[Bioperl-l] BioSQL and Bioperl-db inching towards release

[Jason Stajich]

On Fri, 23 May 2003, Hilmar Lapp wrote:

> I got the Oracle version of the biosql schema fully migrated, at least
> as far as I can tell from here. I'm going to commit the new version
> some time today. There will also be a sql*plus migration script from
> pre-Singapore to the current version that supposedly keeps your data
> intact (be sure to read the disclaimer though).
>
> This means we're getting ready to release Biosql 1.0, possibly as early
> :) as next week. If anyone sees any problems with the current schema
> that he/she thinks should be corrected before this release, please
> speak up now. I guess I should make an effort and generate an updated
> ERD before release; the dated ones are confusing wrt the current
> schema. If there is consensus I'll put out a release candidate early
> next week.
>
> Bioperl-db should be working against the mysql, PostgreSQL, and Oracle
> versions (once I've committed that one). The major deficiency here is
> POD documentation of the modules, specifically updating old modules,
> and adding/updating the SYNOPSIS sections. I guess a programmer's guide
> would also be helpful. For the next weeks to come I'm unfortunately not
> in a position to be able to spend the time it would require to bring
> the POD documentation up to speed. Would anyone else care to help out?
> What is generally people's take on how good the documentation should be
> before we release this? Maybe not care too much and just go ahead to
> have something officially blessed that can be downloaded?
>
> Jason, with respect to the marker database in bioperl-db, what is your
> vote on keeping it in the distribution? The problem is that the schema
> is MySQL-specific, so if someone wants biosql on Pg or Oracle you still
> have to set up Mysql in order to make all tests pass. An option could
> be to check the driver in the markerdb-related tests and skip
> everything if it's not mysql.

Drop it - drop it all. =)

The comparative map questions it was intended answer are really better
dealt with in Ken's/GMOD's CMap stuff and new work on
pedigrees/markers/popstats means that all my old adaptors aren't very
useful.  Hopefully adaptors to a CMap db can interface with the Bioperl
object model of map/marker objects in some sensible way one day.

>
> The next feature I'm going to add to biosql is a table for expression
> data that basically resembles the data cube with various dimensions
> (roughly, bioentry, term [quantitation type], term [sample
> annotation]). No LIMS info (yet) other than sample annotation as far as
> it fits the term table. In my view, this would be a post-1.0 thing. Do
> people agree?
>
> 	-hilmar
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu