The Description Logic Handbook
The Description Logic Handbook
GFO-Bio: A biological core ontology
Applied Ontology - Towards a Metaontology for the Biomedical Domain
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In chemistry, advances in computational technologies have allowed research into molecules that have not been synthesized yet, and may never be, to become widespread. These are described in terms of their structures, which are expressed as chemical graphs. Chemical graphs are a representational artifact, and as such are of a different ontological nature than the molecular entities which they describe. ChEBI (Chemical Entities of Biological Interest) is an ontology of chemical entities such as atoms, ions and molecules. ChEBI is being developed within a realist framework, explicitly incorporating only those entities which are known to exist. However, its molecular entities are described with chemical graphs, and ChEBI makes use of two IUPAC 'derivation' relations, which are defined partly in terms of chemical graphs and names rather than real molecules. Many modern chemical databases do not make explicit a distinction between the structures of chemical entities which do not exist (predicted molecules) and those which do exist (experimentally verified molecules), with both similarly described by chemical graphs. We therefore here analyse the ontological nature of these chemical graphs and the relations which hold between them. We interpret chemical graphs as representations of mathematical “connectivity” objects that can be used to precisely and exhaustively define many classes of molecule based on known properties of the connection of parts within molecules. We furthermore scrutinize the contentious relations in ChEBI and address their formal definitions both in terms of the graphs which represent their structures, and in terms of the molecular entities themselves. Finally, we show how these relations can be expressed using description logics.