A unified approach for debugging is-a structure and mappings in networked taxonomies

Patrick Lambrix,Valentina Ivanova

doi:10.1186/2041-1480-4-10

Abstract

BackgroundWith the increased use of ontologies and ontology mappings in semantically-enabled applications such as ontology-based search and data integration, the issue of detecting and repairing defects in ontologies and ontology mappings has become increasingly important. These defects can lead to wrong or incomplete results for the applications.ResultsWe propose a unified framework for debugging the is-a structure of and mappings between taxonomies, the most used kind of ontologies. We present theory and algorithms as well as an implemented system RepOSE, that supports a domain expert in detecting and repairing missing and wrong is-a relations and mappings. We also discuss two experiments performed by domain experts: an experiment on the Anatomy ontologies from the Ontology Alignment Evaluation Initiative, and a debugging session for the Swedish National Food Agency.ConclusionsSemantically-enabled applications need high quality ontologies and ontology mappings. One key aspect is the detection and removal of defects in the ontologies and ontology mappings. Our system RepOSE provides an environment that supports domain experts to deal with this issue. We have shown the usefulness of the approach in two experiments by detecting and repairing circa 200 and 30 defects, respectively.

Highlights

With the increased use of ontologies and ontology mappings in semantically-enabled applications such as ontology-based search and data integration, the issue of detecting and repairing defects in ontologies and ontology mappings has become increasingly important
In the remainder of this Subsection we describe the detection and repairing in more details and compare the manual repairing with the repairing using RepOSE
For 3 of these term pairs the change came after the domain experts realized that metabolism in MeSH has a different meaning than metabolism in ToxOntology

Summary

Introduction

With the increased use of ontologies and ontology mappings in semantically-enabled applications such as ontology-based search and data integration, the issue of detecting and repairing defects in ontologies and ontology mappings has become increasingly important These defects can lead to wrong or incomplete results for the applications. Ontologies can be seen as defining the basic terms and relations of a domain of interest, as well as the rules for combining these terms and relations [2]. They are a key technology for the Semantic Web. The benefits of using ontologies include reuse, sharing and portability of knowledge across platforms, and improved documentation, maintenance, and reliability. The work on ontologies is recognized as essential in some of the grand challenges of genomics research [3] and there is much international research cooperation for the development of ontologies

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