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oborel / obo-relations

RO is an ontology of relations for use with biological ontologies
http://oborel.github.io/
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has_skeleton - add domain and range #700

Open dosumis opened 1 year ago

dosumis commented 1 year ago

has_skeleton - RO:0002551 should have: domain: UBERON:0000475 ! organism subdivision range: UBERON:0010912 ! subdivision of skeleton

See https://github.com/obophenotype/uberon/issues/2453#issuecomment-1383824700

cmungall commented 1 year ago

uberon query -q "SELECT * FROM edge WHERE predicate='RO:0002551' AND object NOT IN (SELECT subject FROM entailed_edge WHERE predicate='rdfs:subClassOf' AND object='UBERON:0010912')"

A few exceptions:

subject subject_label predicate predicate_label object object_label
UBERON:0000376 hindlimb stylopod RO:0002551 has skeleton UBERON:0015052 femur endochondral element
UBERON:0003822 forelimb stylopod RO:0002551 has skeleton UBERON:0015053 humerus endochondral element
UBERON:0005473 sacral region RO:0002551 has skeleton UBERON:0006075 sacral region of vertebral column
UBERON:0006071 caudal region RO:0002551 has skeleton UBERON:0006076 caudal region of vertebral column
UBERON:0015875 heel RO:0002551 has skeleton UBERON:0001450 calcaneus

the femur/humerus axioms look odd but they reflect the fact we have avoided naming subdivisions where there is only a single bone. We could revisit this decision but if we add a hindlimb stylopod subdivision of skeleton we should make it clear that curators should avoid this term for annotation and instead use the appropriate femur term.

The heel situation is similar. The "heel skeleton" is just the calcaneous (not sure if this holds for all species with a "heel")

The vertebral column ones are a bit odd, they are a consequence of the distinction between skeletal system (includes joints, such as intervertebral joints) and skeleton (no joints).

unfortunately resolving this will take a bit of work. We could choose to have parallel subdivisions (one including joints, one excluding). Or we could choose to center on the most inclusive one - but this would be a huge refactor, and may introduce disconnect with FMA.

ghost commented 1 year ago

Of note- this issue is dependent on the completion of https://github.com/oborel/obo-relations/issues/695 as there is currently no Uberon import to RO. Without the import, the requested domain and range can not fully be added.

wdduncan commented 1 year ago

@bvarner-ebi The issue of whether RO needs to explicitly include classes mentioned as domains/ranges is important. See #701.

wdduncan commented 1 year ago

Does this issue need to be add to the RO agenda for 03/28 or can it be handled off line?

wdduncan commented 1 year ago

Notes from RO call:

dosumis commented 1 year ago

@cmungall - you comment above is a bit worrying as it looks like this causes some problems and we don't have a clear plan to fix. OTOH - this axiom is still in Uberon, so moving here would just continue the status quo.

Suggestion for how to proceed: If you are happy to keep this domain, could you add a ticket to Uberon with some details of the edits needed to fix any problems it causes. Otherwise maybe we should drop this ticket and drop the axiom from Uberon?