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

Trish Whetzel whetzel at stanford.edu
Mon Dec 17 11:17:21 PST 2012


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.
> 
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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