Autogenerating OBO format files (fwd)

[Sue Rhee]

---------- 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