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.