Samuel's Tech Blog

Pellet, the reasoning system already integrated in Bioclipse, is based on so called "Description Logics".

I finally found a summary that contrasts RDF, RDF Schema, OWL, and rule languages (SWRL in this case) in a few sentences:

http://syntheticbiology.org/Semantic_web_ontology/Semantic_Web.html

Read up on:

• First-order logics
• Ontologies (OWL book?)
• OWL (OWL book)
• Description logics (Description logics handbook, chapter 1-2)
• Tableu / Tabling

• Pellet is coupled with a Datalog reasoner. 1. Sirin E, Parsia B, Grau BC, Kalyanpur A, Katz Y: Pellet: A practical OWL-DL reasoner. World Wide Web Internet And Web Information Systems 2007, 5:51-53.
• Datalog is a subset of Prolog
• Jena too seems to have a datalog implementation, according to http://en.wikipedia.org/wiki/Datalog
• DLP is the intersection of Horn logic and OWL, where as SWRL is (roughly) the union of them. <fn>1. Parsia B, Sirin E, Grau BC, Ruckhaus E, Hewlett D: Cautiously Approaching SWRL.

• Read up on Thea / OWL (paper by Mungall et. al.)
• Read up a little bit on DL (Descriptive Logic)
• Try some examples of more advanced Prolog rules, like recursive ones, querying the user interace, and possibly some list operations.
• Test and understand the "RNA Knot" rule in the Mungall paper.
• Install Blipkit submodules.
• Test reasoning with some RDF data.
• Create slides for presentation.
  • Use RNA knot examle (distinction between Prolog and DL reasoning)

This is how to create a "Hello World" kind of program in SWI-Prolog, as installed on Ubuntu (Jaunty).

PROLOG usage can be divided into two phases, one in which you write the Prolog program, and the other in which you query the program. The first phase is easiest done in a separate file. So create a file, i.e. test.pl, in you home folder, and edit it with a text editor like GEdit or Kate (Kate is much more powerful).

Was fighting with installation of Installing Telia 3G Mobile Broadband with Option 505 3G on Ubuntu Jaunty (9.04) this weekend.

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.

I discovered Mendeley today. Except for it's citation organization features, for which it is not unique (there are CiteUlike, JabRef and more) it works as a desktop app that indexes all your local PDF documents, and has an internal PDF viewer that lets you annotate the documents. These two are killer features that I've been looking for since a long time.

It's a pity though that it is proprietary. It would naturally feel better to put your work in the hands of an open system.

I just read a paper on BlipKit/BioProlog, (July 2009). This is interesting stuff!

I'll collect some quotes from the paper, that give some key info about the system's capabilities:

• "Logic programming can provide a means of both performing integrative queries and rule-based inference to accound for implicit knowledge"
  • These are key concepts.