @@ id: UBERON:2001615 name: sphenotic spine def: "Process of the sphenotic. The process may project antero-laterally or laterally or ventro-laterally and it has different development in different fish groups. The sphenotic spine is paired." [TAO:GA_TG] synonym: "sphenotic process" EXACT [TAO:0001615] -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:4100000 ! skeletal element projection relationship: part_of UBERON:2000587 ! sphenotic @@ -254237,7 +254480,7 @@ name: lateral ethmoid wing def: "Superficial and lateral bony projection anterior to orbital region. Sometimes with superficial ornamentation where in direct contact with skin." [TAO:wd] comment: Synonym of lateral ethmoid wing: lateral ethmoid ventral wing (characiforms). synonym: "lateral ethmoid ventral wing" EXACT [TAO:0001616] -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:4100000 ! skeletal element projection relationship: part_of UBERON:2000226 ! lateral ethmoid bone @@ -254600,7 +254843,7 @@ def: "Bony projection that extends from the mesethmoid anteriorly. Mesethmoid co synonym: "cornu" EXACT [TAO:0001675] synonym: "cornua" EXACT PLURAL [TAO:0001675] synonym: "cornuae" EXACT PLURAL [TAO:0001675] -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:4100000 ! skeletal element projection relationship: part_of UBERON:0011238 ! mesethmoid bone @@ -254666,7 +254909,7 @@ relationship: connects UBERON:0011238 ! mesethmoid bone id: UBERON:2001681 name: cornu mesial process def: "Bony projection that is mesially-directed and off the anteromedial corner of each mesethmoid cornu." [TAO:pem] -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:4100000 ! skeletal element projection relationship: part_of UBERON:2001675 ! mesethmoid cornu @@ -255083,7 +255326,7 @@ id: UBERON:2001733 name: mesethmoid ventral diverging lamella def: "Bony projection that is the posterolaterally oriented projection on the ventral region of the mesethmoid. Mesethmoid ventral diverging lamellae are paired and posteriorly contact the lateral ethmoid bones." [TAO:wd] comment: Reference: Weitzman 1962. -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:4100000 ! skeletal element projection relationship: part_of UBERON:0011238 ! mesethmoid bone @@ -255178,7 +255421,7 @@ def: "Bony projection located on the anteroventral region of the mesethmoid whic comment: Synonyms: mesethmoid lateral wing (Zanata and Vari 2005) lateral ethmoid wing (Weitzman 1962) premaxillary articular process (Fink and Fink 1996). synonym: "mesethmoid lateral wing" EXACT [TAO:0001747] synonym: "premaxillary articular process" EXACT [TAO:0001747] -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:4100000 ! skeletal element projection relationship: part_of UBERON:0011238 ! mesethmoid bone @@ -255456,7 +255699,7 @@ def: "Process that is part of the supraoccipital. It is a posteriorly directed a comment: The supraoccipital crest may be small and restricted to the dorsal part of the supraoccipital, or may be large and long and extending ventrally to the dorsal margin of the foramen magnum. The supraoccipital crest may be a large process extending above the skull roof in some teleostean subgroups. synonym: "supraoccipital process" EXACT [TAO:0001783] synonym: "supraoccipital spine" EXACT [TAO:0001783] -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:4100000 ! skeletal element projection relationship: part_of UBERON:0004747 ! supraoccipital bone @@ -256528,7 +256771,6 @@ id: UBERON:2001921 name: adipose eyelid def: "Surface structure that is a fleshy membrane covering part of the eye." [TAO:wd] is_a: UBERON:0003102 ! surface structure -relationship: never_in_taxon NCBITaxon:40674 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Mammalia relationship: part_of UBERON:0000033 ! head [Term] @@ -256584,7 +256826,6 @@ name: epioccipital posterior process def: "Process of the epioccipital that extends posteriorly, is laminar in form and is usually attached to Weberian apparatus." [TAO:wd] is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004530 ! bony projection -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:2001412 ! epiotic [Term] @@ -257214,7 +257455,6 @@ synonym: "anterior thorn of dorsal fin spine 2" EXACT [TAO:0002004] synonym: "anterior tooth of dorsal fin spine 2" EXACT [TAO:0002004] synonym: "dorsal fin spine 2 anterior dentation" EXACT [TAO:0002004] is_a: UBERON:0004529 ! anatomical projection -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda [Term] id: UBERON:2002005 @@ -257381,7 +257621,6 @@ id: UBERON:2002023 name: second preethmoid bone def: "Endochondral bone found between the preethmoid and maxilla." [TAO:wd] is_a: UBERON:0002513 ! endochondral bone -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011164 ! neurocranium bone is_a: UBERON:4300286 ! second preethmoid element relationship: develops_from UBERON:4300285 ! second preethmoid cartilage @@ -257640,7 +257879,6 @@ synonym: "opercular opening" EXACT [TAO:0002057] xref: ZFA:0005389 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000464 ! anatomical space -relationship: never_in_taxon NCBITaxon:40674 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Mammalia relationship: part_of UBERON:0001042 ! chordate pharynx [Term] @@ -257831,7 +258069,7 @@ is_a: UBERON:0002548 ! larva id: UBERON:2002080 name: spina occipitalis def: "Process that is a ventral projection from the supraoccipital that extends between the exoccipitals to the dorsal margin of the foramen magnum." [TAO:wd] -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:4100000 ! skeletal element projection relationship: part_of UBERON:0004747 ! supraoccipital bone @@ -258056,6 +258294,7 @@ relationship: part_of UBERON:0002028 ! hindbrain id: UBERON:2002108 name: buccal papilla def: "Papilla that is part of the mouth." [TAO:wd] +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:2001995 ! papilla relationship: part_of UBERON:0000165 ! mouth @@ -258202,7 +258441,6 @@ comment: Definition reference: Albert, JS and WL Fink. 2007. PHYLOGENETIC\nRELAT synonym: "hypural-opisthural rod" EXACT [TAO:0002129] is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000481 ! multi-tissue structure -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda relationship: part_of UBERON:0002090 ! postcranial axial skeleton [Term] @@ -258254,7 +258492,6 @@ name: anterior swim bladder bud def: "Portion of tissue that forms from the swim bladder epithelium at the anterior end of the swim bladder." [ZFIN:090511-18] xref: ZFA:0005337 is_a: UBERON:0000479 ! tissue -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda [Term] id: UBERON:2002147 @@ -258461,7 +258698,6 @@ synonym: "dorsal