From eb439f82627fc6c4229c225c4aaa61a4312304d0 Mon Sep 17 00:00:00 2001 From: paulacalipho Date: Mon, 18 Sep 2023 11:50:18 +0200 Subject: [PATCH] Update uberon-edit.obo --- src/ontology/uberon-edit.obo | 72 ++++++++++++++++++++---------------- 1 file changed, 40 insertions(+), 32 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 5d32a92508..87bbf21981 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -2649,7 +2649,7 @@ subset: grouping_class subset: non_informative xref: Wikipedia:Sulcus_(anatomy) is_a: UBERON:0000464 ! anatomical space -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-09T06:23:22Z [Term] @@ -2661,7 +2661,7 @@ synonym: "membrane of organ" EXACT [] xref: FMA:7145 is_a: UBERON:0000062 ! organ relationship: composed_primarily_of UBERON:0011823 {source="FMA-def"} ! dense connective tissue -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-07-30T05:19:13Z [Term] @@ -2676,7 +2676,7 @@ xref: Wikipedia:Cardiac_neural_crest xref: XAO:0004190 xref: ZFA:0001648 is_a: UBERON:0000479 ! tissue -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 relationship: overlaps UBERON:0005428 {source="Wikipedia"} ! vagal neural crest relationship: part_of UBERON:0002342 ! neural crest property_value: external_definition "A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751]." xsd:string {source="DOI:10.1242/dev.091751"} @@ -3918,7 +3918,7 @@ xref: CARO:0000081 is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa creation_date: 2009-04-08T04:38:19Z @@ -3994,7 +3994,7 @@ def: "A blood brain barrier that is composed of endothelial cells." [https://orc xref: NIF_Subcellular:nlx_subcell_100205 intersection_of: UBERON:0000120 ! blood brain barrier intersection_of: composed_primarily_of CL:0000115 ! endothelial cell -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-10T08:15:44Z [Term] @@ -4003,7 +4003,7 @@ name: glial blood brain barrier def: "A blood brain barrier composed of glial cells." [https://orcid.org/0000-0002-6601-2165] intersection_of: UBERON:0000120 ! blood brain barrier intersection_of: composed_primarily_of CL:0000125 ! glial cell -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-10T08:42:24Z [Term] @@ -4028,7 +4028,7 @@ xref: Wikipedia:Avian_pallium xref: Wikipedia:Pallium_(neuroanatomy) xref: ZFA:0000505 is_a: UBERON:0002616 ! regional part of brain -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 relationship: part_of UBERON:0001893 ! telencephalon relationship: present_in_taxon NCBITaxon:7762 {source="PMID:8932866"} ! Myxinidae property_value: homology_notes "In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume." xsd:string {source="Wikipedia:Avian_pallium", taxon="NCBITaxon:8782"} @@ -4052,7 +4052,7 @@ xref: EFO:0003522 xref: TAO:0000304 xref: ZFA:0000304 is_a: UBERON:0002616 ! regional part of brain -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 relationship: dorsal_to UBERON:0000203 {notes="separated by cell-free region"} ! pallium relationship: part_of UBERON:0001893 ! telencephalon property_value: external_ontology_notes "BTO term refers specifically to the avian structure" xsd:string {external_ontology="BTO"} @@ -4066,7 +4066,7 @@ synonym: "papulae" EXACT PLURAL [ISBN:0030229073] synonym: "papulli" EXACT PLURAL [] xref: Wikipedia:Papula is_a: UBERON:0002535 ! gill -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata creation_date: 2009-04-18T01:13:57Z @@ -4078,7 +4078,7 @@ xref: ANISEED:1235300 xref: Wikipedia:Gill#Vertebrate_gills is_a: UBERON:0002535 ! gill relationship: adjacent_to UBERON:0001042 ! chordate pharynx -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 property_value: function_notes "Gills are made of filaments which help increase surface area for oxygen exchange" xsd:string property_value: taxon_notes "In bony fish, the gills are covered by a bony cover called an operculum. When a fish breathes, it opens its mouth at regular times and draws in a mouthful of water. It then draws the sides of its throat together, forcing the water through the gill openings. The water passes over the gills on the outside. Valves inside the mouth keep