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

Patrick Meidl pmeidl at cemm.oeaw.ac.at
Thu Dec 2 09:53:36 GMT 2010


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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Research Centre for Molecular Medicine
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