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[bioontology-support] SPARQL Query

Manuel Salvadores Olaizola manuelso at stanford.edu
Mon May 4 11:38:29 PDT 2015


Hi alex,

Not all classes and all ontologies have rdfs:label defined. BCGO does not any rdfs:label triples. We generate one using the predicate <http://bioportal.bioontology.org/metadata/def/prefLabel> . In this case the labels are just the last fragment of the class IRI.

This is the query that you need for that ontology:

PREFIX owl:  <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
SELECT DISTINCT ?s ?label WHERE {
   GRAPH <http://bioportal.bioontology.org/ontologies/BCGO> {
       ?s a owl:Class . ?s <http://bioportal.bioontology.org/metadata/def/prefLabel> ?label .
   }
}


Manuel

----- Original Message -----
From: "Alex Hardy" <alex-t-hardy at hotmail.com>
To: support at bioontology.org
Sent: Monday, May 4, 2015 7:03:32 AM
Subject: [bioontology-support] SPARQL Query

Hi 
I have been using the example SPARQL query (shown below - 2 examples one ontology working, one not) for some coding on a university project across all the ontologies on the Bioportal. However, I have noticed that this SPARQL query code does not work for about 100 ontologies. I therefore looked at the characteristics of the ontologies where the query doesn’t function. It appears that it only functions for an ontology that has been updated since 2014. 
I notice that many ontolgies that existed in the early days of the Bioportal have been updated after 2014 so these work with the SPARQL query code. Do you know: 
- if there is there an ongoing programme to update the remaining old ontologies on the BioPortal? 
- the reason why the SPARQL query code doesn’t work and if so, is there some sample code that would work with these ontologies. 
Thank you for your help 
Kind regards, 
Alex 
Example – that works 
PREFIX owl: < http://www.w3.org/2002/07/owl# > 
PREFIX rdfs: < http://www.w3.org/2000/01/rdf-schema# > 
SELECT DISTINCT ?s ?label WHERE { 
GRAPH < http://bioportal.bioontology.org/ontologies/ABA > { 
?s a owl:Class . 
?s rdfs:label ?label . 
} 
} 
Example - that does not work 
PREFIX owl: < http://www.w3.org/2002/07/owl# > 
PREFIX rdfs: < http://www.w3.org/2000/01/rdf-schema# > 
SELECT DISTINCT ?s ?label WHERE { 
GRAPH < http://bioportal.bioontology.org/ontologies/ BCGO > { 
?s a owl:Class . 
?s rdfs:label ?label . 
} 
} 

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