the water from escaping through the mouth again. The operculum can be very important in adjusting the pressure of water inside of the pharynx to allow proper ventilation of the gills. Lampreys and sharks lack an operculum, they have multiple gill openings. Also, they must use different methods to force water over the gills. In sharks and rays, this ventilation of the gills is achieved either by the use of spiracles or ram ventilation (ventilation by constantly swimming). Although some animals use this method it is much better for animals to use a spiracle because they are less susceptible to injury" xsd:string creation_date: 2009-04-18T01:18:17Z @@ -4092,7 +4092,7 @@ xref: TADS:0000304 is_a: UBERON:0000476 ! acellular anatomical structure is_a: UBERON:0005389 ! transparent eye structure disjoint_from: UBERON:0000965 ! lens of camera-type eye -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 relationship: part_of UBERON:0000018 ! compound eye creation_date: 2009-04-18T01:35:32Z @@ -4209,7 +4209,7 @@ xref: Wikipedia:Toilet-claw is_a: UBERON:0001705 ! nail relationship: capable_of_part_of GO:0007625 ! grooming behavior relationship: capable_of_part_of NBO:0000451 {source="Wikipedia"} ! personal grooming -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-05-19T08:19:58Z [Term] @@ -190417,7 +190417,7 @@ name: digestive tract junction def: "An anatomical junction between two parts of the digestive tract." [https://orcid.org/0000-0002-7073-9172] intersection_of: UBERON:0007651 ! anatomical junction intersection_of: connects UBERON:0004921 ! subdivision of digestive tract -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 ! David Osumi-Sutherland +relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2021-02-05T11:19:31Z [Term] @@ -221598,7 +221598,7 @@ id: UBERON:8200002 name: copepodite stage 1 def: "A development stage of copepods which immediately follows the nauplius stage. It is characterized by the presence of 2 swimming legs." [http://orcid.org/0000-0002-2908-3327] is_a: UBERON:0000105 ! life cycle stage -relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 ! Anne Thessen +relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 relationship: only_in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0014860 ! copepodite stage relationship: part_of UBERON:0018378 ! crustacean larval stage @@ -221610,7 +221610,7 @@ id: UBERON:8200003 name: copepodite stage 2 def: "A development stage of copepods which immediately follows copepodite stage 1. It is characterized by the presence of 3 swimming legs." [http://orcid.org/0000-0002-2908-3327] is_a: UBERON:0000105 ! life cycle stage -relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 ! Anne Thessen +relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 relationship: only_in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0014860 ! copepodite stage relationship: part_of UBERON:0018378 ! crustacean larval stage @@ -221622,7 +221622,7 @@ id: UBERON:8200004 name: copepodite stage 3 def: "A development stage of copepods which immediately follows copepodite stage 2. It is characterized by the presence of 4 swimming legs." [http://orcid.org/0000-0002-2908-3327] is_a: UBERON:0000105 ! life cycle stage -relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 ! Anne Thessen +relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 relationship: only_in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0014860 ! copepodite stage relationship: part_of UBERON:0018378 ! crustacean larval stage @@ -221634,7 +221634,7 @@ id: UBERON:8200005 name: copepodite stage 4 def: "A development stage of copepods which immediately follows copepodite stage 3. It is characterized by the presence of 5 swimming legs." [http://orcid.org/0000-0002-2908-3327] is_a: UBERON:0000105 ! life cycle stage -relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 ! Anne Thessen +relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 relationship: only_in_taxon NCBITaxon:6830 ! Copepoda relationship: part_of UBERON:0014860 ! copepodite stage relationship: part_of UBERON:0018378 ! crustacean