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GO slim

Suzanna Lewis suzi at fruitfly.org
Mon Jun 21 09:36:06 PDT 2004


Hi Evelyn,

Before starting, let me be sure I understand correctly.

1. Where does the list of genes come from?
    a. from those already available on the GO site?
    b. from the user? (if it is from the user, then
       is it an associations file?)
    c. both of the above options?

2. Would there be a default slim? Or could the user
    select/create their own slim?

The easiest way is 1a and a default-slim. Perhaps
start with this and then add the others? 1b will
be both harder because it might have syntax errors
that haven't already been removed, but simpler
because it is just uploading a file. Brad has some
way of creating slims already and so this might
not be hard to do either.

But is any of the above what is needed?

-S

Evelyn Camon wrote:
> Dear Xinghua,
> 
> I'm not sure that there is one but I should like to know too.
> At GOA we release a file of GO annotations mapped to a very small defined
> GO dataset but that does not solve your problem.
> 
> Suzi.....could this also be nice a GO Consortium tool to create
> for non-techy people like me :-)))
> Mind you I have never tried to use the map2slim script.
> This is a common user request.
> We discussed the issue briefly at the GO Advisary meeting.
> 
>>put a list of GO and get slim version back.
> 
> it would be nice to also then map the slim to an association file via an easy
> web
> interface.
> 
> cheers
> 
> Evelyn
> 
> Xinghua Lu wrote:
> 
> 
>>Dear all,
>>
>>I am wondering if there is any web site that runs map2slim so that I can
>>put a list of GO and get slim version back.  Thanks in advance for your
>>help.
>>
>>Best,
>>Xinghua
>>
>>--
>>Xinghua Lu MD, PhD
>>Assistant Professor
>>Dept of Biostatistics, Bioinformatics and Epidemiology
>>Medical University of South Carolina
>>135 Cannon St, Suite 303
>>Charleston, SC 29425
>>Tel: 843-876-1111
>>FAX: 843-876-1126
>>
>>--
>>This message is from the GOFriends moderated mailing list.  A list of public
>>announcements and discussion of the Gene Ontology (GO) project.
>>Problems with the list?           E-mail: owner-gofriends at geneontology.org
>>Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
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> 
> 


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