Ontologies in Practice

This is an extension of an old post An Extensible System for Discovery Data. As I've been thinking more about what constitute the Simplest Building Blocks, I've begun to realize that they designate something very close to an ontology in the "middle distance." That is, it isn't about an ontology down to the fundamental constituents of matter, nor is it about specifying things in sufficient detail to adequately compare and track what's going on between organizations (see Barry Smith's presentation for a discussion of these issues), rather it is an ontology of the stuff we deal with in our day to day activities.

For example, an experiment has

• A protocol consisting of:
  
  • a set of initial conditions
  
  
  • one or more intermediate steps
  
  
  • each step may have a set of operators, equipment, constituents/ingredients etc.


• A result set consisting of one or more members,
  • any of which might be invalid for one or more reasons


• A set of analysis results
  
  • with methods
  
  
  • parameters
  
  
  • derived results (results that are based upon this result)
  
  
  • supporting results (results upon which this result is based, such as calibration curves)

My basis for claiming that these are constituents of a "middle distance" ontology is twofold:

1. Each component is ontologically necessary. That is, an experiment cannot exist without these components.


2. When analyzing these constituents we do not need to go into further detail. We can hide that detail behind an opaque identifier and need not give it further meaning. This opacity allows us to stop our analysis at that point; we don't have to analyze down to the constituent quarks (or chiral forms, for that matter, if they don't have any impact on our current goals).

In future posts I'll cover the entities and relationships that I take as being important in this middle distance and how to identify them (which, like most modularization efforts, is a more of an art than a science).