[ensembl-dev] Missing UniProt ACs for fruitfly?

[Gary Bader]

Hi Andy,
	Thanks for the reply.  Looks like we should use EnsemblMetazoa, since all the expected UniProt ACs seem to be there for Drosophila melanogaster.  Not all of them seem to be there in the main Ensembl, but maybe that will improve in the future (I would have thought that both Drosophila melanogaster instances should be the same, but I guess they have different pipelines).

Cheers,
Gary

On 2012-01-18, at 4:16 AM, Andy Yates wrote:

> Hi Gary,
> 
> UniProt references are linked into Ensembl at the translation layer. You can see your UniProt AC at the following page with a 100% identity between Ensembl and UniProt:
> 
> http://www.ensembl.org/Drosophila_melanogaster/Transcript/Similarity?db=core;g=FBgn0000017;r=3L:16615461-16641674;t=FBtr0075357
> 
> I've just run your query against our mart database and have encountered an error which I'll raise to our BioMart team. For the moment you could always try using Ensembl Genomes' metazoa mart (http://metazoa.ensembl.org/biomart/martview/) where a query against UniProt does not seem to result in the same error.
> 
> Hope this has helped
> 
> Best regards,
> 
> Andy
> 
> On 17 Jan 2012, at 23:03, Gary Bader wrote:
> 
>> Hello,
>> 	We use ensembl fruitfly as a basis for our www.genemania.org website and we have noticed that UniProt ACs are missing for fruitfly.
>> 
>> For instance, for gene: Abl (flybase ID: FBgn0000017), the flybase entry at:
>> http://flybase.org/reports/FBgn0000017.html
>> 
>> has a UniProt AC of P00522 and ID of ABL_DROME
>> http://www.uniprot.org/uniprot/P00522.txt
>> 
>> However, the ensembl gene page (external references section) has the ID ABL_DROME, but is missing the AC P00522:
>> http://useast.ensembl.org/Drosophila_melanogaster/Gene/Summary?g=FBgn0000017;r=3L:16615461-16641674
>> 
>> If you search for P00522 in ensembl, you just find a genomic alignment (protein alignment feature).
>> 
>> I also get a stacktrace from biomart if I try to select "UniProt/SwissProt Accession" or "UniProt/TrEMBL Accession" as an attribute to get for any set of fly genes.
>> 
>> We have also noticed that almost no uniprot IDs or ACs were present until recent ensembl releases - is this still a work in progress?
>> 
>> Thanks,
>> Gary
>> 
>> http://baderlab.org
>> The Donnelly Centre - http://www.thedonnellycentre.utoronto.ca/
>> University of Toronto
>> 
>> 
>> 
>> 
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> 
> ---
> Andrew Yates                   Ensembl Core Software Project Leader
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensembl.org/
> 

http://baderlab.org
The Donnelly Centre - http://www.thedonnellycentre.utoronto.ca/
University of Toronto