[Biojava-l] BioSQL observations

[Keith James]

In no particular order...

This is very nice and is going to make certain annotation tasks much
easier even at the level of populating a DB with a dozen bacterial
chromosomes and hacking on them with raw SQL.

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.

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?"

I've noticed that it is possible to save an EMBL entry which has no AC
line despite accession being 'NOT NULL' because an empty string is
inserted instead. I guess this should throw an Exception - shall I
make it so?

Keith

-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK