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

Hong Sun hong.sun at agfa.com
Mon Jul 29 12:21:43 PDT 2013


 Hi Manuel,

Thank you very much for your explanation!

best regards,
Hong



-----manuelso <manuelso at stanford.edu> wrote: -----
To: Hong Sun/AXIFX/AGFA at AGFA
From: manuelso <manuelso at stanford.edu>
Date: 07/29/2013 06:48PM
Cc: support at bioontology.org
Subject: Re: Failing to filter with umls/cui in the bioportal sparql endpoint

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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