Samuel's Tech Blog

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.

As kindly hinted to by Chen Li, I learned to know the BioModels initiative, which they're directing in the Le Novère group at EBI.

Before going to EBI, I wrote a blog post about "wrapping simulations in semantics", in order to make retrievement of knowledge from simulations automatable.

I had not imagined that the building blocks for this was already done, which is what I realized when looking at the picture at the bottom of the page on the BioModels website.

The BioModels initiative itself (which collects systems biology models which can be used by others) is highly interesting, but what I found extra interesting was that obviously they have both data formats and ontologies for the three main parts which probably need to be addressed, for wrapping simulations in semantics:

1. Model description (Format: SBML, SBGN | Ontology: SBO)
2. Simulation description (Format: SED-ML | Ontology: KiSAO)
3. Simulation results description (Format: SBRML | Ontology: TEDDY)

So, it seems that the idea (to wrap simulations in semantics in order to create an automated system for answering questions whose answers are hidden in simulation results) might not be so unrealistic after all.