OWL 2 is commonly used to represent objects with complex structure, such as complex assemblies in engineering applications, human anatomy or the structure of chemical molecules [2]. Towards that direction, the European Bioinformatics Institute (EBI) has developed the ChEBI ontology as a public dictionary of molecular entities, which is used to ensure interoperability of applications supporting tasks such as drug discovery. In order to automate the classification of molecules, ChEBI descriptions have been translated into OWL and then classified using state of the art Semantic Web reasoners. While this has uncovered numerous implicit subsumptions between ChEBI classes, the usefulness of the approach was somewhat limited by a fundamental inability of OWL 2 to correctly represent the structure of complex molecular entities. OWL 2 exhibits a so-called tree-model property, which prevents one from describing non-tree-like relationships using OWL 2 schema axioms. For example, OWL 2 axioms can state that butane molecules have four carbon atoms, but they cannot state that the four atoms in a cyclobutane molecule are arranged in a ring.
