Journal of Computing Science and Engineering

Korean Institute of Information Scientists and Engineers (한국정보과학회)
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Merging Taxonomies under RCC-5 Algebraic Articulations

  • Thau, David (Dept. of Computer Science, University of California at Davis) ;
  • Bowers, Shawn (Genome Center, University of California at Davis) ;
  • Ludaescher, Bertram (Dept. of Computer Science, University of California at Davis)
  • Published : 2009.06.30
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Abstract

Taxonomies are widely used to classify information, and multiple (possibly competing) taxonomies often exist for the same domain. Given a set of correspondences between two taxonomies, it is often necessary to "merge" the taxonomies, thereby creating a unied taxonomy (e.g., that can then be used by data integration and discovery applications). We present an algorithm for merging taxonomies that have been related using articulations given as RCC-5 constraints. Two taxa Nand M can be related using (disjunctions of) the ve base relations in RCC-5: M; N ${\subseteq}$M; N ${\supseteq}$; N ${\oplus}$M (partial overlap of Nand M); and N ! M (disjointness: N ${\cap}$M = ${\varnothing}$). RCC-5 is increasingly being adopted by scientists to specify mappings between large biological taxonomies. We discuss the properties of the proposed merge algorithm and evaluate our approach using real-world taxonomies.

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References

  1. AHO, A. V., M. R. GAREY, AND J. D. ULLMAN. 1972. The transitive reduction of a directed graph. SIAM Journal on Computing 1, 2:131-137. https://doi.org/10.1137/0201008
  2. BAILEY, K. D. 1994. Typologies and Taxonomies: An Introduction to Classification Techniques. Sage Publications, Inc.
  3. BERENDSOHN, W. G. 2003. MoReTax - Handling Factual Information Linked to Taxonomic Concepts in Biology. Number 39 in Schriftenreihe fur Vegetationskunde. Bundesamt fur Naturschutz.
  4. BRACHMAN, R. 1983. What is-a is and isn't: An analysis of taxonomic links in semantic networks. IEEE Computer 16:30-36. https://doi.org/10.1109/MC.1983.1654194
  5. COTE, R., D. ROTHWELL, AND L. BROCHU, Eds. 1993. SNOMED international: the systematized nomenclature of human and veterinary medicine, 3rd ed. College of American Pathologists, Northfield, Ill.
  6. DOOLITTLE, W. F. 1999. Phylogenetic classification and the universal tree. Science 284, 5423: 2124-2128. https://doi.org/10.1126/science.284.5423.2124
  7. DOU, D., D. MCDERMOTT, AND P. QI. 2004. Ontology translation on the semantic web. In International Conference on Ontologies, Databases and Applications.
  8. EHRIG, M. 2007. Ontology Alignment: Bridging the Semantic Gap. Semantic Web and Beyond Computing for Human Experience, vol. 4. Springer.
  9. EUZENAT, J. 2004. State of the art on ontology alignment. http://www.starlab.vub.ac.be/publications/kweb-223.pdf.
  10. FRANZ, N. M., R. K. PEET, AND A. S. WEAKLEY. 2007. On the use of taxonomic concepts in support of biodiversity research and taxonomy. In The New Taxonomy, Systematics Association Special Volume Series 74, Q. D. Wheeler, Ed. Taylor and Francis, Boca Raton, FL., 61-84.
  11. HENIKOFF, S., E. A. GREENE, S. PIETROKOVSKI, P. BORK, T. K. ATTWOOD, AND L. HOOD. 1997. Gene families: The taxonomy of protein paralogs and chimeras. Science 278, 5338:609-614. https://doi.org/10.1126/science.278.5338.609
  12. IOANNIDIS, Y. E. AND R. RAMAKRISHNAN. 1988. An efficient transitive closure algorithm. In Proceedings of the 14th International Conference Very Large Databases. Los Angeles, California, 382-394.
  13. JONSSON, P. AND T. DRAKENGREN. 1997. A complete classification of tractability in RCC-5. Journal of Artificial Intelligence Research 6, 211-221.
  14. JUNG, J. J. 2006. Taxonomy alignment for interoperability between heterogeneous digital libraries. In Digital Libraries: Achievements, Challenges and Opportunities (2006-11-20), S. Sugimoto, J. Hunter, A. Rauber, and A. Morishima, Eds. Lecture Notes in Computer Science, vol. 4312/2006. Springer, Berlin/Heidelberg, 274-282. https://doi.org/10.1007/11931584_30
  15. KENNEDY, J., R. KUKLA, AND T. PATERSON. 2005. Scientific names are ambiguous as identifiers for biological taxa: Their context and definition are required for accurate data integration. In Second International Workshop on Data Integration in the Life Sciences (DILS). LNCS 3615. 80-95. https://doi.org/10.1007/11530084_8
  16. KIM, J., M. JANG, Y.-G. HA, J.-C. SOHN, AND S.-J. LEE. 2005. MoA: OWL ontology merging and alignment tool for the semantic web. In Proceedings of the International Conference on Industrial and Engineering Applications of Artificial Intelligence and Expert Systems, IEA/AIE (2005-07-13), M. Ali and F. Esposito, Eds. Lecture Notes in Computer Science, vol. 3533. Springer, 722-731. https://doi.org/10.1007/11504894_100
  17. KLEIN, M. 2001. Combining and relating ontologies: an analysis of problems and solutions. In Workshop on Ontologies and Information Sharing, IJCAI-2001, A. Gomez-Perez, M. Gruninger, H. Stuckenschmidt, and M. Uschold, Eds. Seattle, USA.
  18. KOPERSKI, M., M. SAUER, W. BRAUN, AND S. GRADSTEIN, 2000. Referenzliste der Moose Deutschlands. Vol. 34. Schriftenreihe Vegetationsk.
  19. KOTIS, K. AND G. A. VOUROS. 2004. The HCONE approach to ontology merging. In Proceedings of the First European Semantic Web Symposium (2004-09-16), C. Bussler, J. Davies, D. Fensel, and R. Studer, Eds. Lecture Notes in Computer Science, vol. 3053. Springer, 137-151.
  20. KOTIS, K., G. A. VOUROS, AND K. STERGIOU. 2006. Towards automatic merging of domain ontologies: The HCONE-merge approach. J. Web Sem. 4, 1:60-79. https://doi.org/10.1016/j.websem.2005.09.004
  21. LINNAEUS, C. 1758. Systema Naturae. Laurentii Salvii, Stockholm.
  22. MCGUINNESS, D. L., R. FIKES, J. RICE, AND S. WILDER. 2000a. The Chimaera ontology environment. In Proceedings of the 17th National Conference on Artificial Intelligence (2002-01-03). AAAI Press/The MIT Press, 1123-1124.
  23. MCGUINNESS, D. L., R. FIKES, J. RICE, AND S. WILDER. 2000b. An environment for merging and testing large ontologies. In Proceedings of the 16th European Conference on Artificial Intelligence (ECAI-04) of the Seventh International Conference on Principles of Knowledge. Breckenridge, Colorado.
  24. NOY, N. F. AND M. A. MUSEN. 2003. The PROMPT suite: interactive tools for ontology merging and mapping. International Journal of Human-Computer Studies 59, 6:983-1024. https://doi.org/10.1016/j.ijhcs.2003.08.002
  25. ORENGO, C., A. MICHIE, S. JONES, D. JONES, M. SWINDELLS, AND J. THORNTON. 1997. CATH- a hierarchic classification of protein domain structures. Structure 5, 8 (August), 1093-1108. https://doi.org/10.1016/S0969-2126(97)00260-8
  26. PEET, R. K. 2005. Ranunculus dataset.
  27. RANDELL, D. A., Z. CUI, AND A. COHN. 1992. A spatial logic based on regions and connection. In KR'92. Principles of Knowledge Representation and Reasoning: Proceedings of the Third International Conference, B. Nebel, C. Rich, and W. Swartout, Eds. Morgan Kaufmann, San Mateo, California, 165-176.
  28. RENZ, J. AND B. NEBEL. 1999. On the complexity of qualitative spatial reasoning: A maximal tractable fragment of the region connection calculus. Artificial Intelligence 108, 1-2:69-123. https://doi.org/10.1016/S0004-3702(99)00002-8
  29. RIAZANOV, A. AND A. VORONKOV. 2002. The design and implementation of VAMPIRE. AI Communications 15, 2-3:91-110.
  30. STAFF, S. S. 1975. Soil taxonomy. A basic system of soil classification for making and interpreting soil surveys. Number 436 in Soil Conservation Service Agricultural Handbook. United States Department of Agriculture.
  31. STUMME, G. AND A. MAEDCHE. 2001a. FCA-MERGE: Bottom-Up Merging of Ontologies. In Proceedings of the 17th International Joint Conference on Artificial Intelligence. 225-234.
  32. STUMME, G. AND A. MAEDCHE. 2001b. Ontology merging for federated ontologies on the semantic web. In Proceedings of the International Workshop for Foundations of Models for Information Integration (FMII-2001). 413-418.
  33. THAU, D. 2008. Reasoning about taxonomies and articulations. In Ph.D. '08: Proceedings of the 2008 EDBT Ph.D. workshop. ACM, New York, NY, USA, 11-19. https://doi.org/10.1145/1387150.1387153
  34. THAU, D. AND B. LUDASCHER. 2007. Reasoning about taxonomies in first-order logic. Ecological Informatics 2, 3:195-209. https://doi.org/10.1016/j.ecoinf.2007.07.005
  35. W.W. McCune. 2008. Prover 9: http://www.cs.unm.edu/ mccune/prover9/.