To get the meaning and value
of the systems biology graphical notation (SBGN), one need to see
its home-made ontology, http://www.ebi.ac.uk/sbo/. Interestingly,
the notation was suggested by a team of biochemists, modelers, logicians and
computer scientists but ontologists. The project is mostly funded by
Japanese agencies because of involvement of Sony.
Presented as the "circuit
diagram" for biology, the SBNG is composed of three orthogonally different
modeling languages (maps):
the Entity Relationship
Diagrams (all the relationships in which a given entity participates, its
influence on the behavior of others),
the Process Diagrams (temporal
courses of biochemical interactions in a network of biochemical entities),
the Activity Flow Diagrams
(the flow of information between biochemical entities in the network of
biochemical entities), http://precedings.nature.com/documents/3719/version/1.
Some relevant comments on the
use of formalization in the life sciences.
The hallmark of the last
century is that the entire intellectual content of science and
engineering, including ontology engineering, can be captured (expressed, or
represented) in a formal system (symbolism and symbolic
processes). Intelligence and knowledge are largely equated with the
capacity to learn, understand and manipulate formal representations, be it
mathematical formalism, logical systems or graphical representations
The formal logical structures
have a tendency to be static, to resist the inherent property
of intellectual development and conceptual change.
Another warning: no
natural phenomena could be truly described by using unrelated languages for
entities, states, processes, and relationships, lacking logical, semantic and
ontological unities. We again return to the fundamental issue of semantic
and ontology standards, for life sciences now.