I hacked in a new extension point for Bioclipse yesterday, based on a proposal I made earlier. The new extension point (EP) is called ChildResourceCreator and allows creating child resources for a given IBioResource. One application where this is very useful is the CMLRSS application (earlier blog), or any RSS or Atom enriched with any other XML language. Here, child resources are created for each feed entry resource with as content the foreign XML, e.g. the CML bits in the blog.
Other applications involve complex documents, which is basically most existing documents. Take, for example, the PDB format from the PDB database. These PDB files contain a pletory of information including one or more protein structures, sequences and bibliographic information. Bioclipse supports each of those using the CDK, BioJava and JabRef libraries.
By making extension for the ChildResourceCreator EP, I am able to setup a general PDBResource (with Bioclipse's syntax highlighted PDB editor), and child resources for the different bits of information. Bioclipse 1.0, however, only allow looking at the molecular structure(s) in the file, not at the sequence, nor the references. Will post the obligatory screenshot asap.