Chemical databases: curation or integration by user-defined equivalence?

•A rich variety of data on millions of diverse compounds are now available in public databases that can be used in drug discovery.•Differences in database business rules and software limitations mean there will be differences in the structural representation and properties of the same compound in different databases.•The size and growth of some databases and the available resources mean manual curation is becoming an increasingly unfeasible task.•Resources are available that enable compounds to be matched between databases where they have the same connectivity but other differences in their structures or representations.