[Bioperl-l] Bio::EnsemblLite::UpdateableDB

Ewan Birney birney@ebi.ac.uk
Tue, 1 Aug 2000 09:17:16 +0100 (GMT)

On Thu, 27 Jul 2000, Jason Stajich wrote:

I'm sorry I haven't replied to this yet...

> So my first attempt was too divergent from the ensembl base so I wouldn't
> really be getting any advantages from ensembl other than the association
> with the name.

This reassures me; I thought you were heading at too much of a tangent to

> So I revised the UpdateableDB to create 'anonymous' ensembl clones,contigs
> with one sequence per contig, one contig per clone.  I still needed extra
> tables for the generic features, which are attached using the contig
> internal_id field.  If I made any weird assumptions or didn't follow the
> schema correctly Ewan and I WILL have a quick whiteboard discussion at
> BOSC to set me straight...  These extra tables are defined in
> sql/ensembl-lite-mysql-addons.sql.  I also revised code to handle the
> updates to the ensembl schema.

I really want to reuse this table structure inside Ensembl to allow us to
support some other things; eg, people who want to write in generic

So - I would be happy to see this table structured merged with the main
trunk of Ensembl.

> Took my old code and made it Bio::DB:BasicUpdateableDB which is
> essentially a standalone seqdb which supports generic features. The schema
> for this db is in sql/basicseqdb-mysql.  I'm not sure how useful it is,
> but displays another example of an updateable seq db.  I imagine if
> someone wants to write an updatabledb that deals with text files or acedb
> files this should all fall into the Bio::DB::UpdateableSeqI and would
> work.

This is what we should talk about at BOSC, with probably Hilmar as well.

> I gave a description of how to set it up, once you get the code, in the
> README file.
> I have lots of things in mind where this can go, but it will depend on how
> much interest (and help) I get as to the exact direction.  I hope to hash
> this over with many of you at BOSC and see what the interest level is.
> [ for those coming in late to this discussion, all the code is in
>   the bioperl repository and the module is called bioperl-db ]
> -Jason
> Jason Stajich
> jason@chg.mc.duke.edu
> http://galton.mc.duke.edu/~jason/
> (919)684-1806 (office) 
> (919)684-2275 (fax) 
> Center for Human Genetics - Duke University Medical Center
> http://wwwchg.mc.duke.edu/ 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420