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

[Andreas Kahari]

On Thu, Dec 02, 2010 at 01:47:34PM +0000, Matthew Astley wrote:
> On Thu, Dec 02, 2010 at 11:00:11AM +0000, Andreas Kahari wrote:
> 
> > Do you think that get_all_xrefs() is a good alias name for
> > get_all_DBLinks()?
> 
> Does get_all_related_xrefs() better describe the meaning?  Is it worth
> 21 characters?

Hmm...  It's not entirely true.  The existing method will always get the
xrefs for the current object and for all its parts recursively, i.e.
when called on a gene object, it will return the xrefs on the gene and
on all its transcripts and translations, but when called on a transcript
object, it will not return the gene xrefs even though these are arguably
"related".

> Also, is it useful to accept parameters to a) limit the search type or
> depth and b) cause the results to return in a way that indicates the
> relationship? </featurecreep>

We will address additional features in future releases.  To simply add
an alias is something we can easily do for release 61.  In fact, it's
already committed on the HEAD with the suggestions that I had (but I may
still, until the end of the week, change the names of the alias methods
if something better comes up).

> > And can we use get_all_object_xrefs() (i.e. "get all xrefs from this
> > object, not from its constituent parts") as an alias for
> > get_all_DBEntries()?
> 
> get_all_direct_xrefs() would describe this better for me.

Ouch, we always have something called "direct xrefs", and this is not
it.  In the xref pipeline, a direct xref is an xref that is related
directly to the Ensembl object, usually by an external team.

Andreas


> 
> 
> > Any better suggestions?
> 
> (My suggestions are based what I've read in this thread.  I have no
> special understanding of Ensembl's xrefs, nor have I used them much
> yet.)
> 
> -- 
> Matthew
> 
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-- 
Andreas Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, United Kingdom