- From: Matthias Samwald <samwald@gmx.at>
- Date: Tue, 31 Mar 2009 11:09:07 +0200
- To: "Oliver Ruebenacker" <curoli@gmail.com>, "public-semweb-lifesci" <public-semweb-lifesci@w3.org>
> There recent discussion has made me wonder, whether OWL is at all > useful to do quantitative science, if we insist that it is used > correctly (incorrect OWL seems to be useful). I don't think that incorrect OWL is necessary to deal with quantitative science. BioPAX has been criticized by ontology-enthusiasts for several reasons. Many of the design decisions that are criticized in BioPAX are not necessitated by use-cases from quantitative science / systems biology (I was quite involved in the BioPAX community in 2006-2007). > I have tried to come up with a simple example. Feel free to come up > with a simpler one: > > Express in correct OWL: Washington DC is further away from Boston > than New York City > > Use case: I want to fly with my helicopter from Boston to either DC > or NYC, whichever is closer. Why should this be hard? If I take your example by word and I am free to come up with arbitrary OWL DL, we could simply use an n-ary design pattern to SAY it in OWL. E.g., create a class "is farther away than", with three properties "reference place", "nearer place", "place that is farther away" -- and create an instance accordingly. Problem solved. But I guess what we really would want to do is to describe each city with geo-tags (latitude and longitude). Then we can use SPARQL to query for cities and calculate their distance from Boston. You might also be interested in looking at SPIN, an extension of OWL and SPARQL that uses an extended SPARQL syntax to create new inferences, run simulations etc. It is only part of TopBraid Composer so far (a commercial application). Holger Knublauch gives some examples of using SPIN in his blog: http://composing-the-semantic-web.blogspot.com/ He demonstrates how you can do simple maths with it (e.g., calculating the area of a square), but I am sure that much more sophisticated and complex things would also be possible in the hands of, say, a systems biologist. Make sure you also watch the video of using SPIN for running a computer game: http://tinyurl.com/95mftw Applying this technology to biological modeling would be interesting. Cheers, Matthias Samwald DERI Galway, Ireland http://deri.ie/ Konrad Lorenz Institute for Evolution & Cognition Research, Austria http://kli.ac.at/
Received on Tuesday, 31 March 2009 09:10:04 UTC