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[BioRDF] Mapping MeSH to DBpedia

From: Matthias Samwald <samwald@gmx.at>
Date: Mon, 14 Sep 2009 16:35:40 +0200
Message-ID: <293484F1436941E5B3A7345CCE2B3A24@ms>
To: "public-semweb-lifesci" <public-semweb-lifesci@w3.org>
Cc: "Anja Jentzsch" <anja@anjeve.de>
I created a mapping between MeSH and DBpedia. The mapping is based on 
explicit mentions of MeSH entries that can be extracted Wikipedia/DBpedia. 
The preliminary result of this effort is a Turtle file with 2600 
rdfs:seeAlso. It can be found at
http://samwald.info/res/dbpedia_mesh_mapping.ttl

The statements look like this:
<http://dbpedia.org/resource/Primary_motor_cortex> rdfs:seeAlso 
<http://purl.org/commons/record/mesh/D009044> .


I added the mapping to the HCLS Knowledge Base 
(http://hcls.deri.org/sparql ). It can be queried like this:

=====
SELECT * WHERE {
GRAPH <http://samwald.info/res/dbpedia_mesh_mapping.ttl>
  {?s ?p ?o}
}
LIMIT 10
=====


For example, this allows us to use the DBpedia-MeSH-PubMed connection to 
find PubMed abstracts that match a certain DBpedia entry. E.g, for 
http://dbpedia.org/resource/Primary_motor_cortex, we can query the HCLS 
Knowledge Base like this:

=====
PREFIX dbpedia_uri: <http://dbpedia.org/resource/Primary_motor_cortex>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?pubmed_uri WHERE {
GRAPH <http://samwald.info/res/dbpedia_mesh_mapping.ttl>
{ dbpedia_uri: rdfs:seeAlso ?mesh_uri . }

GRAPH <http://purl.org/science/graph/medline/subject-headings>
{ ?pubmed_uri ?o ?mesh_uri . }
}
LIMIT 5
=====


Result:
http://purl.org/commons/record/pmid/4319929
http://purl.org/commons/record/pmid/4951845
http://purl.org/commons/record/pmid/6015242
http://purl.org/commons/record/pmid/4999957
http://purl.org/commons/record/pmid/5633926
[...]


Further documentation and a link to the PHP script that was used to generate 
the mapping: 
http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/DBpedia_to_OBO_mapping
I hope this is helpful to some people reading this list.


Cheers,
Matthias Samwald

DERI Galway, Ireland
http://deri.ie/

Konrad Lorenz Institute for Evolution & Cognition Research, Austria
http://kli.ac.at/ 
Received on Monday, 14 September 2009 14:36:21 UTC

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