Bioinformatician / Developer at UPPMAX HPC Center, Uppsala University. Interested in Semantic Web, Bioinformatics and Computational Systems Biology, Java, Python, Go, Prolog, Domain Driven Design, Model Driven Development, MediaWiki and Drupal.
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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.
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.
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.
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:
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: