Fix hierarchy under anatomical cluster (part 1) #2862
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Align the definition of 'anatomical cluster' with the one used in FBbt.
Remove cross-references on 'anatomical cluster' that no longer match the updated meaning of the term. This includes FMA:49443 and CARO:0000041, as well as all the terms in other ontologies that are merely "copies" of CARO:0000041.
Re-classify a handful of terms that were classified as 'anatomical cluster' but do not fit the meaning of that term.
ghost
reviewed
Apr 5, 2023
ghost
reviewed
Apr 5, 2023
| @@ -209360,7 +209348,7 @@ property_value: provenance_notes "This class was sourced from an external ontolo | |||
| id: UBERON:3000809 | |||
| name: accessory articulation | |||
| def: "Paired, additional vertebral articulations located medial to the intervertebral space, adjacent to the vertebral centrum." [AAO:Cannatella_1985] | |||
| is_a: UBERON:0000477 ! anatomical cluster | |||
| is_a: UBERON:0034921 ! multi organ part structure | |||
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Unsure if this refers to something that is "multi organ".
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Each vertebra is individually considered as a separate “organ” (a vertebra is a vertebral element, which is a skeletal element, which is an organ), so I think it is consistent to say that an articulation between two vertebrae is a “multi organ part structure“ – it involves subparts of two different organs, which fits the definition of “multi organ part structure“.
But this makes me realise that this term can be classified even more precisely under articulation (UBERON:0004905), which is a subclass of multi organ part structure. I’ll do that now.
ghost
approved these changes
Apr 5, 2023
The EHDAA2:0003041 cross-reference points to a term that can't be found anywhere, so we remove it.
'articulation' is a more precise parent for 'accessory articulation' than 'multi organ part structure'.
To avoid needless confusion, terms that are not classified as 'anatomical cluster' should not use the word 'cluster' in their definition.
ghost
approved these changes
Apr 5, 2023
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This PR is a first step towards fixing the hierarchy under anatomical cluster, as discussed in #2819 (especially this comment.
It clarifies the definition of anatomical cluster to align it with the one used in FBbt, and moves out of the hierarchy all the terms that undoubtedly do not fit the definition.
Importantly, the re-classification of hard palate as something else than an anatomical cluster fixes the unsatisfiability of uvular muscle and related terms, because that muscle
has_muscle_insertionto the hard palate, and thehas_muscle_insertionrelation applies to connected anatomical structures only (which a cluster is not).