Samuel's Project Blog

I presented my MSc thesis project "SWI-Prolog as a Semantic Web tool for semantic querying in Bioclipse" today. (Report for download here

Find the slides below. I expected a very non-informatics audience (though some of my fellow Bioclipse:rs showed up =) ), had only 20 minutes, and lots of non-common-knowledge things to introduce, so these are really mostly a bunch of pictures for talking through the basics of semantic web, prolog and Bioclipse.

Turning back to the GSoC project now!

Have started actual coding for GSoC this wednesday (start was 2 weeks delayed because of exams, which I'll catch up). Still just getting up to speed, but looking now into the PHP RDF framework ARC, whose RDF store will replace the currently used RAP store in Semantic Mediawiki. Usage ARC itself looks very straightforward. Just have to figure out the SMW Store API. Looking at the SMWRapStore2.php now, to get an idea.

If you want to follow my progress in (approximate) real-time, then see my twitter.

My degree project, titled "SWI-Prolog as a Semantic Web tool for semantic querying in Bioclipse" is getting closer to finish. Now my report is approved by the Scientific Reviewer (thanks, Prof. Mats Gustafsson), so I wanted to make it available here (Download PDF). Reports on typos are welcome of course! :)

Coding for my GSoC project will start for real in June, 9th or so, but I just had a first look at code, to start wrapping my head around the things involved. I installed the following on my local SMW:

• RAP Connector + SPARQL Endpoint
• PageObjectModel (rev 63243)
• SMWWriter
• SparqlExtension

I tested the RAP based SPARQL endpoint, played a bit with SMWWriter, and tried to get some grips of how to best use existing functionality for implementing RDF import/export.

Some questions that arose (for Denny in the first place, I guess, but feel free to comment):

1. For implementing a SPARQL endpoint, should the ARC RDF store be implemented, similar to how RAP implements a separate store that mirrors the content in the SMW, or is there any way to get around the need for an extra store?
2. An alternative starting point to implementing an ARC store, In addition to the RAP store connector already available in SMW, seems to be the JosekiStore connector in SparqlExtension. But of course, one can look at both.
3. Where to find the relevant functionality related to the equivalent URI property found? In SMW_Exporter.php? other places too? 
4. SMWWriter depends on an outdated version of PageObjectModel, while the latter
   seems to have stabilized (no changes since 2008). What to do about that?

We are probably going to use SMWWriter for extending the RDF import/export functionality of Semantic MediaWiki, so I wanted to test it out a bit.

With some copy and paste of code from this page, I quickly had a MediaWiki Special Page set up, where I could make use SMWWriters internal API to implement a crude form for adding or removing "triples" in my Semantic MediaWiki. See Screenshot:

And the result, on the Methane page:

Looks promising. Connecting this with some ARC functionality for parsing SPARQL and RDF/XML, should make a big step in the right direction.

(For my internal documentation, mostly)

Got Eclipse for PHP up running now, with XDebug. Yay :) It was a snap to install on my Ubuntu box. I basically followed this and this blog post. (The Ubuntu package for XDebug is php5-xdebug).

The Eclipse dialogs had changed location and structure a little, so for my documentation, I included a screenshot of the dialog under "Run > Debug configurations" below.

Interesting: "Scientists Seeking NSF Funding Will Soon Be Required to Submit Data Management Plans". Is this a new trend? If so, it should be an area where Bioclipse can help, I gues, not least through the planned ability to export semantic data to a Semantic MediaWiki (That will require me to finish my GSoC first, though).