OLS not showing full axioms (nor synonym metadata)

EBISPOT / OLS

Ontology Lookup Service from SPOT at EBI

http://www.ebi.ac.uk/ols

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OLS not showing full axioms (nor synonym metadata) #229

Open paolaroncaglia opened 5 years ago

paolaroncaglia commented 5 years ago

I can't remember if this was discussed before, and I can't find relevant tickets or emails. It looks like full axioms for UBERON terms are not visible in OLS. E.g. the OLS entry for MONDO:0005071 'nervous system disorder' lacks the axiom "disease or disorder and (disease has location some nervous system)" in the "Term relations" box (https://www.ebi.ac.uk/ols/ontologies/mondo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMONDO_0005071); compare with Ontobee (http://www.ontobee.org/ontology/MONDO?iri=http://purl.obolibrary.org/obo/MONDO_0005071). Thanks.

paolaroncaglia commented 5 years ago

Also see https://github.com/EBISPOT/efo/issues/310

paolaroncaglia commented 5 years ago

The same issue was raised again today i.e. OLS not showing, in particular, disease location axioms for MONDO terms. Compare e.g. 'liver disease' in MONDO OLS vs Ontobee (same MONDO version):
https://www.ebi.ac.uk/ols/ontologies/mondo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMONDO_0005154 http://www.ontobee.org/ontology/MONDO?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMONDO_0005154 It's an important piece of information that many users would look for. Can this ticket be escalated to the 'Next' queue please? Thanks!

paolaroncaglia commented 5 years ago

@simonjupp Another example where axioms that may well be relevant for users (and for EFO) are not shown in OLS: Compare MONDO:0021166 'inflammatory disease' in OLS and Ontobee The former doesn't show 1) disease has inflammation site some anatomical structure 2) disease disrupts some inflammatory response

This ticket is in the Backlog queue, wondering if it shouldn't be given a bit more priority :-)

paolaroncaglia commented 5 years ago

Also, a reminder that "Unfortunately OLS doesn't show all of the metadata associated with a synonym. @simonjupp is aware of this" (see https://github.com/monarch-initiative/mondo/issues/739#issuecomment-522844894).

henrietteharmse commented 5 years ago

The reason why these axioms are missing from Mondo in OLS is because OLS loads the .obo file rather than the .owl file. These axioms are missing from the .obo file. Below I have screenshots from Protege usages for disease has location with IRI http://purl.obolibrary.org/obo/RO_0004026 for .obo vs .owl. mondo.obo

mondo.owl