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

Ray Fergerson ray.fergerson at stanford.edu
Fri Jun 28 16:45:45 PDT 2013


Dave,

The current SPARQL endpoint will not be updated. The new endpoint, when it
becomes available, will use the newer purls, as will with rest of the
system. Note that currently many of the purls in bioportal are not
working. We are working on this problem but it will be next week before it
is resolved. The MedDRA one in your message has been fixed manually but
there are many others that do not work.

Ray

-----Original Message-----
From: Dave Reynolds [mailto:dave.e.reynolds at gmail.com] 
Sent: Monday, June 24, 2013 2:25 PM
To: Ray Fergerson
Cc: bioontology-support at lists.stanford.edu
Subject: Re: [bioontology-support] MedDRA URL namespace - MDR or MEDDRA?

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
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>



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