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Wednesday, March 01, 2006


Challenge problem

The Taos Discussion


Generative Methodology Glass Bead Games


On the limits of the OWL standard [184]

Reading material [1]

Reading material [2]

Reading material [3]

Summary of the discussion up to this point [186]



On ontological modeling of biological expression


On Formal verses Natural systems [206]


Hi Paul,


You said in the BioPAX forum


BioPAX is not a model of gene and cell expression, in the sense that the model is everything that the natural science community needs in a model. In engineering, a formal mathematical model is often everything one needs, but we do not need to make a false claim regarding BioPAX. Please Gary and Allan, correct me if I am presenting this improperly.


Yes, the "pathway abstraction" that BioPAX uses (that is used by many pathway databases e.g. www.pathguide.org and also most cell/molecular biology textbooks) has major limitations for describing real biological systems. The abstraction is as useful for modeling biological systems as a flowchart is for modeling a factory. You capture the components, types of processes/events and how they connect. This is extremely useful for understanding the system because it abstracts away much of the detail that would otherwise confuse you.


You do not capture the detailed mechanics of the parts, the speed/rates of the processes and the number of parts flowing through the system per unit of time. The rates and dynamics are much better described by mathematical equations (as you mention). Bringing this analogy back to biology, BioPAX cannot describe anything related to concentration and concentration changes over time and space. For instance, you can't say much about the electric current traveling along a neuron in BioPAX (even though this is pretty important). SBML and CellML, which capture these processes as mathematical equations are able to deal with that level of information very well, though you need a lot of detail at this level. E.g.




The more realist you get, the more detailed you get and the more impractical the model becomes for describing the whole cell. For instance, it is not practical to enumerate the actual molecules in the cell. Instead, you just say protein P53 and understand it to mean the "pool" of P53 molecules in some defined biological context.


Ideally, the pathway abstraction (BioPAX) is a component in a larger system that uses multiple abstractions at different scales to get a complete description of a system.






[1] http://dip.semanticweb.org/documents/ECIS2005-A-Methodology-for-Deriving-OWL-Ontologies-from-Products-and-Services-Categorization.pdf

[2] http://www.mindswap.org/2005/OWLWorkshop/sub1.pdf

[3] http://bip.cnrs-mrs.fr/bip10/rosen.pdf