Skip to main content

Investigating Ontological Similarity Theoretically with Fuzzy Set Theory, Information Content, and Tversky Similarity and Empirically with the Gene Ontology

  • Conference paper
Scalable Uncertainty Management (SUM 2011)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 6929))

Included in the following conference series:

Abstract

This paper theoretically and empirically investigates ontological similarity. Tversky’s parameterized ratio model of similarity [3] is shown as a unifying basis of many of the well-known ontological similarity measures. A new family of ontological similarity measures is proposed that allows parameterizing the characteristic set used to represent an ontological concept. The three subontologies of the prominent GO are used in an empirical investigation of several ontological similarity measures. A new ontological similarity measure derived from the proposed family is also empirically studied. A detailed discussion of the correlation among the measures is presented as well as a comparison of the effects of two different methods of determining a concept’s information content, corpus-based and ontology-based.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Cross, V.: Ontological Similarity. In: Popescu, M., Xu, D. (eds.) Data Mining in Biomedicine Using Ontologies, pp. 23–43. Artech House, Norwood, MA (2009)

    Google Scholar 

  2. Pesquita, C., Faria, D., Falcão, A.O., Lord, P., Couto, F.M.: Semantic Similarity in Biomedical Ontologies. PLoS Comput. Biol. 5(7), e1000443, doi:10.1371/journal.p(c)bi.1000443 (2009)

    Google Scholar 

  3. Tversky, A.: Features of Similarity. Psychological Rev. 84, 327–352 (1977)

    Article  Google Scholar 

  4. Pirrò, G., Seco, N.: Design, Implementation and Evaluation of a New Semantic Similarity Metric Combining Features and Intrinsic Information Content. In: Chung, S. (ed.) OTM 2008, Part II. LNCS, vol. 5332, pp. 1271–1288. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  5. Pirrò, G., Euzenat, J.: A Feature and Information Theoretic Framework for Semantic Similarity and Relatedness. In: Proceedings of International Semantic Web Conference, vol. (1), pp. 615–630 (2010)

    Google Scholar 

  6. Cross, V.: Tversky’s Parameterized Similarity Ratio Model: A Basis for Semantic Relatedness. In: Proceedings of the 2006 Conference of North American Fuzzy Information Processing Society (NAFIPS), Montreal, Canada (June 3-6, 2006)

    Google Scholar 

  7. Cazzanti, L., Gupta, M.R.: Information-theoretic and Set-theoretic Similarity. In: Proc. IEEE Intl. Symposium on Information Theory (2006)

    Google Scholar 

  8. Budanitsky, A., Hirst, G.: Semantic Distance in WordNet: An Experimental, Application-oriented Evaluation of Five Measures. In: Workshop on WordNet and Other Lexical Resources, Second meeting of the NAACL, Pittsburgh (2001)

    Google Scholar 

  9. The Gene Ontology Consortium, http://www.geneontology.org/

  10. Lord, P., Stevens, R., Brass, A., Goble, C.: Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19, 1275–1283 (2003)

    Article  Google Scholar 

  11. Wei, M.: An Analysis of Word Relatedness Correlation Measures. Master’s thesis, University of Western Ontario, London, Ontario (May 1993)

    Google Scholar 

  12. Lin, D.: An information-theoretic definition of similarity. In: Proc. of the 15th Int. Conf. on Machine Learning, pp. 296–304. Morgan Kaufmann, San Francisco (1998)

    Google Scholar 

  13. Attneave, F.: Dimensions of Similarity. American J. of Psychology 63, 516–556 (1950)

    Article  Google Scholar 

  14. Goodman, N.: Seven strictures on similarity. In: Goodman, N. (ed.) Problems and projects, pp. 437–447. Bobbs-Merrill, New York (1972)

    Google Scholar 

  15. Medin, D.L., Goldstone, R.L., Gentner, D.: Respects for Similarity. Psychological Review 100(2), 254–278 (1993)

    Article  Google Scholar 

  16. Cross, V.: An Analysis of Fuzzy Set Aggregators and Compatibility Measures, Ph.D. Dissertation, Computer Science and Engineering, Wright State University, Dayton, OH, 264 pages (March 1993)

    Google Scholar 

  17. Cross, V., Sudkamp, T.: Similarity and Compatibility in Fuzzy Set Theory: Assessment and Applications. Physica-Verlag, New York (2002) ISBN: 3-7908-1458

    Book  MATH  Google Scholar 

  18. Resnik, P.: Using information content to evaluate semantic similarity in taxonomy. In: Proc. of the 14th Intl Joint Conference on Artificial Intelligence, pp. 448–453 (1995)

    Google Scholar 

  19. Seco, N., Veale, T., Hayes, J.: An Intrinsic Information Content Metric for Semantic Similarity in WordNet. In: ECAI, pp. 1089–1090 (2004)

    Google Scholar 

  20. Jiang, J., Conrath, D.: Semantic similarity based on corpus statistics and lexical taxonomy, In: Proc. of the 10th International Conference on Research (1997)

    Google Scholar 

  21. Wu, Z., Palmer, M.: Verb semantics and lexical selection. In: Proc. of the 32nd Annual Meeting of the Assoc. for Computational Ling, NM, Las Cruces, pp. 133–138 (1994)

    Google Scholar 

  22. Yu, X.: A Mathematical and Experimental Investigation of Ontological Similarity Measures and their Use in Biomedical Domains. Master’s Thesis, Computer Science and Software Engineering, Miami University, Oxford OH (2010)

    Google Scholar 

  23. Cross, V., Sun, Y.: Semantic, Fuzzy Set and Fuzzy Measure Similarity for the Gene Ontology. In: Proceedings of the IEEE International Conference on Fuzzy Systems. Imperial College, London (2007)

    Google Scholar 

  24. Rodriguez, M.A., Egenhofer, M.J.: Determining Semantic Similarity among Entity Classes from Different Ontologies. IEEE Transactions on Knowledge and Data Engineering 15(2), 442–456 (2003)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Cross, V., Yu, X. (2011). Investigating Ontological Similarity Theoretically with Fuzzy Set Theory, Information Content, and Tversky Similarity and Empirically with the Gene Ontology. In: Benferhat, S., Grant, J. (eds) Scalable Uncertainty Management. SUM 2011. Lecture Notes in Computer Science(), vol 6929. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-23963-2_30

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-23963-2_30

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-23962-5

  • Online ISBN: 978-3-642-23963-2

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics