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[go-helpdesk] Relations and Visualization GO Help query (from website)

Paola Roncaglia paola at ebi.ac.uk
Wed Jun 27 13:38:39 PDT 2012


Dear Hector,

Thank you for contacting GO.

Indeed it seems that there is an error in the section below:
http://www.geneontology.org/GO.ontology.relations.shtml#regulates-trans

"If we switch the relations around, so that A is a B, and B regulates C, 
we can again infer that A regulates C."
should read:
"If we switch the relations around, so that A regulates B, and B is a C, 
we can again infer that A regulates C."

Thanks for pointing this out. I'm cc-ing Chris Mungall to double-check 
this with him before I make the correction.

As for your second question, you could use the Visualization tool in AmiGO:
http://amigo.geneontology.org/cgi-bin/amigo/visualize?mode=client&session_id=

You may find a list of tools to visualize GO terms here:
http://www.geneontology.org/GO.tools_by_type.visualization.shtml

I hope this answers your question. If not, please feel free to contact 
us again.
With best regards,

Paola Roncaglia, for GO help.


> Subject:
> GO Help query (from website)
> From:
> hurbinas at gmail.com
> Date:
> Tue, 26 Jun 2012 13:51:01 -0700
>
> To:
> go-helpdesk at mailman.stanford.edu
>
>
> Email:hurbinas at gmail.com
> Name: Ontology (from Hector Urbina)
> Text: Hello,
> I would comment that inhttp://www.geneontology.org/GO.ontology.relations.shtml  there is an error where it says: "If we switch the relations around, so that A is a B, and B regulates C, we can again infer that A regulates C"; but it should say "If we switch the relations around, so that A regulates, and B is a C..."
>
> I also would like to ask if there is any tool which receive two (and hopefully more) GO codes and gives their inferred relationships in some way? (at least a graph where I can infer their relationships, if any.)  Thanks, Hector.

-- 
Dr Paola Roncaglia
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD
p: +44 1223 492600
f: +44 1223 494468

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