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

[Glenn Proctor]

On Thu, Dec 2, 2010 at 1:47 PM, Matthew Astley <mca at sanger.ac.uk> 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?

These methods will be called on a Gene, Transcript or Translation
object, so I think the "related" is redundant here.

> 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>

This is under consideration, but for now we're limiting ourselves to
implementing aliases of the existing methods, in the interests of
getting this out quickly.

>> 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.

We use the phrase "direct xrefs" elsewhere in Ensembl to mean
something different (a category of xrefs we assign directly, rather
than by sequence matching). I'm not 100% happy with the
"get_all_object_xrefs()" name either though, so keep the suggestions
coming ...

Glenn.