[Bioperl-l] Proposal: SemanticMapping and call for info on GeneObjects

[Matthew Pocock]

Hilmar Lapp wrote:

> That's a perl implementation right? :)
> 
> BTW has anyone checked where BioJava stands in this regard? How does actually Apollo deal with that, i.e., does Apollo have a class hierarchy representing Genes and constituents? I think Dave is checking into that. Dave?
> 


> 	-hilmar

Hum.

We have the interfaces for things like genes (in 
org.biojava.bio.seq.genomic). We have the flexible pipe-lined sequence 
IO API (SeqIOListener & SeqIOBuilder & SeqIOFilter). We haven't yet 
written the sequence IO handlers that intercept flat feature creation 
events (like CDS) and emit tree feature creation events (like gene 
models). We would extends SeqIOFilter and it would consume feature 
creation requests of particular types untill the endSequence method was 
called. Then, it would pattern-match its internal data-structure of 
requests against some rules, pass on the feature creation requests to 
the wrapped listener, clear any caches and then lastly pass on the 
endSequence notification. The thing it passes events on to may be 
another feature re-writing filter, or something else, so we could layer 
rules and transforms arbitrarily deep. I think that's similar to the 
bioperl plan.

This all sort of smells like xslt.

Matthew