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[bioontology-support] inconsistent issues between BioPortal and MeSH

Natasha F. Noy noy at stanford.edu
Fri Oct 15 16:36:16 PDT 2010


I think I understood your question correctly. What I was saying was  
that BioPortal cannot distinguish the two sets of children that show  
up in different subtrees on the NIH site. In other words, what you  
will see as children of "Neoplasm, Experimental" would be the union of  
these two sets of children. And indeed that is what you see in  
BioPortal:

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Some of these subclasses of "Neoplasm, Experimental" appear in one of  
the trees on the NIH site and some in the other. Unfortunately, our  
underlying data model does not enable us to distinguish between the  
different sets of children of  a class, as in: "show these subclasses  
of X if you are viewing X as a child of Y; and show different  
subclasses of X if you are viewing X as a child of Z". The NIH browser  
does make this distinction though.

Natasha


On Oct 15, 2010, at 3:42 PM, Eugene wrote:

> Natasha,
>
> I think you misunderstood my point.
>
> My previous email (see enclosed file) said that those disease terms  
> unexpectedly appear in Investigation Techniques sub-branch in  
> **BioPortal**. The top root of those terms are "Analysis, ..."  
> That's nothing to do with disease branch.
>
> Can the BioPortal team at Stanford fix this kind of problem?
>
> Eugene
>
>
> -----Original Message-----
> From: Natasha F. Noy [mailto:noy at stanford.edu]
> Sent: Friday, October 15, 2010 2:54 PM
> To: Eugene
> Cc: support at bioontology.org; nigam at stanford.edu
> Subject: Re: [bioontology-support] inconsistent issues between  
> BioPortal and MeSH
> Importance: High
>
> Eugene,
>
> Here is what is happening: in the MSH browser on the NLM page, a  
> term gets different children depending on how you got to the term.  
> See for example http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&term=Neoplasms,+Experimental&field=entry
>
> This is the page for your term: Neoplasm, Experimental.
>
> It shows two trees: one with this term under Diseases and another  
> one under Investigative Techniques. There, "Neoplasm, Experimental"  
> has different children in these two different tress:
>
>
>
> From: Eugene <eugene at nextbio.com>
> Date: October 15, 2010 11:44:02 AM PDT
> To: "support at bioontology.org" <support at bioontology.org>
> Cc: "nigam at stanford.edu" <nigam at stanford.edu>
> Subject: inconsistent issues between BioPortal and MeSH
>
>
> Dear Sir or Madam,
>
> Yesterday I have posted an inconsistency issue. Today we just found  
> another similar issue described in the following after we download  
> the ontology from BioPortal. There is inconsistency  
> betweenBioPortaland official MeSH and UMLS portal.
>
> In the following, those circled terms are diseases, but they are put  
> under Technique/Procedure ontology.
>
> <image003.png>
>
>
> I have checked MeSH and UMLS portals. The actual children of  
> ?Nepolasms, Experimental? is shown in the following:
>
> <image002.png>
>
> Could you evaluate and fix if that?s a bug?
>
> Please let us know what you want to do for this issue and  
> yesterday?s (I posted similar issue yesterday).
>
> Thanks
>
> Eugene
>
>
>



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