= The Problem =

One of the goals of BioSQL was to provide an interchange platform for the Bio* objects. This has not yet succeeded due to differences in the way the Bio* projects interpret an individual sequence record and how they persist it to the database.

Common sequence semantics and object/ format handling would probably be of great benefit to many other WS providers and consumers. If Bio* can agree on semantics it would be a good reference for many other projects.


= Possible Tasks =
 * Choose some 'reference' sequences to see how the Bio* projects 'round-trip' them. 
   * Where are the differences and why are there differences?
 * Find out where each Bio* project persists it's data into BioSQL during ORM. 
   * Why are there differences?
 * Establish guidelines for where things should go in BioSQL, eg given a Genbank file, what bits should go where.
   * UML diagrams?
 * Define an interchange format for the Bio* projects. Probably XML, probably borrow something already existing (XEMBL etc).
 * Decide on a restricted vocab for annotations and feature types. Probably use SO.
 * Define a middleware API for uniform I/O access to sequence database.
   * Intially backed by BioSQL.
   * Could be backed by any DB.
 * Derby version of the BioSQL schema (Derby is the Java reference database).
 * A BioSQL release.



= Participants =
 * Mark Schreiber
 * Jan Aerts
 * Richard Holland
 * Hilmar Lapp
 * Heikki Lehvaslaiho
 * Richard Bruskiewich
 * Jan Byrne
 * Raoul J.P. Bonnal


= Random ideas from Jan Aerts =
Mind that this is *very* incomplete. Just to help my really bad memory.
As the issue is interoperability of the Bio* toolkits, we don't have to synchronize the toolkits at the object level, but rather at the interface level.

First thing to check: what types of objects do we want to synchronize? Of course sequence objects; but what else? The results of a BLAST parsing?

== For sequences ==
Check if each toolkit reads and writes a GenBank/Fasta/... serialization in the same way. Input can either be an original GenBank/Fasta/... file or a dbfetch from any database.

 * What should be conserved:
  * Tags
  * for a sequence: lower/uppercase
    * Withing a project it is desirable to mask an alphabet, for transfer between bio* projects this is not a good idea.

 * What not necessarily should be conserved:
  * for a sequence over multiple lines: length of each line

= Task achieved =
== Tuesday ==
 * Initial planning.
 * Approved a BioSQL logo.

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