Dan Cook (U Washington): Ontology design: added value of organizing principles (CBO 2009)

Theory-based ontologies (FMA, OPB, SemSin semantic biosimulation models, GO, Cell Type ontology) for multiscale structure. The OPB is the Ontology of Physics for Biology, where domains include fluids, solids, chemical kinetics, electrochemistry, diffusion, heat transfer.

They have created OPB:physical_property as a child of continuant. These include terms like force, resistance, flow, etc.

Personal Note: I was really glad to see someone else using BFO for their terms in a practical sense like OBI does, rather than in a theoretical sense like most of the other OBO Foundry ontologies.

They have developed SemSim, which is a lightweight mapping schema in OWL from the physics biosimulation code to the semantic knowledge (Gennari JH et al 2008 PSB: Integration of multiscale biosimulation models via lightweight semantics; and another PSB article from 2009 about merging/recombining models – Neal et al.). Very interesting.

You could say that any change in property values is a consequence of a thermodynamically driven state property changes. A change in property can have structural and existential consequences.

Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!

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