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[bioontology-support] Combining a sparql endpoint to bioontology with one to the sparql endpoint of wikipathways

Waagmeester Andra (BIGCAT) andra.waagmeester at maastrichtuniversity.nl
Mon Dec 17 12:08:24 PST 2012


Hi Trish,

      I am assuming that your triple store doesn't need to support SERVICE. The query is sent to our own internal triple store, which does support SERVICE and handles the outgoing query towards your triple store. We did similar queries to Genewiki for example: http://www.wikipathways.org/index.php/Help:WikiPathways_Sparql_queries#WikiPathways_with_GeneWiki

So far I only managed to send the query through the browser interface at http://sparql.bioontology.org. Would it be possible to sent the following query directly to your sparql endpoint without going through the website (and a programming language)?
PREFIX omv: <http://omv.ontoware.org/2005/05/ontology#>
prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT *
WHERE {
    <http://purl.obolibrary.org/obo/PW_0000100> rdfs:label ?ontologyLabel .
    <http://purl.obolibrary.org/obo/PW_0000100> rdfs:subClassOf ?superClassOntology .
    ?superClassOntology rdfs:label ?superClassLabel
}

Regards,

Andra




From: Trish Whetzel <whetzel at stanford.edu<mailto:whetzel at stanford.edu>>
Date: Mon, 17 Dec 2012 20:17:21 +0100
To: Andra Waagmeester <andra.waagmeester at maastrichtuniversity.nl<mailto:andra.waagmeester at maastrichtuniversity.nl>>
Cc: "support at bioontology.org<mailto:support at bioontology.org> Support" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] Combining a sparql endpoint to bioontology with one to the sparql endpoint of wikipathways

Dear Andra,

I believe the issue is that the RDF backend we are using does not support SERVICE.

Trish


On Dec 17, 2012, at 9:42 AM, Waagmeester Andra (BIGCAT) wrote:

Hi,
   We are working towards exposing wikipathways (http://www.wikipathways.org) content through a Sparql endpoint. Different pathways within WikiPathways are classified according to the Pathway ontology. The following sparql query list the different pathways and their pathway ontology term:

SELECT ?title ?ontology ?species
WHERE {
?pathway dc:title ?title .
        ?pathway wp:organism ?species .
        ?pathway wp:pathwayOntology ?ontology .
}

(For the complete results see: http://sparqlbin.com/#f8c0a108ac733acc0ce10d109a137196 and press Execute).

I would very much like to integrate those results with the following sparql query sent to your endpoint:

PREFIX omv: <http://omv.ontoware.org/2005/05/ontology#>
PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
SELECT DISTINCT *
WHERE {
    <http://purl.obolibrary.org/obo/PW_0000100> rdfs:label ?ontologyLabel .
    <http://purl.obolibrary.org/obo/PW_0000100> rdfs:subClassOf ?superClassOntology .
    ?superClassOntology rdfs:label ?superClassLabel
}

I have integrated both queries into the following query:
SELECT ?title ?ontology ?species
WHERE {
?pathway dc:title ?title .
        ?pathway wp:organism ?species .
        ?pathway wp:pathwayOntology ?ontology .

        SERVICE <http://sparql.bioontology.org> {
           ?ontology rdfs:label ?ontologyLabel .
           ?ontology rdfs:subClassOf ?superClassOntology .
           ?superClassOntology rdfs:label ?superClassLabel .
       }
}

This query does not return the expected results. According to your documentation, automatic querying could be done with an API key and through different code examples (Java, etc).

Does this imply that sending direct queries to your sparql endpoint, without doing this through a programming language, is not supported?

Any help here would be appreciated.

Kind regards,


Andra Waagmeester
Maastricht University.


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