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[go-ontology] TG 1 ready for testing

Tanya Berardini tberardi at
Fri Dec 2 16:40:35 PST 2011

I am away next week and back Thurs mid afternoon.  (David is away too, back
Fri. am) If someone else wants to test TG1 in the commit stage, please go
ahead and do so.  Gatekeeper instructions follow below so that someone else
can do the commits to the live ontology in my place.

Here are the instructions that I follow.  I usually run the test mode first
and then the for real one.  This is my set up on my Mac.  Your directory
for OBO-Edit2 may be somewhere else.  And yes, I still use OE2 and not any
of the other newer versions.

QUICK SUMMARY. Do this to pull in submissions, make sure that all your
terms are in there, they might not have made it if they were added less
than an hour before you start because the cvs repository only updates on
the hour.

>cd go/ontology/editors/xp_submit
>cvs update


>perl ./ --dry-run --obo2obo /Applications/OBO-Edit2


>perl ./ --obo2obo /Applications/OBO-Edit2
>cd ..
>cvs diff
>cvs commit gene_ontology_write.obo
>cvs commit xp_submit/


Make sure you do the last two steps otherwise the new terms will not end up
in the ontology.  The last step resets the 'new term' file to a blank one.


Good luck!  I'm looking forward to TG1 in action.  I'll do one last commit
to the live file in about 2 mins and then that will be it for this week.


Tanya Berardini
TAIR Curator

On Fri, Dec 2, 2011 at 4:31 PM, Chris Mungall <cjmungall at> wrote:

> [Apologies for the delay, it turns out that integrating with CVS turned
> out to be much harder than with SVN.]
> TG 1 is ready to be tested. The URL is:
> At the moment, it's hooked up to a test cvs repo and test ontology at
> Berkeley, _not_ the live one. Anything you do in TG1 will be lost for now.
> Here's what I suggest for monday and tuesday for testing. We should add
> some terms using one or more of:
>        regulates
>        involved in
>        occurs in
> (hopefully we have some sensible ones)
> What I suggest is that you add these *twice*. Once in the test TG1
> environment (be sure to log in and commit, and then in the live TG0
> environment. If you like, you can try adding some dubious ones into TG1. Go
> wild! We can ditch them at the gatekeeper stage.
> I have already submitted 3 terms for regulation of "metanephric late
> distal convoluted tubule development"
> Then on wednesday during the meeting we can have Tanya release the actual
> TG0 requests into the main ontology (using the soon to be retired
> gatekeeper script), and then at the same time release the test TG1 requests
> into the test ontology.
> The gatekeeper review page for TG1 is:
> Try it now and you should see the 3 terms I submitted, eagerly waiting to
> be passed or rejected. If you don't have permission then email Heiko your
> TG1 login. D&T should be gatekeepers already. The Cambridge go editors
> should send their logins to Heiko.
> Remember, the TG0 and TG1 environments are completely separate. Your TG0
> logins will not work with TG1. It's very easy to see what tool you're in,
> the URLs are completely separate and the look and feel is completely
> different. TG0 is live and is working (or not working) as usual. TG1 is not
> hooked to the main GO cvs yet, so you can do what you like on it.
> _______________________________________________
> go-ontology mailing list
> go-ontology at
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