Fix composite unsats #3099
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Fix composite unsats #3099
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The local CTENO mirror, used to produce composite-metazoan, contains several axioms coming from an old version of Uberon (CTENO has not been updated since 2016). One such axiom is 'surface groove' SubClassOf: 'surface structure' which *may* have been correct in 2016 but is clearly bogus now, since 'surface groove' (UBERON:0006846) is an immaterial anatomical entity whereas 'surface structure' (UBERON:0003102) is an anatomical structure (and thus a material anatomical entity). That single axiom is causing massive unsatisfiability issues when building composite-metazoan.
The local EHDAA2 mirror, used to build composite-metazoan, contains the following axiom: 'extra embryonic coelum' SubClassOf: 'attached to' some 'coelomic cavity lumen' This is wrong as 'attached to' (RO:0002371) is range- and domain-restricted to anatomical structures, while both 'extra embryonic coelum' (EHDAA2:0004739) and 'coelomic cavity lumen' (EHDAA2:0000267) are anatomical spaces (immaterial entities). This should really be fixed in EHDAA2, but the ontology is officially marked as inactive and has not seen any really meaningful edit for the past 8 years.
'serous sac' (UBERON:0005906) is mapped with EMAPA:16060. This is wrong, because the Uberon term represents an entire organ, made of a serous membrane surrounding an anatomical cavity, while the EMAPA term refers to a body cavity OR the lining that surrounds it. The Uberon term is necessarily a material entity, while the EMAPA term is not committed to being either a material entity or an immaterial entity. Mapping the two terms together results, when building composite-metazoan, in the EMAPA term becoming a subclass of the Uberon term, thereby forcing the EMAPA term to be a material entity. This causes several unsatisfiability issues because there are other Uberon terms that are mapped to subclasses of the EMAPA term but represent immaterial entities. Likewise for MA:0000005.
matentzn
approved these changes
Oct 26, 2023
anitacaron
approved these changes
Oct 26, 2023
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Amazing.. 😅 |
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While I am here, note to my future self and to anyone attempting to debug unsatisfiability issues in composite-metazoan (or any other composite-* product):
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This PR fixes unsatisfiable classes recently found in composite-metazoan by:
serous sacand EMAPA:16060 and MA:0000005.See individual commit messages for more details about each issue.