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[go-friends] Grouping GO terms according to evolutionary appearance

Thomas, Paul pdthomas at usc.edu
Fri Feb 3 09:41:29 PST 2012


Dr Cambridge,

You may find the GO "taxon constraints" file useful for your purpose— we are using it for a similar purpose in inferring GO annotations by homology.  The file specifies the taxonomic range to which many of the GO terms apply.  It can be found at:
http://www.geneontology.org/quality_control/annotation_checks/taxon_checks/taxon_go_triggers.obo
There is also a publication that describes the taxon constraints in more detail:
http://www.ncbi.nlm.nih.gov/pubmed/20973947
The paper describes how you can suggest additional entries to the file, in case it does not cover all the classes you're interested in.

Best,
Paul.
--
Paul D. Thomas, Ph.D.
Associate Professor and Director
Division of Bioinformatics
Department of Preventive Medicine
University of Southern California
1450 Biggy Street, NRT 2502
Los Angeles, CA 90089-9601
* please use zip code 90033 for FedEx deliveries
ph.: (323) 442-7799
fax: (323) 442-7995
email: pdthomas at usc.edu


From: Susan Tweedie <sart2 at gen.cam.ac.uk<mailto:sart2 at gen.cam.ac.uk>>
Date: Thu, 2 Feb 2012 12:24:54 +0000
To: <cambridge at ana.uni-heidelberg.de<mailto:cambridge at ana.uni-heidelberg.de>>
Cc: GO_helpdesk <go-helpdesk at mailman.stanford.edu<mailto:go-helpdesk at mailman.stanford.edu>>, <gofriends at geneontology.org<mailto:gofriends at geneontology.org>>
Subject: Re: [go-friends] Grouping GO terms according to evolutionary appearance

Dear Dr Cambridge

Thank you for contacting the GO consortium - sorry for the delay in getting back to you.

I don't know of a way to do this but I have cc'd my colleagues on the help desk and the GO friends list in the hope that someone may be able to help you.

However, you should bear in mind that the annotation set is still far from complete and experimentally based annotations are skewed towards a relatively small number of species. I would be wary about drawing conclusions from lack of annotation.

Best wishes,
Susan Tweedie


On 2 Feb 2012, at 2/Feb/2012 11:39:06, go-helpdesk-bounces at lists.stanford.edu<mailto:go-helpdesk-bounces at lists.stanford.edu> wrote:


From: Sidney Cambridge <cambridge at ana.uni-heidelberg.de<mailto:cambridge at ana.uni-heidelberg.de>>
Date: 31 January 2012 12:44:33 GMT
To: gohelp at genome.stanford.edu<mailto:gohelp at genome.stanford.edu>
Subject: Grouping GO terms according to evolutionary appearance



Hello,

I was wondering if there is any way to group GO biological processes according to an evolutionary timeline. I am thus looking for information that says for example, GO:123456 first appeared in unicellular eukaryotes, GO:234567 first appeared in invertebrates, GO:345678 first appeared in mammals, etc.
I have a few hundred GO terms that I am analyzing and it would be nice if I could quickly identify the taxonomic/evolutionary time when they first evolved in nature.

Is there any source out there that provides such information ?

Thank you very much in advance !

With kind regards,
Sidney


**************************************************************
Dr. Sidney Cambridge
University of Heidelberg
Department of Anatomy and Cell Biology
Im Neuenheimer Feld 307/Rm. 403
69120 Heidelberg
Germany
Tel: +49-6221-54-8659
Fax: +49-6221-54-4952

What would you attempt to do if you knew you could not fail ?
**************************************************************








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