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[bioontology-support] inconsistent issues between BioPortal and MeSH

Nigam Shah nigam at stanford.edu
Mon Oct 18 22:38:44 PDT 2010


Hi Eugene,

The context information is in the MRHIER tables from UMLS sources. We
currently compute our hierarchy only from the MRREL tables (by a recursive
'get parent' call). MRREL does not distinguish b/w parent/child
relationships based on context. (You can verify in UMLSKS by seeing the "Raw
view" and then the mrhier and mrrel data). So for a term such as "Carcinoma,
Ehrlich Tumor" you get a parent term "Neoplasms, Experimental', which has
two parents

- Disease Model, Animal
- Neoplasms

.. both of which get assigned as grand-parents of "Carcinoma, Ehrlich
Tumor", causing it to show up under Disease Model, Animal. We'll get back to
you with a plan on how to handle this issue of differing parent nodes based
on "context". My guesstimate is that this issue affects a small number of
paths and would be localized to MeSH.

Regards,
Nigam.

On Fri, Oct 15, 2010 at 10:15 PM, Eugene <eugene at nextbio.com> wrote:

>  Nigam,
>
> Your screen shot shows the children of "carcinoma, experimental". But the
> context information for that screen shot is probably under "disease" branch.
> Certainly, in that disease branch, BioPortal is matched with UMLS. However,
> if we look at the children of "carcinoma, experimental" under "analytical ..
> technique" branch in UMLS, we find that BioPortal is not matched with UMLS.
>
> Enclosed is the screen shot that I have captured from UMLS. The screen shot
> explains what I said above. Context 1 is for "analytical.. technique"
> branch. Context 2 is for disease branch. The children of "carcinoma,
> experimental" are different under different context.
>
> The screen shots attached in my previous email were captured from BioPortal
> (1st screen shot) and MeSH portal (2nd screen shot). Both were under
> "Analytical... technique" root concept, but the children of  "carcinoma,
> experimental" are different between BipoPortal and MeSH portal.
>
> Eugene
>
>
>
>  ------------------------------
> *From:* Nigam Shah [nigam at stanford.edu]
> *Sent:* Friday, October 15, 2010 9:58 PM
>
> *To:* Eugene
> *Cc:* support at bioontology.org
> *Subject:* Re: inconsistent issues between BioPortal and MeSH
>
>  Hi Eugene,
>
>  UMLS has the relations exactly the same way we have them. See attached
> screen shot from UMLSKS as of tonight. Where is the screenshot you provided
> from? Natasha and I will discuss this further Monday, but right now, we show
> exactly what the UMLSKS is showing.
>
>  --Nigam.
>
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