An Upper-Level Ontology for Chemistry

Chemical entities are the foundation of biochemistry and biology, but until now there have been few coherent attempts to produce a top-level ontology for chemistry to connect ontological descriptions of reality at the molecular level, such as ChEBI, with upper-level ontologies such as BFO, or indeed familiar laboratoryscale concepts such as mixtures. We work out relationships between chemical types that are compatible with the OBO Relation Ontology, describe macroscopic chemical systems in terms of grains and collectives, and propose a top-level ontology for chemically-relevant continuants and discuss it in relation to BFO and BioTop.