larval stage @@ -221646,7 +221646,7 @@ id: UBERON:8200006 name: copepodite stage 5 def: "A pre-adult stage of copepods which immediately follows copepodite stage 4. It is characterized by enlargement of the urosome and development of sexual organs." [http://orcid.org/0000-0002-2908-3327] is_a: UBERON:0000105 ! life cycle stage -relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 ! Anne Thessen +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 @@ -221657,7 +221657,7 @@ id: UBERON:8200007 name: copepodite stage 6 def: "A fully formed stage of copepods which immediately follows copepodite stage 5. It is characterized by the complete development of the fifth swimming leg." [http://orcid.org/0000-0002-2908-3327] is_a: UBERON:0000105 ! life cycle stage -relationship: dc-contributor https://orcid.org/0000-0002-2908-3327 ! Anne Thessen +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 @@ -222849,7 +222849,7 @@ is_a: UBERON:0035014 {source="NIFSTD"} ! functional part of brain relationship: capable_of_part_of GO:0007601 ! visual perception relationship: contributes_to_morphology_of UBERON:0000956 ! cerebral cortex relationship: contributes_to_morphology_of UBERON:0002021 ! occipital lobe -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 ! Shawn Zheng Kai Tan +relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: in_taxon NCBITaxon:9443 ! Primates relationship: part_of UBERON:0000411 {source="WP"} ! visual cortex property_value: depicted_by "http://upload.wikimedia.org/wikipedia/commons/7/70/Brodmann_areas_17_18_19.png" xsd:anyURI @@ -222861,7 +222861,7 @@ def: "The part of the cortex that is responsible for processing visual informati intersection_of: UBERON:0035014 ! functional part of brain intersection_of: capable_of_part_of GO:0007601 ! visual perception intersection_of: part_of UBERON:0000956 ! cerebral cortex -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 ! Shawn Zheng Kai Tan +relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 [Term] id: UBERON:8440012 @@ -223143,7 +223143,7 @@ synonym: "lateral tuberal nucleus (sensu Rodentia)" EXACT [PMID:29976812] xref: DMBA:16271 xref: MBA:614 is_a: UBERON:0002308 ! nucleus of brain -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 ! Shawn Zheng Kai Tan +relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: in_taxon NCBITaxon:9989 ! Rodentia relationship: part_of UBERON:0001898 ! hypothalamus property_value: curator_notes "Lateral tuberal nucleus is listed as both an exact synonym and related synonym as the term has been used in both ways. See https://github.com/obophenotype/uberon/issues/2439 for more details. No homology links has been made as this is unclear from the literature." xsd:string @@ -223155,7 +223155,7 @@ def: "A prominent nucleus located in the ventral tuberal area of Teleostei that comment: This term is used specifically for fish (or Teleostei in general) as lateral tuberal nucleus (UBERON:0000435) refers to a structure that is specific to humans and higher primates. See https://github.com/obophenotype/uberon/issues/2439 for more details. {xref="PMID:1362279"} synonym: "NLT system (sensu Teleostei)" EXACT [DOI:10.1016/0016-6480(71)90165-1] is_a: UBERON:0001937 ! lateral hypothalamic nucleus -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 ! Shawn Zheng Kai Tan +relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: in_taxon NCBITaxon:32443 ! Teleostei [Term] @@ -223164,14 +223164,14 @@ name: superior paraolivary nucleus def: "A structure embedded in the superior olivary complex that is driven by input pathways from the octopus cells in the cochlear nucleus and the neurons of the medial nucleus of the trapezoid body." [DOI:10.1093/oxfordhb/9780190849061.013.11] synonym: "SPON" EXACT [DOI:10.1093/oxfordhb/9780190849061.013.11] is_a: UBERON:0007247 ! nucleus of superior olivary complex -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 ! Shawn Zheng Kai Tan +relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 [Term] id: UBERON:8440044 name: upper layers of the cortex def: "A laminar subdivision of the neocortex