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[BioRDF] playing with Microarray RDF

From: Eric Prud'hommeaux <eric@w3.org>
Date: Mon, 16 Aug 2010 16:42:08 -0400
To: public-semweb-lifesci@w3.org
Cc: mdmiller <mdmiller53@comcast.net>, Helena Deus <helenadeus@gmail.com>, "M. Scott Marshall" <mscottmarshall@gmail.com>, James Malone <malone@ebi.ac.uk>, Helen Parkinson <parkinson@ebi.ac.uk>, "ostolop@ebi.ac.uk" <ostolop@ebi.ac.uk>, Kei Cheung <kei.cheung@yale.edu>, Satya Sahoo <satyasahoo@gmail.com>, Matthias Samwald <samwald@gmx.at>, Jun Zhao <jun.zhao@zoo.ox.ac.uk>
Message-ID: <20100816204206.GB6268@w3.org>
Poking around in the genelists work, I arbitrarily decided to unify
genelists_20100815_lena.ttl with Lena's sample query:

SPARQL11 -d genelists_20100815_lena.ttl -e '
  PREFIX : <http://purl.org/net/biordfmicroarray/ns#> 
  PREFIX diseasome: <http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/>
  PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
  PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
  SELECT ?diseaseName ?geneName WHERE { ?gene a :gene ; rdfs:label ?geneName
    SERVICE <http://ibl.mdanderson.org/~mhdeus/sparql_federation/endpoint2.php>
      { ?gene rdf:type :gene .  ?gene rdfs:label ?geneName . }
    SERVICE <http://hcls.deri.org/sparql>
      { ?diseasomeGene rdfs:label ?geneName .
        ?disease diseasome:associatedGene ?diseasomeGene.
        ?disease rdfs:label ?diseaseName . }
  }'
and got a couple answers:
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┯━━━━━━━━━━━┓
┃ ?diseaseName                                            │ ?geneName ┃
┃ "Congenital disorder of glycosylation, type Ii, 607906" │    "ALG2" ┃
┃                  "Congenital_disorder_of_glycosylation" │    "ALG2" ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┷━━━━━━━━━━━┛
This is mostly to show how to use the SWObjects code. I await Lena's
wisdom on the query.
-- 
-ericP
Received on Monday, 16 August 2010 20:42:45 GMT

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