diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 5ffc9efb67..b01ee2b4ac 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -927,7 +927,7 @@ intersection_of: UBERON:0000026 ! appendage intersection_of: has_quality PATO:0002236 ! aliform relationship: capable_of_part_of GO:0060361 ! flight 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:186634 {source="bgee", seeAlso="Wikipedia:Flying_fish"} ! 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 @@ -7752,7 +7752,7 @@ xref: ENVO:02000026 xref: FMA:62961 xref: Wikipedia:Chyme is_a: UBERON:0006314 {source="WP"} ! bodily fluid -is_a: UBERON:0012112 {editor_note="consider changing to derivation relationship", source="FMA"} ! ingested food +is_a: UBERON:0012112 {IAO:0000116="consider changing to derivation relationship", source="FMA"} ! ingested food disjoint_from: UBERON:0012113 ! bolus of food relationship: has_quality PATO:0001429 {gci_relation="part_of", gci_filler="UBERON:0000945"} ! acidic relationship: located_in UBERON:0004908 ! upper digestive tract @@ -15949,7 +15949,7 @@ xref: Wikipedia:Peyer's_patch is_a: UBERON:0001962 {source="FMA", source="MA"} ! gut-associated lymphoid tissue relationship: never_in_taxon NCBITaxon:8459 {source="PMID:PMID:20181529"} ! Testudines relationship: only_in_taxon NCBITaxon:32524 {source="PMID:PMID:20181529"} ! Amniota -relationship: part_of UBERON:0000030 {editor_note="check this"} ! lamina propria +relationship: part_of UBERON:0000030 {IAO:0000116="check this"} ! lamina propria relationship: part_of UBERON:0001242 ! intestinal mucosa property_value: external_ontology_notes "FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc]" xsd:string {external_ontology="FMA"} property_value: external_ontology_notes "Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part. WP says duodenum and jejunum lack PPs" xsd:string {external_ontology="MA"} @@ -22423,7 +22423,7 @@ relationship: preaxialmost_part_of UBERON:0002398 ! manus property_value: depicted_by "http://upload.wikimedia.org/wikipedia/commons/6/64/Thumb-up.jpg" xsd:anyURI property_value: depicted_by "https://upload.wikimedia.org/wikipedia/commons/2/2c/Thumbs_up.jpg" xsd:anyURI property_value: taxon_notes "Not present in Anurans (Phenotype RCN Oct 2012)" xsd:string -property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", seeAlso="UBERON:0012260", source="PMID:10220427", source="PhenoscapeRCN"} +property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012260"} [Term] id: UBERON:0001464 @@ -28121,7 +28121,7 @@ relationship: part_of UBERON:0010272 ! hyoid apparatus property_value: axiom_lost_from_external_ontology "relationship loss: part_of hyoid plate (AAO:0000664)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000684", ontology="AAO"} property_value: depicted_by "http://upload.wikimedia.org/wikipedia/commons/1/1f/Gray186.png" xsd:anyURI property_value: external_definition "Paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes are the ossified posteromedial processes and invest the laryngeal apparatus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000684", ontology="AAO", source="AAO:LAP"} -property_value: taxon_notes "The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia." xsd:string {seeAlso="https://github.com/obophenotype/uberon/issues/548", source="WP"} +property_value: taxon_notes "The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia." xsd:string {source="WP", seeAlso="https://github.com/obophenotype/uberon/issues/548"} [Term] id: UBERON:0001686 @@ -34095,7 +34095,7 @@ xref: VHOG:0001625 xref: Wikipedia:Olfactory_tubercle is_a: UBERON:0000125 {source="EHDAA2"} ! neural nucleus relationship: contributes_to_morphology_of UBERON:0002894 ! olfactory cortex -relationship: dubious_for_taxon NCBITaxon:9443 {editor_note="check EHDAA2", source="MP"} ! Primates +relationship: dubious_for_taxon NCBITaxon:9443 {IAO:0000116="check EHDAA2", source="MP"} ! Primates relationship: mutually_spatially_disjoint_with UBERON:0001882 {source="ABA"} ! nucleus accumbens relationship: part_of UBERON:0002894 {source="EHDAA2-inferred", source="MA", source="VHOG", source="Wikipedia"} ! olfactory cortex relationship: part_of UBERON:0005401 {source="BTO"} ! cerebral hemisphere gray matter @@ -35074,7 +35074,7 @@ xref: Wikipedia:Pineal_gland xref: XAO:0000160 xref: ZFA:0000019 is_a: UBERON:0010134 {source="MA"} ! secretory circumventricular organ -relationship: capable_of GO:0030187 {editor_note="add secretion"} ! melatonin biosynthetic process +relationship: capable_of GO:0030187 {IAO:0000116="add secretion"} ! melatonin biosynthetic process relationship: contributes_to_morphology_of UBERON:0001899 ! epithalamus relationship: has_part CL:0000652 ! pinealocyte relationship: has_part CL:0002220 ! interstitial cell of pineal gland @@ -38619,7 +38619,7 @@ xref: Wikipedia:Spinal_accessory_nerve xref: XAO:0004214 intersection_of: UBERON:0001021 ! nerve intersection_of: extends_fibers_into UBERON:0020358 ! accessory XI nerve nucleus -relationship: dubious_for_taxon NCBITaxon:8292 {seeAlso="http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7", source="VHOG", source="Wikipedia"} ! Amphibia +relationship: dubious_for_taxon NCBITaxon:8292 {source="VHOG", source="Wikipedia", seeAlso="http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7"} ! Amphibia relationship: innervates UBERON:0001737 ! larynx relationship: innervates UBERON:3010692 {gci_relation="part_of", gci_filler="NCBITaxon:8292", source="ISBN:080184780X"} ! m. cucullaris relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda @@ -44580,7 +44580,7 @@ xref: Wikipedia:Nerve_root is_a: UBERON:0000122 ! neuron projection bundle relationship: extends_fibers_into UBERON:0001017 ! central nervous system relationship: extends_fibers_into UBERON:0001021 ! nerve -relationship: part_of UBERON:0001016 {editor_note="we do not commit to CNS or PNS to allow for flexibility with this class"} ! nervous system +relationship: part_of UBERON:0001016 {IAO:0000116="we do not commit to CNS or PNS to allow for flexibility with this class"} ! nervous system property_value: editor_note "We consider cranial nerve roots to be primarily CNS structures, but model spinal nerve roots as PNS structures, due to the existence of ganglia on the roots." xsd:string property_value: external_definition "The continuation of the neurite bundle and associated glia of a nerve, inside the central nervous system[FBbt:00007602, FBC:DOS]." xsd:string {source="FBbt:00007602, FBC:DOS"} property_value: external_ontology_notes "FMA has 'central zone of nerve' which is the superclass of cranial nerve tracts, which the FMA sometimes calls roots" xsd:string {external_ontology="FMA"} @@ -74713,7 +74713,7 @@ relationship: part_of UBERON:5003622 ! manual digit 2 plus metapodial segment property_value: depicted_by "https://upload.wikimedia.org/wikipedia/commons/d/d5/Index_finger.JPG" xsd:anyURI property_value: has_relational_adjective "indicis" xsd:string property_value: taxon_notes "Anurans lack manual digit 1, so manual digit 2 is the digit after the prepollex (Phenotype RCN Oct 2012)" xsd:string -property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", seeAlso="UBERON:0012261", source="PMID:10220427", source="PhenoscapeRCN"} +property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012261"} [Term] id: UBERON:0003623 @@ -74750,7 +74750,7 @@ relationship: ambiguous_for_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0012141 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! manual digitopodium region relationship: part_of UBERON:5003623 ! manual digit 3 plus metapodial segment property_value: depicted_by "https://upload.wikimedia.org/wikipedia/commons/f/fd/Middle_finger.jpg" xsd:anyURI -property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", seeAlso="UBERON:0012262", source="PMID:10220427", source="PhenoscapeRCN"} +property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012262"} [Term] id: UBERON:0003624 @@ -76083,7 +76083,7 @@ xref: Wikipedia:Canine_tooth intersection_of: UBERON:0001091 ! calcareous tooth 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_part UBERON:0006844 {IAO:0000116="cardinality not allowed with transitivity in OWL", count="1"} ! 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="Wikipedia:Cricetidae"} ! Muroidea relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia property_value: depicted_by "https://upload.wikimedia.org/wikipedia/commons/5/57/Azawakh_K9.jpg" xsd:anyURI @@ -113227,7 +113227,7 @@ name: seminal fluid def: "A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended." [http://orcid.org/0000-0002-6601-2165] synonym: "male genital fluid" RELATED [] synonym: "male genital secretion" RELATED [] -synonym: "milt" NARROW [PMID:31287811, PMID:35203131] {http://purl.obolibrary.org/obo/IAO_0000232="A secretion from the glands of the male reproductive system in some aquatic animals that contains sperm and is sprayed onto the eggs."} +synonym: "milt" NARROW [PMID:31287811, PMID:35203131] {IAO:0000232="A secretion from the glands of the male reproductive system in some aquatic animals that contains sperm and is sprayed onto the eggs."