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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
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39 changes: 39 additions & 0 deletions src/ontology/uberon-edit.obo
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Expand Up @@ -184,6 +184,7 @@ property_value: doap-SVNRepository "https://obo.svn.sourceforge.net/svnroot/obo/
property_value: foaf-homepage "http://uberon.org" xsd:anyURI
property_value: has_ontology_root_term UBERON:0000104
property_value: has_ontology_root_term UBERON:0001062
owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001474>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/UBERON_0007681>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/UBERON_4200133>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/UBERON_4200230>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/UBERON_7500131>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/UBERON_8500006>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>))\n\n############################\n# Classes\n############################\n\n# Class: <http://purl.obolibrary.org/obo/UBERON_7500131> (<http://purl.obolibrary.org/obo/UBERON_7500131>)\n\nSubClassOf(<http://purl.obolibrary.org/obo/UBERON_7500131> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_4200133> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0007681>)))\n\n# Class: <http://purl.obolibrary.org/obo/UBERON_8500006> (<http://purl.obolibrary.org/obo/UBERON_8500006>)\n\nSubClassOf(<http://purl.obolibrary.org/obo/UBERON_8500006> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UBERON_4200230> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001474>)))\n\n\n)
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@gouttegd gouttegd May 2, 2025

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You are trying to insert the following axiom:

'facial crest' SubClassOf: 'crest' and ('part of' some 'facial neural crest')

Such an axiom cannot be represented in “pure” OBO format, hence the introduction of this owl-axioms tag.

If you intended to say a 'facial crest' is both a 'crest' and something that is 'part of' some 'facial neural crest', you should do so in two independent SubClassOf axioms, there is no need for an ObjectIntersectionOf.

If you intended to say that any 'crest' that is 'part of' some 'facial neural crest' is a 'facial crest', then what you need is a EquivalentTo axiom, not a SubClassOf axiom. Such an axiom is representable in “pure” OBO.

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@meghalithic meghalithic May 2, 2025

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@gouttegd do you have any guidance for when EquivalentTo should be used ('crest' and 'part of' some 'facial neural crest') or SubClaseOf ('crest', 'part of' some 'facial neural crest')? The facial crest is not a crest can pop up anywhere (as seems to be facial neural crest), it is specifically on the lateral side between the maxilla and zygomatic arch.

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@gouttegd gouttegd May 2, 2025

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There are some pages on the OBOOK about the issue (for example here and here), though it’s nowhere near as complete as it should be IMHO.

But the most important rule of thumb, I believe, is: When in doubt, use SubClassOf. :) Whenever you are unsure which of SubClassOf or EquivalentTo is more appropriate, it can never be wrong to use SubClassOf (the worst that can happen is that you will make a statement that won’t be as “strong” as it should be, but that will be correct all the same).

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@gouttegd gouttegd May 2, 2025

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However, independently of the choice between SubClassOf and EquivalentTo, there may also be a problem with the term involved: are you sure this 'facial crest' is 'part of' some 'facial neural crest'?

'facial neural crest' is a part of the neural crest, an embryonic structure. That does not seem to fit well with the text definition.

Of note, the original term requested had proposed a logical definition involving 'facial skeleton', not 'facial neural crest'.

treat-xrefs-as-has-subclass: EHDAA
treat-xrefs-as-has-subclass: EV
treat-xrefs-as-has-subclass: NCIT
Expand Down Expand Up @@ -221503,6 +221504,16 @@ relationship: dc-contributor https://orcid.org/0000-0001-8415-4848
relationship: dc-contributor https://orcid.org/0000-0003-2699-3066
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 []
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 @@ -224249,6 +224260,34 @@ is_a: UBERON:0006983 ! anatomical point
relationship: dc-contributor https://orcid.org/0000-0001-8415-4848
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 []
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: Facial crest
def: "A ridge or similar projection rising above the surface of the lateral side of the cranium that crosses the zygomatic bone, extends to the maxilla and end on the facial tuberble." [https://orcid.org/0000-0001-8415-4848]
synonym: "crista facialis" EXACT []
intersection_of: UBERON:4200133 ! crest
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@gouttegd gouttegd May 6, 2025

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Given that the term has never made it into a public release (it did not even make it into the master branch!), it would have been perfectly acceptable to simply delete it without leaving a trace.

intersection_of: part_of UBERON:0011156 ! facial skeleton
relationship: part_of UBERON:0002397 ! maxilla
relationship: part_of UBERON:0004654 ! temporal process of zygomatic bone
property_value: dc-contributor "https://orcid.org/0000-0001-8415-4848" xsd:string

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