Posted at: http://wwmm.ch.cam.ac.uk/blogs/adams/?p=195
Making the distinction between a substance and a molecule is indeed important and valuable from an ontological perspective, particularly when it comes to reasoning about the domain. The distinction is often blurred simply because it is more pragmatic not to consider them different. Indeed, most chemists might agree that while there is a conceptual distinction, they don’t want to navigate through a set of high-brow concepts to find such simple (indirect) relationships. Have you considered the impact of representing knowledge in this way with respect to usability?
Another important issue is that of identity - you are making the argument that every different feature effectively warrants a different identifier. That if i want to make a statement about glucose in one form versus another, i need two different identifiers. This will lead to enormous numbers of different “concepts”, which may affect reasoning capability (especially in OWL!) and potentially also lead to sparsely populated knowledge bases. An alternative is to capture the semantics of non-structural features in relations to the main component. For instance, I could reuse the “Glucose” class by adding additional restrictions, in the context of some process or experimental result. e.g. in my experiment i found glucose to be in its chair form. Indeed, expressing the behaviour (or structural conformation in this case) wrt to the context leads itself to modular reuse and also improves our representation of knowledge.
A couple of pointers that you might find interesting:
1 - Contextual knowledge representation - http://dumontierlab.com/pdf/2008_OWLEDEU_MR.pdf
2 - Biochemical Identifiers - http://www.slideshare.net/micheldumontier/accurate-biochemical-knowledge-starting-with-precise-structurebased-criteria-for-molecular-identity
We’ve also worked on chemical ontologies in OWL - you can see them here:
it would be nice to merge the two and work towards a comprehensive OWL-based ontology for the chemistry domain. Let me know if that would interest you.