[BiO BB] Programmatic access to pubmed

Dan Bolser dan.bolser at gmail.com
Thu Apr 29 13:52:13 EDT 2010

There was a related discussion on the bio2RDF mailing list (below).


From: Marc-Alexandre Nolin <manolin at gmail.com>
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I've finally put online a new version of Pubmed/medline at


The release information and copyrights notice are available on the
release endpoint http://release.bio2rdf.org/sparql or throw the
Bio2RDF service with the URI http://bio2rdf.org/release:pubmed

This release use nquads, so you can get the complete triples from a
single document whatever its depth from the main URI by specifying its
graph. For example, take a random pubmed ID, 17472304, so to get the
complete information about this record, you can ask the sparql query

select * where {graph <http://bio2rdf.org/pubmed_record:17472304> {?s ?p ?o}}

The RDFizer program used to create it is indicated in the release information.

Comments, request for change, anythings are welcome.


Marc-Alexandre Nolin

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On 28 April 2010 07:11, Manjula P. Thimma <Manjula.Thimma at kaust.edu.sa> wrote:
> Dear All,
> I am heading to create a list of reference articles that discuss about Cancer Metabonomics/Metabolomics using NMR (either in the abstract, or in any part of the text) from pubmed. Since Manual fishing is cumbersome, I am wondering is there any programmatic access for this database?
> Any pointers towards this is much appreciated.
> Best Regards
> Manjula
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb

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