[Biojava-dev] Suggestions for the BioJava project

[mark.schreiber at novartis.com]

It's probably premature to announce this but Richard Holland and I have 
been working on a new object model that will pesist very easily to BioSQL. 
It extends the core interfaces and miraculously doesn't break anything so 
you can still use the core stuff or you can use the new models if you want 
to. 

For example we have the RichSequence interface which closely follows 
biosql but also extends Sequence, so anywhere you can use Sequence you can 
happily use a RichSequence (or just a plain old Sequence). The really cool 
stuff is the work Richard has done with Hibernate. The whole of BioSQL can 
now be happily transported back and forth to biojava via hibernate. It's 
amazingly painless and seems to avoid many of the problems of our old SQL 
system. The model is also decoupled from hibernate completely so you can 
use the objects for your normal biojava stuff without ever having a 
database for persistence.

We also have a NCBITaxon class to handle all the issues Andreas brought 
up.

The whole thing is available from CVS under the org.biojavax.bio package. 
We chose the name biojavax to be analogous to the relationship between 
java and javax. The javax packages are extensions to the core java. They 
improve it, they sometimes deprecate it, they use it, but they don't 
replace it. The same is true for biojavax. It is not a replacement. It is 
an extension that gives better functionality but still gets a lot of 
milage out of biojava. Importantly, they are not seperate packages. There 
is also a genetic algorithm framework under org.biojavax.ga but that's an 
entirely different story : )

The biojavax packages should be considered highly unstable at the moment 
as we are still working out the kinks. More later.

- Mark

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910





Len Trigg <len at reeltwo.com>
Sent by: biojava-dev-bounces at portal.open-bio.org
08/15/2005 06:22 AM

 
        To:     Andreas Dräger <andreas.draeger at clever-telefonieren.de>
        cc:     biojava-dev at biojava.org, (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-dev] Suggestions for the BioJava project



Andreas Dräger wrote:
> I am and currently working with BioSQL and BioJava. Trying to insert
> the NCBI taxon hierachy and also different kinds of biosequences into
> the database I got to know that there are still some open problems in
> BioJava. Since I wrote some classes anyway, I would like to contribute
> them to the community.

Good stuff.  The work that I did with the TaxonSQL classes was based
on the fairly simple requirements of the project I was working on,
which is why you found the current implementation a bit limited. (I
don't have projects involving BioJava at the moment, so haven't been
doing much other than following the mailing list.)


> I modified the functions to put and retrieve taxa into the database so
> that they consider that the names Map could sometimes point to a Set of
> names instead of  normal name Strings.
> In addition I considered the other information that can be inserted in
> the database like genetic code and so on.

Excellent improvements.


> However, there are some methods in TaxonSQL.java that are defined to be
> private. If they were protected, an extension of this class could call 
them.
> But because they're private, I had to copy and paste them.

That class isn't really designed for extension, since it's plugged
directly into calls from BioSQLSequenceAnnotation and BioSQLSequenceDB
(you presumably had to change these to point to your MySQLTaxon) and
there's no need for multiple implementations.  I'd say that your
changes should instead be folded directly as improvements to TaxonSQL
itself so that everyone gets the improvements out of the box.


Cheers,
Len.

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