Ontological dependence, dispositions and institutional reality in chemistry

Authors:
Colin Batchelor;Janna Hastings;Christoph Steinbeck
Affiliations:
Royal Society of Chemistry, Thomas Graham House, Cambridge, UK CB4 0WF;European Bioinformatics Institute, Hinxton, UK CB10 1SD;European Bioinformatics Institute, Hinxton, UK CB10 1SD
Venue:
Proceedings of the 2010 conference on Formal Ontology in Information Systems: Proceedings of the Sixth International Conference (FOIS 2010)
Year:
2010

Citing 3
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Abstract

Biochemical 'small molecules' are involved in all living processes across all biological domains. Chemical ontologies provide structured chemical data and thereby support cross-disciplinary and integrative research across systems biology, chemogenomics and metabolomics. Efforts are underway to align ChEBI with upper level ontologies such as BFO, but confusion persists as to the ontological status of the ChEBI 'role' entities, which refer to continuants which inhere in chemical entities by virtue of the activity of the chemical entities. We provide a formal classification of these 'role' entities according to the continuants and endurants on which they ontologically depend, discuss the nature of chemical dispositions and the relevance of institutional reality, and address granularity issues in modelling chemical activity.