On May 17, 2007, at 6:34 PM, Eric Jain wrote:
There does indeed seem to be an existing has_participant predicate, but is there also a "protein expression process" class? This would seem rather contrived, from a biologists (if not an ontologists) point of view (all we want to say, after all, is that the protein can be found in some tissue)!
If you want to say that the protein is found in some tissue, that's what should be said. However, in your email you wrote that the protein is expressed in the tissue. They are not the same, and I think that in our semweb representations we should take care to not confuse them, though in language they are easily interchanged and we still (often) understand what each other is talking about.
If it is know to be found in the tissue I would make the subclass be the subclass of the protein each instance of which is located in some instance of the tissue. No processes involved at all.
Using widely used concepts and predicates is no doubt a good thing. But if you can instead make do with core RDF features, that's even better -- not everyone uses OBO, no matter how "foundational" it may be :-)
I don't think we can make due with core RDF features, if we want to have agents that make reasonably inferences based on what they are told. RDF is just too weak to do much of anything in this direction. OTOH, if the RDF is always going to be interpreted by a human - essentially you are using RDF as an opaque (from a machine agent point of view) syntax, then there is no problem. I guess I am hoping my machines to help me more than that.
Note that the reification "design pattern" allows you to add attribution information on statements that you did not at first think would ever need such information, without breaking the data model.
As long as those statements are single triples. It gets more involved when statements are more than a single triple, as they often will be.
-Alan
