[Bioperl-l] Bio::Ontology & Bio::OntologyIO

[Hilmar Lapp]

I've committed a series of further fixes and standardization to the 
Bioperl ontology modules. My feeling is they are now ready for prime 
time use. Everyone who is interested in using ontologies in bioperl can 
start toying around with them - ideally within the next days to help 
smooth out the sharp edges before it gets back-ported over to the 1.2.x 
branch. Checkout Bio::Ontology::Ontology[I], Bio::Ontology::Term[I], 
Bio::Ontology::Relationship[I], and Bio::OntologyIO.

What is still missing is

	- a SO parser (but now the GO parser should be SO-ready, so that a SO 
parser supposedly can be created with minimal effort from it)
	- generalizing to the base Ontology::Term implementation a number of 
properties the Ontology::GOterm class adds, such that eventually 
Ontology::GOterm becomes a very thin derivation of Term (that either 
covers SOterm, too, or can be copied with minimal modifications to 
obtain the SOterm class)

I'll address both within the next days.

	-hilmar

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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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