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[bioontology-support] Help

Manuel Salvadores Olaizola manuelso at stanford.edu
Thu May 7 10:51:36 PDT 2015


Hello Szenasi,

The SPARQL endpoint it is not efficient for keyword search. Unless you really have to use SPARQL we always recommend to use our search enppoint that has been specifically design for that purpose.

You can find documentation for search in BioPortal here:

http://data.bioontology.org/documentation

Best,

Manuel

----- Original Message -----
From: "Szenasi Gyuri" <szenasi.gyuri92 at gmail.com>
To: support at bioontology.org
Sent: Thursday, May 7, 2015 6:46:42 AM
Subject: [bioontology-support] Help

Hello, 

My name is Szenasi Gyuri, and i am student at the Technical University of Cluj-Napoca , Computer Science Department. 
I'm working on a project that has to extract medical information from electronic health records, and for this i use bioontology, but i have a problem with some query and i cannot find a solution. 

I make this query in java: 

String query = " PREFIX rdfs: < http://www.w3.org/2000/01/rdf-schema# > " 
+ "SELECT DISTINCT *" 
+ "FROM < http://bioportal.bioontology.org/ontologies/SNOMEDCT >" 
+ "FROM < http://bioportal.bioontology.org/ontologies/globals >" 
+ "WHERE" 
+ "{" 
+ " ?x rdfs:label ?label ." 
+ "?x rdfs:subClassOf ?parent ." 
+ "?parent rdfs:label ?parentLabel ." 
+ "FILTER (CONTAINS ( UCASE(str(?label)), \""+term+"\") )" 
+ "}"; 

The problem is if i search for the term INTUBATION, i do not get all the results. For example i need to get this result: http://purl.bioontology.org/ontology/SNOMEDCT/52765003 , to identity a term as medical related term, but this isn't among the results of the query however the label of the term contains the word "intubation". 

If you could tell me where my mistake is, or what to change to get all the results, it would be great. 

Thank You, 
Szenasi Gyuri 

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