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[bioontology-support] MeSH in French version

Trish Whetzel whetzel at stanford.edu
Tue Apr 6 15:01:43 PDT 2010


Hi Eugene,

I'm not quite sure I understand the question. The link below is to  
SNOMED CT and is the output from the BioPortal Web services, which is  
in XML.

With respect to any changes in the Web service signatures and/or XML  
content, announcements are sent via the bioportal-announce mailing  
list (https://mailman.stanford.edu/mailman/listinfo/bioportal- 
announce) to let developers know of the changes ahead of time and test  
out code changes on the Stage server prior to the production release.

Trish


On Apr 5, 2010, at 2:48 PM, Eugene wrote:

> Can we use the following link to get French version rather than  
> ViewExtractor? I was aware your View Extractor has download  
> limitation=, but not sure if that has been fixed yet.
>
> http://rest.bioontology.org/bioportal/virtual/ontology/1353/373673007?email=example@example.org
>
> Thanks
>
> Eugene
>
> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> Sent: Friday, April 02, 2010 5:41 PM
> To: Eugene
> Cc: support at bioontology.org
> Subject: Re: [bioontology-support] MeSH in French version
>
> 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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