Samuel's Tech Blog

I was wondering how to express lists in RDF. Here is the answer, in RDF/N3 (there's a nice shorthand version available in N3).

There are many W3C Semantic Web primers, but this one seems to be the one to start with.

Just got to know there is something called "OWL (2) profiles", which basically seems to be certain sets of restrictions one can infer on what you can express, with the aim to make certain usage patterns possible.

OWL 2 RL seems particularly interesting for my concern, since it is (according to the above link) meant to be "a syntactic subset of OWL 2 which is amenable to implementation using rule-based technologies", and rule-based technologies is exactly what I'm looking at with SWI-Prolog and BLIPKIT.

Just got to know the Semantic Science Portal today (though I've read with keen interest the papers of some of the people behind it, and know SADI and Bio2RDF from before, since Egon W told me about them).

On the portal I found some interesting new things though, including:

France24, a french news website, recently upgraded from Drupal 5 to Drupal 6, taking benefit of improved performance and functionality. In the course, they have developed a seemingly quite impressive set of modules that provide the functionality that was missing in Drupal in order to create a highly flexibly layouted, and easy-worked news website - features which are highly general to many categories of websites. The good news is that they now have released most, if not all, of their custom modules as open source, as reported on drupal.org. Great news!

Found a very interesting quote:

"Both OWL-DL and function-free Horn rules are decidable fragments of first-order logic with interesting, yet orthogonal expressive power"Motik B, Sattler U, Studer R. Query Answering for OWL-DL with rules. Web Semantics: Science, Services and Agents on the World Wide Web. 2005;3(1):41-60. Available at: http://linkinghub.elsevier.com/retrieve/pii/S157082680500003X.

"Horn rules", is what prolog builds upon (a prolog statement are horn rules, AFAIS), so maybe Prolog fits into the category of "function-free horn rules"? (Gotta try to figure that out), and OWL-DL is the W3C standard for expressive semantics, that reasoners like pellet (which is available in bioclipse build upon.

What do you think of that title? :) To me it sounds like one of the (many) natural next steps forward for Bioclipse sometime in future¹.

Explicit knowledge is too expensive

There are lots of things that can't be answered by a computer from data alone. Maybe the majority of what we humans perceive as knowledge is inferred from a combination of data (simple fact statements about reality) and rules that tell how facts can be combined together to allow making implicit knowledge (knowledge that is not persisted as facts anywhere, but has to be inferred from other facts and rules) become explicit.

One can easily imagine though, that storing every single piece of knowledge that could be stated, as an explicit fact, would require more storage than can probably ever be made available in this universe.

Simulations can make knowledge explicit, from first princples

It is not too hard to come up with some processes which are just too complex and involves too much variability² that it is unrealistic to try to capture every imaginable state of of that system or process in explicit facts. Instead we must seek the "first principles" that defines the process, and through simulations make explicit any knowledge we are looking for, at the time we need it (one can of course cache often accessed knowledge).

Agent based simulation seems highly interesting for biological and/or molecular systems, which are too complex and "high dimensional" to be successfully simulated solely by mathematical means.

Stochastic simulation use to be the way to go then, but it seems agent based computing provide an even more general, and powerful paradigm for simulating this kind of systems.

In light of this, I was delighted to find Mason, a free (how does the "academic free licence" compare against LGPL etc.?) Java based software for agent based simulations, seemingly with many characteristics that make it good for integration in other software (Of course I'm pondering bioclipse integration here)

It seems to be quite working ... see the Conway's "Game Of Life" implementation, further down on the page :)

And, in case MASON is not the right answer to every question, they provide a shortlist of other interesting agent-based simulation software.

Since my last blogpost, about installing the Option 505 3G modem from telia on Ubuntu Jaunty (9.04), I have not got it working on Karmic (9.10).

But hinted from this post (in swedish) to this post, describing the installation in quite some detail, I now got it working on my Asus UL30A laptop.

As work has now started on getting bioclipse.net on Drupal (more on that in a while), it's good to know that Drupal is in to semantic web.

I was wondering what it looks like (since I have not had time to play with it), and to me, this screenshot was clarifying, showing how you can map fields (core fields, or your own custom ones) to rdf types (In drupal you can create both custom fields, and custom content types, which contain many fields).