[ensembl-dev] How to programmatically get ontology go terms for transcript?
Thomason, James
thomason at cshl.edu
Tue Apr 10 00:08:34 BST 2012
Well, that's progress, I guess. But what do I do with a Bio::EnsEMBL::DBEntry object?
Looking at them, they don't appear to contain any of the data in that ontology table. Do I need to hop to some additional objects? Nothing looks obvious to jump to next.
On Apr 9, 2012, at 5:15 PM, Jan Vogel wrote:
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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--
-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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