[ensembl-dev] Gene name synonyms

[Sébastien Moretti]

Hi Mag,

I will skip the grep step with external_db and get all possible synonyms.

Thanks

> Hi Sébastien,
>
> Your solution works if all you want are the synonyms attached to the
> xref used as gene display name.
> These are the synonyms displayed on the main website.
>
> There are however more than one source used, and they can all have
> additional synonyms.
> For example, for human, main gene name sources are HGNC, EntrezGene and
> Uniprot_gn.
> Only the HGNC one, if available, will be used as gene display name, but
> all 3 will have synonyms and the same name.
>
> This is what the REST server shows:
> http://beta.rest.ensembl.org/xrefs/name/human/TAF8?content-type=application/json
>
>
> If you want all the possible synonyms, I would remove the condition on
> the external_db.
>
> For drosophila, FlyBaseName_gene is used to assign display names, but
> flybase_gene_id are additional xrefs which have synonyms.
> On the main website, genes do not display synonyms.
>
> For C. elegans, there are only synonyms for the Uniprot translation xrefs.
>
>
> Hope that helps,
> Magali
>
> On 10/03/2014 13:48, Sébastien Moretti wrote:
>> Hi
>>
>> Usually I try to get gene name synonyms with the API this way:
>>
>> my @synonyms = ...
>>                map  { @{$_->get_all_synonyms} }
>>                grep { $_->dbname() eq $gene->external_db() }
>>                @{ $gene->get_all_xrefs() };
>>
>> I get all xrefs, then keep only those that are from the main
>> external_db of the gene, then get all synonyms from it.
>>
>>
>> Unfortunately this is not always so simple:
>> For D. melanogaster, the main external_db is not the one that contains
>> synonyms according to your REST service.
>> FlyBaseName_gene    should be    flybase_gene_id
>>
>> For C. elegans I don't find any synonyms.
>> Normal?
>>
>> Also not sure I miss some synonyms for other species because the rest
>> service may return several synonym fields according to your REST service.
>>
>>
>> So, what could be the right way to get synonyms?
>> Why the REST and the website/API don't show the same information from
>> time to time?
>>
>> Thanks

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://selectome.unil.ch/ http://bgee.unil.ch/