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

ek at ebi.ac.uk ek at ebi.ac.uk
Tue Apr 10 07:25:55 BST 2012


Hi James

have a look at get_ontology_chart function in

http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/eg-plugins/common/modules/EnsEMBL/Web/Object/Transcript.pm?revision=1.23&root=ensembl&view=markup

it builds a hash containing all the relevant data for the ontology table
and ontology graphs

regards

Eugene


> 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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