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

[Oliver, Gavin]

"I was under the impression that the average user would be interested
in one or a few external databases, say HGNC and EntrezGene, on one
species."

I would agree with this.  

And HGNC and EntrezGene in my experience are the two big ones.  I personally want as much info as possible but our data analysis team and the majority of customers encountered tend to balk at the idea of anything beyond these two IDs.


-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Andreas Kahari
Sent: 02 December 2010 11:35
To: Bert Overduin
Cc: dev at ensembl.org
Subject: Re: [ensembl-dev] getting the entrez gene id from an ensembl record

On Thu, Dec 02, 2010 at 11:11:43AM +0000, Bert Overduin wrote:
> On Thu, Dec 2, 2010 at 10:33 AM, Andreas Kahari <ak at ebi.ac.uk> wrote:
> 
> > 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),
> 
> 
> From the fact that I've seen quite some helpdesk tickets in the past from
> people who are trying to get xrefs from the wrong level and the fact that I
> myself, even though I teach the core API, can never remember which xref is
> done on which level, I I am afraid you're far too optimistic here .... :0

So, it is according to you more common that people deal with multiple
external databases on multiple species?

I was under the impression that the average user would be interested
in one or a few external databases, say HGNC and EntrezGene, on one
species.

However, since these seems to be strong feelings about this (especially
among users on the Hinxton campus), we will obviously implement a good
solution for it.

We will, for release 61, add easy to remember alias method names for
get_all_DBEntries() and get_all_DBLinks(), and for release 62 we will
hopefully be able to speed up the catch-all get_all_DBLinks() method.

Andreas

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

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