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[bioontology-support] sparql endpoint, missing mapping?

Hollink, L. l.hollink at vu.nl
Thu Jan 31 03:13:17 PST 2013


Hi, 

I am using the Bioportal SPARQL endpoint and I am wondering if all the bioportal information is there. 

For example: I am looking for mappings between MDR (MedDRA) and BRO (Biomedical research ontology. According to the website http://bioportal.bioontology.org/mappings, there is one mapping between them. However, the SPARQL endpoint does not return any mappings. 

I've tried:

PREFIX map: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#> 
SELECT ?sourceOntologyId (count(?mappingId) as ?count) WHERE { 
   ?mappingId map:target_ontology <http://bioportal.bioontology.org/ontologies/1422> . 
   ?mappingId map:source_ontology ?sourceOntologyId . }
GROUP BY ?sourceOntologyId ORDER BY DESC(?count) 

This gives a list of ontologies that MDR is linked to, but not BRO.

To be sure, I've also tried: 

PREFIX map: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#> 
SELECT ?mappingId WHERE { 
   ?mappingId map:source_ontology <http://bioportal.bioontology.org/ontologies/1422> . 
   ?mappingId map:target_ontology <http://bioportal.bioontology.org/ontologies/2022> . }

As expected, this gives no results.

So my question is: are these triples missing from the SPARQL endpoint, or am I querying it in the wrong way? 

Thanks in advance for your help,
Laura









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