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Exploring the Role of Deontic Reasoning and World Knowledge in Wason´s Selection Task
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Inferring ontology graph structures using OWL reasoning.

Miguel Ángel Rodríguez-García1,2, Robert Hoehndorf3,4

  • 1Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.

BMC Bioinformatics
|January 7, 2018
PubMed
Summary
This summary is machine-generated.

Onto2Graph transforms ontologies into graphs using automated reasoning, capturing rich semantic content. This method enhances biological data analysis, such as protein-protein interaction inference, by improving performance through deductive inference.

Keywords:
Automated reasoningOWLOntologyOntology visualizationSemantic similarity

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Ontology Engineering

Background:

  • Ontologies represent domain conceptualizations, traditionally as directed acyclic graphs (DAGs).
  • Modern ontologies use formal languages like Web Ontology Language (OWL), defining classes via axioms.
  • Extracting comprehensive graph structures from OWL ontologies that leverage semantic content remains a challenge.

Purpose of the Study:

  • To develop a method for transforming OWL ontologies into expressive graph structures.
  • To exploit the full semantic content of ontologies beyond basic taxonomy.
  • To improve ontology-based data analysis and visualization.

Main Methods:

  • Developed Onto2Graph, a method using automated reasoning to transform OWL ontologies into graphs.
  • Identified implied class relations by searching for patterns in the ontology's deductive closure.
  • Generated graph structures encoding significant semantic information from ontologies.

Main Results:

  • Demonstrated the method's application to infer protein-protein interactions using semantic similarity on the Gene Ontology.
  • Showcased performance improvements in data analysis when using graphs inferred via deductive reasoning.
  • Made the Onto2Graph software and experimental results publicly available.

Conclusions:

  • Onto2Graph provides a novel method for generating graph structures from OWL ontologies via automated reasoning.
  • The resulting graphs enhance ontology visualization and facilitate more effective ontology-based data analysis.