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/
