title: CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules.
abstract: A novel chemical ontology based on chemical functional groups automatically, objectively assigned by a computer program, was developed to categorize small molecules. It has been applied to PubChem and the small molecule interaction database to demonstrate its utility as a basic pharmacophore search system. Molecules can be compared using a semantic similarity score based on functional group assignments rather than 3D shape, which succeeds in identifying small molecules known to bind a common binding site. This ontology will serve as a powerful tool for searching chemical databases and identifying key functional groups responsible for biological activities.
authors.affiliation: The Blueprint Initiative of the Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave., Toronto, ON, Canada.
authors.forename: Howard J
authors.initials: HJ
authors.lastname: Feldman
authors.forename: Michel
authors.initials: M
authors.lastname: Dumontier
authors.forename: Susan
authors.initials: S
authors.lastname: Ling
authors.forename: Norbert
authors.initials: N
authors.lastname: Haider
authors.forename: Christopher W V
authors.initials: CW
authors.lastname: Hogue
mesh_terms: D001665:Binding Sites; D016208:Databases, Factual; D046911:Macromolecular Substances / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D012660:Semantics; D012984:Software
chemical_list: D046911:Macromolecular Substances