that is comprised of the more surface layers, commonly layers two through four." [DOI:10.1101/2022.10.12.511898] is_a: UBERON:8440004 ! laminar subdivision of the cortex -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 ! Shawn Zheng Kai Tan +relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 [Term] id: UBERON:8440045 @@ -223252,7 +223252,7 @@ id: UBERON:8440051 name: lower layers of the cortex def: "A laminar subdivision of the neocortex that is comprised of the deeper layers, commonly layers five and six, however, could also consist part of layer four." [DOI:10.1101/2022.10.12.511898] is_a: UBERON:8440004 ! laminar subdivision of the cortex -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 ! Shawn Zheng Kai Tan +relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 [Term] id: UBERON:8440052 @@ -223445,7 +223445,7 @@ synonym: "LTN" EXACT ABBREVIATION [MBA:283] xref: MBA:283 xref: neuronames:1957 is_a: UBERON:0002308 ! nucleus of brain -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 ! Shawn Zheng Kai Tan +relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: dorsal_to UBERON:0007632 ! Barrington's nucleus relationship: part_of UBERON:0003023 ! pontine tegmentum relationship: ventral_to UBERON:0002148 ! locus ceruleus @@ -223457,7 +223457,7 @@ def: "A nucleus of the brain that is the most ventral portion of the gigantocell synonym: "MARN" EXACT ABBREVIATION [MBA:307] xref: MBA:307 is_a: UBERON:0002308 ! nucleus of brain -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 ! Shawn Zheng Kai Tan +relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: part_of UBERON:0002155 ! gigantocellular nucleus relationship: part_of UBERON:0025525 ! motor system @@ -223471,7 +223471,7 @@ synonym: "ISVe" EXACT ABBREVIATION [NeuroNames:719] xref: MBA:76 xref: NeuroNames:719 is_a: UBERON:0000125 ! neural nucleus -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 ! Shawn Zheng Kai Tan +relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: part_of UBERON:0002731 ! vestibulocochlear nerve root [Term] @@ -223481,7 +223481,7 @@ def: "The part of the cerebral cortex that is responsible for the perception of synonym: "gustatory area" EXACT [MBA:1057] xref: MBA:1057 is_a: UBERON:0002616 ! regional part of brain -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 ! Shawn Zheng Kai Tan +relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: part_of UBERON:0000956 ! cerebral cortex relationship: part_of UBERON:0001033 ! gustatory system @@ -223491,7 +223491,7 @@ name: somatomotor area def: "A part of the cerebral cortex that comprises of the primary motor cortex and the premotor cortex." [MBA:500] xref: MBA:500 is_a: UBERON:0002616 ! regional part of brain -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 ! Shawn Zheng Kai Tan +relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: has_part UBERON:0001384 ! primary motor cortex relationship: has_part UBERON:0016634 ! premotor cortex @@ -223504,7 +223504,7 @@ is_a: UBERON:0000464 ! anatomical space relationship: adjacent_to UBERON:0007193 ! orbital gyrus relationship: adjacent_to UBERON:0015800 ! taenia tectum of brain relationship: adjacent_to UBERON:8440033 ! infralimbic area -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 ! Shawn Zheng Kai Tan +relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: present_in_taxon NCBITaxon:10090 {xref="MBA:1078"} ! Mus musculus relationship: present_in_taxon NCBITaxon:10114 {xref="NeuroNames:1975"} ! Rattus @@ -224223,6 +224223,14 @@ intersection_of: part_of UBERON:0007318 ! saphenous vein relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 property_value: dcterms-date "2023-08-31T11:41:09Z" xsd:dateTime +[Term] +id: UBERON:8480069 +name: temporofacial region +def: "The region at each side of the face comprising the temple and the cheek." [https://orcid.org/0000-0002-0819-0473] +is_a: UBERON:0001444 ! subdivision of head +relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 +property_value: dcterms-date "2023-09-18T06:03:43Z" xsd:dateTime + [Term] id: UBERON:8480071 name: skin of lobe of tail