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FlyBase / drosophila-anatomy-developmental-ontology

The home of the Drosophila anatomy ontology
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sort out muscles #1128

Open Clare72 opened 3 years ago

Clare72 commented 3 years ago

All existing muscle terms are for cells, however most authors use the word 'muscle' to refer to a complete muscle containing all the muscle cells of the same type. This is a potentially confusing discrepancy between the ontology and common usage.

For clarity, we should add 'cell' to the label of each existing term. We also have a mixture of 'somatic' and 'skeletal' in muscle names - these should probably all be 'somatic' based on usage (from research for #915).

We may also want a term to represent the complete muscle for each somatic muscle.

We currently use 'attached to' for linking muscle cells to their attachment sites, but it is actually the tendon cell that is attached to both. It would be more accurate to move these relationships to the complete muscle terms (including tendons as part of the muscle).

There also seem to be some redundant terms - we have some grouping terms with only one direct subclass e.g. 'adductor muscle', 'tergal remotor muscle', so the hierarchy could probably be simplified a bit. We also have a term 'occlusor muscle' with no definition, no references and no associated curation in FlyBase - so not a very useful term! I suspect there are other examples where terms can be merged/obsoleted.

SianGramates commented 3 years ago

I'm concerned that this (adding 'cell' to each muscle term) conflicts with decades-old common usage. Muscles are a weird cell case, being multinucleate syncytia. I'm wondering if this change is better left as part of the definition of individual muscles, and not included in the name.

Clare72 commented 3 years ago

Adding cell to each term will make the labels better match the existing meanings of these terms (reducing ambiguity) and this also matches usage in the cell ontology. It will also allow the previous names to be reused to refer to the 'complete' muscles, including tendon cells.