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Yep, this is separate from the GA = PA-2 formula (which is all correct and synchronized across ontologies, with the exception of some remaining confusion in XAO).
This issue is entirely about the relation used and the confusion arising from the fact that some people use the term "arch" to denote the sekeletal subdivision - so switching from part_of to develops_from should not be a problem then.
currently (in ext):
gill arch 1 skeleton part_of some part_of some 'pharyngeal arch 3'
this was inherited from TAO. In fact the arches as embryonic in uberon - replace with develops_from?
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