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Volume 3 Issue 2
Apr.  2016

IEEE/CAA Journal of Automatica Sinica

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Article Navigation >  IEEE/CAA Journal of Automatica Sinica  > 2016  >  3(2): 132-140
Qingpeng Zhang and David Haglin, "Semantic Similarity between Ontologies at Different Scales," IEEE/CAA J. of Autom. Sinica, vol. 3, no. 2, pp. 132-140, 2016.
Citation: Qingpeng Zhang and David Haglin, "Semantic Similarity between Ontologies at Different Scales," IEEE/CAA J. of Autom. Sinica, vol. 3, no. 2, pp. 132-140, 2016.
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Semantic Similarity between Ontologies at Different Scales

  • 1. Department of Systems Engineering and Engineering Management, City University of Hong Kong, Kowloon, Hong Kong SAR, China;

  • 2. Pacific Northwest National Laboratory, Seattle WA 98109, USA

Funds:

This work was supported by National Natural Science Foundation of China (71402157), the Natural Science Foundation of Guangdong Province, China (2014A030313753), CityU Start-up (7200399), the Center for Adaptive Super Computing Software -MultiThreaded Architectures (CASS-MT) at the U. S. Department of Energy's Pacific Northwest National Laboratory. Pacific Northwest National Laboratory Is Operated by Battelle Memorial Institute (Contract DE-ACO6-76RL01830).

    Abstract
  • In the past decade, existing and new knowledge and datasets have been encoded in different ontologies for semantic web and biomedical research. The size of ontologies is often very large in terms of number of concepts and relationships, which makes the analysis of ontologies and the represented knowledge graph computational and time consuming. As the ontologies of various semantic web and biomedical applications usually show explicit hierarchical structures, it is interesting to explore the trade-offs between ontological scales and preservation/precision of results when we analyze ontologies. This paper presents the first effort of examining the capability of this idea via studying the relationship between scaling biomedical ontologies at different levels and the semantic similarity values. We evaluate the semantic similarity between three gene ontology slims (plant, yeast, and candida, among which the latter two belong to the same kingdom - fungi) using four popular measures commonly applied to biomedical ontologies (Resnik, Lin, Jiang-Conrath, and SimRel). The results of this study demonstrate that with proper selection of scaling levels and similarity measures, we can significantly reduce the size of ontologies without losing substantial detail. In particular, the performances of Jiang- Conrath and Lin are more reliable and stable than that of the other two in this experiment, as proven by 1) consistently showing that yeast and candida are more similar (as compared to plant) at different scales, and 2) small deviations of the similarity values after excluding a majority of nodes from several lower scales. This study provides a deeper understanding of the application of semantic similarity to biomedical ontologies, and shed light on how to choose appropriate semantic similarity measures for biomedical engineering.

     

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