MOTIVATION: The existing connections between large databases of chemicals, proteins, metabolites and assays offer valuable resources for research in fields ranging from drug design to metabolomics. Transparent search across multiple databases provides a way to efficiently utilize these resources. To simplify such searches, many databases have adopted semantic technologies that allow interoperable querying of the datasets using SPARQL query language. However, the interoperable interfaces of the chemical databases still lack the functionality of structure-driven chemical search, which is a fundamental method of data discovery in the chemical search space. RESULTS: We present a SPARQL service that augments existing semantic services by making interoperable substructure and similarity searches in small-molecule databases possible. The service thus offers new possibilities for querying interoperable databases, and simplifies writing of heterogeneous queries that include chemical-structure search terms. AVAILABILITY: The service is freely available and accessible using a standard SPARQL endpoint interface. The service documentation and user-oriented demonstration interfaces that allow quick explorative querying of datasets are available at https://idsm.elixir-czech.cz .

Department of Software Engineering Faculty of Mathematics and Physics Charles University Malostranské náměstí 25 118 00 Prague 1 Czech Republic

Institute of Organic Chemistry and Biochemistry of the CAS Flemingovo náměstí 2 166 10 Prague 6 Czech Republic

J Cheminform. 2020 Feb 13;12(1):13. doi: 10.1186/s13321-020-0418-8. PubMed

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Correction to: Interoperable chemical structure search service