[ensembl-dev] getting the entrez gene id from an ensembl record

[Patrick Meidl]

On Thu, Dec 02 2010, ian Longden <ianl at ebi.ac.uk> wrote:

> Use $gene->get_all_DBLinks as this gets the external database
> references on the transcripts and translations of the gene too.
> 
> DBEntries only gets the ones attached to the gene directly.

I'm not sure if there are any stats, but this misunderstanding must rank
in the top 10 of the most frequently asked questions about the Ensembl
core API.

in combination with the fact that these methods are also among the very
few where there is no naming consistency between the database tables and
the model object names (xref vs DBEntry), it might be a good idea to
think about more expressive names for the methods (and possibly the
models as well). the old names could be deprecated but kept as
aliases/proxies for backward compatibility.

just my 2c...

    patrick

-- 
Patrick Meidl, Mag.
Bioinformatician

Ce-M-M-
Research Centre for Molecular Medicine
of the Austrian Academy of Science

Lazarettgasse 14 / AKH BT 25.3
Vienna, Austria

room 02.205
phone +43 1 40160 70016
email pmeidl at cemm.oeaw.ac.at
web http://www.cemm.at/