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

[Glenn Proctor]

Hi

These are all good points - for release 61 we'll add methods that are
aliases of get_all_DBLinks/Entries but have more intuitive names.

Glenn.


On Thu, Dec 2, 2010 at 9:53 AM, Patrick Meidl <pmeidl at cemm.oeaw.ac.at> wrote:
> On Thu, Dec 02 2010, Andy Jenkinson <andy.jenkinson at ebi.ac.uk> 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.
>>
>> 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?
>
> exactly. I therefore think that what is now called get_all_DBLinks()
> should have an intuitive name which highlights that in most cases,
> _this_ is the right method for getting xrefs.
>
> get_all_DBEntries() is a special case which most users won't need, and
> the name should indicate its nature as well (and maybe have a less
> catchy name so that people don't use it by accident, as is the case
> now).
>
> sure, all this is documented in the POD, but the beauty of the Ensembl
> core API is that object and method names are so intuitive that in 95% of
> the use cases you don't have to read the documentation. so, ironing out
> the few wriggles would be cool.
>
> cheers
>
>    patrick
>
> --
> Patrick Meidl, Mag.
> Bioinformatician
>
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