bar" RELATED [TAO:0002193] xref: ZFA:0001672 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001841 ! anterior semicircular canal relationship: part_of UBERON:0001842 ! posterior semicircular canal @@ -258575,7 +258811,6 @@ name: otic vesicle protrusion xref: ZFA:0001715 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0003051 ! ear vesicle [Term] @@ -258631,7 +258866,6 @@ name: pillar of the semicircular canal xref: ZFA:0001717 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001840 ! semicircular canal [Term] @@ -259024,7 +259258,6 @@ def: "Dermal bone that is an unpaired, scale-like structure. Arratia, G. 2009. I comment: temporarily relabeled 'fish scute' to distinguish from reptilian scute class. To DO: reconcile definitions for the two sets of classes. synonym: "ridge scale" EXACT [TAO:0002294] is_a: UBERON:0008907 ! dermal bone -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda relationship: part_of UBERON:0002416 ! integumental system [Term] @@ -259522,7 +259755,6 @@ def: "An elaborate set of vessels that branche off caudally from the anterior me synonym: "SBA" EXACT [TAO:0005089] xref: ZFA:0005089 is_a: UBERON:0001637 ! artery -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda [Term] id: UBERON:2005093 @@ -259538,7 +259770,6 @@ id: UBERON:2005097 name: caudal fin vasculature xref: ZFA:0005097 is_a: UBERON:0007304 ! appendage vasculature -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda [Term] id: UBERON:2005098 @@ -259546,7 +259777,6 @@ name: central ray artery def: "Positioned in the intraray mesenchym between the hemirays of the lepidotrichia,. Huang et al. 2003." [ZFIN:curator] xref: ZFA:0005098 is_a: UBERON:0007304 ! appendage vasculature -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda [Term] id: UBERON:2005099 @@ -259554,7 +259784,6 @@ name: ray vein def: "Lie flanking and just lateral to the fin ray, in the interray mesenchyme. Huang et al. 2003." [ZFIN:curator] xref: ZFA:0005099 is_a: UBERON:0007304 ! appendage vasculature -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda [Term] id: UBERON:2005100 @@ -259563,7 +259792,6 @@ def: "Vessels that travel between artery and veins or vein and vein in a single synonym: "intervessel comisures" EXACT PLURAL [TAO:0005100] xref: ZFA:0005100 is_a: UBERON:0007304 ! appendage vasculature -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda [Term] id: UBERON:2005101 @@ -259572,7 +259800,6 @@ def: "Vessels that travel between veins in adjacent rays." [ZFIN:curator] synonym: "interray vessels" EXACT PLURAL [TAO:0005101] xref: ZFA:0005101 is_a: UBERON:0007304 ! appendage vasculature -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda [Term] id: UBERON:2005102 @@ -259580,7 +259807,6 @@ name: presumptive median fin fold synonym: "presumptive median fin-fold" EXACT [TAO:0005102] xref: ZFA:0005102 is_a: UBERON:0006598 ! presumptive structure -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda [Term] id: UBERON:2005103 @@ -259764,7 +259990,6 @@ synonym: "third lobe" EXACT [TAO:0005174] xref: ZFA:0005174 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004119 ! endoderm-derived structure -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda relationship: part_of UBERON:0002107 ! liver [Term] @@ -260536,7 +260761,6 @@ xref: ZFA:0005316 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: develops_from UBERON:0005421 ! pectoral appendage apical ectodermal ridge -relationship: never_in_taxon NCBITaxon:32523 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Tetrapoda relationship: part_of UBERON:0005419 ! pectoral appendage bud [Term] @@ -260891,7 +261115,6 @@ name: common crus xref: ZFA:0005411 is_a: UBERON:0000058 ! duct is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:2005409 ! pars superior ear [Term] @@ -260909,7 +261132,6 @@ def: "Foramen in the inner ear." [ZFIN:curator] xref: ZFA:0005415 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005744 ! bone foramen -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001846 ! internal ear [Term] @@ -261271,6 +261493,7 @@ synonym: "ventral bar" EXACT [TAO:0007055] synonym: "ventral pillar" EXACT [TAO:0007055] synonym: "ventral piller of the semicircular canal" EXACT [TAO:0007055] xref: ZFA:0007055 +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:2002223 ! pillar of the semicircular canal relationship: develops_from UBERON:2001716 ! caudal principal ray 4 relationship: part_of UBERON:0001843 ! lateral semicircular canal @@ -262465,7 +262688,6 @@ id: UBERON:3000141 name: endolymphatic system is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001846 ! internal ear [Term] @@ -262551,7 +262773,8 @@ synonym: "otostapes" RELATED [UBERON:3000178] synonym: "pars otica columellae" RELATED [UBERON:3000178] synonym: "pseudooperculum" RELATED [UBERON:3000178] is_a: UBERON:0000064 ! organ part -is_a: UBERON:0010313 ! neural crest-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:3000408 ! pars media plectri [Term] @@ -263026,7 +263249,6 @@ id: UBERON:3000393 name: pars amphibiorum is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001854 ! saccule of membranous labyrinth [Term] @@ -263042,7 +263264,6 @@ id: UBERON:3000395 name: pars basilaris is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001854 ! saccule of membranous labyrinth [Term] @@ -263071,7 +263292,8 @@ synonym: "hyostapes" RELATED [UBERON:3000399] synonym: "medio-stapedial" RELATED [UBERON:3000399] synonym: "pars quadrata columellae" RELATED [UBERON:3000399] is_a: UBERON:0000064 ! organ part -is_a: UBERON:0010313 ! neural crest-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:3000443 ! plectral apparatus [Term] @@ -263093,7 +263315,6 @@ id: UBERON:3000405 name: pars inferior of labyrinth is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001846 ! internal ear [Term] @@ -263103,14 +263324,16 @@ def: "Plate-like structure that lies in the fenestra ovalis. It arises within th synonym: "operculum auris" RELATED [UBERON:3000406] synonym: "operculum fenestrae ovalis" RELATED [UBERON:3000406] is_a: UBERON:0000064 ! organ part -is_a: UBERON:0010313 ! neural crest-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:3000443 ! plectral apparatus [Term] id: UBERON:3000408 name: pars media plectri is_a: UBERON:0000064 ! organ part -is_a: UBERON:0010313 ! neural crest-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:3000443 ! plectral apparatus [Term] @@ -263134,7 +263357,6 @@ name: perilymphatic system def: "Consists of enlarged cistern against which the operculum and footplate of the columella rest in the oval window. Together with the endolymphatic systems comprises the membranous