[ensembl-dev] How to get the GO evidence code and qualifier

[Jan Vogel]

Hi Mei, 

ensembl stores annotation data such as GO, SO etc  and provides adaptors  to access it - please find some entry points below. I don't have exact code to directly fetch IDA. 

http://www.ensembl.org/info/docs/Doxygen/external-api/classBio_1_1EnsEMBL_1_1ExternalData_1_1GO_1_1GOAdaptor.html

There's also a module in CPAN which allows you to access sub trees of GO: 

http://search.cpan.org/~cmungall/go-db-perl/GO/AppHandle.pm

The ensembl go db can be found here : 

 ./mysql -hensembldb.ensembl.org -P5306 -uanonymous -Densembl_go_5

It's not upgraded every release …. 


Hth, 

      jan 



On Sep 14, 2012, at 2:29 AM, JiangMei wrote:

Hi All.

Does anyone know how to get the GO evidence code, such as IDA (Inferred from direct assay), or qualifier, such as NOT? Did Ensembl API store these GO information?

Wish your help! Thanks a bunch!


Best, Mei
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