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

[Patrick Meidl]

On Thu, Dec 02 2010, Andreas Kahari <ak at ebi.ac.uk> wrote:

> > 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.

fair point. but since the level of storage is often counter-intuitive
(from an end-user perspective, see the comments about EntrezGene IDs),
there is a trade-off...

besides, an API should, IMHO, expose as little implementation details to
the user as possible; so if get_all_DBLinks() is too slow, it would be a
good candidate for optimising the db representation or API methods :)

    patrick

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Patrick Meidl, Mag.
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