Autogenerating OBO format files (fwd)

[Pankaj Jaiswal]

In one of my earlier mails I suggested on releasing the OBO format with 
every major release. However, depending on the situation, and user 
liking we can start having it frequently (once a day), until everything 
shifts to the OBO format completely.

Pankaj

Sue Rhee wrote:

> ---------- Forwarded message ----------
> Date: Sun, 8 Feb 2004 14:03:53 -0800
> From: Mike Cherry <cherry at genome.stanford.edu>
> To: John Day-Richter <john.richter at aya.yale.edu>
> Cc: "go at geneontology.org List" <go at genome.stanford.edu>
> Subject: Re: Autogenerating OBO format files
> 
> John,
> 
> Thanks for the instructions and thanks for a great tool.  The flat2obo
> script works great on our Solaris server.  I can easily generate the
> go.obo file to the go/ontology directory in the CVS repository as
> whatever frequency is useful.  I'm sending this message to the GO list
> for discussion of this topic.  The other question is how long should I
> plan on generating the go.obo file, before the curators will be
> switching to committing that file.  Obviously, I will need to include
> checks in my script so that if the go.obo file is newer than the
> process, function or component files I do not over write.
> 
> Then after the curators switch to writing go.obo I'll switch to making
> the flat  files from the OBO file for the repository.
> 
> This is a big change.  What other issues does the group need to discuss?
> 
> -Mike
> 
> On Feb 7, 2004, at 2:20 PM, John Day-Richter wrote:
> 
> 
>>Hi, Mike. I should have gotten to you earlier with this, but I've been
>>engrossed in some new DAG-Edit features for the last week.
>>
>>At the last meeting, we talked about autogenerating the GO files in
>>OBO format
>>and posting them on the website. You said you'd be able to write a
>>script for
>>that once I sent you some instructions on how to use the conversion
>>scripts.
>>Here are those instructions:
>>
>>1) Download DAG-Edit 1.410 from sourceforge.net/projects/geneontology
>>. I
>>suggest the .tar.gz format.
>>
>>2) Unpack the archive wherever you'd like. You'll want to be able to
>>run the
>>flat2obo script that's in the main installation directory. If you need
>>to,
>>you can create a link to the flat2obo script in one of your system path
>>directories.
>>
>>3) Run flat2obo with the following options:
>>
>>flat2obo --gopresets {path-to-component.ontology}
>>{path-to-process.ontology}
>>{path-to-function.ontology} -def {path-to-GO.defs} -o
>>{path-to-create-go.obo}
>>
>>The GO ontology files can be listed in any order.
>>
>>Let me know if you have any questions.
>>
>>	Thanks,
>>
>>		John
>>
> 
> J. Michael Cherry, Ph.D.         Internet: cherry at stanford.edu
> Associate Professor (Research)   Department of Genetics
> Medical Center, Room M341        Stanford University School of Medicine
> Voice:    650-723-7541           Stanford, California  94305-5120
> FAX:      650-723-1534           http://genome-www.stanford.edu/~cherry
> 
> 

-- 
******************************
Pankaj Jaiswal, PhD
Gramene Database
Department of Plant Breeding
G-15 Bradfield Hall
Cornell University
Ithaca, NY-14853

tel: +1-607-255-3103
fax: +1-607-255-6683
web: http://www.gramene.org
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