Supporting the analysis of ontology evolution processes through the combination of static and dynamic scaling functions in OQuaRE View Full Text


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Article Info

DATE

2016-10-17

AUTHORS

Astrid Duque-Ramos, Manuel Quesada-Martínez, Miguela Iniesta-Moreno, Jesualdo Tomás Fernández-Breis, Robert Stevens

ABSTRACT

BACKGROUND: The biomedical community has now developed a significant number of ontologies. The curation of biomedical ontologies is a complex task and biomedical ontologies evolve rapidly, so new versions are regularly and frequently published in ontology repositories. This has the implication of there being a high number of ontology versions over a short time span. Given this level of activity, ontology designers need to be supported in the effective management of the evolution of biomedical ontologies as the different changes may affect the engineering and quality of the ontology. This is why there is a need for methods that contribute to the analysis of the effects of changes and evolution of ontologies. RESULTS: In this paper we approach this issue from the ontology quality perspective. In previous work we have developed an ontology evaluation framework based on quantitative metrics, called OQuaRE. Here, OQuaRE is used as a core component in a method that enables the analysis of the different versions of biomedical ontologies using the quality dimensions included in OQuaRE. Moreover, we describe and use two scales for evaluating the changes between the versions of a given ontology. The first one is the static scale used in OQuaRE and the second one is a new, dynamic scale, based on the observed values of the quality metrics of a corpus defined by all the versions of a given ontology (life-cycle). In this work we explain how OQuaRE can be adapted for understanding the evolution of ontologies. Its use has been illustrated with the ontology of bioinformatics operations, types of data, formats, and topics (EDAM). CONCLUSIONS: The two scales included in OQuaRE provide complementary information about the evolution of the ontologies. The application of the static scale, which is the original OQuaRE scale, to the versions of the EDAM ontology reveals a design based on good ontological engineering principles. The application of the dynamic scale has enabled a more detailed analysis of the evolution of the ontology, measured through differences between versions. The statistics of change based on the OQuaRE quality scores make possible to identify key versions where some changes in the engineering of the ontology triggered a change from the OQuaRE quality perspective. In the case of the EDAM, this study let us to identify that the fifth version of the ontology has the largest impact in the quality metrics of the ontology, when comparative analyses between the pairs of consecutive versions are performed. More... »

PAGES

63

References to SciGraph publications

  • 2015-01-28. Aber-OWL: a framework for ontology-based data access in biology in BMC BIOINFORMATICS
  • 2014-03-06. Thematic series on biomedical ontologies in JBMS: challenges and new directions in JOURNAL OF BIOMEDICAL SEMANTICS
  • 2011. K-Means Clustering in ENCYCLOPEDIA OF MACHINE LEARNING
  • 2006. Modelling Ontology Evaluation and Validation in THE SEMANTIC WEB: RESEARCH AND APPLICATIONS
  • 2009-05-22. Application of Ontologies in Bioinformatics in HANDBOOK ON ONTOLOGIES
  • 2004. Tracking Changes During Ontology Evolution in THE SEMANTIC WEB – ISWC 2004
  • 2013. Finding Fault: Detecting Issues in a Versioned Ontology in ADVANCED INFORMATION SYSTEMS ENGINEERING
  • 2015-06-01. Region Evolution eXplorer – A tool for discovering evolution trends in ontology regions in JOURNAL OF BIOMEDICAL SEMANTICS
  • 2015-01-16. Predicting protein functions using incomplete hierarchical labels in BMC BIOINFORMATICS
  • 2004-07-01. Ontology Evolution: Not the Same as Schema Evolution in KNOWLEDGE AND INFORMATION SYSTEMS
  • 2009-05-22. What Is an Ontology? in HANDBOOK ON ONTOLOGIES
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    http://scigraph.springernature.com/pub.10.1186/s13326-016-0091-z

    DOI

    http://dx.doi.org/10.1186/s13326-016-0091-z

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/27751176


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