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

Jason Stajich jason@chg.mc.duke.edu
Thu, 27 Jul 2000 14:42:44 -0400 (EDT)

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.

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.

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

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 Stajich
(919)684-1806 (office) 
(919)684-2275 (fax) 
Center for Human Genetics - Duke University Medical Center