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

[Lincoln Stein]

Wow.  Great news.  This is a big step forward.

Lincoln

On Thursday 06 March 2003 08:32 pm, Hilmar Lapp wrote:
> I just committed an extensive test of the SO parser, added to
> simpleGOparser.t (as I said, GO and SO parsers use the same codebase,
> namely the dagflat parser). It did reveal a few problems where
> identifiers where checked to strictly for being beginning with 'GO:'. I
> corrected that.
>
> All tests pass, indicating that the OntologyEngine that works behind it
> (Graph.pm-based SimpleGOEngine) is relatively (in fact surprisingly)
> flawless. Note that the test runs directly off of the latest SOFA from
> song.sf.net, which hereby becomes part of bioperl
> (t/data/sofa.ontology).
>
> So, bioperl is ready for GO and SO from the framework perspective.
> Again, if you're considering using ontologies in bioperl, check out in
> particular the following interfaces: Bio::Ontology::OntologyI and
> Bio::Ontology::TermI. If you think there's an API function missing,
> speak up *now*.
>
> 	-hilmar
>
> On Thursday, March 6, 2003, at 01:14  AM, Hilmar Lapp wrote:
> > 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
> >> -------------------------------------------------------------
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at bioperl.org
> >> http://bioperl.org/mailman/listinfo/bioperl-l
> >
> > --
> > -------------------------------------------------------------
> > Hilmar Lapp                            email: lapp at gnf.org
> > GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> > -------------------------------------------------------------
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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