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

[Thomason, James]

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/