[Biojava-l] BioSQL observations

[Emig, Robin]

	Oh, cool. Could we also have an "Authentication" module. Ie given a authenticated token (ie username/password), allow only access to certain sequence ids.
	or how about a folder representation, where you could have nested folders of sequences....
	or even better yet, a virtual folder/sequence representation where sequences could exist in multiple folders...
	extensible modules.....yummmm
-Robin


-----Original Message-----
From: Thomas Down [mailto:td2@sanger.ac.uk]
Sent: Thursday, March 14, 2002 4:39 AM
To: biojava-l@biojava.org
Subject: Re: [Biojava-l] BioSQL observations


On Thu, Mar 14, 2002 at 09:56:01AM +0000, Keith James wrote:
> 
> In the longer term I think that BioSQLSequenceDB should use a
> DataSource or some new interface which wraps a DataSource or
> DriverManager (instead of using the JDBCConnectionPool class). That
> way anyone can plug in their own e.g. their vendor's
> ConnectionPoolDataSource.

Yes, this is definitely on my todo list.  My one concern
with this. originally, was that it led to an extra compile-time
dependancy for the BioJava package.  But since the javax.sql
interfaces are included in JDK1.4, this is going to become
less of an issue over time.

> On the schema itself, was there any discussion on being able to track
> changes to Features? I'm thinking of situations where the a number of
> people are applying annotation to a genome and want to know "when was
> this Feature last modified?"

>Hmmm, I'd really like to see the core schema stay fairly
stable and general-purpose.  That said, at the Hackathon we
discussed an idea of `extension modules' -- extra schema
files which get loaded into the database on top of the core
schema.  There are already a couple of these proposed (for
ontologies and genome assemblies).  The BioJava code auto-detects
whether the assembly module is available, and uses it if so.
Same sort of thing will probably happen for the ontologies.

>A change-tracking module sounds like a good candidate for
this kind of treatment -- I'd be happy to work with you on
this if there's a bit of spare time during the bootcamp
development sessions.