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[bioontology-support] MeSH in French version

Eugene eugene at nextbio.com
Tue Apr 6 15:08:52 PDT 2010


Trish,

That link I give was just an example. My point is we'd like to get MeSH for French download through that kind of API rather than ViewExtractor API.

Eugene

From: Trish Whetzel [mailto:whetzel at stanford.edu]
Sent: Tuesday, April 06, 2010 3:02 PM
To: Eugene
Cc: support at bioontology.org
Subject: Re: [bioontology-support] MeSH in French version

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<mailto: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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