[BioSQL-l] BioSQL documentation

[Richard HOLLAND]

I just think the BioSQL 1.0 standard should include a reference as to
the 'official' way to store the different bits of various file formats
within the schema, which all apps talking to BioSQL can be expected to
comply with (and hence behave well with each other's data).

Richard.

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: mark.schreiber at novartis.com 
> [mailto:mark.schreiber at novartis.com] 
> Sent: Wednesday, April 27, 2005 5:33 PM
> To: Richard HOLLAND
> Cc: biosql-l at open-bio.org; 
> biosql-l-bounces at portal.open-bio.org; Hilmar Lapp
> Subject: Re: [BioSQL-l] BioSQL documentation
> 
> 
> 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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> This email is confidential and may be privileged. If you are not the 
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> not copy or use it for any purpose, or disclose its content 
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