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

Andy Jenkinson andy.jenkinson at ebi.ac.uk
Thu Dec 2 16:07:39 GMT 2010


On 2 Dec 2010, at 14:40, Andreas Kahari wrote:

> On Thu, Dec 02, 2010 at 02:05:03PM +0000, Bert Overduin wrote:
>> On Thu, Dec 2, 2010 at 1:59 PM, Andy Jenkinson <andy.jenkinson at ebi.ac.uk>wrote:
>> 
>>> On 2 Dec 2010, at 13:52, Glenn Proctor wrote:
>>>> I'm not 100% happy with the
>>>> "get_all_object_xrefs()" name either though, so keep the suggestions
>>>> coming ...
>>> 
>>> $gene->get_all_gene_xrefs()  etc?
>>> 
>>> At the risk of adding a large number of redundant methods, theoretically
>>> this is possible:
>>> $transcript->get_all_gene_xrefs();
>>> $gene->get_all_transcript_xrefs();
>>> etc
>>> 
>> 
>> Personally I find this the most transparent from a user perspective ....
> 
> Notice that today, the get_all_DBLinks() method does not get gene xrefs
> when called on a transcript object.  We will not change the semantics of
> the method, only add an alias name for it.

It's incredibly difficult to come up with a good name then: get_all_xrefs isn't true.

> 
> Andreas
> 
>> 
>> Cheers,
>> Bert
>> 
>> 
>>> _______________________________________________
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>>> 
>> 
>> 
>> 
>> -- 
>> Bert Overduin, Ph.D.
>> PANDA Coordination & Outreach
>> 
>> EMBL - European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton, Cambridge CB10 1SD
>> United Kingdom
>> 
>> http://www.ebi.ac.uk/~bert <http://www.ebi.ac.uk/%7Ebert>
> 
>> _______________________________________________
>> 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
> 
> _______________________________________________
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