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[bioontology-support] Questions about SPARQL endpoint

manuelso manuelso at stanford.edu
Fri May 25 15:43:58 PDT 2012


Hi Josh,


> Two more questions :-)  Please let me know if there's a public mailing
> ist that's a more appropriate place; I'm happy to post wherever.

bioontology-support at lists.stanford.edu is the best place for all kind of technical questions related to BioPortal.

> 
> 1.  For reproducibility, could  you include a copy of your
> MetamorphSys "Configuration Properties File" with umls2rdf?  (Selected
> sources, suppressions, precedence...)

I need to get this from our sysadmins. I'll include it in the umls2rdf project once I get it.

> 
> 2.  Have you thought about how to distinguish concepts vs. atoms in
> source vocabs like RxNorm?  E.g. right now you're generating RDF like
> 
> <http://purl.bioontology.org/ontology/RXNORM/259047>
>     <http://purl.bioontology.org/ontology/RXNORM/ORIG_CODE>
>            "0338-0500", "MTHU005081", "00326";
>    <http://purl.bioontology.org/ontology/RXNORM/ORIG_SOURCE>
>            "MMX", "VANDF", "NDDF".
> 
> so it's impossible to tell which ORIG_SOURCE corresponds to which ORIG_CODE.
> 
> (Reading through your python exporter, I don't think this is the same
> as the distinction between codes vs. cuis...)

Interesting I need to investigate this further. It seems that the RDF we generate is similar to what we have now in BioPortal see here:

http://purl.bioontology.org/ontology/RXNORM/259047
(this information is not extracted from the triple store, it is extracted from LexEVS)

I'll get back to you with more information soon.

Manuel

> 
> 
> Thanks!
> 
>  -Josh



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