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

[Hilmar Lapp]

I've just committed another series of fixes and changes. This should 
complete the Ontology module reorganization and clean-up.

	- moved more generally useful methods into an expanded TermI/Term; 
GOterm is now a very thin layer on top of Term (basically, it provided 
an alias GO_id to identifier() which format-checks)

	- the GO parser doesn't contain anything restricted to GO anymore; I 
renamed it to a base parser dagflat, from which the goflat and soflat 
parsers inherit. All they add is essentially a default for the term 
factory and for the ontology name.

	- as just mentioned, there is now a SO parser, which still needs a 
test written for it though (provided SO flat format is the same as GO 
flat format, there shouldn't be any surprises):

		$ontio = Bio::OntologyIO->new(-format => 'so', # or 'soflat'
                                       -file => 'sofa.ontology');
		$so = $ontio->next_ontology();

I recommend that interested parties have a look at this and if possible 
test-drive it, because it will go into the stable branch within the 
next days probably.

	-hilmar

On Tuesday, March 4, 2003, at 02:18  AM, Hilmar Lapp wrote:

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