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

Marijane White whimar at ohsu.edu
Thu Jul 22 11:47:11 PDT 2021


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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