[ensembl-dev] How to programmatically get ontology go terms for transcript?

[Jan Vogel]

Hi James, 

check out the doxygen ensembl api doc: 

http://uswest.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Transcript.html#afbe0947fe458e2f2739f78852c292f7c

Bio::EnsEMBL::Transcript::get_all_DBLinks( )  is your friend - for Ensembl annotation on www.ensembl.org, this should return http://www.geneontology.org/GO.slims.shtml#whatIs annotations. 
Another way would be to use biomart. 

I'm unsure if this is set up for the gramene website … 

Hope  this helps, 

         Jan Vogel 

          
On Apr 9, 2012, at 2:56 PM, Thomason, James wrote:

> Hi all,
> 
> I'm completely stumped. I've been charged with programmatically extracting out ontology go terms from our ensembl installation. A relevant link would be:
> 
> http://www.gramene.org/Arabidopsis_thaliana/Transcript/Ontology/Table?db=core;g=AT3G52430;oid=1;r=3:19431371-19434403;t=AT3G52430.1
> 
> I want to pull out everything inside that "Ontology Table" bit. But I'm utterly stumped as to how to go about doing it. I dug through the code enough to find that the page is generated through an EnsEMBL::Web::Component::Transcript::Go object, but I don't know how to instantiate one on the command line to get at the info. Presumably, since it's in the Web sub-tree, I really shouldn't be doing that on the command line anyway. Is there some way to link to that data through a Bio::EnsEMBL::Transcript object, perhaps? An xref or something?
> 
> For now, I basically just want to dump out that data in a tab delimited format, so I don't need anything fancy other than actually getting to it.
> 
> Any pointers in the right direction would be greatly appreciated.
> 
> Thanks,
> 
> --
> -Jim Thomason...
> 
> Scientific Informatics Developer @ The Ware Lab,
> a USDA-ARS Laboratory at Cold Spring Harbor Laboratory
> http://www.warelab.org/
> http://www.cshl.edu/
> 
> 
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