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

Sean Davis sdavis2 at mail.nih.gov
Mon Apr 19 13:31:25 EDT 2010


On Mon, Apr 19, 2010 at 12:49 PM, Robert Bradbury <robert.bradbury at gmail.com
> wrote:

> Are there any interfaces from BioPerl to the data in the HGNC data at
> genenames.org?
>
> 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.
>
>
Hi, Robert.

I think the format is tab-delimited text.  These should be pretty easy to
parse.

Sean


> 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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