Scaling alignment of large ontologies

International Journal of Bioinformatics Research and Applications

Volumn 6, Issue 4, 2010, Pages 384-401

  Stoutenburg, Suzette K ^a   Kalita, Jugal ^a   Ewing, Kaily ^b   Hines, Lisa M ^b  

^a University of Colorado at Colorado Springs   (United States)

^b UNIVERSITY OF COLORADO   (United States)

Author keywords

Knowledge acquisition; Knowledge management; Machine learning; Ontology; Ontology alignment; Semantic technology; Support Vector Machines; SVMs

Indexed keywords

EID: 77958018994     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2010.036001     Document Type: Article

References (31)

1. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M. and Sherlock, G. (2000) 'The gene ontology consortium, gene ontology: tool for the unification of biology', Nature Genetics, Vol. 25, No. 1, pp. 25-29.
2. Caracciolo, C., Euzenat, J., Hollink, L., Ichise, R., Isaac, A., Malaisé, V., Meilicke, C., Pane, J., Shvaiko, P., Stuckenschmidt, H., Šváb-Zamazal, O. and Svátek, N. (2008) Results of the Ontology Alignment Evaluation Initiative 2008, http://www.dit.unitn. it/p2p/OM2008/oaei08-paper0.pdf
3. Cuenca-Grau, B., Horrocks, I., Kazakov, Y. and Sattler, U. (2007) 'Just the right amount: extracting modules from ontologies', 16th WWW Conference, Banff, Alberta, Canada, pp. 717-726.
4. Doan, A., Madhavan, J., Domingos, P. and Halevy, A. (2004) 'Chapter 18 ontology matching: a machine-learning approach', Handbook on Ontologies, Springer-Verlag, Berlin, Germany, pp. 385-404.
5. Ehrig, M. (2007) Ontology Alignment: Bridging the Semantic Gap, Science + Business Media, Springer, New York, NY.
6. Elmasri, R., Fu, J., Ji, F. and Li, Q. (2007) 'BioSO: bioinformatic service ontology for dynamic biomedical web services integration', Proc. of the Fourth Biotechnology and Bioinformatics Symposium (BIOT 2007), pp. 60-62.
7. Euzenat, J. and Shvaiko, P. (2007) Ontology Matching, Springer-Verlag, Heidelberg.
8. Euzenat, J., Isaac, A., Meilicke, C., Shvaiko, P., Stuckenschmidt, H., Šváb, O., Svátek, V., van Hage, W. R. and Yatskevich, M. (2007) Results of the Ontology Alignment Evaluation Initiative 2007, http://www.dit.unitn. it/p2p/OM-2007/0ooaei2007.pdf
9. Giunchiglia, F., Yatskevich, M., Avesani, P. and Shvaiko, P. (2009) 'A large scale dataset for the evaluation of ontology matching systems', The Knowledge Engineering Review, Vol. 24, No. 2, pp. 1-22.
10. Hepp, M., De Leenheer, P., de Moor, A. and Sure, Y. (2008) Ontology Management: Semantic Web, Semantic Web Services and Business Applications, Springer, New York, NY.
11. Hu, W., Qu, Y. and Cheng, G. (2008) 'Matching large ontologies: a divide-and-conquer approach', Data and Knowledge Engineering, Vol. 67, No. 1, pp. 140-160.
12. Kirsten, T., Thor, A. and Rahm, E. (2007) 'Instance-based matching of large life science ontologies', 4th International Workshop on Data Integration in the Life Sciences, Philadelphia, PA, pp. 172-187.
13. Mao, M. and Peng, Y. (2007) 'The prior+: results for OAEI campaign 2007', Proc. of ISWC + ASWC Workshop on Ontology Matching, Busan, Korea, pp. 219-226.
14. Mork, P. and Bernstein, P. (2004) 'Adapting a generic match algorithm to align ontologies of human anatomy', Proc. of the 20th International Conference on Data Engineering, Busan, Korea, pp. 787-790.
