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[Gohelp] GO term information

Rachael Huntley huntley at ebi.ac.uk
Thu May 22 03:08:21 PDT 2008


Dear Tania,

You can find details of multiple terms in a couple of ways. Firstly, 
there is a file of GO Terms and IDs on the GO Consortium website 
(http://www.geneontology.org/GO.downloads.files.shtml) which contains 
GO:ID, GO term names and ontologies which you can grep for your required 
GO:IDs.

Alternatively, you can compare several terms in the EBI's GO browser 
QuickGO (www.ebi.ac.uk/quickgo) - on the home page list your GO:IDs in 
the 'Compare GO terms' search box. This will give you a list of GO:IDs, 
their term names and ontology together with a graph showing their 
relationship with each other. (Note: there is a limit to how many terms 
can be shown on the graph, depending how widely dispersed they are in 
the ontology, so if you have lots of terms throughout the three 
ontologies you may not be able to display these). Once on this results 
page you can add or remove terms to your search as well as find 
annotation to the terms.

You mentioned that you used Chris Mungall's map2slim.pl script to obtain 
your GOslim - AmiGO has a new feature, GO Slimmer 
(http://amigo.geneontology.org/cgi-bin/amigo/slimmer), which is an 
adaptation of this script, the results page of the GO Slimmer will show 
you GO:ID, term name and ontology as well.

I hope this has answered your question. Please do not hesitate to 
contact us if you have further queries.

Best wishes,
Rachael Huntley
GO Curator.

>
> ------------------------------------------------------------------------
>
> Subject:
> GO Help query (from Tania Oh)
> From:
> tania.oh at dpag.ox.ac.uk
> Date:
> Thu, 22 May 2008 02:25:14 -0700 (PDT)
> To:
> gohelp at genome.stanford.edu
>
> To:
> gohelp at genome.stanford.edu
>
>
>contactName: Tania Oh
>contactEmail: tania.oh at dpag.ox.ac.uk
>contactText: hi, 
>Would you happen to know if there is a a tool or some method of obtaining GO information of GO terms mapped to GOslim terms? 
>
>I used Chris Mungall's map2slim.pl program to obtain the GOslim mappings of my go terms and this is one example:
>
>GO:0006979 => GO:0006950 // GO:0006950 GO:0050896 GO:0008150
>
>see also: 
>http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0006979 
>I would like to be able to obtain the following information for each of the above GOids, as such:
>
>biol_process    GO:0006979      response to oxidative stress    
>biol_process     GO:0006950    response to stress
>biol_process     GO:0050896    response to stimulus
>biol_process     GO:0008150    biological_process
>
>is there a simple way of doing this? 
>
>many thanks in advance,
>tania
>  
>





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