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EBISPOT / OLS

Ontology Lookup Service from SPOT at EBI
http://www.ebi.ac.uk/ols
Apache License 2.0
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Can't find (existing) mapping in OLS #323

Open paolaroncaglia opened 4 years ago

paolaroncaglia commented 4 years ago

Hi,

If I search for OMIM:612431 in https://www.ebi.ac.uk/ols/ontologies/efo, I can't retrieve any meaningful entry. But OMIM:612431 is indeed a database cross reference in EFO > Orphanet:90635. I had noticed this behaviour before a handful of times, but I can't quite pin-point it - e.g. searching for OMIM:616568 will correctly retrieve EFO:0000326 as top match. (UniProt routinely needs OMIM mappings to be added to EFO, for Open Targets, so it's not ideal not being able to find mappings that already exist.) Could you advice, please?

Thanks! Paola

paolaroncaglia commented 4 years ago

Another example: if I search EFO in OLS for OMIM:613608 I can't find it, but OMIM:613608 is a dbxref for EFO > Orphanet:86814.

henrietteharmse commented 4 years ago

@paolaroncaglia There is an occasional issue regarding indexes that I have not been able to pinpoint exactly to be able to reproduce consistently. Without being able to reproduce consistently, a fix may be elusive.

For the moment I am still gathering evidence. Please can I ask you to add to this as you notice further issues?

paolaroncaglia commented 4 years ago

@henrietteharmse sure, will do if/as I come across similar issues. Thanks.

paolaroncaglia commented 4 years ago

@henrietteharmse As requested, here's one more example: If I search https://www.ebi.ac.uk/ols/ontologies/efo for 'isolated trigonocephaly', I retrieve EFO > Orphanet:3366 Isolated trigonocephaly; This has the dbxref MONDO:0018065; If I search https://www.ebi.ac.uk/ols/ontologies/efo for MONDO:0018065, I can't retrieve the right term.