Algorithms and Software for Collaborative Development and Use of Modular Ontologies

Project Summary

The success of the world wide web can be attributed to the network effect: The absence of central control on content and organization of the web allows thousands of independent actors to contribute resources (web pages) that are interlinked to constitute the web. Recent efforts to extend the web into a semantic web are aimed at enriching the web with machine interpretable content and interoperable resources and services. Realizing the full potential of the semantic web requires the large-scale adoption and use of ontology based approaches to sharing of information and resources. In such a setting, instead of a single, centralized ontology, it is much more natural to have multiple distributed ontologies that cover different, perhaps partially overlapping, domains (e.g., biology, medicine, pharmacology). Such ontologies represent the local knowledge of the ontology designers, that is, knowledge that is applicable within a specific context. Hence, there is an urgent need for theoretically sound yet practical approaches that support user, context, or application-specific adaptation and reuse of knowledge from multiple autonomously developed ontologies in specific applications. Ontologies on the semantic web need to satisfy apparently conflicting objectives: Selective sharing or reuse of knowledge across autonomously developed ontologies on the one hand and accommodation of the local points of view or contextuality of knowledge on the other. Our research on modular ontologies has led to:

• The development of modular variants of description logics that provide mechanisms for semantic importing of names (including concept, role and nominal names) across ontology modules and contextualized interpretation of reused knowledge . The resulting family of ontology languages, namely, package-based description logics (P-DL), frees the ontology designer from the burden of ensuring the reusability of an ontology module in contexts that are hard to foresee at the time of construction of the module in question. A natural consequence of contextualized interpretation is that inferences that are drawn are always from the point of view of a witness module. Thus, different modules might infer different consequences, based on the knowledge that they import from other modules.
• The development of distributed tableaux-based reasoning algorithms for P-DL which provide support for inference from the point of view of an ontology module, using knowledge that is imported from other modules, without the need for complete integration of multiple ontology modules.

Work in progress is aimed at:

• Design and implementation of a P-DL based software prototype for collaborative ontology building environment; Development of efficient distributed reasoning algorithms for P-DL.
• The development of a framework for strategies for protecting private knowledge while truthfully answering queries.
• Implementation of a suite of tools for collaborative development and use of package-based partial order ontologies for applications in biomedical informatics and comparative genomics.

Anticipated results of this research includes open source software for rapid, collaborative construction of modular ontologies including support for distributed reasoning with modular ontologies.

A long-term goal of our research on modular ontologies is to transform distributed data and knowledge base applications in the same way that the World-Wide Web has transformed the construction, sharing and use of hyperlinked documents and Wiki has transformed encyclopedia construction.

Funding

At present, the primary sources of funding for this project are:

• IIS-0639230 SGER: Exploratory Investigation of Modular Ontologies. National Science Foundation Vasant Honavar (PI), Giora Slutzki (Co-PI), and Doina Caragea (Co-PI).
• A Collaborative Building Environment for Animal Trait Ontologies, Vasant Honavar (PI), James Reecy, (Co-PI), Center for Integrative Animal Genomics and Center for Computational Intelligence, Learning, and Discovery, Iowa State University.

Personnel

Dr. Vasant Honavar, Professor of Computer Science and of Bioinformatics and Computational Biology, Iowa State University, Principal Investigator.

Dr. Giora Slutzki, Professor of Computer Science, Iowa State University, Co-Principal Investigator.

Doina Caragea, Assistant Professor of Computer Science, Kansas State University, Co-Principal Investigator.

George Voutsadakis, Assistant Professor of Mathematics and Computer Science, Lake Superior State University, Collaborator

Jim Reecy, Assistant Professor of Animal Science, Iowa State University, Collaborator

Jie Bao, Ph.D. Student, Computer Science.

LaRon Hughes, Ph.D. Student, Bioinformatics and Computational Biology.

Zhiliang Hu, National Animal Genome Research Program, Collaborator.

Publications

1. Bao, J., Slutzki, G., and Honavar, V. (2007). A Semantic Importing Approach to Knowledge Reuse from Multiple Ontologies.. In: Proceedings of the 22nd Conference on Artificial Intelligence (AAAI-2007). Vancouver, Canada. In Press.

2. Bao, J., Caragea, D., and Honavar, V. A Tableau Based Federated Reasoning Algorithm for Modular Ontologies. In: Proceedings of the ACM/IEEE/WIC Conference on Web Intelligence. IEEE Press. pp. 404-410.
   

3. Bao, J., Caragea, D., and Honavar, V. On the Semantics of Linking and Importing in Modular Ontologies.In: Proceedings of the International Semantic Web Conference (ISWC 2006), Lecture Notes in Computer Science, Vol. 4273. pp. 72-86. Berlin: Springer.
   

4. Bao, J., Hu, Z., Caragea, D., Reecy, J., and Honavar, V. A Tool for Collaborative Construction of Large Biological Ontologies. Fourth International Workshop on Biological Data Management (BIDM 2006), Krakov, Poland, DEXA Workshops. IEEE Press. pp. 191-195. 2006.
   

5. Bao, J., Caragea, D., and Honavar, V. A Distributed Tableau Algorithm for Package-based Description Logics. Proceedings of the Second International Workshop on Context Representation and Reasoning (CRR 2006), Riva del Garda, Italy, CEUR. Vol. 2006.
   

6. Bao, J., Caragea, D., and Honavar, V. Modular Ontologies - A Formal Investigation of Semantics and Expressivity. In Proceedings of the First Asian Semantic Web Conference, Beijing, China, Springer-Verlag. Vol. Vol. 4185, pp. 616-631, 2006. Best Paper Award

7. Bao, J., Caragea, D., and Honavar, V. Towards Collaborative Environments for Ontology Construction and Sharing. Proceedings of the International Symposium on Collaborative Technologies and Systems., Las Vegas, 2006. Slides

Software

In progress.