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Use of uberon classes for generic anatomical structures means taxon restrictions are too strict #13898
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Chris will work out importing the CARO term. |
interesting, this is revealing previously cryptic inconsistencies in GO: This was not revealed before; we already had an axiom classifying CL cell under CARO anatomical structure, but because we weren't using CARO in GO there was no linkage and hence this problem went unnoticed. Good choice to go with CARO everyone! I'll remove the disjoints in this PR cc @dosumis |
Ahh, we even annotated this disjointness axiom with a comment:
It seems we have reverted from this, and now consider 'anatomical structure P' in GO to be consistently about generic anatomical structures. We could bring in a gross AS later but not clear if this worth it |
I have done my bit See the linked PR. Merging this will result in a few new classifications under 'anatomical structure maturation', since cells are now anatomical structures |
I think I found another problem. 'zygote asymmetric cell division' is linked to 'animal zygote' (CL term for zygote) but has a child 'zygote asymmetric cell division in embryo sac'. The latter is a plant term. http://amigo.geneontology.org/amigo/term/GO:0010070#display-lineage-tab Is there a CARO term for 'zygote'? @cmungall, how to fix this one? |
Arose from this: obophenotype/cell-ontology#454 "We will not add a new generic class now, though we can explore this in future if a use case arises (note we would need an inter-ontology subclass with PO)" guess we have the use case now |
From
geneontology/go-site#403
this introduces an existential dependence between ASs and zygotes, causing problems for use of terms like cell morphogenesis in yeast
We should either
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