[BioSQL-l] BioSQL documentation

[mark.schreiber at novartis.com]

I don't know if this means there cannot be a 1.0 release. The BioSQL 1.0 
will be a standard. It's up to the bio* projects to play well with it.

- Mark





"Richard HOLLAND" <hollandr at gis.a-star.edu.sg>
Sent by: biosql-l-bounces at portal.open-bio.org
04/27/2005 02:57 PM

 
        To:     "Hilmar Lapp" <hlapp at gnf.org>
        cc:     biosql-l at open-bio.org, (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [BioSQL-l] BioSQL documentation


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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