Wednesday, March 01, 2006
Generative Methodology Glass Bead Games
On the limits of the OWL standard à [184]
Reading material [1]
Reading material [2]
Reading material [3]
Summary of the discussion up to this point à [186]
On ontological modeling of biological expression
On Formal verses Natural systems à [206]
From “Paul Prueitt” to BioPAX forum and others
It this point, the BioPAX discussion has become focused on the nature of scientific investigations where distributed Internet interactions are occurring and the meaning of vocabularies is critically important.
Dick, there is an opportunity here to understand specifically “where” the bioinformatics community is in broad based attempts to extend the role that mathematics has played for empirical science. This role is being extended by using "ontological models".
For example, Frank Schacherer is suggesting that OWL might not be the right tool for some aspects of the cell and gene expression "communication aid". The use of n-ary based ontology as a "sign system" (without entangled logical impositions) would seem to have three classes of contributions
1) The single n-ary when viewed as a graph neighborhood provides a sign that can be given shared interpretations by humans
2) The n-aries arise as the product of co-occurrence algorithms (ie in various forms of latent semantic indexing)
3) A collection of n-aries can be easily associated with OWL indexes and the data associated with the assertions made in an OWL index.
It is fascinating to observe.
The consequences of how issues are discovered and worked within a community of biologists, have direct impact on the current massive service oriented architecture developments in the federal government and private sector.
My group is generalizing and cross referencing the BioPAX (and other bioinformatics) work with the new clarity that we see over SOA ( service oriented architecture) in the transaction spaces (Customs, B-2-B, G-2-G).