My last post was an attempt to drag myself out of the realism debate; unfortunately, Chris Mungall replied, and he deserves an answer. Fortunately, his comment addressed an issue that I have been meaning to post for a while, which is the use of “not”, or “absent” in an ontology. I’ll make a brief aside into realism, then describe the pragmatic design decisions that lie at the heart of the issue. Feel free to skip the realism bit.

Following the publication of a number of papers, Gary Merrill, Michel Dumontier and Robert Hoehndorf (also as PDF) and myself (also on PLoS One), there has been an enormous amount of discussion on what is realism in ontology building, and whether it appropriate for use in scientific ontology building. As I have documented previously, I had now left the BFO discuss mailing list, and more latter OBO discuss, as I felt that these discussions have reached a finishing point. In this post, I want to spell out clearly my reasons why I think that it is not appropriate. I want to try and avoid re-iterating the positions in my paper, and earlier postings, as well as provide a direct answer to David Sutherland who has posted why he is a realist.

I don’t normally use my blog to engage in conversations the way that some people do. I already spend enough time on mailing lists, so using the blog seems redundant for this. However, I will change the habit of a life-time this once, because of an interesting discussion on institutional repositories, which I have previously written about myself.

While travelling on Elba, I suffered the misfortune of a virus attack; I don’t use AV software these days, since it tends to break other things which take a long time to fix, and it’s been many years since I’ve lost a machine to malicious software.

Elba was a lot of fun; it’s very biased toward beaches, but there are plenty of these, they are easy to get to and, generally, free. For my money, the best of these ones that we went to were Aquavivata (or something like that) and Sansone (next to each other — I swam to the latter) and Capo Bianco. Both of these are withing spitting distance of Portoferraio. which is the biggest town. It turns out that Capo Bianco is part of a marine reserve, which explains, with no fishing; this probably explains why the place was so rich with life that otherwise would have ended up on pasta. But, with a pebble beach, a slow sloping seabed still only 1 or 2m in depth some 50m from shore and with many rocks, and a headland it’s ideal for swimming and snorkelling.