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Extending a Multi-agent System for Genomic Annotation

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Book cover Cooperative Information Agents V (CIA 2001)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 2182))

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Abstract

The explosive growth in genomic (and soon, expression and proteomic) data, exemplified by the Human Genome Project, is a fertile domain for the application of multi-agent information gathering technologies. Furthermore, hundreds of smaller-profile, yet still economically important organisms are being studied that require the efficient and inexpensive automated analysis tools that multi-agent approaches can provide. In this paper we give a progress report on the use of the DECAF multi-agent toolkit to build reusable information gathering systems for bioinformatics. We will briefly summarize why bioinformatics is a classic application for information gathering, how DECAF supports it, and recent extensions underway to support new analysis paths for genomic information.

This work was supported by the National Science Foundation under grants IIS-9812764, IIS- 9733004 and BDI-0092336.

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References

  1. Y. Arens and C.A. Knoblock. Intelligent caching: Selecting, representing, and reusing data in an information server. In Proc. 3rd Intl. Conf. on Info. and Know. Mgmt., 1994.

    Google Scholar 

  2. D.A. Benson and et al. Genbank. Nucleic Acids Res., 28:15–18, 2000.

    Article  Google Scholar 

  3. K. Bryson, M. Luck, M. Joy, and D.T. Jones. Applying agents to bioinformatics in geneweaver. In Proc. 4th Int. Wksp. Collab. Info. Agents, 2000.

    Google Scholar 

  4. S. Chawathe, H. Garcia-Molina, J. Hammer, K. Ireland, Y. Papakonstantinou, J. Ullman, and J. Widom. The TSIMMIS project: integration of heterogeneous information sources. In Proc. 10th Mtg. Info. Proc. Soc. Japan, Dec. 1994.

    Google Scholar 

  5. S. B. Davidson and et al. Biokleisli:a digital library for biomedical researchers. Intnl. J. on Digital Libraries, 1(1):36–53, 1997.

    Google Scholar 

  6. K. Decker, X. Zheng, and C. Schmidt. A multi-agent system for automated genomic annotation. In Proceedings of the 5th Intl. Conf. on Autonomous Agents, Montreal, 2001.

    Google Scholar 

  7. K. S. Decker, A. Pannu, K. Sycara, and M.W illiamson. Designing behaviors for information agents. In Proc. 1st Intl. Conf. on Autonomous Agents, pages 404–413, 1997.

    Google Scholar 

  8. K. S. Decker, K. Sycara, and M. Williamson. Middle-agents for the internet. In Proc. 15th IJCAI, pages 578–583, 1997.

    Google Scholar 

  9. K. S. Decker and V. R. Lesser. Quantitative modeling of complex computational task environments. In Proc. 11th AAAI, pages 217–224, 1993.

    Google Scholar 

  10. K. S. Decker and K. Sycara. Intelligent adaptive information agents. Journal of Intelligent Information Systems, 9(3):239–260, 1997.

    Article  Google Scholar 

  11. L. Deschaine, R. Brice, and M. Nodine. Use of infosleuth to coordinate information acquisition, tracking, and analysis in complex applications. MCC-INSL-008-00, 2000.

    Google Scholar 

  12. M.B. Eisen, P.T. Spellman, P.O. Brown, and D. Botstein. Cluster analysis and display of genome-wide expression patterns. Proc. Nat. Acad. Sci.

    Google Scholar 

  13. J. Graham and K.S. Decker. Towards a distributed, environment-centered agent framework. In Intelligent Agents VI, LNAI-1757, pages 290–304. Springer Verlag, 2000.

    Google Scholar 

  14. J. Graham. Real-time Scheduling in Multi-agent Systems. PhD thesis, University of Delaware, 2001.

    Google Scholar 

  15. J. Hendler and M. Taylor K. Stoffel. Advances in high performance knowledge representation. Technical Report CS-TR-3672, University of Maryland Institute for Advanced Computer Studies, 1996. Also cross-referenced as UMIACS-TR-96-56.

    Google Scholar 

  16. C.A. Knoblock, Y. Arens, and C. Hsu. Cooperating agents for information retrieval. In Proc. 2nd Intl. Conf. on Cooperative Information Systems. Univ. of Toronto Press, 1994.

    Google Scholar 

  17. S. Möller and M. Schroeder. Consistent integration of non-reliable heterogeneous information applied to the annotation of transmembrane proteins. Journal of Computing and Chemistry, to appear, 2001.

    Google Scholar 

  18. I. Muslea, S. Minton, and C. Knoblock. Stalker: Learning expectation rules for simistructured web-based information sources. In Papers from the 1998 Workshop on AI and Information Gathering, 1998. also Technical Report ws-98-14, University of Southern California.

    Google Scholar 

  19. M. Nodine and A. Unruh. Facilitating open communication in agent systems: the infosleuth infrastructure. In Intelligent Agents IV, pages 281–295. Springer-Verlag, 1998.

    Google Scholar 

  20. R. Stevens and et al. Tambis: Transparent access to multiple bioinformatics information sources. Bioinformatics, 16(2):184–185, 2000.

    Article  MathSciNet  Google Scholar 

  21. K. Sycara, K. S. Decker, A. Pannu, M. Williamson, and D. Zeng. Distributed intelligent agents. IEEE Expert, 11(6):36–46, December 1996.

    Article  Google Scholar 

  22. The Gene Ontology Consortium. Gene ontolgy: tool for the unification of biology. Nature Genetics, 25(1):25–29, May 2000.

    Google Scholar 

  23. T. Wagner, A. Garvey, and V. Lesser. Complex goal criteria and its application in design-tocriteria scheduling. In Proc. 14th AAAI, 1997.

    Google Scholar 

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Decker, K., Khan, S., Schmidt, C., Michaud, D. (2001). Extending a Multi-agent System for Genomic Annotation. In: Klusch, M., Zambonelli, F. (eds) Cooperative Information Agents V. CIA 2001. Lecture Notes in Computer Science(), vol 2182. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44799-7_12

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  • DOI: https://doi.org/10.1007/3-540-44799-7_12

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