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

mwilliam mwilliam at ebi.ac.uk
Thu Jul 22 16:27:27 PDT 2021


Hi Jennifer and Marijane,

Thank you both for looking into this.

At the end of day, Dogs and cats need parity :-)

Have a lovely evening. It's past midnight in the UK and we are still 
sweltering.

Cheers,

Mark


On 2021-07-22 19:58, Jennifer Leigh Vendetti wrote:
> 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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>>    https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> 


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