Presented at the 2010 Formal Ontology in Information Systems conference (FOIS 2010). Discusses different classifications of the activity of chemical entities (in the context of the ChEBI ontology).

1. Ontological dependence, dispositions and institutional reality in chemistry Colin Batchelor 1 , Janna Hastings 2 and Christoph Steinbeck 2 1 Royal Society of Chemistry, Cambridge, UK 2 EBI Cheminformatics and Metabolism, UK

2. Some initial questions ChEBI ontology 20.10.10 What are the different kinds of active properties of chemical entities that are relevant in a biological context? In what kinds of processes are those active properties realized? What are the necessary aspects of a full formal description thereof?

6. Realizable (active) properties 20.10.10 Ontological dependence, dispositions and institutional reality in chemistry

8. Dispositions Dispositions specifically depend on their bearers solely by virtue of the sort of things they are. Examples: fragility , malleability , ductility .

10. Status functions Roles, by contrast, not only depend for their existence on the sort of thing their bearers are (pigs cannot graduate), but on social conventions , and speech acts that brings them into being. (BFO calls these roles .)

12. Mutual dispositions Many dispositions come in pairs. The bearer of one disposition, or the realization of that disposition, is part of the circumstances for the other. General examples: locks and keys , hosts and parasites (see Cowell et al. ). Chemical examples: acids and bases , ligands and binding sites , donors and acceptors .

13. portion of wine portion of water portion of ethanol water CHEBI:15377 water–hydroxide + proton equilibrium ethanol CHEBI:16236 ethanol–ethoxide ion + proton equilibrium hydroxide CHEBI:16234 proton CHEBI:24636 ethoxide CHEBI:52092 icbo icao has_participant has_grain has_part Bulk granularity Molecular granularity hydrogen atom oxygen atom has_part icbo icao proton transfer from ethanol to ethoxide proton transfer from ethoxide to ethanol has_participant has_participant Ontological dependence, dispositions and institutional reality in chemistry

15. Results 20.10.10

21. An example of a drug in ChEBI Ontological dependence, dispositions and institutional reality in chemistry

26. Thank you for your attention