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

[Andreas Kahari]

On Thu, Dec 02, 2010 at 10:53:36AM +0100, Patrick Meidl 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.

On the contrary.  If the users knows what external database they are
querying for (which they often do), and they know what level the xref
are annotated on (which they also often do), then get_all_DBEntries()
is definitely the most correct method to call.  It is lots quicker than
get_all_DBLinks().  The DBLinks method is a lazy catch-all.

> 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).

See above.

Cheers,
Andreas


> 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
> 
> 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/
> 
> 
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev
> 

-- 
Andreas Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, United Kingdom