Samuel's Tech Blog

As a side-note, this looks interesting (Googled up by Egon), a Prolog Eclipse Plugin:

• http://eclipse.ime.usp.br/projetos/grad/plugin-prolog/index.html#Screenshots

Could be interesting to combine that, in the future, with the results of my current project. Worth thinking about at least.

EDIT: Se solution at the bottom of the page

I'm trying to set the java.library.path system setting for my Bioclipse manager/Eclipse plugin.

Normally, if running java from command line, this variable should be set like so (According to what I've googled up):

java -Djava.library.path=/usr/local/lib/pl-5.7.15/lib/i686-linux/JavaClassName

so I have tried to add the line

-Djava.library.path="/usr/local/lib/pl-5.7.15/lib/i686-linux/"

Being completely new to development for Bioclipse, I'm trying to dig into the developer-centric information available, primarily on the Bioclipse Wiki. Thinking that the feedback from a newcomer might be of some value, I'll below share my reflections and ideas for the wiki.

MediaWiki as platform

I think it has been a wise choice to use MediaWiki as a backend. since it is today becoming a de facto standard, both for huge community-driven knowledge bases with millions of users, as well as in the industry.

I switched laptop recently, so I needed to set up my development environment for Bioclipse 2.2 plugin development from scratch. Since the instructions for how to do this are spread over a couple of blogs and the wiki, I used the occasion to create an integrated howto, for my own documentation as well as for anyone interested.

When trying to build swi-prolog packages from source, the xpce package complains:

I ran into the trouble that I needed to clean up some software built from source, that did not have the "make uninstall" option, what a mess!

Just found a solution though: paco. Paco keeps track of installed files if you run "make install" through it. Later you can easily remove the installed packages.

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.

Install notes for SWI Prolog JPL on Ubuntu Jaunty (9.04)

JPL is a bi-directional Java/Prolog interface for SWI-Prolog, which I hope to be able to use for integrating Blipkit into Bioclipse, so I'm happy to have got it up running tonight. Below are some notes from the installation procedure.

NOTE: These are still rather incomplete notes about how to get this to work.

I Just read this paper on using thea for OWL (Web Ontology Language) reasoning from within Prolog.

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