[Biojava-l] Integrating Biojava into an organism Database System

[Ewan Birney]

On Tue, 23 Jan 2001, Arnaud Kerhornou wrote:

> Hi
> 
> I work for the Pathogen Sequencing Unit at the Sanger Centre. One of our
> projects is to set a database. This database will store publicly
> available data regarding several organisms.
> We are interested in implementing the Database Interface  with Java.
> 
> So I was thinking how to integrate BioJava, in other words our objects
> would behave as BioJava objects, following two ways :
> 
> The first one is our own objects would inherit from the BioJava
> Interface. This implies to implement them, and thus we'll have
> difficulties to keep them compliant iwth the future development within
> BioJava.

I would take this route. It is up to biojava to keep interface definitions
stable and you will want to have control of your own implementation 


This is the route Ensembl takes with Bioperl (ie, Ensembl implements
Bioperl interfaces) and it works very well. Bioperl might be more stable
than biojava, but you always have the option of walking down the corridor
and beating up Matt and Thomas if they don't behave ;)



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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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