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Merged
matentzn merged 11 commits into from
Jan 16, 2026
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Merged

Issue 3027 #3516

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89524d4
adding nasal notch, staphylon, and facial crest
helenamachado Aug 18, 2023
1416dd6
Update uberon-edit.obo
meghalithic May 2, 2025
e648107
Update uberon-edit.obo
meghalithic May 2, 2025
c29061d
Merge branch 'master' into issue3027-fm
gouttegd May 6, 2025
bb926eb
Update uberon-edit.obo
meghalithic May 7, 2025
235cda7
Update uberon-edit.obo
meghalithic May 9, 2025
2fd2775
Update uberon-edit.obo
meghalithic May 10, 2025
063c7e1
Merge branch 'master' into issue-3027
matentzn Jan 16, 2026
7bcafd1
Normalise OBO EDIT source
matentzn Jan 16, 2026
4effce6
Update facial crest term and remove obsolete duplicate
matentzn Jan 16, 2026
a3547b2
Fix typo in nasal notch synonym
matentzn Jan 16, 2026
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55 changes: 46 additions & 9 deletions src/ontology/uberon-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -928,7 +928,7 @@ intersection_of: has_quality PATO:0002236 ! aliform
relationship: capable_of_part_of GO:0060361 ! flight
relationship: in_taxon NCBITaxon:33213 ! Bilateria
relationship: never_in_taxon NCBITaxon:118072 {source="bgee"} ! Coelacanthimorpha
relationship: never_in_taxon NCBITaxon:186634 {source="bgee", seeAlso="Wikipedia:Flying_fish"} ! Otomorpha
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
Expand Down Expand Up @@ -22373,7 +22373,7 @@ relationship: preaxialmost_part_of UBERON:0002398 ! manus
property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Thumb-up.jpg" xsd:anyURI
property_value: depiction "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", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012260"}
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"}

[Term]
id: UBERON:0001464
Expand Down Expand Up @@ -28057,7 +28057,7 @@ 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: depiction "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 {source="WP", seeAlso="https://github.com/obophenotype/uberon/issues/548"}
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"}

[Term]
id: UBERON:0001686
Expand Down Expand Up @@ -38532,7 +38532,7 @@ 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 {source="VHOG", source="Wikipedia", seeAlso="http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7"} ! Amphibia
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: in_taxon NCBITaxon:32523 ! Tetrapoda
relationship: innervates UBERON:0001737 ! larynx
relationship: innervates UBERON:3010692 {gci_relation="part_of", gci_filler="NCBITaxon:8292", source="ISBN:080184780X"} ! m. cucullaris
Expand Down Expand Up @@ -72964,8 +72964,8 @@ id: UBERON:0003532
name: hindlimb skin
def: "A zone of skin that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic]
synonym: "hind limb skin" EXACT [OBOL:automatic]
synonym: "lower limb skin" EXACT [FMA:23102]
synonym: "lower limb skin" EXACT [https://orcid.org/0000-0002-0819-0473]
synonym: "lower limb skin" EXACT [FMA:23102]
synonym: "skin of hind limb" EXACT [OBOL:automatic]
synonym: "skin of hindlimb" EXACT [OBOL:automatic]
synonym: "skin of lower extremity" EXACT [OBOL:automatic]
Expand Down Expand Up @@ -74529,7 +74529,7 @@ relationship: part_of UBERON:5003622 ! manual digit 2 plus metapodial segment
property_value: depiction "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", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012261"}
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"}

[Term]
id: UBERON:0003623
Expand Down Expand Up @@ -74566,7 +74566,7 @@ 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: depiction "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", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012262"}
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"}

[Term]
id: UBERON:0003624
Expand Down Expand Up @@ -138777,7 +138777,7 @@ 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 {seeAlso="https://github.com/obophenotype/mouse-anatomy-ontology/issues/117", source="MA:th"}
xref: EMAPA:37964 {source="MA:th", seeAlso="https://github.com/obophenotype/mouse-anatomy-ontology/issues/117"}
xref: MA:0000754
xref: NCIT:C49776
xref: UMLS:C1710157 {source="ncithesaurus:Splenic_Marginal_Sinus"}
Expand Down Expand Up @@ -151538,7 +151538,7 @@ 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", source="UBERON:skansa", seeAlso="UBERON:0004410"}
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"}

[Term]
id: UBERON:0012292
Expand Down Expand Up @@ -221095,6 +221095,18 @@ relationship: dc-contributor https://orcid.org/0000-0001-8415-4848 ! Helena Mach
relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 ! Meghan Balk
property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/2882" xsd:anyURI

[Term]
id: UBERON:7500131
name: facial crest
def: "A ridge or similar projection on the lateral side of the cranium that crosses the zygomatic bone and extends to the maxilla and ends on the facial tubercle (tuber faciale)." [https://orcid.org/0000-0001-8415-4848]
synonym: "crista facialis" EXACT []
intersection_of: UBERON:4200133 ! crest
intersection_of: part_of UBERON:0007681 ! facial neural crest
relationship: part_of UBERON:0002397 ! maxilla
relationship: part_of UBERON:0004654 ! temporal process of zygomatic bone
property_value: curator_notes "very prominent in ruminants and equids; short in carnivorans and pigs: https://www.imaios.com/en/vet-anatomy/anatomical-structures/facial-crest-11073890400#" xsd:string
property_value: dc-contributor "https://orcid.org/0000-0003-2699-3066" xsd:string

[Term]
id: UBERON:8000000
name: first instar larva stage
Expand Down Expand Up @@ -223972,6 +223984,31 @@ is_a: UBERON:0006983 ! anatomical point
relationship: dc-contributor https://orcid.org/0000-0001-8415-4848 ! Helena Machado
relationship: part_of UBERON:0001697 ! orbit of skull

[Term]
id: UBERON:8500006
name: nasal notch
def: "Anatomical point of cranium between nasal process of premaxilla and nasal bone, at the anteriormost end of the suture." [isbn:9783830410690]
synonym: "nasoincisve notch" EXACT []
is_a: UBERON:0006983 ! anatomical point
relationship: part_of UBERON:0001681 ! nasal bone
relationship: part_of UBERON:0002244 ! premaxilla
property_value: dc-contributor "https://orcid.org/0000-0001-8415-4848" xsd:string

[Term]
id: UBERON:8500007
name: staphylon
def: "Anatomical point of cranium; the most aboral point of the horizontal part of the palate in the median plane." [isbn:9780873659505]
is_a: UBERON:0006983 ! anatomical point
relationship: part_of UBERON:0012071 ! palate bone
property_value: dc-contributor "https://orcid.org/0000-0001-8415-4848" xsd:string

[Term]
id: UBERON:8500008
name: DEPRECATED Facial crest
comment: accidentally duplicated term
relationship: seeAlso UBERON:7500131 ! facial crest
is_obsolete: true

[Term]
id: UBERON:8600000
name: lobular bronchiole
Expand Down
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