[Bioperl-l] Interfaces to HGNC/genenames.org?

Robert Bradbury robert.bradbury at gmail.com
Mon Apr 19 12:49:24 EDT 2010

Are there any interfaces from BioPerl to the data in the HGNC data at

I don't know if genenames.org has a documented program interface like NCBI
(it would seem like they should).

One could of course use the web interface and parse their web pages but that
would be dependent on their not changing the information format in them over
the long term.

Alternately, one could parse the downloaded data files they provide.  I
think they allow you to download the data in specific formats which might
make the BioPerl interface less subject to external changes.

If these interfaces don't exist, might I suggest a Google SOC project?

The reason this could be useful is that it would allow the parsing of
genomic data (e.g. PubMed records or even PDF references), perhaps something
like CPAN's Peptide-PubMed and have some confidence in separating real gene
names (or their alternates) from English or scientific terms (though perhaps
something like CPAN's WWW::Dictionary can do this)..


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