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

References

Formats

•  GenBank sample

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
    • Within 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
    • Proposal for a common default value, 60bp ?

Task achieved

Tuesday

• Initial planning.
• Approved a BioSQL logo.
• Hilmar initiated BioSQL release discussion
• Selected sequence files to roundtrip
• BioRuby has no way of exporting Bio::Sequence objects to GenBank, EMBL, ...
• Began roundtrips
  • BioPerlRoundTripFirstPass
  • BioJavaRoundTripFirstPass
• Started UML diagram to describe object model with Richard Bruskiewich.

Wednesday

• Continue roundtrips
  • BioPerlRoundTripSecondPass
  • BioJavaRoundTripSecondPass
• BioRuby: started work on creating export filters to GenBank? and EMBL
• BioJava: Fixing issues with UniprotXML format and updating EMBLxml to new xsd.
• Adding BioSQL schema documentation to BioSQL wiki page.

Thursday

• Continue roundtrips
  • BioJavaRoundTripThirdPass
• Translation of BioSQL to Derby RDBMS.
• -- Would like to know why BioSQL can't add multi dbxrefs to one docref.
• -- Would like to work out how best to store EMBL assembly data in BioSQL.

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