[ensembl-dev] mapping miRBase -> Ensembl

[Rhoda Kinsella]

Hi Julian
I will add miRBase filter and attribute for Danio rerio to the release  
61 mart. Thank you for bringing this to our attention.
Kind regards
Rhoda

On 25 Nov 2010, at 15:44, Julien Roux wrote:

> Thanks Andy for the answer
> Yes you're right...
> Then I find it strange that it is not possible to retrieve this info  
> from Biomart
> Am I missing something?
>
> Le 25.11.10 16:12, Andy Yates a écrit :
>> Hi Julien,
>>
>> It seems that the mirBase accession is available from the  
>> transcript and not the gene.
>>
>> http://www.ensembl.org/Danio_rerio/Transcript/Similarity?db=core;g=ENSDARG00000082738;r=25:1688203-1688297;t=ENSDART00000116791
>>
>> Andy
>>
>> On 25 Nov 2010, at 15:02, Julien Roux wrote:
>>
>>> Dear Ensembl team
>>>
>>> For zebrafish Ensembl genes, it does not seem possible to retrieve  
>>> the miRbase Accessions via Biomart. nothing appears in the  
>>> "External References" section.
>>> However I checked that it is possible for other species (human,  
>>> mouse etc)
>>> How does it come?
>>> Is there another way to retrieve this mapping?
>>> The data seem to be in Ensembl since the description of some genes  
>>> mention the mirBase accession (http://www.ensembl.org/Danio_rerio/Gene/Summary?db=core;g=ENSDARG00000082738 
>>>  for example)
>>> Thnaks for your help
>>> Julien
>>> -- 
>>> Julien Roux, PhD
>>>
>>> http://www.unil.ch/dee/page38327.html
>>>
>>> Keller group, Department of Ecology and Evolution
>>> Biophore, University of Lausanne, 1015 Lausanne, Switzerland
>>> tel: +41 21 692 4221    fax: +41 21 692 4165
>>>
>>> _______________________________________________
>>> Dev mailing list
>>> Dev at ensembl.org
>>> http://lists.ensembl.org/mailman/listinfo/dev
>
>
> -- 
> Julien Roux, PhD
> http://www.unil.ch/dee/page38327.html
> Keller group, Department of Ecology and Evolution
> Biophore, University of Lausanne, 1015 Lausanne, Switzerland
> tel: +41 21 692 4221    fax: +41 21 692 4165
>
>
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev

Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.