Samuel's Tech Blog

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. (Possibly though, the Defeasible Reasoning feature of DR-PROLOG might be worth integrating later).

This change means a slightly updated project plan:

Project Title

Integration of Blipkit/BioProlog for semantic reasoning in Bioclipse

Aim

To integrate a PROLOG based tool for integrating and reasoning with data in semantic formats. Reasoning experiments will be performed with real-world use cases in order to assess the supportiveness of the tool in everyday science.

PROLOG

PROLOG is interesting as a platform in this area because it's syntax is declarative rather than predicative in nature, being much closer to natural language than traditional programming languages. This makes it very well suited for work with semantics. Complex semantic relationships can more easily be grasped and dealt with even in an interactive manner.

Blipkit/BioProlog

Blipkit/BioProlog is a capable PROLOG based reasoning system tailored towards bioinformatics, some of it's main features being:

• Lightweight, fast and scalable
• Open Source
• Active development and usage within bioinformatics
• Parsers to handle a plethora of bioinformatics formats and convert them to semantic ditto, as well as a library for quickly writing own mapping code.
• Takes care of fetching remote data across HTTP, maintaining a local cache.
• Package for dealing with systems biology data, including a db model strongly influenced by the SBML standard.
• Relational database integration
• Wrappers for querying Google, Yahoo and Wikipedia.
• Two means of visualizing such data (GraphViz and XPCE).
• Bundled web server, serval.
• Based on SWI-Prolog which can be installed on many different OS's