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Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
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IDSM ChemWebRDF: SPARQLing small-molecule datasets.

Jakub Galgonek1, Jiří Vondrášek2

  • 1Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic. jakub.galgonek@uochb.cas.cz.

Journal of Cheminformatics
|May 13, 2021
PubMed
Summary

We created the Integrated Database of Small Molecules (IDSM) with a SPARQL endpoint, enhancing data interoperability for chemical and biological datasets. This enables complex federated queries, unlocking new insights from combined sources.

Keywords:
Resource Descriptor FrameworkSPARQLSmall-molecule datasets

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Area of Science:

  • * Cheminformatics and bioinformatics data integration.
  • * Semantic web technologies for chemical data.
  • * Database development for molecular information.

Background:

  • * Resource Description Framework (RDF) and SPARQL enhance data interoperability.
  • * Biological and chemical databases increasingly use RDF.
  • * Lack of official SPARQL endpoints for key datasets like PubChem, ChEMBL, and ChEBI hinders federated querying.

Purpose of the Study:

  • * Integrate PubChem, ChEMBL, and ChEBI small-molecule datasets into a unified database (IDSM).
  • * Provide a SPARQL endpoint for IDSM to enable complex and federated queries.
  • * Enhance mutual interoperability between the integrated datasets.

Main Methods:

  • * Developed an in-house SPARQL engine utilizing PostgreSQL for data storage.
  • * Stored RDF data in a relational format, translating SPARQL queries to optimized SQL.
  • * Integrated compound substructure and similarity search capabilities via the Sachem project.

Main Results:

  • * Established the Integrated Database of Small Molecules (IDSM) with a functional SPARQL endpoint.
  • * Achieved efficient SPARQL query evaluation through SQL translation and query optimization.
  • * Enabled programmatic access for federated queries and offered a web application (ChemWebRDF) for user interaction.

Conclusions:

  • * The IDSM addresses the gap in SPARQL accessibility for major chemical datasets.
  • * The developed system facilitates advanced data analysis and discovery through federated querying.
  • * Enhanced data interoperability and usability are achieved for small-molecule research.