Interoperable chemical structure search service

0507389 - ÚOCHB 2020 RIV GB eng J - Journal Article
Kratochvíl, Miroslav - Vondrášek, Jiří - Galgonek, Jakub
Interoperable chemical structure search service.
Journal of Cheminformatics. Roč. 11, Jun 28 (2019), č. článku 45. ISSN 1758-2946. E-ISSN 1758-2946
R&D Projects: GA MŠMT(CZ) LM2015047
Institutional support: RVO:61388963
Keywords : substructure search * small molecule databases * interoperability * linked data
OECD category: Biochemistry and molecular biology
Impact factor: 5.326, year: 2019
Method of publishing: Open access
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0367-2

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.
Permanent Link: http://hdl.handle.net/11104/0298382