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[bioontology-support] sparql endpoint, missing mapping?

manuelso manuelso at stanford.edu
Thu Jan 31 11:57:03 PST 2013


Hi Laura,

Notice that the BRO ontology IRI is :

http://bioportal.bioontology.org/ontologies/1104

The one you refer to (2022) is an ontology view and AFAIK we do not generate mappings for views. Trish can correct me here if I am wrong.

For your first query, the BRO (1104) mapping does come back.

On your second query replace 2022 with 1104 and you will see that mapping. See here:

http://goo.gl/87eNe

We just released a new version of the mapping data and from now on we will have two separate databases; one for terms and metadata and a second just for mappings. In our web front end there is an option to run your query against terms or mappings.

If you run your queries programmatically, to query the mapping KB, direct your queries to:

http://sparql.bioontology.org/mappings/sparql

Documentation here:

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

Best,

Manuel


On Jan 31, 2013, at 3:13 AM, "Hollink, L." <l.hollink at vu.nl> wrote:

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

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