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Re: [Gmod-schema] Re: Action points from yesterday's conversation on the modular schema
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From: Scott C. <ca...@cs...> - 2002-10-18 19:31:49
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Chris, I agree; best to get it set up right to begin with. I don't have a problem with the structure you propose. Anyone else? Scott On Fri, 2002-10-18 at 15:25, Chris Mungall wrote: > > > 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 > > > > > > > > > > > > ------------------------------------------------------- > > > This sf.net email is sponsored by:ThinkGeek > > > Welcome to geek heaven. > > > http://thinkgeek.com/sf > > > _______________________________________________ > > > Gmod-schema mailing list > > > Gmo...@li... > > > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > > > > > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. ca...@cs... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory |