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

[Hilmar Lapp]

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.

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
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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