Autogenerating OBO format files (fwd)

[Sue Rhee]

Hi, all

This is a heads up on the switch of Dag-edit to use OBO flat files. There
is a script that will convert a GO flat file into OBO flat file and I
think this could be done perhaps by Shuly once before we switch to have
the curators using the OBO flat file? I will forward a message that
describes where the how to run the script.

Sue

---------- Forwarded message ----------
Date: Sun, 8 Feb 2004 16:33:46 -0700 (MST)
From: John Day-Richter <jrichter at yossarian.colorado.edu>
To: Mike Cherry <cherry at genome.stanford.edu>
Cc: "go at geneontology.org List" <go at genome.stanford.edu>
Subject: Re: Autogenerating OBO format files



On Sun, 8 Feb 2004, Mike Cherry wrote:

> 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.

Thanks for setting this up! Is it possible to have the script
automatically generate the obo file on the server-side every time there's
a commit to the cvs repository? If not (or if that's too much of a
hassle), I vote to generate the obo file at midnight every night.

> 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.

Now that the new version of DAG-Edit is out, I am planning to publish some
protocols for the obo adapter beta-test I'd like the Cambridge curators
to do. (Hopefully I'll send out that document some time tomorrow). Once
we've deemed the obo adapter completely stable (which I hope will be done
in one or two weeks), I think we should immediately switch to the new
format.

	-John