Saturday, January 07, 2006
New
discussion about signal pathways
and complex ontology
This is part of a discussion that will be moved to a Wiki page soon.
Communication to BioPAX
discussion, from BCNGroup.
Responding to ŕ [123]
1. Observation of state is often a matter of granularity. (stratification of coherence))
2. The notion of state can be localized, or the non-local effects can be observed. (separation of causes)
3. State has a fixed, but sometimes not completely known, history and a constrained path moving into the future. (embedding)
Let us assume that these three “ontological statements” are a cover for a set of open issues related to modeling any complex system, a system existing in a natural setting.
One additional “ontological statement” is needed and this is called the “modeling statement.”
4. “Modeling Statement”: Abstractions in the form of concepts are made “about” real systems. These abstractions “refer” to properties observed “about” the formation, the stable continuant, and the dissolution of real systems.
By cover, we mean that the element of the cover as sufficient to social discourse about complex systems. The modeling statement is not placed with the other three ontological statements, and sets “off to the side”.
Nested context leads myself and a few other “non-standard ontologists” to develop informal (non-formalizable) theories. Non-formalization does not imply that a controlled vocabulary cannot be put into place where the context can be clearly communicated between domain specialists.
The purpose of the current effort by the BioPAX group is to develop both controlled vocabulary, and data ontology. The data ontology is referred to by the human use of language from the controlled vocabulary. (My opinion.)
The generalization of architecture for modeling complex natural phenomenon seems to be on the near horizon. A metaphor between biological expression and knowledge management between entities within a business/market environment is being made.