Abstract
Ontologies are heavily used in life sciences and evolve continuously to incorporate new or changed insights. Often ontology changes affect only specific parts (regions) of ontologies making it valuable for ontology users and applications to know the heavily changed regions on the one hand and stable regions on the other hand. However, the size and complexity of life science ontologies renders manual approaches to localize changing or stable regions impossible. We therefore propose an approach to automatically discover evolving or stable ontology regions. We evaluate the approach by studying evolving regions in the Gene Ontology and the NCI Thesaurus.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Bodenreider, O., Stevens, R.: Bio-ontologies: current trends and future directions. Briefings in Bioinformatics 7(3), 256–274 (2006)
Boutet, E., Lieberherr, D., Tognolli, M.: UniProtKB/Swiss-Prot. Methods in Molecular Biology 406, 89–112 (2007)
Boyle, E.I., Weng, S., Gollub, J., et al.: GO:TermFinder - open source software for ac-cessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20(18), 3710–3715 (2004)
caBIG Strategic Planning Workspace: The Cancer Biomedical Informatics Grid (caBIG): infrastructure and applications for a worldwide research community. Studies Health Technology and Informatics 129, 330-334 (2007)
Euzenat, J., Shvaiko, P.: Ontology matching. Springer, Heidelberg (2007)
Floris, G., Manakanatas, D., Kondylakis, H., et al.: Ontology change: classification and survey. The Knowledge Engineering Review 23(2), 117–152 (2008)
The Gene Ontology Consortium: The Gene Ontology project in 2008. Nucleic Acids Research 36(Database issue), D440–D444 (2008)
Hartung, M., Kirsten, T., Gross, A., Rahm, E.: OnEX – Exploring changes in life science ontologies. BMC Bioinformatics 10, 250 (2009)
Hartung, M., Kirsten, T., Rahm, E.: Analyzing the Evolution of Life Science Ontologies and Mappings. In: Bairoch, A., Cohen-Boulakia, S., Froidevaux, C. (eds.) DILS 2008. LNCS (LNBI), vol. 5109, pp. 11–27. Springer, Heidelberg (2008)
Hubbard, T.J., Aken, B.L., Ayling, S., et al.: Ensembl 2009. Nucleic Acids Research 37(Database issue), D690–D697 (2009)
Kirsten, T., Hartung, M., Gross, A., Rahm, E.: Efficient Management of Biomedical Ontology Versions. In: Meersman, R., Herrero, P., Dillon, T.S. (eds.) OTM 2009 Workshops. LNCS, vol. 5872, pp. 574–583. Springer, Heidelberg (2009)
Klein, M., Fensel, D.: Ontology versioning on the Semantic Web. In: Proceedings of the International Semantic Web Working Symposium (SWWS), pp. 75–91 (2001)
Komatsoulis, G.A., Warzel, D.B., Hartel, F.W., et al.: caCORE version 3: Implementation of a model driven, service-oriented architecture for semantic interoperability. Journal of Biomedical Informatics 41(1), 106–123 (2008)
Lambrix, P., Tan, H., Jakoniene, V., Strömbäck, L.: Biological Ontologies. In: Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences, pp. 85–99 (2007)
Noy, N., Chugh, A., Liu, W., et al.: A Framework for Ontology Evolution in Collaborative Environments. In: Cruz, I., Decker, S., Allemang, D., Preist, C., Schwabe, D., Mika, P., Uschold, M., Aroyo, L.M. (eds.) ISWC 2006. LNCS, vol. 4273, pp. 544–558. Springer, Heidelberg (2006)
Noy, N., Klein, M.: Ontology evolution: Not the same as schema evolution. Knowledge and Information Systems 6(4), 428–440 (2004)
Noy, N., Musen, M.: Promptdiff: a fixed-point algorithm for comparing ontology versions. In: Proc. 18th Intl. Conference on Artificial Intelligence, pp. 744–750 (2002)
Noy, N., Musen, M.: Ontology versioning in an ontology management framework. IEEE Intelligent Systems 19(4), 6–13 (2004)
Papavassiliou, V., Flouris, G., Fundulaki, I., et al.: On Detecting High-Level Changes in RDF/S KBs. In: Bernstein, A., Karger, D.R., Heath, T., Feigenbaum, L., Maynard, D., Motta, E., Thirunarayan, K. (eds.) ISWC 2009. LNCS, vol. 5823, pp. 473–488. Springer, Heidelberg (2009)
Plessers, P., De Troyer, O.: Ontology Change Detection Using a Version Log. In: Gil, Y., Motta, E., Benjamins, V.R., Musen, M.A. (eds.) ISWC 2005. LNCS, vol. 3729, pp. 578–592. Springer, Heidelberg (2005)
Prüfer, K., Muetzel, B., Do, H.H., et al.: FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics 8, 41 (2007)
Sioutos, N., de Coronado, S., Haber, M.W., et al.: NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information. Journal of Biomedical Informatics 40(1), 30–43 (2007)
Smith, B., Ashburner, M., Rosse, C., et al.: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology 25(11), 1251–1255 (2007)
Stojanovic, L., Maedche, A., Motik, B., et al.: User-driven ontology evolution management. In: Gómez-Pérez, A., Benjamins, V.R. (eds.) EKAW 2002. LNCS (LNAI), vol. 2473, pp. 285–300. Springer, Heidelberg (2002)
Stojanovic, L., Motik, B.: Ontology evolution within ontology editors. In: Proceedings of the International Workshop on Evaluation of Ontology-based Tools, pp. 53–62 (2002)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Hartung, M., Gross, A., Kirsten, T., Rahm, E. (2010). Discovering Evolving Regions in Life Science Ontologies. In: Lambrix, P., Kemp, G. (eds) Data Integration in the Life Sciences. DILS 2010. Lecture Notes in Computer Science(), vol 6254. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15120-0_3
Download citation
DOI: https://doi.org/10.1007/978-3-642-15120-0_3
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-15119-4
Online ISBN: 978-3-642-15120-0
eBook Packages: Computer ScienceComputer Science (R0)