[Biojava-l] Re: This tangled web on which I'm laid intwined

[Tony Obermeit]

No problem!  I've just tried it again and ended up with a pdf file that had 
no content.  In my browser, the url became:

http://prometheus.frii.com//open-bio-database.pdf

cheers

Tony

At 10:18 AM 4/02/2002 +0000, Thomas Down wrote:
>
>On Sat, Feb 02, 2002 at 06:26:14AM +1000, Tony Obermeit wrote:
> > I'm interested in SequenceDB and a port to MS-Access and Oracle, I've got
> > years of Oracle experience and am happy to review what would be necessary
> > to get it working in either of those environments.  I was not able to
> > download the draft document at
> > http://www.technophage.com/open-bio-database.pdf  The document was
> > blank.
>
>Could you try it once more, just in case there was a transient
>server problem?  I've just re-downloaded it and didn't have
>any trouble.
>
>(If you're still having trouble, I can mail you a copy or
>something).
>
> > At the moment I'm new to BioJava and have only just joined the
> > list.  Do I need to join any other area of BioJava to access the cvs
> > SequenceDB code?
>
>No, the BioSQL SequenceDB implementation is part of the main
>CVS module: biojava-live.  If you're going to be checking much
>code into the CVS repositiory, you'll want to contact either
>myself or David to get an account created.  But if you
>want to look at the code and experiment with it, you can just
>follow the instructions at:
>
>    http://cvs.biojava.org/
>
>The BioSQL code can be found in the package:
>
>   org.biojava.bio.seq.db.biosql
>
>The complication with BioSQL is that the current schemas don't
>yet have a proper home on the web.  As a /very/ temporary
>measure, I've placed them in the BioJava download area:
>
>    http://www.biojava.org/download/
>
>But please don't expect them to stay there for too long.  Note
>that the mysql version is currently `authoratative'.  PostgreSQL
>was generated by an automatic script.
>
>
>I'd be very interested in seeing ports to other databases.  The
>job ought to be pretty simple:
>
>   - Edit the MySQL schema so that it loads into your database.
>
>   - Do a quick check through the SQL in the code to make sure
>     it doesn't do anything really stupid.  If it does, please
>     let me know -- I'd like to work out a set of queries which
>     will work in as many popular databases as possible.
>
>   - Implement the DBHelper interface for your database.  This
>     is the database-abstraction layer I'm using for the BioSQL
>     code.  Right now, it just has one method, which is used to
>     discover auto-generated IDs after an INSERT query.  I don't
>     have any Oracle experience myself, but I showed the interface
>     to someone who does, and he said it would be no trouble
>     to implement.
>
>
>Let me know how this goes!
>
>     Thomas.