[Bioperl-l] Another implementation

J. H. Park jong@ebi.ac.uk
Wed, 13 Sep 2000 00:42:37 +0100


> > Does the Perl/BioTK work off SeqI/PrimarySeqI/SeqFeatureI stuff or does it
> > straight to DBI to the database? It would be great if the BioTK stuff
> > could work against the SeqI interfaces - we could then just point it at
> > other SeqI implementing databases (eg, Flat file indexed GenBank or my
> > ever favourite ensembl)
> The problem I am seeing now is that we import data from our non-standard
> database, and importing stuff from other dbs may break parts of our
> non-bioperl code.  I will attempt to make this more robust.

I think the best solution is you spend a little time
in designing more general form(schema) for your DB and
perhaps suggest the BioXX community a fairly acceptable
format. This will save a lot of time in the end(not only
for your but also for the next generation developers).

I am interested in DB interface and representation of
BioEntities for DBs. Why don't you share you experience
on certain problems to tackle to make things more general
and standard.

> Our database is quite hairy right now, but the whole thing is built around
> a few primary tables, primarily a GFF-like feature table.  I'll figure out
> a visual DB schema if anyone is interested.  The database came first, and

I am, very much so. 

> this application is adapting to it, rather than the other way around.

Too much specifics to your DB will hurt your application's
future flexibility and standardization in my opinion.
A bit of thinking on that matter (interface between DB and parsers and
visualizations) will be good.



"It is easier to fight for principles than to live up to them."
-- Alfred Adler