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[bioontology-support] MeSH in French version

Trish Whetzel whetzel at stanford.edu
Fri Apr 2 17:41:28 PDT 2010


Hi Eugene,

I put in a request to load the French version of MeSH. BioPortal does  
accommodate foreign language versions of ontologies using the Views  
mechanism. If you go to MeSH at:
-http://bioportal.bioontology.org/ontologies/42142
-click on 'Views' in the menu above the metadata description, i.e. the  
menu above the row starting with Ontology Name
-click on 'Expand All', the information on the Spanish version of MeSH  
is displayed. This should be visible from: http://bioportal.bioontology.org/ontologies/42142#views

The French version will also be loaded as a View and listed on this  
page.

Trish


On Apr 2, 2010, at 1:19 PM, Eugene wrote:

>
> I wonder if it is possible for us to download foreign language  
> ontologies from your website? Such as MeSH French, etc. I know  
> currently you don’t have this feature. Can you add this feature?
>
> Thanks
>
> Eugene
>
>
>
>
>
> From: Nigam Shah [mailto:drnigam at gmail.com]
> Sent: Friday, April 02, 2010 12:43 PM
> To: Eugene
> Subject: Re: MeSH in French version
>
> No one asked for it. If you make a request to support it can get  
> added.
>
> From my phone.
>
> On Apr 2, 2010, at 12:27 PM, Eugene <eugene at nextbio.com> wrote:
>
> Nigam,
>
> Thanks.
>
> It seems the bioontology website only lists English version of MeSH.  
> Do you have French version?
>
> Eugene
>
> From: drnigam at gmail.com [mailto:drnigam at gmail.com] On Behalf Of  
> Nigam Shah
> Sent: Thursday, April 01, 2010 3:02 PM
> To: Eugene
> Subject: Re: View extractor in OWL format
>
> Here is the code: http://smi-protege.stanford.edu/svn/bp-view-extractor/?rev=18182#dirlist 
>  that drives the view extractor. Most of the work is happening in:
>
> http://smi-protege.stanford.edu/svn/bp-view-extractor/trunk/src/org/ncbo/stanford/extractor/OntologyExtractor.java?rev=18000&view=markup
>
> --Nigam.
>
> On Wed, Mar 31, 2010 at 10:27 PM, Eugene <eugene at nextbio.com> wrote:
> Nigam,
>
> Your ViewExtractor writes to OWL format. Do you use some open source  
> such as Jena? Would you mind doing us a favor? Could you give us  
> some coding example?
>
> It’s not easy to find coding examples for generating OWL format in  
> the internet.
>
> Thank you very much
>
> Eugene
>
>
> From: drnigam at gmail.com [mailto:drnigam at gmail.com] On Behalf Of  
> Nigam Shah
> Sent: Wednesday, March 24, 2010 11:13 AM
> To: Eugene
> Subject: Re: view extractor in bioontology
>
> Also see http://bioportal.bioontology.org/visualize/42142/?conceptid=D000820 
>  .. for the example you were trying to use. The UMLS cui is what you  
> were using, its not the MSH id.
>
> --n.
>
> On Wed, Mar 24, 2010 at 11:10 AM, Nigam Shah <nigam at stanford.edu>  
> wrote:
> Yes. C000304 is not an ID from MSH. You are using a CUI, those are  
> assigned by the UMLS metathesaurus .. MSH ids are of the form  
> D008545 (e.g. for Melanoma). So the call would be http://rest.bioontology.org/bioportal/virtual/ontology/1351/D008545?email=example@example.org
>
> --Nigam.
>
> On Wed, Mar 24, 2010 at 11:04 AM, Eugene <eugene at nextbio.com> wrote:
> Hi,
>
> I have a question.
>
> The following url is working for SnoMed CT ontology.
>
> http://rest.bioontology.org/bioportal/virtual/ontology/1353/2704003?email=example@example.org
>
> However, I am changing to use MeSH to the following:
>
> http://rest.bioontology.org/bioportal/virtual/ontology/1351/C0003047?email=example@example.org
>
> 1351: MeSH ontology id
> C0003047: “animal disease” concept id.
>
> Now, it doesn’t work. Is the parameter wrong?
>
> Thanks
>
> Eugene
>
>
>
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> bioontology-support at lists.stanford.edu
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