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[bioontology-support] MedDRA URL namespace - MDR or MEDDRA?

Dave Reynolds dave.e.reynolds at gmail.com
Mon Jun 24 14:25:20 PDT 2013


Ray,

Thanks.

So will the reindexing include updating the triple store?  I was hoping 
to use the SPARQL endpoint as my definitive source but that currently 
uses MDR URLs. Seems like a tricky change since that will break 
everyone's SPARQL queries.

Does that also mean the MEDDRA URLs will resolve at some point?

Dave

On 24/06/13 21:36, Ray Fergerson wrote:
> Dave,
>
> As part of a general cleanup we have recently changed the names and
> abbreviations for a number of ontologies to be more recognizable. MedDRA
> is one of these. Unfortunately the search service has not been updated and
> is still using the old ontology names. Thanks for pointing this out. We
> will kick off a reindexing of all ontologies that should pick this up. The
> abbreviation should be "MEDDRA".
>
> Ray
>
> -----Original Message-----
> From: bioontology-support-bounces at lists.stanford.edu
> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Dave
> Reynolds
> Sent: Monday, June 24, 2013 3:55 AM
> To: bioontology-support at lists.stanford.edu
> Subject: [bioontology-support] MedDRA URL namespace - MDR or MEDDRA?
>
> I'm trying to use the RDF translation of some of the terms from the MedDRA
> ontology from Bioportal.
>
> However, I'm seeing some inconsistency in the namespaces and wondered what
> the right one is.
>
> If I use the search service or the SPARQL service then I get URLs of the
> form:
>
>     http://purl.bioontology.org/ontology/MDR/{concept}
>
> But if I dereference those URLs they link to terms using the namespace:
>
>     http://purl.bioontology.org/ontology/MEDDRA/{concept}
>
> For example, fetching (conneg to RDF/XML):
>
>       http://purl.bioontology.org/ontology/MDR/10002086
>
> Returns
>
>       <owl:Class
> rdf:about="http://purl.bioontology.org/ontology/MEDDRA/10002086">
>           <rdfs:label>Anaemias nonhaemolytic and marrow
> depression</rdfs:label>
>           <rdfs:subClassOf
> rdf:resource="http://purl.bioontology.org/ontology/MEDDRA/10005329"/>
>           <skos:notation>10002086</skos:notation>
>           <umls-skos:TUI>T047</umls-skos:TUI>
>           <skos:prefLabel>Anaemias nonhaemolytic and marrow
> depression</skos:prefLabel>
>           <umls-skos:UMLS_CUI>C0851368</umls-skos:UMLS_CUI>
>           <skos:altLabel>Anemias nonhemolytic and marrow
> depression</skos:altLabel>
>           <skos:broader
> rdf:resource="http://purl.bioontology.org/ontology/MEDDRA/10005329"/>
>       </owl:Class>
>
> Those are also the URL patterns shown by the interactive browser.
>
> Trying to dereference any of the MEDDRA (as opposed to MDR) URLs gives a
> 500 error.
>
> [Sorry if this is the wrong list for this sort of question, is there a
> better place to ask?]
>
> Dave
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