[ensembl-dev] Bulk download of Microarray Probe mapping via MySQL

[njohnson]

Hi Alex

I'd like to pre-fix my response by stating that  (as I'm sure you are aware), the safest way to access the data is via the API, as this will protect you against any schema changes that might occur in the future. However, the probe and xref tables are probably the most stable in the whole schema. So for your purpose I think this is probably the right choice.

I do get these specific questions occasionally, so I will write a script which does the necessary direct SQL queries and check this into our scripts folder. I'll let you know asap. 


Nathan Johnson
Ensembl Regulation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD

http://www.ensembl.info/
http://twitter.com/#!/ensembl

On 11 Jul 2013, at 21:56, Alex Holman <aholman at jimmy.harvard.edu> wrote:

> Hi Nathan, 
> Thanks for the reply.
> I'd like to get both the alignment coordinates (which I *think* I have by joining on the probe_feature table) as well as the probe/set -> transcript annotations.  
> 
> I'm part of the team working on an updated version of the MeV (Multiple Experiment Viewer) software for microarray analysis (http://mev-tm4.sourceforge.net/).  We incorporate the ability to display probe gene annotations as well as basic probe IDs, and I'd like to include the Ensembl mappings as well as those supplied directly from Affy, Illumina, etc.  To do this I'm hoping to mirror a local copy of the Ensembl mappings for all chips to incorporate into the tool as an annotation set.
> 
> Thanks,
> Alex
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/