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[Gohelp] GO structure query

Jane Lomax jane at ebi.ac.uk
Thu Oct 29 04:55:01 PDT 2009


Dear feng gao,

Thanks for your interest in GO. To answer your first question, you can 
either view the term in a browser such as the GO tool AmiGO:

http://amigo.geneontology.org/cgi-bin/amigo/go.cgi

If after you've found your term you view in in any of the tree views 
you'll be able to see the parent and child terms.

e.g. for mitochondrion:

http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0005739&session_id=5006amigo1256815858#lineage

or you can directly query the GO database here:

http://berkeleybop.org/goose

You'll find example queries in the pulldown menu.

Regarding your other two questions, GO is structured as a directed 
graph, where each term can have one or more parents. As such, any term 
can have multiple paths back to the root which is probably why you can 
see the same term in different locations in the tree. This also means 
that GO terms do not occupy strict fixed levels in the hierarchy so it 
is not possible to create a file like the one you describe I'm afraid. 
There's more information on GO structure here:

http://www.geneontology.org/GO.ontology.structure.shtml

Hope this helps,

Jane Lomax
GO helpdesk
>
> ------------------------------------------------------------------------
>
> Subject:
> GO Help query (from website)
> From:
> gaomoutaint at gmail.com
> Date:
> Wed, 28 Oct 2009 18:27:05 -0700
> To:
> gohelp at genome.stanford.edu
>
> To:
> gohelp at genome.stanford.edu
>
>
> Email: gaomoutaint at gmail.com
> Name: Ontology (from feng gao)
> Text: how can i know a random GO term's father level or its children level?
> can i find the relationship map of all the GO term in excel format? such as GO 000005  1.1
>                       GO 000054  1.1.3
>
> another question, why same GO term has different location in the GO trees?
>   


-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
f: +44 1223 494468




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