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

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Jul 22 11:58:20 PDT 2021


OK, thanks for this clarification Marijane. 

I didn’t see this until after I sent another message detailing the fact that BioPortal imports the NCBI Taxonomy from a different source than OLS and Ontobee.

So, it appears that there are two separate issues:

1). We’re serving an older version of NCBI Taxonomy from May of last year (sourced from the UMLS Metathesaurus)

2). The UMLS Metathesaurus version of NCBI Taxonomy doesn’t include concepts below the species level

Again, I’ll speak with our technical program manager about our import process to see if BioPortal should be modified to retrieve NCBI Taxonomy from an alternate source.

Kind regards,
Jennifer



> On Jul 22, 2021, at 11:47 AM, Marijane White <whimar at ohsu.edu> wrote:
> 
> The UMLS Metathesaurus vocabulary documentation for the NCBI Taxonomy indicates that it does not include concepts below the species level in the taxonomy, and Canis lupis familiaris is a subspecies of the Canis lupus species. So yes, the UMLS Metathesaurus version of the NCBI Taxonomy is not complete.
> 
> https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NCBI/index.html
> 
> 
> Marijane White, M.S.L.I.S.
> Data and Research Engagement Librarian, Assistant Professor
> Oregon Health & Science University Library
> 
> Email: whimar at ohsu.edu
> ORCiD: https://orcid.org/0000-0001-5059-4132
> 
> 
> On 7/22/21, 10:55 AM, "bioontology-support on behalf of mwilliam" <bioontology-support-bounces at lists.stanford.edu on behalf of mwilliam at ebi.ac.uk> wrote:
> 
> 
>    Hi Jennifer,
> 
>    The term exists here:
>    http://purl.obolibrary.org/obo/NCBITaxon_9615
> 
>    Also in the NCBI Taxonomy browser:
>    https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9615
> 
>    Also here:
>    https://www.ebi.ac.uk/ols/search?exact=true&q=NCBITaxon_9615
> 
>    So it could well be that the version of NCBITAXON accessed by bioportal 
>    is incomplete.
> 
>    Cheers,
> 
>    Mark
> 
> 
> 
>    On 2021-07-22 18:18, Jennifer Leigh Vendetti wrote:
>> Hello Mark,
>> 
>>> On Jul 21, 2021, at 8:47 AM, support at bioontology.org wrote:
>>> 
>>> Feedback:
>>> 
>>> Hi,
>>> The NCBITAXON term for dog, Canis lupus familiaris, is not returned.
>> 
>> We import the NCBI Taxonomy from the National Library of Medicine’s
>> UMLS Metathesaurus. I used their browser software to search for the
>> term you listed above of "Canis lupus familiaris”. I only see one
>> result where this string occurs: "Wolbachia endosymbiont of Canis
>> lupus familiaris” (screenshot below). This matches what BioPortal
>> returns if you execute the same search against our NCBITAXON entry.
>> 
>> Could you offer more clarification on what you expected to see here?
>> 
>> Thanks,
>> Jennifer
>> 
>> UMLS Metathesaurus browser search result:
>> 
>> BioPortal search result:
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