labryinth of the inner ear. Duellman and Trueb 1994." [PHENOSCAPE] is_a: UBERON:0001032 ! sensory system is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001846 ! internal ear [Term] @@ -263304,7 +263526,8 @@ synonym: "processus ascendens columellae" RELATED [UBERON:3000486] synonym: "processus dorsalis columellae" RELATED [UBERON:3000486] synonym: "processus superior columellae" RELATED [UBERON:3000486] synonym: "suprastapediale" RELATED [UBERON:3000486] -is_a: UBERON:0010313 ! neural crest-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:4100000 ! skeletal element projection relationship: part_of UBERON:3000399 ! pars externa plectri @@ -263435,7 +263658,6 @@ id: UBERON:3000538 name: recessus fenestrae ovalis is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:3000428 ! perilymphatic system [Term] @@ -263478,7 +263700,6 @@ name: septum semicircularium anterior def: "The anterior connective tissue partition between walls of otic capsule around which the membranous semicircular canals pass." [PHENOSCAPE] is_a: UBERON:0003037 ! septum is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001846 ! internal ear [Term] @@ -263487,7 +263708,6 @@ name: septum semicircularium laterale def: "The lateral connective tissue partition between walls of otic capsule around which the membranous semicircular canals pass." [PHENOSCAPE] is_a: UBERON:0003037 ! septum is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001846 ! internal ear [Term] @@ -263496,7 +263716,6 @@ name: septum semircularium posterior def: "The posterior connective tissue partition between walls of otic capsule around which the membranous semicircular canals pass." [PHENOSCAPE] is_a: UBERON:0003037 ! septum is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001846 ! internal ear [Term] @@ -263530,7 +263749,6 @@ id: UBERON:3000570 name: spatium sacculare is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:3000428 ! perilymphatic system [Term] @@ -263563,7 +263781,8 @@ synonym: "stapes" RELATED [UBERON:3000580] synonym: "stelidium" RELATED [UBERON:3000580] synonym: "stilus columellare" RELATED [UBERON:3000580] is_a: UBERON:0000064 ! organ part -is_a: UBERON:0010313 ! neural crest-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:3000408 ! pars media plectri [Term] @@ -263755,7 +263974,8 @@ relationship: part_of UBERON:3000492 ! processus infrafenestralis id: UBERON:3000648 name: crista praeopercularis def: "Synchondrotic or synostotic connection between the footplate of the pars media plectri and the ventral margin of the fenestra ovalis." [AAO:LAP] -is_a: UBERON:0010313 ! neural crest-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:4100000 ! skeletal element projection relationship: part_of UBERON:3000408 ! pars media plectri @@ -265377,6 +265597,7 @@ relationship: part_of UBERON:0002100 ! trunk id: UBERON:3000981 name: limb external integument structure def: "Dermal, epidermal, glandular and pigment structures of the limb integument." [AAO:EJS] +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:3000961 ! external integument structure intersection_of: UBERON:3000961 ! external integument structure intersection_of: part_of UBERON:0002101 ! limb @@ -265386,6 +265607,7 @@ relationship: part_of UBERON:0002101 ! limb id: UBERON:3000982 name: tail external integument structure def: "Dermal, epidermal, glandular and pigment structures of the tail integument." [AAO:EJS] +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:3000961 ! external integument structure intersection_of: UBERON:3000961 ! external integument structure intersection_of: part_of UBERON:0007812 ! post-anal tail @@ -265458,6 +265680,7 @@ is_a: UBERON:0010721 ! distal tarsal bone [Term] id: UBERON:3001003 name: cloacal fold +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:3000977 ! body external integument structure relationship: part_of UBERON:0000162 ! cloaca @@ -265974,8 +266197,8 @@ relationship: part_of UBERON:3000993 ! otic and occipital id: UBERON:3010144 name: odontoids def: "Toothlike processes found on the mandible of some anurans; can be formed by dentary or dentary + mentomeckelian bones; odontoids lack enamel and dentine present in true teeth." [AAO:EJS] +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000064 ! organ part -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001710 ! lower jaw region [Term] @@ -267810,7 +268033,6 @@ name: ramus anterior of CN VIII def: "Formed by fibers from the anterior semicircular canal and sacculus." [AAO:EJS] is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004529 ! anatomical projection -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001648 ! vestibulocochlear nerve [Term] @@ -267819,7 +268041,6 @@ name: ramus posterior of CN VIII def: "Composed of two rami: a short ventral ramus innervating the cochlea (lagena and papille basilar), and a long dorsal ramus innervating the posterior semicircular canal." [AAO:EJS] is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004529 ! anatomical projection -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001648 ! vestibulocochlear nerve [Term] @@ -270510,8 +270731,9 @@ is_obsolete: true [Term] id: UBERON:4200169 -name: process 2 +name: process 2 of entepicondyle def: "Process on the humerus of basal tetrapods, anterior to the entepicondyle and associated with subscapularis muscle (based on Coates 1996)." [PHENOSCAPE] +synonym: "process 2" BROAD [] is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:4100000 ! skeletal element projection relationship: part_of UBERON:0000976 ! humerus @@ -271127,7 +271349,6 @@ relationship: part_of UBERON:0000970 ! eye id: UBERON:4300006 name: scale row def: "A series of scales in alignment with each other along some axis of the body." [PHENOSCAPE:BF] -is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0000477 ! anatomical cluster property_value: dc-contributor https://orcid.org/0000-0003-3162-7490 relationship: has_part UBERON:0002542 ! scale @@ -271685,7 +271906,6 @@ name: tectorial restraint system def: "Tectorial restraint system is a type of ciliary restraint system for hair cells in the inner ear. In tectorial restraint systems, the tectorial membrane restrains the cilia of the hair cells by attaching either directly to ciliary tufts or indirectly through various kinds of fibrous structure (simple fibers, fibrous strands, finger-like processes, tectorial plates) [Phylogenetic Relationships of the Lizard Families: Essays Commemorating Charles L. Camp. 1988. Eds. R Estes, GK Pregill. Stanford University Press]." [PHENOSCAPE] is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest property_value: dc-contributor https://orcid.org/0000-0003-3162-7490 relationship: part_of UBERON:0001846 ! internal ear @@ -272492,7 +272712,7 @@ id: UBERON:4300249 name: lateral occipital foramen def: "Foramen that has the exoccipital as the anterior and dorsal rim. The occipital forms the anterior rim during early development. [database_cross_reference: GOC:cvs][database_cross_reference: https://orcid.org/0000-0002-2244-7917][database_cross_reference: ZFIN:ZDB-PUB-961014-192]." [ZFIN:ZDB-PUB-961014-192] xref: ZFA:0005892 -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0013685 ! foramen of skull relationship: part_of UBERON:0001693 ! exoccipital bone @@ -272594,7 +272814,6 @@ def: "Extension of the exoccipital that extends over the posttemporal fossa." [h synonym: "epiotic bridge" EXACT [] is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005913 ! zone of bone organ -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest property_value: dc-contributor https://orcid.org/0000-0003-3162-7490 relationship: part_of UBERON:2001412 ! epiotic @@ -273795,12 +274014,12 @@ consider: FBbt:00000000 [Term] id: UBERON:6000002 -name: panarthropod tagma -def: "The three main divisions of the whole organism formed from groups of segments." [FBC:gg] +name: arthropod tagma +def: "One of the main divisions of the whole organism of arthropods formed from groups of segments." [https://doi.org/10.1016/B978-0-12-385026-3.00024-3] +comment: Strictly speaking the term "tagma" cam be used for any metameric organism, however we follow the common usage which is to restrict the term to arthropods. xref: FBbt:00000002 -is_a: UBERON:6057001 ! insect anterior-posterior subdivision of organism -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: only_in_taxon NCBITaxon:88770 ! Panarthropoda +is_a: UBERON:0011676 ! subdivision of organism along main body axis +relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0000468 ! multicellular organism [Term] @@ -273819,7 +274038,6 @@ def: "Head segment derived from the second embryonic segment (between the labral synonym: "acron" RELATED [] xref: FBbt:00000005 is_a: UBERON:6000007 ! procephalic segment -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata relationship: only_in_taxon NCBITaxon:50557 {source="cjm"} ! Insecta [Term] @@ -273830,7 +274048,6 @@ xref: FBbt:00000006 is_a: UBERON:0000914 ! organismal segment intersection_of: UBERON:0000914 ! organismal segment intersection_of: part_of UBERON:0000033 ! head -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000033 ! head [Term] @@ -273843,7 +274060,6 @@ synonym: "preoral segment" EXACT [] synonym: "procephalon" RELATED [] xref: FBbt:00000007 is_a: UBERON:6000006 ! insect head segment -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000033 ! head [Term] @@ -273882,7 +274098,7 @@ id: UBERON:6000015 name: insect thorax def: "The main middle section of the insect body comprising three thoracic rings: the pro-, the meso- and the metathoraces which are more or less well fused and cask-like sometimes having on the upper lateral part one of two pairs of wings, while on the ventrolateral part each thoracic ring bears a pair of legs." [FlyBase:FBrf0166419] xref: FBbt:00000015 -is_a: UBERON:6000002 ! panarthropod tagma +is_a: UBERON:6000002 ! arthropod tagma relationship: only_in_taxon NCBITaxon:50557 ! Insecta [Term] @@ -273933,7 +274149,7 @@ id: UBERON:6000020 name: insect abdomen def: "The most posterior of the three tagma (UBERON:6000002)." [FlyBase:FBrf0166419] xref: FBbt:00000020 -is_a: UBERON:6000002 ! panarthropod tagma +is_a: UBERON:6000002 ! arthropod tagma relationship: only_in_taxon NCBITaxon:50557 ! Insecta [Term] @@ -273972,11 +274188,10 @@ is_a: UBERON:6007248 ! insect chorionic specialization [Term] id: UBERON:6000094 -name: clypeo-labral anlage in statu nascendi -synonym: "Asn Cly" RELATED [FBC:DOS] +name: obsolete clypeo-labral anlage in statu nascendi +comment: No need for such a specific term in Uberon. See https://github.com/obophenotype/uberon/issues/2154. xref: FBbt:00000094 -is_a: UBERON:6005413 ! insect anlage in statu nascendi -relationship: part_of FBbt:01000119 +is_obsolete: true [Term] id: UBERON:6000096 @@ -274070,8 +274285,8 @@ id: UBERON:6000137 name: embryonic tagma def: "Any tagma (UBERON:6000002) that is part of some embryo (UBERON:6000052)." [FBC:auto_generated_definition] xref: FBbt:00000137 -is_a: UBERON:6000002 ! panarthropod tagma -intersection_of: UBERON:6000002 ! panarthropod tagma +is_a: UBERON:6000002 ! arthropod tagma +intersection_of: UBERON:6000002 ! arthropod tagma intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo @@ -274288,7 +274503,6 @@ relationship: part_of UBERON:6001055 ! insect presumptive embryonic/larval nervo [Term] id: UBERON:6001057 name: insect neurogenic region -xref: FBbt:00001057 is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure relationship: only_in_taxon NCBITaxon:50557 ! Insecta @@ -274481,8 +274695,8 @@ id: UBERON:6001728 name: insect larval tagma def: "Any tagma (UBERON:6000002) that is part of some larva (UBERON:6001727)." [FBC:auto_generated_definition] xref: FBbt:00001728 -is_a: UBERON:6000002 ! panarthropod tagma -intersection_of: UBERON:6000002 ! panarthropod tagma +is_a: UBERON:6000002 ! arthropod tagma +intersection_of: UBERON:6000002 ! arthropod tagma intersection_of: part_of UBERON:0002548 ! larva relationship: part_of UBERON:0002548 ! larva @@ -274974,8 +275188,8 @@ id: UBERON:6003005 name: insect adult tagma def: "Any tagma (UBERON:6000002) that is part of some adult (UBERON:6003004)." [FBC:auto_generated_definition] xref: FBbt:00003005 -is_a: UBERON:6000002 ! panarthropod tagma -intersection_of: UBERON:6000002 ! panarthropod tagma +is_a: UBERON:6000002 ! arthropod tagma +intersection_of: UBERON:6000002 ! arthropod tagma intersection_of: part_of UBERON:0007023 ! adult organism relationship: part_of UBERON:0007023 ! adult organism @@ -275254,7 +275468,7 @@ name: insect tergite def: "The dorsal plate (sclerite) of an adult abdominal segment." [FlyBase:FBrf0007734, FlyBase:FBrf0111704] synonym: "abdominal tergite" EXACT [] xref: FBbt:00004476 -is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:6004475 ! insect sclerite relationship: develops_from UBERON:6001792 ! insect anterior dorsal histoblast nest abdominal relationship: develops_from UBERON:6001809 ! insect posterior dorsal histoblast nest abdominal @@ -275610,11 +275824,10 @@ relationship: only_in_taxon NCBITaxon:50557 ! Insecta [Term] id: UBERON:6005425 -name: insect visual anlage in statu nascendi -synonym: "A0Vis" RELATED [] -synonym: "Asn VisSys" RELATED [FBC:DOS] +name: obsolete insect visual anlage in statu nascendi +comment: No need for such a specific term in Uberon. See https://github.com/obophenotype/uberon/issues/2154. xref: FBbt:00005425 -is_a: UBERON:6005413 ! insect anlage in statu nascendi +is_obsolete: true [Term] id: UBERON:6005427 @@ -275640,7 +275853,6 @@ is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage -relationship: develops_from UBERON:6005425 ! insect visual anlage in statu nascendi relationship: part_of UBERON:6000119 ! insect anterior ectoderm [Term] @@ -275664,7 +275876,6 @@ is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage -relationship: develops_from UBERON:6000094 ! clypeo-labral anlage in statu nascendi relationship: part_of UBERON:6000119 ! insect anterior ectoderm [Term] @@ -275852,7 +276063,7 @@ relationship: part_of UBERON:0000924 ! ectoderm id: UBERON:6007046 name: insect dorsal ectoderm derivative xref: FBbt:00007046 -is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0010000 ! multicellular anatomical structure relationship: develops_from UBERON:6000112 ! insect dorsal ectoderm @@ -276062,8 +276273,8 @@ relationship: part_of UBERON:0000922 ! embryo id: UBERON:6017021 name: insect abdominal histoblast anlage xref: FBbt:00017021 +is_a: CARO:0000000 ! anatomical entity is_a: UBERON:0002050 ! embryonic structure -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage relationship: develops_from UBERON:6005526 ! insect dorsal epidermis primordium @@ -276140,10 +276351,11 @@ relationship: part_of UBERON:6040005 ! insect synaptic neuropil [Term] id: UBERON:6057001 -name: insect anterior-posterior subdivision of organism +name: obsolete insect anterior-posterior subdivision of organism +comment: Obsoleted as it is redundant with 'subdivision of organism along main body axis', which is not restricted to insects. xref: FBbt:00057001 -is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +is_obsolete: true +consider: UBERON:0011676 [Term] id: UBERON:6100153 @@ -276224,39 +276436,27 @@ relationship: part_of UBERON:0002415 ! tail [Term] id: UBERON:7500036 -name: line from caundal-sacral region of the vertebral column to the last vertebra -def: "An anatomical line along a tail that extends from the first caudal vertebra to the last cuadal vertebra." [https://orcid.org/0000-0003-2699-3066] -is_a: UBERON:0006800 ! anatomical line -intersection_of: UBERON:0006800 ! anatomical line -intersection_of: connects UBERON:0011271 ! caudal-sacral region of vertebral column -intersection_of: connects UBERON:7500035 ! tip of tail -relationship: connects UBERON:0011271 ! caudal-sacral region of vertebral column -relationship: connects UBERON:7500035 ! tip of tail -property_value: dc-contributor https://orcid.org/0000-0003-2699-3066 +name: obsolete line from caundal-sacral region of the vertebral column to the last vertebra +def: "OBSOLETE An anatomical line along a tail that extends from the first caudal vertebra to the last cuadal vertebra." [https://orcid.org/0000-0003-2699-3066] +comment: No longer part of the pattern design for lengths of lines. Can be found in OBA as tail length (http://purl.obolibrary.org/obo/OBA_VT0002758). +is_obsolete: true +consider: OBA:VT0002758 [Term] id: UBERON:7500037 -name: line from helix of outer ear to intertragus incisure -def: "An anatomical line of a ear that connects the helix of the outer ear to the intertragus incisure of an ear." [https://orcid.org/0000-0003-2699-3066] -is_a: UBERON:0006800 ! anatomical line -intersection_of: UBERON:0006800 ! anatomical line -intersection_of: connects UBERON:0002488 ! helix of outer ear -intersection_of: connects UBERON:0036212 ! intertragic incisure -relationship: connects UBERON:0002488 ! helix of outer ear -relationship: connects UBERON:0036212 ! intertragic incisure -property_value: dc-contributor https://orcid.org/0000-0003-2699-3066 +name: obsolete line from helix of outer ear to intertragus incisure +def: "OBSOLETE An anatomical line of a ear that connects the helix of the outer ear to the intertragus incisure of an ear." [https://orcid.org/0000-0003-2699-3066] +comment: No longer part of the pattern design for lengths of lines. Can be found in FOVT as ear length to notch (FOVT:0000005). +is_obsolete: true +consider: FOVT:0000005 [Term] id: UBERON:7500038 -name: line from the distal-most end of the longest nail to the posterior-most part of the foot -def: "An anatomical line of a hindfoot that connects the distal-most part of the longest nail to the posterior-most part of a foot." [https://orcid.org/0000-0003-2699-3066] -is_a: UBERON:0006800 ! anatomical line -intersection_of: UBERON:0006800 ! anatomical line -intersection_of: connects UBERON:7500039 ! posterior of pes -intersection_of: connects UBERON:7500040 ! tip of nail -relationship: connects UBERON:7500039 ! posterior of pes -relationship: connects UBERON:7500040 ! tip of nail -property_value: dc-contributor https://orcid.org/0000-0003-2699-3066 +name: obsolete line from the distal-most end of the longest nail to the posterior-most part of the foot +def: "OBSOLETE An anatomical line of a hindfoot that connects the distal-most part of the longest nail to the posterior-most part of a foot." [https://orcid.org/0000-0003-2699-3066] +comment: No longer part of the pattern design for lengths of lines. Can be found in FOVT as pes length with nail (FOVT:0000003). +is_obsolete: true +consider: FOVT:0000003 [Term] id: UBERON:7500039 @@ -276291,51 +276491,35 @@ consider: UBERON:0009551 [Term] id: UBERON:7500042 -name: line from the distal-most end of the longest phalax of the foot to the posterior-most part of the foot -def: "An anatomical line of a hindfoot that connects the end of the longest digit to the posterior-most part of a foot." [https://orcid.org/0000-0003-2699-3066] -is_a: UBERON:0006800 ! anatomical line -intersection_of: UBERON:0006800 ! anatomical line -intersection_of: connects UBERON:0009551 ! distal segment of digit -intersection_of: connects UBERON:7500039 ! posterior of pes -relationship: connects UBERON:0009551 ! distal segment of digit -relationship: connects UBERON:7500039 ! posterior of pes -property_value: dc-contributor https://orcid.org/0000-0003-2699-3066 +name: obsolete line from the distal-most end of the longest phalax of the foot to the posterior-most part of the foot +def: "OBSOLETE An anatomical line of a hindfoot that connects the end of the longest digit to the posterior-most part of a foot." [https://orcid.org/0000-0003-2699-3066] +comment: No longer part of the pattern design for lengths of lines. Can be found in FOVT as pes length without nail (FOVT:0000004). +is_obsolete: true +consider: FOVT:0000004 [Term] id: UBERON:7500043 -name: line from tip of nose to the caudal-sacral region of the vertebral column -def: "An anatomical line of a body that connects the tip of the nose to the posterior-most part of the sacrum." [https://orcid.org/0000-0003-2699-3066] -is_a: UBERON:0006800 ! anatomical line -intersection_of: UBERON:0006800 ! anatomical line -intersection_of: connects UBERON:0011271 ! caudal-sacral region of vertebral column -intersection_of: connects UBERON:0012128 ! nose tip -relationship: connects UBERON:0011271 ! caudal-sacral region of vertebral column -relationship: connects UBERON:0012128 ! nose tip -property_value: dc-contributor https://orcid.org/0000-0003-2699-3066 +name: obsolete line from tip of nose to the caudal-sacral region of the vertebral column +def: "OBSOLETE An anatomical line of a body that connects the tip of the nose to the posterior-most part of the sacrum." [https://orcid.org/0000-0003-2699-3066] +comment: No longer part of the pattern design for lengths of lines. Can be found in FOVT as body length without tail (FOVT:0000002). +is_obsolete: true +consider: FOVT:0000002 [Term] id: UBERON:7500044 -name: line from tip of nose to the posterior-most part of the last caudal vertebra -def: "An anatomical line of a body that connects the tip of the nose to the posterior-most part of a tail." [https://orcid.org/0000-0003-2699-3066] -is_a: UBERON:0006800 ! anatomical line -intersection_of: UBERON:0006800 ! anatomical line -intersection_of: connects UBERON:0012128 ! nose tip -intersection_of: connects UBERON:7500035 ! tip of tail -relationship: connects UBERON:0012128 ! nose tip -relationship: connects UBERON:7500035 ! tip of tail -property_value: dc-contributor https://orcid.org/0000-0003-2699-3066 +name: obsolete line from tip of nose to the posterior-most part of the last caudal vertebra +def: "OBSOLETE An anatomical line of a body that connects the tip of the nose to the posterior-most part of a tail." [https://orcid.org/0000-0003-2699-3066] +comment: No longer part of the pattern design for lengths of lines. Can be found in FOVT as body length with tail (FOVT:0000001). +is_obsolete: true +consider: FOVT:0000001 [Term] id: UBERON:7500045 -name: line of medial condyle of femur to greater trochanter -def: "An anatomical line of a femur that connects the medial condyle to the greater trochanter." [https://orcid.org/0000-0003-2699-3066] -is_a: UBERON:0006800 ! anatomical line -intersection_of: UBERON:0006800 ! anatomical line -intersection_of: connects UBERON:7500033 ! distal-most point of medial condyle of femur -intersection_of: connects UBERON:7500049 ! proximal-most point of greater trochanter of femur -relationship: connects UBERON:7500033 ! distal-most point of medial condyle of femur -relationship: connects UBERON:7500049 ! proximal-most point of greater trochanter of femur -property_value: dc-contributor https://orcid.org/0000-0003-2699-3066 +name: obsolete line of medial condyle of femur to greater trochanter +def: "OBSOLETE An anatomical line of a femur that connects the medial condyle to the greater trochanter." [https://orcid.org/0000-0003-2699-3066] +comment: No longer part of the pattern design for lengths of lines. Can be found in FOVT as femur length from greater trochanter to medial condyle (FOVT:0000006). +is_obsolete: true +consider: FOVT:0000006 [Term] id: UBERON:7500046 @@ -276387,27 +276571,19 @@ relationship: proximalmost_part_of UBERON:0002503 ! greater trochanter [Term] id: UBERON:7500050 -name: line of medial condyle of femur to head of femur -def: "An anatomical line of a femur that connects the medial condyle to the head of a femur." [https://orcid.org/0000-0003-2699-3066] -is_a: UBERON:0006800 ! anatomical line -intersection_of: UBERON:0006800 ! anatomical line -intersection_of: connects UBERON:7500033 ! distal-most point of medial condyle of femur -intersection_of: connects UBERON:7500046 ! proximal-most point of head of femur -relationship: connects UBERON:7500033 ! distal-most point of medial condyle of femur -relationship: connects UBERON:7500046 ! proximal-most point of head of femur -property_value: dc-contributor https://orcid.org/0000-0003-2699-3066 +name: obsolete line of medial condyle of femur to head of femur +def: "OBSOLETE An anatomical line of a femur that connects the medial condyle to the head of a femur." [https://orcid.org/0000-0003-2699-3066] +comment: No longer part of the pattern design for lengths of lines. Can be found in FOVT as femur length from caput to medial condyle (FOVT:0000007). +is_obsolete: true +consider: FOVT:0000007 [Term] id: UBERON:7500051 -name: line from trochlea of humerus to proximal head of humerus -def: "An anatomical line of a humerus that connects the trochlea to the proximal head." [https://orcid.org/0000-0003-2699-3066] -is_a: UBERON:0006800 ! anatomical line -intersection_of: UBERON:0006800 ! anatomical line -intersection_of: connects UBERON:7500034 ! distal-most point of trochlea of humerus -intersection_of: connects UBERON:7500047 ! proximal-most point of head of humerus -relationship: connects UBERON:7500034 ! distal-most point of trochlea of humerus -relationship: connects UBERON:7500047 ! proximal-most point of head of humerus -property_value: dc-contributor https://orcid.org/0000-0003-2699-3066 +name: obsolete line from trochlea of humerus to proximal head of humerus +def: "OBSOLETE An anatomical line of a humerus that connects the trochlea to the proximal head." [https://orcid.org/0000-0003-2699-3066] +comment: No longer part of the pattern design for lengths of lines. Can be found in FOVT as humerus length from trochlea to caput (FOVT:0000008). +is_obsolete: true +consider: FOVT:0000008 [Term] id: UBERON:7500052 @@ -276490,15 +276666,11 @@ property_value: dc-contributor https://orcid.org/0000-0003-2699-3066 [Term] id: UBERON:7500060 -name: line from trochlea of humerus to ventral tubercle of humerus -def: "An anatomical line of a humerus that connects the trochlea to the ventral tubercle." [https://orcid.org/0000-0003-2699-3066] -is_a: UBERON:0006800 ! anatomical line -intersection_of: UBERON:0006800 ! anatomical line -intersection_of: connects UBERON:7500034 ! distal-most point of trochlea of humerus -intersection_of: connects UBERON:7500048 ! proximal-most point of ventral tubercle of humerus -relationship: connects UBERON:7500034 ! distal-most point of trochlea of humerus -relationship: connects UBERON:7500048 ! proximal-most point of ventral tubercle of humerus -property_value: dc-contributor https://orcid.org/0000-0003-2699-3066 +name: obsolete line from trochlea of humerus to ventral tubercle of humerus +def: "OBSOLETE An anatomical line of a humerus that connects the trochlea to the ventral tubercle." [https://orcid.org/0000-0003-2699-3066] +comment: No longer part of the pattern design for lengths of lines. Can be found in FOVT as humerus length from trochlea to ventral tubercle (FOVT:0000009). +is_obsolete: true +consider: FOVT:0000009 [Term] id: UBERON:7500061 @@ -276611,7 +276783,6 @@ synonym: "muzzle" RELATED [] synonym: "snout" RELATED [] is_a: UBERON:0000475 ! organism subdivision property_value: dc-contributor https://orcid.org/0000-0003-2699-3066 -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: part_of UBERON:0003128 ! cranium relationship: part_of UBERON:0004089 ! midface @@ -276728,6 +276899,18 @@ is_a: UBERON:0013685 ! foramen of skull property_value: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:0001682 ! palatine bone +[Term] +id: UBERON:7500085 +name: endodontium +def: "A pulp-dentin complex or endodont that is part of a calcareous tooth." [https://en.wikipedia.org/wiki/Pulp_(tooth)] {comment="PMID: 29345716"} +synonym: "endodont" EXACT [] +synonym: "pulp-dentin complex" EXACT [] +is_a: UBERON:0010365 ! odontoid tissue +property_value: dc-contributor http://orcid.org/0000-0003-2699-3066 +relationship: has_part UBERON:0001751 ! dentine +relationship: has_part UBERON:0001754 ! dental pulp +relationship: part_of UBERON:0001091 ! calcareous tooth + [Term] id: UBERON:7500088 name: obsolete distal articular surface of radius @@ -277719,10 +277902,7 @@ synonym: "airway submucosal gland" BROAD [] synonym: "bronchial submucosal gland" EXACT [] synonym: "submucosal bronchial gland" EXACT [] synonym: "submucosal bronchus gland" EXACT [] -xref: EFO:0010666 -is_a: UBERON:0004119 ! endoderm-derived structure -is_a: UBERON:0011148 ! submucosal gland -is_a: UBERON:0036225 ! respiratory system gland +is_a: UBERON:8410077 ! airway submucosal gland intersection_of: UBERON:0011148 ! submucosal gland intersection_of: part_of UBERON:0002185 ! bronchus property_value: dc-contributor https://orcid.org/0000-0002-2825-0621 @@ -278024,9 +278204,11 @@ relationship: in_taxon NCBITaxon:8782 ! Aves [Term] id: UBERON:8410070 -name: levatores costarum +name: levator costarum def: "A chest muscle with a role in forceful inspiration. In human, there are twelve levatores costarum on either side of the chest; they are small tendinous and fleshy bundles arising from the ends of the transverse processes of the seventh cervical and upper eleven thoracic vertebrae. They pass obliquely downward and laterally, like the fibers of the intercostales externi, and each is inserted into the outer surface of the rib immediately below the vertebra from which it takes origin, between the tubercle and the angle (levatores costarum breves). Each of the four lower muscles divides into two fasciculi, one of which is inserted as above described; the other passes down to the second rib below its origin (levatores costarum longi)." [WikipediaVersioned:Levatores_costarum_muscles&oldid=876138804] -synonym: "levatores costarum muscle" EXACT [] +synonym: "levator costarum muscle" EXACT [] +synonym: "levatores costarum" EXACT [] +synonym: "levatores costarum muscles" EXACT [] synonym: "musculi levatores costarum" EXACT LATIN [] xref: FMA:71312 is_a: CARO:0000003 @@ -278037,6 +278219,33 @@ relationship: has_muscle_origin UBERON:0001077 ! transverse process of vertebra relationship: part_of RO:0002577 ! system relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +[Term] +id: UBERON:8410071 +name: subcapsular sinus ceiling +def: "The section of the lymph node capsule that faces the subcapsular sinus. In human, it's characterized by specific protein markers." [http://www.ncbi.nlm.nih.gov/pubmed/31402260] +synonym: "ceiling of subcapsular sinus of lymph node" EXACT [] +synonym: "floor of capsule of lymph node" EXACT [] +synonym: "subcapsular sinus of lymph node ceiling" EXACT [] +is_a: CARO:0000000 ! anatomical entity +is_a: UBERON:0000064 ! organ part +relationship: adjacent_to UBERON:0005463 ! subcapsular sinus of lymph node +property_value: dc-contributor http://orcid.org/0000-0002-2825-0621 +relationship: part_of UBERON:0002194 ! capsule of lymph node +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens + +[Term] +id: UBERON:8410072 +name: subcapsular sinus floor +def: "The section of the lymph node cortex that faces the subcapsular sinus. In human, it's characterized by specific protein markers." [http://www.ncbi.nlm.nih.gov/pubmed/31402260] +synonym: "ceiling of cortex of lymph node" EXACT [] +synonym: "floor of subcapsular sinus of lymph node" EXACT [] +synonym: "subcapsular sinus of lymph node floor" EXACT [] +is_a: CARO:0000000 ! anatomical entity +is_a: UBERON:0000064 ! organ part +relationship: adjacent_to UBERON:0005463 ! subcapsular sinus of lymph node +property_value: dc-contributor http://orcid.org/0000-0002-2825-0621 +relationship: part_of UBERON:0002006 ! cortex of lymph node + [Term] id: UBERON:8410073 name: medullary region of kidney @@ -278050,6 +278259,71 @@ relationship: has_part UBERON:0004200 ! kidney pyramid relationship: part_of UBERON:0002113 ! kidney created_by: http://orcid.org/0000-0002-2825-0621 +[Term] +id: UBERON:8410074 +name: lymph node paracortical sinus +def: "A lymph node sinus intimately associated with paracortical cords that originate in the interfollicular cortex and extend into the medullary cords." [http://www.ncbi.nlm.nih.gov/pubmed/17067937, http://www.ncbi.nlm.nih.gov/pubmed/9176696] +synonym: "cortical sinus" RELATED [] +synonym: "lymphatic labyrinth" RELATED [] +synonym: "paracortical sinus" BROAD [] +synonym: "peripheral sinus" RELATED [] +is_a: CARO:0000000 ! anatomical entity +is_a: UBERON:0004111 ! anatomical conduit +property_value: dc-contributor http://orcid.org/0000-0002-2825-0621 +relationship: part_of UBERON:8410066 ! lymph node paracortex +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens + +[Term] +id: UBERON:8410075 +name: lymph node paracortical cord +def: "Lymph node paracortical parenchyma containing dense networks of T cells, B cells, fibroblastic reticular cells, and dendritic cells." [http://www.ncbi.nlm.nih.gov/pubmed/17067937, http://www.ncbi.nlm.nih.gov/pubmed/49306] +synonym: "paracortical cord" BROAD [] +is_a: CARO:0000000 ! anatomical entity +is_a: UBERON:0000353 ! parenchyma +property_value: dc-contributor http://orcid.org/0000-0002-2825-0621 +relationship: part_of UBERON:8410066 ! lymph node paracortex +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens + +[Term] +id: UBERON:8410076 +name: glomus coccygeum +def: "A glomus-like dermal microanatomical structure found in human and placed in front of, or immediately below, the tip of the coccyx. Each glomus