[BioSQL-l] BioSQL documentation

[Richard HOLLAND]

Hilmar,

I read through the doc/schema_overview.txt and it looks fine, nothing has changed much since it was written. It's fine to leave it as it is.

Now that BioJava will play nicely with the Clobs in the official BioSQL schema for Oracle, I will rewrite the BioJava/BioSQL/Oracle HowTo and remove references to Len's schema as it is no longer relevant. The official schema will now function perfectly well with BioJava out-of-the-box (but only if you are using biojava-live, for now, until the change gets into the main release branch). I will post the URL to this list when it is complete and updated.

Mark Schreiber and I have asked if we might attend the Open Bio Hackathon this year. If we are accepted, one of our projects is to get all the Bio* projects to play nicely with BioSQL and store various bits of information in the same columns of the same tables as each other. If this does not happen, we still intend to do it, but it might take longer. If you or anyone else working with BioSQL interfaces in the Bio* projects will also be attending then we'd love to work with you on this. There are three stages: (1) identify where things should be going for all the common data formats (Genbank, Swissprot, plain fasta etc.), then (2) identify where they are actually going at the moment when loaded into BioSQL by the various Bio* projects, and finally (3) modify the various Bio* projects to use the correct locations (and hopefully retain checks for backwards compatibility so that if they can't find that information in its correct location, they'll check the old one just in case). Hopefully that's not too much work for a small group of people to finish together in a couple of days.

I was wondering if it would be a good idea to delay the official BioSQL 1.0 release until after the above standardisations have taken place. Then we can include in the distribution a document detailing exactly what goes where when loading various data formats, both for reference and for the guidance of future projects not yet written.

cheers,
Richard

Richard Holland
Bioinformatics Specialist
Genome Institute of Singapore
60 Biopolis Street, #02-01 Genome, Singapore 138672
Tel: (65) 6478 8000   DID: (65) 6478 8199
Email: hollandr at gis.a-star.edu.sg
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