Samuel's Tech Blog

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

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 technologies in the Life Sciences:

• Biological knowledgemanagement: the emerging role of the Semantic Web technologies

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?!

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

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.

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.

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). ..."

• Full Physorg article

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.