I have a new blog!

Semantic web for LAMP systems

Just aquainted myself a tiny bit with ARC, RDF Classes for PHP. Might be useful in the Bioclipse / Semantic MediaWiki integration that is in the thoughts for the coming months. ARC "framework", or RDF API used by RDF modules in Drupal, and has been talked about being the substitute for the currently used RAP framework in Semantic MediaWiki (used if one wants to set up a SPARQL endpoint for a Semantic MediaWiki).

On a different note, there are a bunch of nice web apps built on ARC over at semsol.com, most notably trice, a semantic web application framework.

GSoC project suggestion

Is there general enough import/export support for RDF data in Semantic MediaWiki that one could use SMW as a general collaborative RDF editor, as part of workflows?

(I know SMW has RDF export, but haven't yet found much about import (Except for OWL), and also wonder what is required to maintain the same RDF format "before and after" importing data for editing, and then exporting?)

I'm asking, firstly because we're interested in this functionality for integration with workflows made in Bioclipse's scripting environment (Since Bioclipse already has support for RDF storage, SPARQL querying,

Querying multiple SPARQL endpoints from single query, with Jena SERVICE extension

Egon pointed to an interesting blog post about a feature that is available as a an extension to Jena, the semantic web framework available in Bioclipse. It allows to very easily query multiple SPARQL endpoints from a single SPARQL query (using the SERVICE keyword), and use variable bound from one endpoint when querying the next.

This is very useful in general. I was also thinking of the specific scenario (along the lines we have partly already been thinking) to use multiple Semantic MediaWikis as community maintained databanks, for querying back into Bioclipse. Being able to use multiple MediaWiki installs is very useful because it is hard to incorporate a very efficient access restriction system in MediaWiki (due to the nature of how it works, with template calls and all), so then it is better to be able to have separate wikis for content which needs special restrictions.

Need to add "colon dash" before rdf_register_ns

I could not get the rdf_db:rdf_register_ns/2 function of SWI-Prolog's semweb package to work ... getting errors like "No permission to redefine static method ..." etc.

Now I finally figured out one has to add ":-" before the line with the rdf_db:rdf_register_ns predicate, like so:

:- rdf_db:rdf_register_ns(nmr, 'http://www.nmrshiftdb.org/onto#').

or ... inside Bioclipse:
swipl.loadPrologCode(":- rdf_db:rdf_register_ns(nmr, 'http://www.nmrshiftdb.org/onto#').");

Spatial indexing for SWI-Prolog can be useful for modelling embryology with semantics

Just found out that there is a Spatial Indexing package available for SWI-Prolog! How cool! That would come extremely handy if wanting to model the embryologic process of developmental biology with semantics (as I dream of doing :) ) ... and of course combining it with the ontologies and formats of the BioModels initiative.

Jena/SPARQL outperformed Prolog for spectrum similarity search

UPDATE 29/3: See new results here

I was a bit worried over the performance of the RDF facilities in Bioclipse, as a SPARQL query for doing NMR Spectrum similarity search, including a numerical comparison run in Pellet (against datasets which are attached), were quite unsatisfactory, being some 2 orders of magnitude worse than some Prolog code I wrote for doing the same task (But of course, pure SPARQL with filtering is probably not what pellet is optimized for ...).

Getting the Blipstart files right

I managed to fiddle a bit with my blipkit startup files, so I just need to document again
I use the files blipstart (a shell script), which loads the other file: blipstart.pl.

blipstart, the shell script, just contains the following line:


blipstart.pl is basically a copy of the blipkit/bin/blip file, removing the first line, and adding the following line at the end:

:- use_module(library('semweb/rdf_db')).

Bioclipse is finalist for the Eclipse Community Awards 2010

See more info here. Congrats!

Screencast: Experimental Prolog integration in Bioclipse

I wanted to test out some screen casting, so I chose to demo the (still experimental) SWI-Prolog integration into Bioclipse, showing how Prolog code (or a "Prolog knowledge base") can conveniently be stored inside Bioclipse's JavaScript environment (in a JS variable), loaded into the prolog engine, and then queried, all from the JS environment, and finally the results can be returned as well to the Javascript environment for further processing or output.

Note that this is still at the experimental stage, so things are a bit rough around the edges!

SBML turns 500

SBML, the "Systems Biology Markup Language", has reached over 500 citations, reports physorg.com, indicating the success of the standard. Congrats!