Improving ontologies by automatic reasoning and evaluation of logical definitions

Sebastian Köhler, Sebastian Bauer, Chris Mungall, Gabriele Carletti, Cynthia Smith, Paul Schofield, Georgios Gkoutos, Peter Robinson

Research output: Contribution to journalArticlepeer-review

28 Citations (SciVal)
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Abstract

Background
Ontologies are widely used to represent knowledge in biomedicine. Systematic approaches for detecting errors and disagreements are needed for large ontologies with hundreds or thousands of terms and semantic relationships. A recent approach of defining terms using logical definitions is now increasingly being adopted as a method for quality control as well as for facilitating interoperability and data integration.

Results
We show how automated reasoning over logical definitions of ontology terms can be used to improve ontology structure. We provide the Java software package GULO (Getting an Understanding of LOgical definitions), which allows fast and easy evaluation for any kind of logically decomposed ontology by generating a composite OWL ontology from appropriate subsets of the referenced ontologies and comparing the inferred relationships with the relationships asserted in the target ontology. As a case study we show how to use GULO to evaluate the logical definitions that have been developed for the Mammalian Phenotype Ontology (MPO).

Conclusions
Logical definitions of terms from biomedical ontologies represent an important resource for error and disagreement detection. GULO gives ontology curators a fast and simple tool for validation of their work.
Original languageEnglish
Article number418
JournalBMC Bioinformatics
Volume12
Issue number1
DOIs
Publication statusPublished - 2011

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