Re: [Gmod-schema] Re: Action points from yesterday's conversation on the modular schema

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On 18 Oct 2002, Scott Cain wrote:

> Dave,
>
> We should definitely get this stuff under cvs control.  I was thinking
> of a module named schema with doc, src and image subdirectories to hold
> the information that is in the three tar balls that are currently on the
> website.  If nobody has any objections, that's what I'll do.

That would be great, thanks.

(it is under cvs at the moment, but just in a flat scratch space, the
sooner we get it a real home the better)

just to be pernickity -

i expect code to live under src/ - i'd make it sql/

shall we just stick the images under doc/

should we have the doc directory mirror the modular structure of the sql
directory, or should we just have module-specific docs

the way we have it now is

/sql
    sequence/
             sequence.sql
             use-cases/

and so on

sorry to be a bore about these things but it's important to get a cvs dir
set up right as it's a pain to change the structure once it's underway!

> About the phone meeting, I'll answer for Lincoln, so that you can get an
> answer before you go home today.  Lincoln is teaching a course this week
> and next, so his time during the day is rather limited.  I don't know
> about is plans for the week after, but perhaps that is when we should
> shoot for.
>
> Scott
>
>
> On Fri, 2002-10-18 at 11:34, David Emmert wrote:
> > Hi all,
> >
> > First of all, Scott, I had a look at the Modular Schema info you put on
> > http://www.gmod.org, and it looks great - many thanks.  I wonder if you
> > have any ideas as to how we can go about improving whats there and  making
> > sure it is current.  Should we be thinking about putting the Modular
> > Schema into the sourceforge CVS now, and if so, how organized?
> >
> > Thanks also for setting up the schema mailing list.
> >
> > I wanted to let you all know that I've successfully loaded all of the
> > D.melanogaster "release 3" genome annotation GenBank records into the
> > schema, and the sequence module seems to have worked beautifully.  I
> > finished the loader just last night so I havn't completely evaluated
> > the results, but the annotations I've looked at look good.
> >
> > There's at least one gene model annotation which *didn't* load properly,
> > mod(mdg4), which is a nasty case of trans splicing who's "join" locations
> > my location parser definitely did not appreciate.  Here's what one of the
> > mod(mdg4) GB mRNA features looks like:
> >
> >      mRNA            join(138523..138735,138795..139263,
> >                      complement(154413..154524),complement(153944..154201),
> >                      complement(153727..153866),complement(152185..153037))
> >                      /product="CG32491-PZ"
> >                      /note="trans splicing"
> >
> > Parser go bung!
> >
> > I'm sure this case is workable in the schema, and I'll work on parsing
> > locations of this ilk as soon as I get a chance.
> >
> > Lincoln, I focused on this instead of the WormBase data because in
> > the context of our local (FlyBase) development, and learning how to
> > layer-on the genetic/phenotypic data, we really needed to get a test-bed
> > to work with, and it looks like a proper port of Berkeley's gadfly data
> > is going to take some time coming.
> >
> > I'll take a look at the WormBase GFF and .ace data now.
> >
> > In the meantime, if any of you would like a postgres dump of this
> > data to play with, please let me know.   Please, everyone, be aware
> > that the current D.melanogaster "release 3" genome annotation data
> > in GenBank imperfect, and these imperfections (only, I hope) are
> > obviously going to be in this test data.
> >
> > Once I've convinced myself I've implemented this properly, I want to
> > start writing some practical documents on implementing data in the
> > sequence module.   Scott, others, if you have any opinions on format
> > or content this should have, please let me know.
> >
> > If I get a chance, I'm going to try to get Gbrowse up and running on
> > this data, as I'm very anxious to know how the Modular Schema and
> > Gbrowse play together.   I have no idea how easy or difficult this
> > will be, being totally unfamiliar with Gbrowse;  if anybody wants to
> > give advice or lend a hand, please do!
> >
> > Finally, Lincoln mentioned we set up further conference calls, and
> > I'd like to suggest we shoot for next Wednesday, 22 Oct, 3pm EST -
> > same time as last time.  Would that work for everybody?
> >
> > I'll be out of town on Monday or Tuesday, but checking mail off and
> > on, so apologies in advance if my replies are slow in coming.
> >
> > Best,
> >
> > -Dave
> >
> >
> > >> From ls...@pe... Thu Oct 10 12:56 EDT 2002
> > >> From: Lincoln Stein <ls...@cs...>
> > >> To: wa...@cs..., kc...@cs...
> > >> Subject: Action points from yesterday's conversation on the modular schema
> > >> Date: Thu, 10 Oct 2002 12:57:32 -0400
> > >> User-Agent: KMail/1.4.3
> > >> Cc: Chris Mungall <cj...@fr...>, David Emmert <em...@mo...>,
> > >>         Scott Cain <ca...@cs...>
> > >> MIME-Version: 1.0
> > >> Content-Transfer-Encoding: 8bit
> > >> X-MIME-Autoconverted: from quoted-printable to 8bit by morgan.harvard.edu id MAA10948
> > >>
> > >> Hi All,
> > >>
> > >> I thought our conversation yesterday about the modular schema was very
> > >> productive, and I look forward to David setting up a schedule for further
> > >> talks.  Just a summary of the action points that we ended on:
> > >>
> > >> Because ideally the modular schema should support the application modules that
> > >> we've already contributed to gmod, we're going to put together test sets for
> > >> David and Chris to work with.
> > >>
> > >> 1) Lincoln to provide sequence feature data from WormBase in GFF and .ace
> > >> format
> > >> 2) Ken & Doreen to provide genetic map and correspondence data in the form of
> > >> relational database table dumps
> > >> 3) Doreen to provide curated mutants/phenotypes/alleles in some form (to be
> > >> determined)
> > >> 4) Scott to set up mailing list on gmod site to help coordinate this.
> > >>
> > >> The data sets will be submitted via e-mail to David.  I will do this by
> > >> putting a data set on an FTP site and sending the URL to David.
> > >>
> > >> Lincoln
> >
> >
> >
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