Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

manuelso manuelso at stanford.edu
Mon Dec 17 11:59:24 PST 2012


Trish is right. At the moment we do not support SPARQL query federation.

Best,

Manuel

On Dec 17, 2012, at 11:17 AM, Trish Whetzel <whetzel at stanford.edu> wrote:

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20121217/33f33bda/attachment-0001.html>


More information about the bioontology-support mailing list