Fix incompatibility with ZFA's "head". #3360
Conversation
In ZFA, the "head" (ZFA:0001114) corresponds to what Uberon calls the "craniocervical region" (UBERON:0007811), comprising the head proper and the neck. So we remap ZFA:0001114 to UBERON:0007811, rather than UBERON:0000033). Also, the axiom stating that 'pharyngeal arch' (UBERON:0002539) is part of the 'embryonic head' (UBERON:0008816) is bogus, as some pharyngeal arches are located in the neck rather than the head. So we create a new term 'embryonic craniocervical region' to be the embryonic counterpart of 'craniocervical region' (as 'embryonic head' is the embryonic counterpart of 'head'), and rewrite the aforementioned axiom to state that 'pharyngeal arch' is part of the 'embryonic craniocervical region'. Combined together, these two changes fix about 80 unsatisfiable classes in the merge product of Uberon and ZFA. closes #379
Not really useful for a definition that is merely the English translation of the logical definition, but it keeps the CI checks happy.
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#gogoeditdiff |
Here's a diff of how these changes impact the classified ontology (on -base file):Ontology comparisonLeft
Right
Ontology importsOntology annotations1st arch mesenchyme from head mesenchyme
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Here's a diff of your edit file (unreasoned)Ontology comparisonLeft
Right
Ontology importsOntology annotationscraniocervical region
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I am wondering if it would be benefitial to add a GCI |
Sounds sensible, but unsure about how beneficial it would be. Unfortunately the effects of adding such a GCI wouldn’t be shown by |
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yes, I used DL queries in Protégé and compared the results. |
Add the following GCI axiom
('part of' some embryo) and ('part of' some 'craniocervical region')
SubClassOf: 'part of' some 'embryonic craniocervical region'
In ZFA, the "head" (ZFA:0001114) corresponds to what Uberon calls the "craniocervical region" (UBERON:0007811), comprising the head proper and the neck. So we remap ZFA:0001114 to UBERON:0007811, rather than UBERON:0000033).
Also, the axiom stating that 'pharyngeal arch' (UBERON:0002539) is part of the 'embryonic head' (UBERON:0008816) is bogus, as some pharyngeal arches are located in the neck rather than the head. So we create a new term 'embryonic craniocervical region' to be the embryonic counterpart of 'craniocervical region' (as 'embryonic head' is the embryonic counterpart of 'head'), and rewrite the aforementioned axiom to state that 'pharyngeal arch' is part of the 'embryonic craniocervical region'.
Combined together, these two changes fix about 80 unsatisfiable classes in the merge product of Uberon and ZFA.
closes #379