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[Go-database] Re: GO database

Heather Butler hbutler at
Thu Aug 16 09:15:21 PDT 2001


> right now CGAP are refering to version 1.113 of the ontology 
> which seems
> to me like they have taken the cvs revision number of *one* of the
> ontology files.

I thought that the number 1.113 was most likely refering to the version
number of the GO-Editor that was used to create the ontology and was
used mistakenly instead of the actual ontology version number. Could
this be true?

I also have a vague recollection about the monthly dumps being given
version numbers like: 1.0, 2.0, 3.0 etc so that the ontologies released
at the beginning of each month will have the same version number and I
was wondering if this is still something that is going to happen.



> it seems an easy short term solution would be to cvs tag the 
> repository on
> a, say, montly basis and make this our versioning scheme. it 
> would be easy
> to do a checkout based on these tags and build the database 
> and xml from
> these. Then everything is nicely in sync. (when the database 
> becomes the
> primary source the cvs tag could be replaced by a "publish" 
> button in GO
> Edit or something)
> if we don't have a versioning scheme scheme should we 
> continue the current
> ad hoc (unverified xml nightly and verified mysql dump every 2 or 3
> weeks) way or not?
> sorry if I'm retreading ground, I wasn't at the last meeting and the
> minutes aren't up on the site yet.
> On Wed, 15 Aug 2001, Suzanna Lewis wrote:
> > 
> > Hello Bo and Chris,
> > 
> > I wish I could have heard your talk Bo because Chris doesn't give
> > praise lightly. Hopefully next time.
> > 
> > The earliest that Chris and I will both be in the same place at the
> > same time is August 29-30. In the meantime (once he is 
> back) Chris can
> > at least get web pages updated so that the date on the page reflects
> > the date of the dump.
> > 
> > Right now there are 3 formats that you can download the data in. For
> > someone like you I can understand that what you would want is the
> > one that can go right into your copy of the database.
> > 
> > 1. is the original indented file. i don't recommend this one because
> >    it hasn't been checked for errors. Like Chris said, now that
> >    everyone is using go-edit it is more reliable, but it never hurts
> >    to double check (since we can't guarantee that it passed through
> >    go-edit and thus has no syntax errors). Chris can provide the
> >    details of the cron job that loads this (frequency and 
> success rate)
> >    
> > 2. the tab delimited database dump. best for those using 
> the database.
> >    it still needs to have a cron job to turn the crank and update it
> >    
> > 3. the xml - i think i'll read some more e-mail before i 
> say anything
> >    here, although my recollection is that this is currently 
> automatically
> >    (cron) pulled from the database after the indented-file (#1) is
> >    loaded.
> >    
> > #2 and #3 include definitions too which #1 doesn't
> > 
> > I agree that the web pages could make all of this more obvious. I'm
> > adding that onto the to-do list.
> > 
> > I liked to discuss how to do versioning with Chris first 
> and then send
> > something out at the end of the month to discuss our options.
> > 
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