What is known about HIV using Bio2RDF's SPARQL endpoints ?

Created: 2009-02-05 06:13:53      Last updated: 2009-02-05 06:15:22

To answer this question Bio2RDF Atlas about mouse and human genome sparql endpoint available at http://atlas.bio2rdf.org/sparql is searched.  The selected URIs are then loaded into your local Virtuoso triplestore at http://localhost:8890/sparql. You must enable insert mode into the graph.

Once the mashup is built, two SPARQL queries analyze the obtained graph.  Finally you can submit queries to the RDF mashup about HIV as you like.  Enjoy.

This is the queries present in this workflow :

CONSTRUCT {
  ?s ?p ?o .
}
FROM < geneid,uniprot,omim,pubmed,go >
WHERE {
  ?s ?p ?o .
  ?o bif:contains "hiv" .
}

then

SELECT * WHERE {?s ?p ?o}

then

SELECT ?type, count(*)
WHERE {
?s <rdf:type> ?type .
}

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  • Thursday 05 March 2009 14:48:21 (UTC)

    Dear Francois,

    Firstly, congratulation on the great job! I have been looking forward to this for a long time, a binding between Bio2RDF and Taverna.

    I have download your workflow and tried to run it using Taverna 2.0. However, no results were ever returned to me. I digged into the workflow and found that the value given to the string processor "virtuoso_server" is http://localhost:8890. Is this the reason why I got no results back? What should I fix to make the workflow run on my local desktop?

    Thanks,

    Jun

  • Tuesday 14 September 2010 16:17:15 (UTC)

     Jun,

    I think the workflow assumes that you have a triple-store running locally.  Basically it goes and gets the data for you, sticks it into your server, and then lets you query it.  

     Anyone have this working?

     




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