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Enabling Ontology Based Semantic Queries in Biomedical Database Systems.

Shuai Zheng1, Fusheng Wang2, James Lu1

  • 1Department of Mathematics and Computer Science, Emory University Atlanta, Georgia, USA.

International Journal of Semantic Computing
|December 27, 2014
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Summary
This summary is machine-generated.

DBOntoLink integrates biomedical databases with ontologies, enabling direct semantic queries using standard languages like SQL. This open-source tool enhances data accessibility and query efficiency for biomedical research.

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Semanticsbiomedical databasesontology

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Area of Science:

  • Biomedical Informatics
  • Database Management
  • Semantic Web Technologies

Background:

  • Biomedical databases often use ontology concepts for annotation, but lack tools for direct semantic querying.
  • Integrating ontology-based semantic queries into existing database systems is challenging.

Purpose of the Study:

  • To develop a middleware solution for seamless integration of ontology repositories and semantically annotated biomedical databases.
  • To enable direct semantic querying using standard database languages like SQL and XQuery.

Main Methods:

  • Developed a semantic query engine with reasoning and query processing capabilities.
  • Implemented semantic operators as user-defined functions within the database engine (IBM DB2).
  • Integrated with the National Center for Biomedical Ontology (NCBO) BioPortal for ontology operations.

Main Results:

  • The DBOntoLink system, an open-source software, was implemented and supports major ontologies.
  • Semantic queries were directly specified and executed using standard database query languages.
  • Performance studies demonstrated high expressiveness and efficiency of semantic queries, with caching for performance boosts.

Conclusions:

  • DBOntoLink provides an adaptable and efficient solution for semantic querying in biomedical databases.
  • The system facilitates direct, expressive, and high-performance semantic data retrieval.
  • DBOntoLink enhances the utility of semantically annotated biomedical data for research and analysis.