15. Nagy, M., Vargas-Vera, M. and Motta, E. (2007) 'DSSim managing uncertainty on the semantic web', Proc. of ISWC + ASWC Workshop on Ontology Matching, Busan, Korea, pp. 160-169.
16. Noy, N. and Musen, M. (2003) 'The PROMPT suite: interactive tools for ontology mapping and merging', International Journal of Human-Computer Studies, Vol. 6, No. 59.
17. Noy, N. F. (2004) 'Semantic integration: a survey of ontology-based approaches', ACM SIGMOD Record, Vol. 33, No. 4, pp. 65-70.
18. Paulheim, H. (2008) 'On applying matching tools to large scale ontologies', OM-2008 Held in Conjunction with ISWC 2008, Karlsruhe, Germany, pp. 214-218.
19. Rahm, E. and Bernstein, P. A. (2001) 'A survey of approaches to automatic schema matching', VLDB Journal: Very Large Databases, Vol. 10, No. 4, pp. 334-350.
20. Sahoo, S., Zeng, K., Bodenreider, O. and Sheth, A. (2007) 'From Glycosyltransferase to congenital muscular dystrophy: integrating knowledge from NCBI entrez gene and the gene ontology', Proc. 12th World Congress on Health (Medical) Informatics (MEDINFO 2007), Brisbane, Australia, pp. 1260-1264.
21. Seidenberg, J. and Rector, A. (2006) 'Web ontology segmentation: analysis, classification and use', 15th WWW Conference, Edinburg, Scotland, pp. 13-22.
22. Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L. J., Eilbeck, K., Ireland, A., Mungall, C. J., the OBI Consortium, Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S-A., Scheuermann, R. H., Shah, N., Whetzel, P. L. and Lewis, S. (2004) 'The OBO foundry: coordinated evolution of ontologies to support biomedical data integration', Nature Biotechnology, Vol. 25, pp. 1251-1255.
23. Stoilos, G., Stamou, G. and Kollias, S. (2005) 'A string metric for ontology alignment', Proc. 4th International Semantic Web Conference (ISWC 2005), Galway, Ireland, pp. 624-637.
24. Stoutenburg, S. (2009) Advancing Ontology Alignment: New Methods for Biomedical Ontology Alignment using Non Equivalence Relations, PhD Thesis, University of Colorado at Colorado Springs, Colorado Springs, CO.
25. Stoutenburg, S., Obrst, L., Nichols, D., Samuel, K. and Franklin, P. (2007) 'Ontologies for rapid integration of heterogeneous data sources', Proc. Ontologies for the Intelligence Community (OIC 2007), October, Columbia, MD, pp. 37-42.
26. Stuckenschmidt, H. and Klein, M. (2004) 'Structure-based partitioning of large class hierarchies', 3rd International Semantic Web Conference (ISWC 2004), Hiroshima, Japan, pp. 717-726.
27. Tang, J., Li, B., Liang, X., Huang, Y. L. and Wang, K. (2006) 'Using Bayesian decision for ontology mapping', Journal of Web Semantics, Vol. 4, No. 4, pp. 243-262.
28. Tiffin, N., Kelso, J. F., Powell, A. R., Pan, H., Bajic, V. B. and Hide, W. A. (2005) 'Integration of text-and data-mining using ontologies successfully selects disease gene candidates', Nucleic Acids Research, Vol. 33, No. 5, pp. 1544-1552.
29. Wang, P. and Xu, B. (2008) 'Lily: ontology alignment results for OAEI 2008', Proc. of Ontology Matching Workshop (OM-2008), Held in Conjunction with the 7th International Semantic Web Conference, Karlsruhe, Germany, pp. 167-175.
30. Zhang, S. and Bodenreider, O. (2007) 'Hybrid alignment strategy for anatomical ontologies: results of the 2007 ontology alignment contest', ISWC + ASWC Workshop on Ontology Matching, Busan, South Korea, pp. 139-149.
31. Zhang, X., Cheng, G. and Qu, Y. (2007) 'Ontology summarization based on RDF sentence graph', 16th WWW Conference, Banff, Alberta, Canada, pp. 707-715.