[MOBY-dev] Layering OWL on top of BioMOBY RDF descriptions

[Damian Gessler]

Hi Duncan,

> The next layer in the semantic web cake [1] is to add OWL descriptions.

Totally on board with you here.  To see how it's working, go to 
www.semanticmoby.org and type in "dna".  You'll see that term retrieves, in 
a Google-like manner, four bioinformatic service providers.  Click on the 
RDF icon by their name and you'll see the OWL Resource Description Graph 
(essentially the equivalent of a semantically-wise WSDL, though completely 
unrelated in implementation with WSDL).  [Note: your browser may be set to 
any number of alternative display modes for RDF; do a View Source if it 
isn't easily readable).

You can try the Legume Information Network to see how resources can be 
pipelined.

For shared ontologies--the meat of the middle layer of how resources 
describe themselves and thus how they are discovered and engaged--a few a 
populating at http://ontologies.ncgr.org.  We're currently lining up 
conversions of SO and SOFA (Sequence Ontology), POC (Plant Ontology), and TO 
(Trait Ontology).

D.


----- Original Message ----- 
From: "Duncan Hull" <duncan.hull at cs.man.ac.uk>
To: "Core developer announcements" <moby-dev at biomoby.org>
Sent: Friday, March 03, 2006 2:39 AM
Subject: [MOBY-dev] Layering OWL on top of BioMOBY RDF descriptions


> Gary Schiltz wrote:
>
>>I can then paste that RDF into the converter at 
>>http://www.semanticmoby.org/developer/dev-tools.jsp
>>
>>
> ...and thanks Gary too...
>
> Actually, while we're on the subject of RDF...BioMOBY has done a great
> job of demonstrating some of the strengths and limitations of using RDF
> to represent bioinformatics service metadata.
>
> The next layer in the semantic web cake [1] is to add OWL descriptions.
> Semantic MOBY, BioMOBY and myGrid have all made various moves in this
> direction. With OWL, we get more expressivity and the ability to reason
> over our services, in particular we possibly get more "bang for our
> buck", specifically:
>
> 1. We can distinguish between classes and instances (individuals)
> 2. Properties won't be able to have properties any more (something
> RDF/RDFS lets you do)
> 3. We can distinguish between language constructors and ontology 
> vocabulary
> 4. We have localised range and domain constraints
> 5. We get existence/cardinality constraints
> 6. We get  transitive, inverse and symmetrical properties
> 7. We get better reasoning support using "native" reasoners
>
> (see [2,3] for details)
>
> So, which bits of this rich service metadata are going to be
> a) realist to capture?
> b) useful for biologists and bioinformaticians describing and finding
> services?
> c) useful for registry providers to manage their services?
>
> I realise these are all very open questions, but I'd be interested to
> know what moby-devvers think...
>
> Duncan
>
> [1] 
> http://www.cs.man.ac.uk/~horrocks/Publications/download/2005/HPPH05.pdf
> [2]
> http://www.cs.man.ac.uk/~horrocks/Teaching/cs646/Slides/ontologies.pdf
> (see problems with RDF/RDFS)
> [3] 
> http://www.cs.man.ac.uk/~horrocks/Publications/download/2003/HoPH03a.pdf
>
> -- 
> Duncan Hull
> http://www.cs.man.ac.uk/~hulld/
> Phone: +44 (0) 161 275 0677
>
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