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[bioontology-support] [BioPortal] Feedback from Mark Williams

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Jul 22 11:51:52 PDT 2021


Hi Mark,


On Jul 22, 2021, at 10:55 AM, mwilliam <mwilliam at ebi.ac.uk<mailto:mwilliam at ebi.ac.uk>> wrote:

The term exists here:
http://purl.obolibrary.org/obo/NCBITaxon_9615


This resolved to the term in the Ontobee application. I looked at the Ontobee NCBI homepage. It appears that they import NCBI from a different source than we do. There’s a GitHub repository that contains code for taking the NCBI taxonomy database and translating it to OBO and OWL versions:

https://github.com/obophenotype/ncbitaxon

As I mentioned in my previous reply, we import NCBI Taxonomy from the UMLS Metathesaurus. We’re currently serving the 2020AB release of the metathesaurus. I looked at their vocabulary documentation and it appears that 2020AB contains version “NCBI2020_05_21” of the NCBI Taxonomy:

https://wayback.archive-it.org/4253/20201103055331/https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NCBI/metadata.html

I assume the latter portion of the version string means that it’s a version from May of last year.



Also in the NCBI Taxonomy browser:
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9615


I assume this is the canonical source



Also here:
https://www.ebi.ac.uk/ols/search?exact=true&q=NCBITaxon_9615


It looks like OLS is serving a much more recent version of the ontology from June 10th of this year.



So it could well be that the version of NCBITAXON accessed by bioportal is incomplete.


I think we’re serving the complete version of what was exposed in the 2020AB release of the UMLS Metathesaurus. This appears to be an older version though, compared to what OLS and Ontobee serve. I’ll speak with our technical program manager and see if we can change our process to use the version that’s generated by the GitHub obophenotype/ncbitaxon project.

Kind regards,
Jennifer

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