[BioSQL-l] Re: Singapore schema

[Hilmar Lapp]

On Thursday, February 20, 2003, at 05:13  AM, McCulloch, Alan wrote:

> Hi Hilmar,
>
> Is there a Singapore schema yet ? - just checked
> http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/doc/ 
> ?cv
> sroot=biosql
> but the diagram looks like the old one , although Aaron's docs are
> there.

The diagram is still old. It will not change before I get back home and  
get time to update it. (It is generated by ERwin.)

You need to look at the DDL in sql/biosqldb-{mysql,pg}.sql. The Oracle  
version will also be updated only later.

>   For example , how tightly coupled to this schema are BioJava and
> BioPerl going to be ?
>
>   Is the aim to provide essentially a Genbank repository , or are there
> plans to go beyond that ?

Both. There are different use cases, ranging from a temporary sequence  
cache, a SRS like repository, a toolkit's persistence store, to a rich  
gene annotation database.

>   We have been advised that for our bioinformatics developers to be
> productive with BioJava and BioPerl , we need to change our existing  
> in-house database schema so that it conforms to the BioSQL schema.

This depends entirely on what you want to use Bioperl and Biojava for.  
Biosql is their primary persistence store. If you want to have  
persistent Biojava or bioperl objects, you need to provide a  
biosql-compliant schema in order to use the native APIs. Otherwise  
there is no need for that.

>   we would not be wanting to create dependencies of the Bio* projects  
> on
> any particular database
>   technology (i.e. relational) or schema.
>

The toolkits themselves are not dependent, but their persistence  
mechanisms are.

>   Is it really true that if BioJava and BioPerl want to talk to a DB it
> has in practice to be BioSQL ?

Yes, unless you want to write your own persistence layer. In both  
bioperl and biojava we are striving to provide a relatively generic  
persistence framework, but the physical object-relational mapping will  
have to come from you if you don't run a biosql-compliant database.  
Also, both toolkits have plans to support other schemas, for instance  
Chado. Those are only plans yet though ...

>  Do you have any feel for what people with existing databases are  
> doing ? (I would have thought , writing drivers for their own DB's to  
> support sequence-object construction  with their own DB as source. How  
> hard is it to set up these drivers ?)

It depends on how incompatible your relational model is with the  
bioperl and biojava object models. If your schema is very similar to  
biosql, the idea is you just change the physical OR mapping and you're  
done. Generic OR mapping is hard though, so I'd expect a bumpy ride if  
your schema is a lot different.

> I have a slight concern that BioSQL appears to be being seen by some  
> as a de facto interoperability standard, as well as a handy Genbank  
> repository,

It is meant to be one of the interoperability standards, yes.

> and this might introduce some unfortunate dependencies.

Possibly. We've tried other technologies (BioCORBA), with little  
success over the long run.

	-hilmar

>
>   These might seem like strange questions, but there is some  
> uncertainty
> here about the
>   scope of BioSQL and its relationship to the other Open* projects, and
> we are
>   unsure what to make of the suggestion that we need to change our
> database
>   schema. Perhaps an addition to the docs of an overview section might
> set us straight.
>
>
> Alan McCulloch
> Bioinformatics Software Engineer
> AgResearch NZ
>
> PS
>
> Thanks for all your work ! - the BioSQL schema is great and we have  
> used
> alot of its ideas recently.
>
> PPS sorry for replying to you directly but for some reason I am unable
> to
> post to the list, I get errors about suspicious message header.
>
>
>
> -----Original Message-----
> From: biosql-l-request at open-bio.org
> [mailto:biosql-l-request at open-bio.org]
> Sent: Thursday, 20 February 2003 6:00 a.m.
> To: biosql-l at open-bio.org
> Subject: BioSQL-l Digest, Vol 2, Issue 5
>
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> Today's Topics:
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>    1. BioSQL release candidate (Hilmar Lapp)
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>
> ----------------------------------------------------------------------
>
> Date: Wed, 19 Feb 2003 17:38:45 +0800
> From: Hilmar Lapp <hlapp at gmx.net>
> To: Biosql <biosql-l at open-bio.org>
> Cc: Bioperl <bioperl-l at bioperl.org>
> Subject: [BioSQL-l] BioSQL release candidate
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>
> We're preparing BioSQL for a schema freeze and subsequent release in
> Singapore at the BioHackathon. Based on a lot of feedback and review
> with and by Aaron I introduced quite a number of changes to the schema.
> I committed a release candidate for both MySQL and PostgreSQL to the
> repository.
>
> Aaron also committed a schema documentation in doc/schema-overview.txt.
>
> Please take a look at the changes and make your voice heard if you see
> us heading for trouble or if you've got any comments and/or suggestions
> ...
>
> 	-hilmar
>
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------