consists of one or more arterial segments that branch into a number of glomic arterioles surrounded by rows of round, uniform, epithelioid contractile cells, that drain into a collecting venous plexus." [http://www.ncbi.nlm.nih.gov/pubmed/28545163, http://www.ncbi.nlm.nih.gov/pubmed/30799440, https://orcid.org/0000-0002-1572-1316] +synonym: "coccygeal body" EXACT [FMA:15649] +synonym: "coccygeal gland" EXACT [WikipediaVersioned:Coccygeal_glomus&oldid=1019065130] +synonym: "coccygeal glomus" EXACT [FMA:15649] +synonym: "gland of Luschka" EXACT [FMA:15649] +synonym: "glands of Luschka" EXACT [] +synonym: "glomus body" EXACT [http://www.ncbi.nlm.nih.gov/pubmed/30799440] +synonym: "Luschka's gland" EXACT [WikipediaVersioned:Coccygeal_glomus&oldid=1019065130] +is_a: UBERON:0010000 ! multicellular anatomical structure +property_value: dc-contributor http://orcid.org/0000-0002-2825-0621 + +[Term] +id: UBERON:8410077 +name: airway submucosal gland +def: "A submucosal gland found in a respiratory tract." [http://orcid.org/0000-0003-3440-1876, http://orcid.org/0000-0003-4183-8865] +synonym: "respiratory tract submucosal gland" EXACT [] +synonym: "submucosal gland of respiratory tract" EXACT [] +xref: EFO:0010666 +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0011148 ! submucosal gland +is_a: UBERON:0036225 ! respiratory system gland +intersection_of: UBERON:0011148 ! submucosal gland +intersection_of: part_of UBERON:0000065 ! respiratory tract +property_value: dc-contributor http://orcid.org/0000-0002-2825-0621 +relationship: part_of UBERON:0000065 ! respiratory tract + +[Term] +id: UBERON:8410078 +name: right lymphatic duct +def: "A great lymphatic vessel that empties lymph into one of the subclavian veins. In humans, there are two lymph ducts in the body: the right lymphatic duct and the thoracic duct. The right lymphatic duct drains lymph from the right upper limb, right side of thorax and right halves of head and neck. The thoracic duct drains lymph into the circulatory system at the left brachiocephalic vein between the left subclavian and left internal jugular veins." [http://en.wikipedia.org/wiki/Lymph_duct] +comment: This term ('right lymphatic duct') would not need a 'left' counterpart; the other great lymph duct in the human body is represented by UBERON:0001631 'thoracic duct'. +synonym: "ductus lymphaticus dexter" EXACT LATIN [] +xref: FMA:5832 +is_a: UBERON:0001473 ! lymphatic vessel +property_value: dc-contributor http://orcid.org/0000-0002-2825-0621 +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens + [Term] id: UBERON:8420000 name: hair of scalp @@ -278475,6 +278749,7 @@ xref: by_means [Typedef] id: capable_of name: capable of +namespace: external namespace: protein def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] subset: ro-eco @@ -278704,7 +278979,7 @@ def: "x composed_primarily_of y iff: more than half of the mass of x is made fro xref: RO:0002473 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity -is_a: has_part ! has_part +is_a: has_part ! has part [Typedef] id: conduit_for @@ -278820,6 +279095,12 @@ name: title xref: http://purl.org/dc/elements/1.1/title is_metadata_tag: true +[Typedef] +id: dcterms-date +name: date +xref: http://purl.org/dc/terms/date +is_metadata_tag: true + [Typedef] id: dcterms-isReferencedBy name: is referenced by @@ -278943,12 +279224,10 @@ comment: This is the transitive form of the develops from relation xref: RO:0002202 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant -holds_over_chain: part_of develops_from is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into -transitive_over: part_of ! part_of [Typedef] id: develops_from_part_of @@ -279191,7 +279470,7 @@ xref: RO:0002327 is_a: capable_of ! capable of inverse_of: enabled_by ! enabled by transitive_over: has_component_activity ! has component activity -transitive_over: has_part ! has_part +transitive_over: has_part ! has part [Typedef] id: enables_subfunction @@ -279225,7 +279504,7 @@ name: ends with def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] xref: RO:0002230 is_transitive: true -is_a: has_part ! has_part +is_a: has_part ! has part is_a: temporally_related_to ! temporally related to [Typedef] @@ -279419,7 +279698,7 @@ namespace: protein def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] xref: RO:0002180 is_transitive: false -is_a: has_part ! has_part +is_a: has_part ! has part [Typedef] id: has_component_activity @@ -279533,7 +279812,7 @@ id: has_member name: has member def: "has member is a mereological relation between a collection and an item." [] xref: RO:0002351 -is_a: has_part ! has_part +is_a: has_part ! has part [Typedef] id: has_muscle_antagonist @@ -279582,6 +279861,12 @@ expand_assertion_to: "Class: EquivalentT is_metadata_tag: true is_class_level: true +[Typedef] +id: has_ontology_root_term +name: has ontology root term +xref: IAO:0000700 +is_metadata_tag: true + [Typedef] id: has_output name: has output @@ -279595,18 +279880,14 @@ inverse_of: output_of ! output of id: has_part name: has part name: has_part -namespace: chebi_ontology namespace: external namespace: protein namespace: quality def: "a core relation that holds between a whole and its part" [] -def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [] -comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 -is_cyclic: false is_transitive: true is_a: overlaps ! overlaps @@ -279723,7 +280004,7 @@ domain: CARO:0000003 domain: UBERON:0000475 ! organism subdivision range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} range: UBERON:0010912 ! subdivision of skeleton -is_a: has_part ! has_part +is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -280256,8 +280537,8 @@ name: never_in_taxon def: "S never_in_taxon T iff: S SubClassOf in_taxon only not T." [http://www.ncbi.nlm.nih.gov/pubmed/20973947] def: "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." [] xref: RO:0002161 -expand_assertion_to: "?X DisjointWith RO_0002162 some ?Y " [] expand_assertion_to: "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" [] +expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y " [] is_metadata_tag: true is_class_level: true @@ -280338,7 +280619,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 is_transitive: true is_a: overlaps ! overlaps -inverse_of: has_part ! has_part +inverse_of: has_part ! has part [Typedef] id: part_of_developmental_precursor_of @@ -280738,7 +281019,7 @@ name: starts with def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] xref: RO:0002224 is_transitive: true -is_a: has_part ! has_part +is_a: has_part ! has part is_a: temporally_related_to ! temporally related to [Typedef]