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

[Thomason, James]

Okay, good, I am getting somewhere. Hopefully I'm almost there.

I filtered out my call to get_all_DBLinks() to only look at the OntologyXref objects.

Comparing against thes tables:
http://dev.gramene.org/Arabidopsis_thaliana/Transcript/Ontology/Table?db=core;g=AT3G52430;oid=1;r=3:19431371-19434403;t=AT3G52430.1

it looks like the OntologyXref objects directly give me the accession, term, and evidence codes. So next questions are -

1) How do I get those go slim accessions? They don't appear to be  OntologyXref objects, and I'm assuming they're somehow related. Trying the various get_* methods didn't seem to yield the results I wanted.

2) How can I get the URLs that the accessions link to? For the non-slim ones, I see that for my purposes I could just hardwire to Gramene, but I'd really rather populate it correctly.

3) How do I group the accessions together? Again, that page has multiple tables - descendent of biological process, cellular component, etc.  Is it a matter of looking at each OntologyXref's get_all_masters() values and parsing together a tree from that?

Many thanks for the help and the patience. :-)

On Apr 10, 2012, at 2:52 AM, Andy Yates wrote:

Hi James,

If you are going to use the API to extract this information then you should look at the Bio::EnsEMBL::OntologyXref which extends DBEntry. The API automatically creates these objects when it encounters an object_xref link which also has an entry in the ontology_xref table. As Jan said get_all_DBLinks() is the method to use and will return these OntologyXref objects.

All the best,

Andy

On 10 Apr 2012, at 00:08, "Thomason, James" <thomason at cshl.edu<mailto:thomason at cshl.edu>> wrote:

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<http://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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Dev mailing list    Dev at ensembl.org<mailto:Dev at ensembl.org>
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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/


_______________________________________________
Dev mailing list    Dev at ensembl.org<mailto:Dev at ensembl.org>
List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
Ensembl Blog: http://www.ensembl.info/

_______________________________________________
Dev mailing list    Dev at ensembl.org<mailto:Dev at ensembl.org>
List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
Ensembl Blog: http://www.ensembl.info/

--
-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/