[ensembl-dev] Gene name synonyms

Sébastien Moretti sebastien.moretti at unil.ch
Mon Mar 10 13:48:55 GMT 2014


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/




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