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[bioontology-support] MeSH in French version

Eugene eugene at nextbio.com
Tue Apr 6 14:38:01 PDT 2010


Before you provide MeSH for French download, do you have idea where I can download French version from some website?

Thanks

Eugene

From: Eugene
Sent: Monday, April 05, 2010 2:49 PM
To: 'Trish Whetzel'
Cc: support at bioontology.org
Subject: RE: [bioontology-support] MeSH in French version

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<mailto: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> [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<mailto: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> [mailto: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<mailto: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<mailto: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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