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SPARQL-enabled identifier conversion with Identifiers.org.

Sarala M Wimalaratne1, Jerven Bolleman1, Nick Juty1

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland, Database Center for Life Science (DCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan, Stanford Center for Biomedical Informatics Research, Stanford University, CA 94305-5479, USA and Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.

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This study introduces a new SPARQL service for integrating life science data. It resolves differing International Resource Identifiers (IRIs) to enable seamless federated queries across distributed data resources.

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Area of Science:

  • Bioinformatics
  • Semantic Web Technologies
  • Life Sciences Data Integration

Background:

  • Life science data is often fragmented across multiple resources on the semantic web.
  • Discrepancies in International Resource Identifiers (IRIs) hinder federated SPARQL queries.
  • Lack of identifier correspondence creates a significant barrier for cross-resource data analysis.

Purpose of the Study:

  • To develop a novel SPARQL-based service for on-the-fly integration of life science data.
  • To overcome the challenge of disparate identifiers in federated data querying.
  • To facilitate seamless data access and analysis across diverse life science databases.

Main Methods:

  • Implementation of a SPARQL-based identifier conversion service.
  • Utilization of the Identifiers.org Registry to define identifier patterns.
  • Generation of multiple identifier variants for matching source and target identifiers.
  • Demonstration of the service's utility in answering cross-resource queries.

Main Results:

  • A novel SPARQL service for life science data integration has been introduced.
  • The service successfully generates diverse identifier variants using Identifiers.org patterns.
  • The approach enables effective matching of identifiers across different data sources.
  • The utility is demonstrated by successful querying across major life science Linked Data producers.

Conclusions:

  • The developed SPARQL service effectively integrates distributed life science data.
  • Identifier resolution via Identifiers.org patterns facilitates federated querying.
  • This approach enhances the discoverability and usability of life science Linked Data.