Re: OWL vs RDF

[William Bug]

Hi All, At this week's BIRN All-Hands Meeting, the BIRN Ontology Task Force has been working on ontological representation of neuroanatomy (decomposing the differing senses often wrapped together in a standard neuroanatomical terminological resources), so that in the end we'll be able to recompose an OWL repsentation of the traditionally convolved dualistic structure-function description of neuroanatomy.  If this process proves as promising as it appears to be so far, we'll hopefully be able to include the additional contexts we know we also need to take into account to represent those entities and properties that are also ubiquitous in traditional neuroanatomical studies, such as cytoarchitectural detail, neurochemistry, development, cross-species comparative anatomy, gene & protein _expression_, etc. I would add the work we are doing in neuroanatomy relies heavily on existing knowledge resources in this domain which we've found we cannot use in their current form.  As we've proceeded with the work above over the last year, we've worked hard to stay aligned with these resources as much as is practical. We've also been working on the standard cognitive and behavioral paradigms used now - in the context of the BIRN and many other projects - as an experimental context for functional brain imaging experiments.  This also requires careful decomposition and examination of how to properly create object properties, so that many of the more complex aspects of the ontological graph can be assembled, extended, and maintained via reliance on the DIG reasoners that can be used in ProtegeOWL, for instance. It's pretty clear if we don't proceed by careful consideration of how and when to lean on the reasoners, the issues Robert and Phil discuss below - and others have been discussing in the context of the NCBO/OBO Foundry-associated community biomedical ontology development projects that are on going - we will very quickly overwhelm the limited human resources we have in place to both build, extend, and maintain these ontologies. In both contexts cited above - neuroanatomy and cognitive & behavioral experimental psych. paradigms, we are already working on how to build from the tools being assembled by the community - BFO, CARO, Relations Ontology, etc. - and others of our own creation - the Object Properties we'll need to re-compose a complete ontological representation of these complex domains. This is not to say this work cannot be done using RDF alone, but I don't see how we'll be able to get away without relying on formal rules for constructing constraints and complex, qualified ontological relations. In the end, I suppose the question really will come down to whether the limits, entailments, and computational constraints one can confront when using OWL (specifically OWL-DL) will prove to be more of a hindrance than the additional work required to construct such ontological frameworks in RDF alone. As Phil implies below, if you really just need a formalism for nodes and edges, you don't NEED OWL - in fact, for many types of graphs, you don't need RDF.  On the other hand, if you are clearly going to require a formalism with considerable ontological expressivity, you probably want to give the OWL dialects (and their underlying DLs and the toolsets such as ProtegeOWL  and the Pellet, FACT++, and other reasoners, etc.) serious and in depth consideration. Just to be clear, I'm talking here about ontology construction which I consider just a portion of the required task of semantically formal data representation.  For much of the semantic representation we need to do in large scale biological data repositories, RDF alone will clearly be a sufficient first step, so long as we continue to develop effective means of expressing the triplets in the context of the ontologies and extending the ontologies via analysis (as automatic as is feasible) of the triplet repositories. Cheers, Bill On Oct 26, 2006, at 1:45 PM, Robert Stevens wrote: There's another answer of using the reasoner by building your ontology to take advantage of its capabilities. the conceptual lego approach relies on the reasoner. Anecdotally, I've managed to miss out subsumption relationships by hand in ontologies as small as a dozen classes. Also, when building purely by hand, I've seen people introduce inconsistencies by asserting multiple inheritance across disjoint classes. I would feel nervous at saying "there is a point when you need a reasoner", but I think building to take advantage of it is as close as I can get. robert. At 11:46 26/10/2006, Phillip Lord wrote: >>>>> "Alan" == Alan Ruttenberg <[EMAIL PROTECTED]> writes:   Alan> Well it would be educational to get your view on what you can   Alan> you do with owl without a reasoner that's not easier to do   Alan> without owl? You can do lots of things with OWL without a reasoner. The Gene Ontology is representable in OWL, for example, and uses a simple enough expressivity that you could do without a reasoner easily enough. Of course, you need to use some kind of "reasoning" engine, but something which understands transitive closure is enough. Whether it's "easier" to do without OWL depends on what the alternatives are. You could also represent GO style semantics in RDF (although, I think, the existential nature of part_of would not be explicit), or indeed anything else capable of representing a graph.   Alan> And how are you to know when you do need the reasoner and when   Alan> you don't? When you use enough of the expressivity of OWL, where "enough" is relatively undefined. Phil Bill Bug Senior Research Analyst/Ontological Engineer Laboratory for Bioimaging  & Anatomical Informatics www.neuroterrain.org Department of Neurobiology & Anatomy Drexel University College of Medicine 2900 Queen Lane Philadelphia, PA    19129 215 991 8430 (ph) 610 457 0443 (mobile) 215 843 9367 (fax) Please Note: I now have a new email - [EMAIL PROTECTED]