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.
[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.
[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.
@article{"International Journal of Information, Control and Computer Sciences:56980", author = "Leong Lee and Jennifer Leopold and Julia Albath and Alton Coalter", title = "An Ontology Abstract Machine", 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.", volume = "3", number = "4", pages = "1062-12", }
