[Bioperl-l] Thoughts on bioperl-db

[Ewan Birney]

On Tue, 29 May 2001, Kris Boulez wrote:

> I've been using bioperl-db for the last few weeks and it made part of my
> life a lot easier. I was wondering how hard it would be to use/access a
> different database (which might have a different schema). In this
> approach bioperl-db would be a middle layer betweern different sequence
> databases.
> What would it need other then having a replacement for
> Bio::EnsemblLite::UpdateableDB and changing the sql statements in the
> different Bio::DB::SQL adaptors.

This is the aim of the adaptors. In fact, one could parameterise the Root
DBAdaptor to be able to set "your own" Sequence etc Adaptor whih complied
to the same Adaptor interface, allowing the "business
object" (Bio::DB::Seq) to remain the same.

(Bio::EnsemblLite::UpdateableDB is a defunt module I thought - it
certainly does not work with the Bio::DB::SQL code so far)

(I think in reality changing one adaptor is likely to force a change of
all the adaptors, so an entire new code base will be written)


If this set up is too restrictive, one could aim to use the same basic
approach to link to a different SQL schema that implemented the
Bio::DB::RandomAccessI interface and therefore gave out Bio::SeqI

I think it would be good to think of a 

Bio::DB::QueryableAccessI interface to provide a generic, richer query
langauge we could then layer ontop of database implementations. We could
have a stab at this


all in all --- lots of options. What is your immeadaite problem you are
trying to solve


> 
> Such a setup would allow people to access (sequence) databases in a big
> organization to which they only have access via SQL.
> This might become a poor mans version of IBM's DiscoveryLink
> (http://www-3.ibm.com/solutions/lifesciences/discovery.html)
> 
> Kris,
> 
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> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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