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[bioontology-support] SPARQL endpoint federated query

Manuel Salvadores Olaizola manuelso at stanford.edu
Wed Aug 6 09:04:43 PDT 2014


Hi Sina,

How are you issuing that query ? 

For that query to work you need to use a SPARQL client that can handle SPARQL federation since our server does not support federation remotely. This means that the client will decompose the query in smaller parts and it will the join itself.

JenaARQ supports this. We have an example here:

https://github.com/ncbo/sparql-code-examples/blob/master/java/src/org/ncbo/stanford/sparql/examples/JenaARQFederationExample.java

Manuel

----- Original Message -----
From: "Sina Madani" <AHMadani at mdanderson.org>
To: support at bioontology.org
Sent: Wednesday, August 6, 2014 8:55:54 AM
Subject: [bioontology-support] SPARQL endpoint federated query



Hi, 

We are trying to troubleshoot our updated SPARQL app that supposed to do federated query. 

Should below same query (from NCBO document) work in our environment (querying your endpoint) with my APIkey ? (user: sina) 

We are getting this error 



Executing query failed: Error during SPARQL execution: 'Remote server returned error code 403 . 





http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal 





PREFIX map: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#> 

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

PREFIX skos: <http://www.w3.org/2004/02/skos/core#> 

SELECT DISTINCT ?mappedParent WHERE { 

SERVICE <http://sparql.bioontology.org/mappings/sparql/?apikey=YOUR API KEY HERE> { 

?mapping map:target <http://purl.bioontology.org/ontology/CSP/0468-5952> . 

?mapping map:source ?source . 

} 

SERVICE <http://sparql.bioontology.org/ontologies/sparql/?apikey=YOUR API KEY HERE> { 

?source rdfs:subClassOf ?mappedParent . 

} 

} 





Thanks! 

Sina 









-------------------- 

Sina Madani, MD, PhD 

MD Anderson Cancer Center 

Clinical Analytics & Informatics 

Phone: 713-583-1803 





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