Hello -- I have been following the public-semweb-lifesci discussions for some time (silently) with great interest. By way of introduction, I am the CEO and founder of Sentient Solutions Inc. - a non-profit Colorado company with an affiliated Consulting LLC Sentient Consulting. I worked for UC-computational pharmacology for four years, and for Evolutionary Genomics.
I thought I would chime in for a brief moment. "Sound and Complete" i.e. consistent and complete is proven impossible by Gödel - see http://en.wikipedia.org/wiki/G%C3%B6del's_incompleteness_theorem No use wasting time trying to get both in a perfect Panglosian world :-). but... if the reasoning systems we have on closed world systems (using equality, transitive closure and other formal rules of logic) have enough apriori validation tests, we can achieve something very close. Are the inferences right? Are the facts consistent? Are the answers biologically supported? Hammering each inference with apriori validity tests (same chromosome, same gene, not deprecated, not homonymous...) the "lies" or inconsistencies can be flushed out to a certain level of significance and removed or marked in the graph of triplets that the reasoners use. Completeness is a function of how many triplets can be inferenced over by a reasoner with rules, and also a data integration challenge... Then, I find that the triplet stores become huge, slow to compute over and the reasoners become slow for larger A-boxes. The quality of the answers can be validated by simple logic with a nice list of tests though, and not too surprising, inconsistencies in the logic happen just as Gödel predicts. Then wouldn't the question be how to identify the erroneous triplets and repair them in the overall triplet graph retaining as complete of a graph and thus inferencing capability as possible? Daniel J McGoldrick Ph.D. Sentient Solutions Inc.
