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

[Andy Jenkinson]

On 2 Dec 2010, at 07:51, Patrick Meidl wrote:

> 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.

Also, whether something is attached to a gene or transcript is not always intuitive: as I understand it, it depends on how the mapping was done, not the logical data model relationships. You have to know the internal data model before you can use it. For example, why is an EntrezGene not a gene-related record?

> just my 2c...

And mine :)

> 
>    patrick
> 
> -- 
> Patrick Meidl, Mag.
> Bioinformatician
> 
> Ce-M-M-
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