An Ontology Abstract Machine

Authors: Leong Lee, Jennifer Leopold, Julia Albath, Alton Coalter

Abstract:

As more people from non-technical backgrounds are becoming directly involved with large-scale ontology development, the focal point of ontology research has shifted from the more theoretical ontology issues to problems associated with the actual use of ontologies in real-world, large-scale collaborative applications. Recently the National Science Foundation funded a large collaborative ontology development project for which a new formal ontology model, the Ontology Abstract Machine (OAM), was developed to satisfy some unique functional and data representation requirements. This paper introduces the OAM model and the related algorithms that enable maintenance of an ontology that supports node-based user access. The successful software implementation of the OAM model and its subsequent acceptance by a large research community proves its validity and its real-world application value.

Keywords: Ontology, Abstract Machine, Ontology Editor, WebbasedOntology Management System.

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1334630

References:

[1] Buffalo Ontology Site: http://ontology.buffalo.edu/
[2] V. K. Chaudhri, A. Farquhar, R. Fikes, P. D. Karp, J. P. Rice, "OKBC: A programmatic foundation for knowledge base interoperability," in Proc. 15th national conference on artificial intelligence (AAAI-98), 1998.
[3] M. R. Genesereth, R. E. Fikes, Knowledge Interchange Format Version 3.0 Reference Manual: http://logic.stanford.edu/kif/Hypertext/kifmanual. html
[4] P. Lambrix, M. Habbouche, M. Pérez, "Evaluation of ontology development tools for bioinformatics," Bioinformatics, vol. 19, no. 12, August 2003, pp. 1564-1571.
[5] A. J. Duineveld, R. Stoter, M. R. Weiden, B. Kenepa, V. R. Benjamins, "WonderTools? A comparative study of ontological engineering tools," International Journal of Human-Computer Studies, vol. 52, no. 6, June 2000, pp. 1111-1133.
[6] A. Farquhar, R. Fikes, J. Rice, "The Ontolingua Server: a tool for collaborative ontology construction", International Journal of Human- Computer Studies (1997), pp. 707-727.
[7] J. Lee, R. Goodwin, "Ontology Management for Large-Scale Enterprise Systems", Electronic Commerce Research and Applications, vol. 5, Iss. 1, Spring 2006, pp. 2-15.
[8] B. Smith, et al., "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration," Nature biotechnology, vol. 25, iss.11, pp.1251, 2007.
[9] Open Biological Ontologies: http://www.obofoundry.org/
[10] M. Klein, "Combining and relating ontologies: an analysis of problems and solutions," in Proc. IJCAI workshop on Ontologies (IJCAI-2001).
[11] AmphibAnat: http://www.amphibanat.org/
[12] J. Leopold, A. Coalter, and L. Lee, "A Generic, Functionally Comprehensive Approach to Maintaining an Ontology as a Relational Database", ICOSE 2009: International Conference on Ontological and Semantic Engineering, in review.
[13] J. Bao and V. Honava., "Divide and conquer semantic web with modular ontologies - a brief review of modular ontology language formalisms," in Proc. ISWC2006 International Workshop on Modular Ontologies (WoMo2006).
[14] J. Bao and V. Honavar, "Ontology Language Extensions to Support Localized Semantics, Modular Reasoning, and Collaborative Ontology Design and Ontology Reuse," Technical Report, Department of Computer Science, Iowa State University, 2004.
[15] P. Kodeswaran, S. B. Kodeswaran, A. Joshi, T. Finin, "Enforcing security in semantics driven policy based networks," ICDE Workshops 2008, pp. 490-497.
[16] J. Bao, G. Swlutzki, V. Honavar, "Privacy-Preserving Reasoning on the Semantic Web," IEEE/WIC/ACM International Conference on Web Intelligence, pp. 791-797, 2007.
[17] H. Luong, S. Gauch, and Q. Wang, "Ontology Learning Through Focused Crawling and Information Extraction," International Conference on Information, Process, and Knowledge Management, Cancun, Mexico, Feb. 1-7, 2009.
[18] OBO Edit: http://www.oboedit.org/
[19] OWL Web Ontology Language Guide: http://www.w3.org/TR/2004/REC-owl-guide-20040210/
[20] Stanford medical informatics Home page: http://protege.stanford.edu
[21] T. Finin, A. Joshi, L. Kagal, J. Niu, W. H. Winsborough, B. thuraisingham, "ROWLBAC - Representing Role Based Access Control in OWL", in Proc. SACMAT'08, 2008.
[22] T. R. Gruber, "A translation approach to portable ontology specifications," Knowl .Acquis, vol. 5, no. 2, pp.199-220, June 1993.
[23] J. de Bruijn, M. Ehrig, C. Feier, F. Martíns-Recuerda, F. Scharffe, and M. Weiten, "Ontology Mediation, Merging, and Aligning", in Semantic Web Technologies, July 2006, pp. 95-113.
[24] B. C. Grau, I. Horrocks, Y. Kazakov, and U. Sattler, "Just the right amount: extracting modules from ontologies", in Proc. 16th International Conference on World Wide Web, ACM, New York, NY, pp. 717-726.
[25] P. Linz, "An Introduction to Formal Languages and Automata", Jones & Bartlett, 4th edition, 2006, pp. 49-54.
[26] J. D. Richter, M. A. A. Harris, M. Haendel, S. Lewis, "OBO-EditÔÇöan ontology editor for biologists", Bioinformatics, vol. 23, no. 16, 2007, pp. 2198-2200.