When Ontologies go wrong.
March 21, 2007 2 Comments
Now as part of the polymer informatics project I am currently wworking on an ontology for polymer concepts. Now for those of you who don’t know, an ontology in computer science is a data model that represents a set of concepts within a domain and the relationships between those concepts. It is used to reason about the objects within that domain. This is the Wikipedia definition.
As part of this I am also currently trying to map out which ontologies on the wild wild web contain chemistry terms and to look at those slightly more closely. Now today I had a look at CyC, which claims to be an upper ontology of everything. When looking up the definition of the term “polymer” I found the following:
Now what is wrong with that definition? A whole lot. First of all, the term “PolymerMolecule” is a contradiction in terms. A polymer is a SUBSTANCE, which is composed of different individual MACROMOLECULES, as the definition above quite rightly states. It cannot therefore be a molecule in its own right and hence a concept like “PolymerMolecule” does not make sense. Furthermore, a macromolecule, according to IUPAC is “a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.” So even if the “chemical union of five or more identical combining units” were to refer to a concept
“macromolecule” this particular definition would generate an oligomer at best.
Upon seeing this, my colleague Dr Peter Corbett remarked, that upper ontologies are fundamentally broken. I tend to agree with him.
Scimantica - Semantic Science 
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I am no chemist, and I’ve not worked on this part of the Cyc ontology, but I think a couple of things are going on here:
1. You have to remember that Cyc names are opaque identifiers, used only by the ontologists creating them. There are doubtless issues with the chemistry ontology, but these would have to do with relationships between terms. Names can be infelicitous or confusing, but the only way the ontology can be wrong is in the relationships between terms. I don’t have a running cyc image available to check, but you would need to look at PolymerMolecule and determine that it is a spec of both the collections that represent Polymer and Molecule for Cyc to have the problem you describe.
2. The name PolymerMolecule is, I imagine, a way for a general ontologist to describe a molecule that participates in polymers. Like “car paint” — not a paint that is a car, nor a car that is a paint, but a paint that is related to cars.