[Bioperl-l] Summary about ontologies in bioperl

[Hilmar Lapp]

There is no document really yet. If you can make sense of module 
documentations, check out the PODs of Bio::Ontology::Ontology and 
Bio::Ontology::Term. These are the two basic implementations of their 
respective interfaces (append an 'I' to find the interface) that a 
client will usually have to deal with. If you're wondering how to get 
an ontology into bioperl, check out the POD of Bio::OntologyIO.

Those documents are nowhere near complete and may not even be 
comprehensible ... This is a very area in bioperl where the extent of 
polishing is minimal yet, especially regarding documentation.

As usual, any takers to change this situation are highly welcome ...

If you have little idea what an ontology is, a good place to see and 
explore a concrete one is probably the GO home 
(http://www.geneontology.org/). In bioperl we will move towards relying 
on SO (Sequence Ontology) or its SOFA subset. This is also a more or 
less nascent project with I believe the main entry point so far being 
http://song.sf.net/.

	-hilmar

On Thursday, March 13, 2003, at 08:50  AM, Guillaume Rousse wrote:

> I've seen many discussion on this list about ontologies, but i've been 
> unable
> to follow them, as everyone was refering to some very precise points. 
> So, is
> there anywehre a document, or is anyone willing to summary:
> - what  ontology means exactly in BioPerl context ?
> - what are they useful for ?
> - how are they implemented ?
>
> Thanks for your help.
> -- 
> No matter how many resources you have, it is never enough.
> 	-- Murphy's Computer Laws n°1
>
>
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> Bioperl-l at bioperl.org
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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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