I have a new blog!

Structure and behaviour to co-exist

This, I think, was one of the more interesting quotes I've read for months:

OO, UML, ROOM and RRT make a fundamental distinction between structural modeling and behavioral modeling of computer systems.

Very good review on Semantic Web Tech in Life Sciences

Very good review on Semantic Web technologies in the Life Sciences:

Interestingly they talk some on "Semantic Systems biology" as well, concluding that Systems biology has been predicted, and shown, to be one of the main adopters of semantic technologies within the life sciences, due to it's high need of integration of knowledge from diverse scientific fields.

Surprisingly they are not mentioning any of the projects of the BioModels initiative, of which I just blogged, such as the Systems Biology Ontology. Should be essential?!

Most of the work is already? (Along the way to model the embryologic process with a semantics/simulation combination)

I've had the idea that I'd like to model the embryologic process with semantics (combined with simulations, which would be wrapped in semantics), into a general query answering system for the developmental process of a given species, but having thought that too many ontologies etc. are still missing, such as for expressing time and space.

Well, in addition to realizing that there are ontologies for describing systems biology models, simulations, and simulation results, already (see blog post), I now also realize that work on the above mentioned ontologies (for time and space e.g.) are there as well, and that tons of work along the line of integrate biological knowledge and systems level simulations, is already done (though they don't seem to address embryology specifically, so far).

Gotta think of what that means. Most probably somebody will soon address the embryology process as well, using the mentioned groundwork, and so I don't have to do it! =P

Chemical ring and cage structures need rules (seemingly)

During my short stay at EBI, Egon had kindly arranged an opportunity to talk to Janna from the Steinbeck group, about some interesting work she has done on searching for cage structures in molecules, using Prolog, so we met over a coffee, together with Nico who's now at the Steinbeck group (visiting).

Bot Nico and Janna kindly gave a lot of good advice about research in general (as I'm currently looking into possibly doing PhD somewhere), which I highly appreciated. :)

And we talked some about the original topic too :), that is the cage structure problem. The cage structure problem is kind of an extension to the problem of expressing rings, which has previously been reported as a problem for OWL-DL. So because of this, it is interesting that Janna came up with a working solution, using Prolog.

As a highlighting example from the DL-side, Michel Dumontier has done some work on representing molecules, including rings. But they also had to use rules, not plain OWL.

So that seem to be the general conclusion: In order to express ring structures (or extensions of it, such as cage structures), you'll need to use rules in some way.

Unfortunatly my project is now running out of time, so I might not have much time to look more into this topic as part of my project :(. Will see if I can include this as a part of another course I still have to finish ("knowledge based systems in bioinformatics"), but that remains to see.

Building blocks of "wrapping simulations in semantics" already there

I was at EBI last week for PhD interview (though I unfortunately failed the IAA test, and did not enter), but in addition to the opportunity to see EBI, I got to know some interesting stuff.

MIBBI Initiative: Minimum Information about a Biomedical or Biological Investigation

Stumbled upon this, which seems useful to be aware of, and of which physorg.com reports: "More than 20 grass-roots standardisation groups, led by scientists at the European Bioinformatics Institute (EMBL-EBI) and the Centre for Ecology & Hydrology (CEH), have combined forces to form the "Minimum Information about a Biomedical or Biological Investigation" (MIBBI) initiative (www.mibbi.org). ..."

NMR SPARQL search problem solved

The problem I've had, to find a working SPARQL query for doing similarity search for spectra, according to a list of peak shift values (documented on this blog: post1, post 2 and on semanticoverflow) is now finally solved, thanks to helpful advice from Brandon Ibach on the [pellet-users] mailing list.


This is a great SPARQL FAQ, and seemingly a good starting point for finding out anything SPARQL.


Think I finally got it what Horn clauses are good for

The Wikipedia article on Horn clauses states the following: "Horn clauses are relevant to theorem proving by first-order resolution, in that the resolution of two Horn clauses is itself a Horn clause"

That seems to explain why horn clauses are so foundational for prolog, since in prolog one can compose goal functions as compounds of other goals.

(I realize my lack of basic knowledge of Prolog, heavily regretting not having been able to have any formal training in logic programming / prolog at my uni :( (they removed the prolog part of the course where I hoped to learn it, just before I entered that course) ).


Tricky reasnong problem for SPARQL and OWL: Lists of property chains containing numerical value constraints

EDIT (19/2): The problem with doing this with a SPARQL query, is now solved! See this blog post.

Thought I should write up on my NMRSpectrum similarity search problem, which I've got quite stuck with ... even after trying to get some advice from Semantic Overflow. So ... here we go.

I have a problem that I can't seem to express successfully in either pure SPARQL nor using OWL class descriptions, seemingly because the problem combines lists, property chains, and numerical value constraints, in a troublesome mix.