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[bioontology-support] MEDDRA pref label

manuelso manuelso at stanford.edu
Wed Aug 7 20:21:18 PDT 2013


Walt,

The SPARQL endpoint uses a slightly old metadata version and MEDDRA is actually MDR. I would avoid using ORDER BY, with large ontologies you can hit query time outs. If you want to retrieve all labels from MEDRA use something like:

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT DISTINCT ?term ?label
FROM <http://bioportal.bioontology.org/ontologies/MDR>
WHERE
{
?term skos:prefLabel  ?label.
} OFFSET 0 LIMIT 5000

and iteratively increase the OFFSET  until you get no results. This is the safest way to retrieve all labels from a large ontology.

Manuel



On Aug 6, 2013, at 11:38 AM, "Melo, Walt" <Walcelio.Melo at noblis.org> wrote:

> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
> PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
> SELECT DISTINCT ?term ?label
> FROM <http://bioportal.bioontology.org/ontologies/MEDDRA>
> WHERE
> {
> ?term rdfs:label  ?label.
> } order by ?term
>  
> I also tried
>  
> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
> PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
> SELECT DISTINCT ?term ?label
> FROM <http://bioportal.bioontology.org/ontologies/MEDDRA>
> WHERE
> {
> ?term skos:prefLabel  ?label.
> } order by ?term
>  
> From: Manuel Salvadores [mailto:manuelso at stanford.edu] 
> Sent: Tuesday, August 06, 2013 12:49 PM
> To: Melo, Walt
> Cc: support at bioontology.org
> Subject: Re: [bioontology-support] MEDDRA pref label
>  
> Walt,
> 
> Could you please send the SPARQL query you tried ? The one using skos:prefLabel. 
> 
> Thanks,
> 
> Manuel
> 
> "Melo, Walt" <Walcelio.Melo at noblis.org> wrote:
> 
> I am trying to get the preferred label from a set of MEDDRA concepts using bioportal SPARQL endpoint. Unfortunately, skos:prefLabel   nor rdfs:label have returned any results.
>  
> What predicate should I use to get the preferred label from MEDDRA concepts?
>  
> Walt

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