} synonym: "seminal fluid" RELATED [BTO:0001232] synonym: "seminal plasma" EXACT [BTO:0001232] xref: BTO:0001232 @@ -118699,7 +118699,7 @@ xref: SCTID:304572005 xref: UMLS:C1704302 {source="ncithesaurus:Bicuspid_Tooth"} xref: Wikipedia:Premolar 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: has_part UBERON:0006844 {IAO:0000116="cardinality not allowed with transitivity in OWL", UBPROP:0000008="some premolars may have 3 cusps", min_count="2"} ! 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="Wikipedia:Cricetidae"} ! Muroidea property_value: depicted_by "http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray1003.png" xsd:anyURI property_value: taxon_notes "In humans, there are two premolars per quadrant, making eight premolars total in the mouth. They have at least two cusps. Premolars can be considered as a 'transitional tooth' during chewing, or mastication. It has properties of both the anterior canines and posterior molars, and so food can be transferred from the canines to the premolars and finally to the molars for grinding, instead of directly from the canines to the molars. The premolars in humans are the maxillary first premolar, maxillary second premolar, mandibular first premolar, and the mandibular second premolar. There is always one large buccal cusp, especially so in the mandibular first premolar. The lower second premolar almost always presents with two lingual cusps. Premolar teeth by definition are permanent teeth distal to the canines preceded by deciduous molars. In primitive mammals there are four premolars per quadrant. The most mesial two have been lost in Catarrhines. Paleontologists refer to human premolars as Pm3 and Pm4" xsd:string @@ -139085,7 +139085,7 @@ name: spleen marginal sinus def: "The border region surrounding the spleen B cell follicles and the periarteriolar lymphoid sheath that separates it from the marginal zone that mediates lymphocyte entry into the white pulp from the blood." [MP:MP] subset: pheno_slim synonym: "splenic marginal sinus" EXACT [MP:0002363] -xref: EMAPA:37964 {source="MA:th", seeAlso="https://github.com/obophenotype/mouse-anatomy-ontology/issues/117"} +xref: EMAPA:37964 {seeAlso="https://github.com/obophenotype/mouse-anatomy-ontology/issues/117", source="MA:th"} xref: MA:0000754 xref: NCIT:C49776 xref: UMLS:C1710157 {source="ncithesaurus:Splenic_Marginal_Sinus"} @@ -142048,7 +142048,7 @@ synonym: "ventral nasal capsule" EXACT [PMID:21270050] xref: AAO:0000303 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: dubious_for_taxon NCBITaxon:8292 {IAO:0000116="check AAO"} ! Amphibia relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: overlaps UBERON:0001703 {source="TAO"} ! neurocranium relationship: part_of UBERON:0002241 {source="TAO"} ! chondrocranium @@ -151883,7 +151883,7 @@ xref: SCTID:361795009 xref: Wikipedia:Malleolus is_a: UBERON:0005913 ! zone of bone organ relationship: part_of UBERON:0004410 ! distal epiphysis of fibula -property_value: taxon_notes "In bovids, the distal end of the fibula is present only as the lateral malleolus, a separate bone that articulates with the lateral side of the distal tibia." xsd:string {scope="NCBITaxon:9895", seeAlso="UBERON:0004410", source="UBERON:skansa"} +property_value: taxon_notes "In bovids, the distal end of the fibula is present only as the lateral malleolus, a separate bone that articulates with the lateral side of the distal tibia." xsd:string {scope="NCBITaxon:9895", source="UBERON:skansa", seeAlso="UBERON:0004410"} [Term] id: UBERON:0012292 @@ -181505,7 +181505,7 @@ id: UBERON:0034930 name: auricular feather intersection_of: UBERON:0000022 ! feather intersection_of: surrounds UBERON:0001691 ! external ear -relationship: has_quality PATO:0001297 {editor_note="request more specific terms from PATO"} ! reflectivity +relationship: has_quality PATO:0001297 {IAO:0000116="request more specific terms from PATO"} ! reflectivity property_value: function_notes "the auricular feathers play a role in hearing by reflecting and funneling sound into the external acoustic meatus" xsd:string [Term] @@ -223934,7 +223934,7 @@ property_value: dcterms-date "2022-10-31T07:56:47Z" xsd:dateTime id: UBERON:8480041 name: testicular sheath def: "Bilayer sheath that covers both the insect male mature gonad and a portion of genital disc-derived structures. It is composed of an outer pigment cell layer, an inner muscle cell layer, and their respective basal laminae." [PMID:9553045] -synonym: "testis sheath" EXACT [] {http://purl.obolibrary.org/obo/IAO_0000232="https://www.fortunejournals.com/ijpaes/admin/php/uploads/798_pdf.pdf"} +synonym: "testis sheath" EXACT [] {IAO:0000232="https://www.fortunejournals.com/ijpaes/admin/php/uploads/798_pdf.pdf"} is_a: UBERON:0004923 ! organ component layer relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 ! Paula Duek Roggli relationship: in_taxon NCBITaxon:50557 ! Insecta