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Re: URI for MeSH

From: Janos G. Hajagos <risk.limits@gmail.com>
Date: Mon, 06 Jun 2011 11:10:06 -0400
Message-ID: <4DECEDCE.3080907@gmail.com>
To: Helena Deus <helenadeus@gmail.com>
CC: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Helena,

As you can see there are many options for MeSH but no official version. 
Another option is to use the SPARQL endpoint maintained by Stony Brook 
University Department of Medical Informatics for the public sources of 
the UMLS that have been converted to RDF. As MeSH is part of the UMLS 
you also get the ability to link to other vocabulary sources like NCIt.

http://link.informatics.sunysb.edu/sparql/

You could potentially use a URI to the normalized version of the MeSH 
Header (a URI to UMLS CUI (Concept Unique Identifier)

SELECT ?aui ?cui WHERE
{ ?aui rdfs:label "Neoplasms" .
   ?aui <http://link.informatics.stonybrook.edu/umls/hasSAB> 
<http://link.informatics.stonybrook.edu/umls/SAB/MSH> .
   ?aui <http://link.informatics.stonybrook.edu/umls/hasTermType> 
<http://link.informatics.stonybrook.edu/umls/TTY/MH> .
   ?aui <http://link.informatics.stonybrook.edu/umls/hasCUI> ?cui
  }

Running the above query gives the following result.

aui     cui
http://link.informatics.stonybrook.edu/umls/AUI/A0090941     
http://link.informatics.stonybrook.edu/umls/CUI/C0027651

Note: the above links in the result set can be browsed interactively 
from a web browser.

I can only hypothesize that Bioportal issue might be related to the 
D058885 (Multilocus Sequence Typing)  being a term newly introduced to 
the 2011 version of MeSH.  FYI, UMLS version that is being hosted here 
does not contain D058885 the term because it is the 2010 version. See  
http://link.informatics.stonybrook.edu/umls/SAB/MSH for metadata about 
the MeSH source currently being hosted.

-Janos


On 6/6/2011 7:35 AM, Helena Deus wrote:
> Hi all,
>
> I am trying to identify a URI for a concept in MeSH; bioportal URI is 
> http://bioportal.bioontology.org/ontologies/44776?p=terms&conceptid=D058885 
> <http://bioportal.bioontology.org/ontologies/44776?p=terms&conceptid=D058885>
> But BioPortal gives me this very polite message:
>
> "We're sorry but something has gone wrong. We have been notified of 
> this error."
>
> I've looked up the same concept in MeSH site - 
> http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?index=26024 - but it does 
> not seem to be a well-formed URI (not serving RDF data).
>
> Does anyone know of a proper way to build a URI for MeSH terms?
>
> Best,
> Helena
Received on Monday, 6 June 2011 19:21:07 UTC

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