Autogenerating OBO format files (fwd)

[Sue Rhee]

Since we won't be releasing the official PO files until July, I suggest
that we release it as OBO. As for the existing spcies-specific files, your
suggestion sounds fine to me, though I don't know how frequently these
will be updated between now and the PO file release.

Sue

On Mon, 9 Feb 2004, Pankaj Jaiswal wrote:

> 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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Sue Rhee                         	rhee at acoma.stanford.edu
The Arabidopsis Information Resource	URL: www.arabidopsis.org
Carnegie Institution of Washington	FAX: +1-650-325-6857
Department of Plant Biology		Tel: +1-650-325-1521 ext. 251
260 Panama St.
Stanford, CA 94305
U.S.A.
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