Samuel's Tech Blog

A strategy for how to work with the Bioclipse/JPL/Prolog/Blipkit combination I'm setting up, is becoming clear.

The main idea with Bioclipse, as well as with having a prolog engine available in it, is for flexible and "interactive" knitting together of knowledge. One of the main questions regarding how to use a Bioclipse/JPL/Prolog/Blipkit combination, has been where to put the bulk of knowledge integration/reasoning code? There would in principle be three options for that:

1. Bioclipse (Javascript environment)
2. The Blipkit-Prolog/Bioclipse integration plugin (Java code, a.k.a. "Manager methods")
3. The prolog engine (As a prolog file)

I had the problem that in JPL (The java Prolog API) you cannot use namespaces before term (atoms or variables etc.) names, like so:

prologFunction( ns:'atom' ).

The best solution would be to have some kind of "namespace-like" support in the JS console of Bioclipse instead. One easy thing one can do is to just create a simple function that appends the long preceding URL, so a JS Example could be:

function molid ( term ) {
  return "http://pele.farmbio.uu.se/nmrshiftdb/?moleculeId=" + term;
}
blipkit.queryRDF(molid("234"),"X","Y");

As a subproject, I'm now focusing on doing some comparison between reasoning in Prolog and Pellet, using example data from NMRShiftDB.org. Below I'm documenting my planning, + any new findings while I'm digging in to this subpeoject.

My project has been more or less on hold for around a week because of exams and other stuff. Looking forward to getting some concrete things done now. While still reading up a bit on OWL, I've started taken the first steps of the prolog/blipkit integration with a simple method for querying a prolog on the form "subject, a predicate, and an object".

For my own documentation I went ahead and summarized all the steps I had to take

1. In order to start blipkit from java commandline, and
2. In order to start blipkit from an Eclipse plugin.

I now also managed to start blipkit from inside Eclipse.

The trick was to start the whole eclipse (The eclipse using for building Bioclipse) preceded with LD_PRELOAD=...the path to libjpl.so , and before that adding the paths to where libjava.so and libjvm.so are located.

Finally got blipkit started from java via jpl :)

• (Thanks to Andrew Koster on the SWIPL mailing list, who made me continue researching the LD_PRELOAD trick!)

In order to get the jpl java examples to work, LD_LIBRARY_PATH has to contain:

/usr/lib/jvm/java-1.5.0-sun-1.5.0.19/jre/lib/i386/client/:/usr/lib/jvm/java-1.5.0-sun-1.5.0.19/jre/lib/i386/

/usr/local/lib/pl-5.7.15/lib/jpl.jar:/home/samuel/install/swi-prolog/pl57/packages/jpl/examples/java/Test

Now firing up blipkit works, when calling Java from commandline!!!

Egon pointed me to an interesting blog post on RIF and OWL. The post highlights a situation very relevant for my project: The apparent existence of two main approaches in the field of "knowledge representation and reasoning" (maybe it should be called simply handling?) on the Semantic Web.

Talking about BLIPKIT, the Thea library - for reading OWL2 ontologies directly from within SWI-Prolog - seems relevant for this project, as a complement to BLIPKIT. It's written (partly) by the author of BLIPKIT.

Some features I noted:

• SWRL support (SWRL - Semantic Web Rule Language . is a proposed W3C standard for exchange between rule languages on the web)
• Bridge to the java OWL API
• translation of ontologies to Description Logic programs

After installation problems with DR-PROLOG, and after looking closer to Blipkit/BioProlog (Biomedical Logic Programming Knowledge Integration Kit), after a suggestion by Claes Andersson, I now aim to integrate it instead of DR-PROLOG.