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

Thomason, James thomason at cshl.edu
Mon Apr 9 22:56:19 BST 2012

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:


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.


-Jim Thomason...

Scientific Informatics Developer @ The Ware Lab,
a USDA-ARS Laboratory at Cold Spring Harbor Laboratory

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