[ensembl-dev] Gene name synonyms

[mag]

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
>