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April 7, 2013 / admin

Blog move.

I’ve moved all my posts over to my personal website so I don’t have to maintain several different blogs. I’ll delete this blog in a while, so if you want to follow my posts (I’m looking at you, 6 subscribers on Google Reader), change your bookmarks/subscriptions.

March 15, 2013 / admin

I’m a professor.

screenshotAt least according to Jason Lim from the “World Scientific Team”. Clearly a reputable journal which I will be more than happy to advertise to everyone in my pattern recognition knowledge engineering “something with computers” research group.

February 24, 2013 / admin

Removing margins in gnuplot

I’ve had some fun* creating plots in gnuplot lately, and happened across one of those “it works everywhere but not for my setup” type problems. Here’s my setup/aims:

  • using Mac OS X 10.6 and gnuplot 4.6
  • generate plots to use in LaTeX, i.e. either PDF or EPS output
  • change the standard ratio of the plot canvas from around 4:3 to “a bit wider and less high” (in order to fit the standard width of my 1 column LaTeX text without taking up half of the page)
  • have no or only little unnecessary whitespace around the plot

This seems to be impossible in gnuplot, as the usual (since gnuplot 4.4 or so) way to change the plot and canvas size “set size …” works differently for the postscript terminal. You can change the plot size or aspect ratio, but not the canvas size, which results in lots of whitespace around the plot, see the picture below where the blue frame marks the bounding box of the resulting eps.


This is obviously not great, but there seems to be now way around it other than manually removing the whitespace, e.g. in Preview. After some digging, however, I came across the eps2eps tool (happened to be installed on my machine already) which “fixes” the bounding box and removes unnecessary whitespace. Unfortunately, for some unknown reason, it also rotates the resulting image by 90 degrees clockwise and there are no options to rotate or prevent rotation of the output. Ugh.

After some more digging, I found yet another tool, eps2pdf, which converts an EPS image to PDF – and happily accepts a rotation parameter. I simply downloaded the EPS tools package and copied the three files into /usr/bin and made them executable to run them. Et voila, I’ve got a 3-tool-pipeline for generating margin-less plots – see the resulting graphic below.

In the plot file:

set size ratio 0.6
set terminal postscript enhanced color
set output 'frequency.tmp.eps'

My script ( for generating the PDF output:

gnuplot $1.plt
eps2eps $1.tmp.eps $1.eps
eps2pdf -r -90 $1.eps
rm $1.tmp.eps

Run the script with

sh frequency

And here’s the resulting PDF – beautiful, non?



December 13, 2012 / admin

WoDOOM 2013 announced

The 2nd workshop on Debugging Ontologies and Ontology Mappings (WoDOOM 13) will be co-located with ESWC 2013 in Montpellier, France. This year’s workshop was small but had some excellent contributions, and it would be great to see some more papers and attendees next year. After all, there is still plenty of work to be done in the ontology debugging landscape. Deadline for submissions is the 4th March 2013.

November 24, 2012 / admin

Stardog ASCII art power

I’ve just installed the Stardog RDF database for the first time (painless. Download, unzip to some directory, set an environment variable, done. TAKE A NOTE, triple stores.) and on server startup I was greeted with this wonderful peace of ASCII art:

You’ve just won me over.

Edit: Downloaded, installed, and loaded one of the example files with Stardog in 2 minutes. User-friendliness win. Now, if you could perhaps explain what that mysterious “-t D” flag is…

$ ./stardog-admin create -n myDB -t D -u admin -p admin --server \ 
snarl://localhost:5820/ examples/data/University0_0.owl

Without the flag, the loading simply fails with “Authentication failed”. Eh.

November 13, 2012 / admin

WoDOOM 2012: A brief review of the First International Workshop on Debugging Ontologies and Ontology Mappings

I travelled to Galway (Ireland) in early October for the First International Workshop on Debugging Ontologies and Ontology Mappings, or WoDOOM 2012 in short, which was co-located with EKAW 2012. With around 20 attendees and 4 speakers, the half-day workshop was fairly small, but it was definitely an interesting start for, hopefully, more workshops to come.

The invited speaker was Bijan Parsia, who gave a rather awesome talk laying out the landscape of what we generally refer to as ‘errors’ in OWL ontologies. We can categorise errors into logical and non-logical errors. Logical errors include the ‘classical’ errors such as incoherence and inconsistency, wrong entailments, missing entailments, but also less obvious problems such as tautologies and ‘concept idleness’. Non-logical errors are problems that we might not think of straight away when we talk about debugging; these include wrong naming of concepts and properties, structural irregularities, and performance problems.

The first research paper by Valentina Ivanova, Jonas Laurila Bergman, Ulf Hammerling and Patrick Lambrix was dealing with the debugging of ontology alignments based on an interesting use-case (ToxOntology, an ontology describing toxicological information of food). The main idea was to validate mappings based on the structural relations of concepts in the  ontology. Valentina also demoed a prototype of the RepOSE tool which nicely combines the “accept/reject” task of debugging alignments with a graph-based user interface (see screenshot below), making the job slightly less painful.

Next up was Tu Anh Nguyen from the Open University who presented her work on justification-based debugging using patterns and natural language. The approach taken to measuring the cognitive complexity of justifications is very appealing: They first identified a set of frequently occurring patterns in justifications which were sub-sets of justifications of maximally 4 axioms, using justifications from around 500 ontologies. The  50 most frequent patterns were then translated into natural language and evaluated using a mechanical turk style web service by presenting the ‘rule’ to a user, then asking them to decide whether a given entailment followed from that rule. This is quite close to what we did in our complexity study, but with the advantage that the natural language rules could be presented to a much wider audience than our DL/OWL Manchester syntax patterns. The result of the user study was a ranking of the most frequent rules, which can be used to rank the complexity of OWL justifications – at least in their natural language form. It would obviously be interesting to find out whether the complexity measure translates directly to Manchester syntax as used in Protege, for example.

And finally, I presented my paper “Declutter your justifications“, which deals with grouping multiple justifications based on their structural similarities. My talk followed on quite nicely from Tu Anh’s presentation, as she basically solved the problem of “obvious proof steps” using her natural language approach to testing justification sub-patterns. The slides for my presentation are available here.

In summary, this first WoDOOM turned out really well, and the papers presented were very interesting. I also have to admit that I was very pleased with the rate of 75% female speakers / first authors, which is pretty awesome. I’m hoping that we’ll have some more papers next year, as at least two had a very similar approach to debugging (justifications!), especially given Bijan’s highlighting other errors which are currently not considered in most debugging approaches.

[Photo of Galway by Phalinn Ooi, cc-licensed]

October 25, 2012 / admin

Enlightenment: A comparison between EL and EL-top.

I’m glad we clarified this.

[Table from an MSc dissertation of an unnamed student.]