NCIT:Endometabolome, NCIT:Exometabolome not found by OLS?

[jonathan-hunter]

NCIT terms below not returned in OLS? I don't think these are super new or obsolete based on a quick look at the NCIT OWL file. Any ideas what is happening here? Apologies if I am missing something obvious.

NCIT:Endometabolome
NCIT:Exometabolome

To Reproduce
Steps to reproduce the behavior:

1. Navigate to NCIT Ontology page on OLS web.
2. Search 'Endometabolome' or 'Exometabolome' in the 'Search NCIT...' search box.
3. No results!

Expected behavior
Return the terms from NCIT as per bioportal.

[haideriqbal]

@jonathan-hunter both of these terms you have mentioned do not exist in NCIT owl file hence aren't loaded into OLS. At OLS the purl file for NCIT is: http://purl.obolibrary.org/obo/ncit.owl and the file downloaded via this doesn't contain these terms.

It may be that BioPortal is using a different OWL file for NCIT.

[jonathan-hunter]

Hi @haideriqbal Thanks for the response.

On closer inspection I can see that the "ncit-obo-edition" .owl is missing the terms, but the original Thesaurus.OWL does contain them. It appears to be a consequence of the conversion process.

NCIT OWL https://evs.nci.nih.gov/ftp1/NCI_Thesaurus/Thesaurus.OWL.zip

NCIT OBO OWL http://purl.obolibrary.org/obo/ncit.owl

https://github.com/OBOFoundry/purl.obolibrary.org/blob/master/config/ncit.yml

From products:
- ncit.owl: https://github.com/ncit-obo-org/ncit-obo-edition/releases/latest/download/ncit.owl

https://github.com/ncit-obo-org/ncit-obo-edition/blob/7cbc5cb73396cede71ff6c4154042e8dcab567ce/src/ontology/Makefile#L32

Thesaurus.owl:
 	curl -L -O https://evs.nci.nih.gov/ftp1/rdf/Thesaurus.owl

This version does contain the Endo/exometabolome terms also.

Therefore, it appears that the terms are being dropped during the conversion process. I will raise this in the ncit-obo-org/ncit-obo-edition repo also.

[jonathan-hunter]

The ncit-obo-org converter has been updated and a new NCIT(OBO).owl release made. This oughta propogate to OLS at some point in the near future, I believe. Will close this issue when the terms appear.

[haideriqbal]

@jonathan-hunter these terms are now in OLS. Have a look: https://www.ebi.ac.uk/ols4/ontologies/ncit/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FNCIT_C222306

[jonathan-hunter]

Thanks @haideriqbal