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[bioontology-support] Failing to filter with umls/cui in the bioportal sparql endpoint

manuelso manuelso at stanford.edu
Mon Jul 29 09:48:36 PDT 2013


Hi Hong,

The values of the umls:cui property are xsd typed with string. You need to do the following:

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX snomed-term: <http://purl.bioontology.org/ontology/SNOMEDCT/> 
PREFIX skos: <http://www.w3.org/2004/02/skos/core#> 
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

SELECT * 
FROM <http://bioportal.bioontology.org/ontologies/SNOMEDCT> 
WHERE 
{ 
    ?s <http://bioportal.bioontology.org/ontologies/umls/cui> "C0994344"^^xsd:string. 
} limit 500 

It is bad that our web front end hides  xsd types. We plan to fix it so this.

Hope this helps,

Manuel

 
On Jul 29, 2013, at 2:55 AM, Hong Sun <hong.sun at agfa.com> wrote:

> Dear Manuel and all, 
> 
> I found the bioportal SPARQL endpoint fails to filter on the property <http://bioportal.bioontology.org/ontologies/umls/cui> 
> 
> e.g. the query below can return result 
> 
> Query 1: 
> 
> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
> PREFIX snomed-term: <http://purl.bioontology.org/ontology/SNOMEDCT/> 
> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> 
> SELECT * 
> FROM <http://bioportal.bioontology.org/ontologies/SNOMEDCT> 
> WHERE 
> { 
>     <http://purl.bioontology.org/ontology/SNOMEDCT/201794001> <http://bioportal.bioontology.org/ontologies/umls/cui> ?o. 
> } limit 500 
> 
> Result 1" 
> o 
> "C0994344" 
> 
> But when I filter with the returned CUI, no result return. 
> Query 2: 
> 
> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
> PREFIX snomed-term: <http://purl.bioontology.org/ontology/SNOMEDCT/> 
> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> 
> SELECT * 
> FROM <http://bioportal.bioontology.org/ontologies/SNOMEDCT> 
> WHERE 
> { 
>     ?s <http://bioportal.bioontology.org/ontologies/umls/cui> "C0994344". 
> } limit 500 
> 
> Result: 
> Null 
> 
> Could you help to take a look? Thank you very much! 
> 
> Best regards,
> Hong

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