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International Journal of Telemedicine and Applications
Volume 2009 (2009), Article ID 917826, 14 pages
Managing Requirement Volatility in an Ontology-Driven Clinical LIMS Using Category Theory
Department of Computer Science and Software Engineering, Concordia University, 1455 de Maisonneuve Boulevard West, Montreal, QC, Canada H3G 1M8
Received 17 June 2008; Revised 30 October 2008; Accepted 29 December 2008
Academic Editor: Hui Chen
Copyright © 2009 Arash Shaban-Nejad et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- R. D. Mcdowall, “A matrix for the development of a strategic laboratory information management system,” Analytical Chemistry, vol. 65, no. 20, pp. 896A–901A, 1993.
- G. Avery, C. McGee, and S. Falk, “Implementing LIMS: a “how-to” guide,” Analytical Chemistry, vol. 72, no. 1, pp. 57A–62A, 2000.
- J. M. Overhage, J. Suico, and C. J. McDonald, “Electronic laboratory reporting: barriers, solutions and findings,” Journal of Public Health Management and Practice, vol. 7, no. 6, pp. 60–66, 2001.
- R. Wurtz and B. J. Cameron, “Electronic laboratory reporting for the infectious diseases physician and clinical microbiologist,” Clinical Infectious Diseases, vol. 40, no. 11, pp. 1638–1643, 2005.
- M. Eisenbarth and J. Dörr, “Facilitating project management by capturing requirements quality and volatility information,” in Proceedings of Workshop on Measuring Requirements for Project and Product Success (MeReP '07), Palma de Mallorca, Spain, November 2007.
- Y. K. Malaiya and J. Denton, “Requirements volatility and defect density,” in Proceedings of the 10th International Symposium on Software Reliability Engineering (ISSRE '99), pp. 285–294, Boca Raton, Fla, USA, November 1999.
- S. Eilenberg and S. Mac Lane, “General theory of natural equivalences,” Transactions of the American Mathematical Society, vol. 58, no. 2, pp. 231–294, 1945.
- K. E. Wiegers, Software Requirements, Microsoft Press, Wasthington, DC, USA, 2nd edition, 2003.
- T. R. Gruber, “A translation approach to portable ontology specifications,” Knowledge Acquisition, vol. 5, no. 2, pp. 199–220, 1993.
- D. Deridder and T. A. D'Hondt, “Concept-centric approach to software evolution,” in Proceedings of the 19th Annual ACM SIGPLAN Conference on Object-Oriented Programming, Systems, Languages, and Applications (OOPSLA '04), Vancouver, Canada, October 2004.
- G. Dobson and P. Sawyer, “Revisiting ontology-based requirements engineering in the age of the semantic web,” in Proceedings of the International Seminar on Dependable Requirements Engineering of Computerised Systems at NPPs, Halden, Norway, November 2006.
- O. C. Z. Gotel and A. C. W. Finklestein, “An analysis of the requirements traceability problem,” in Proceedings of the 1st International Conference on Requirements Engineering (ICRE '94), pp. 94–101, Colorado Springs, Colo, USA, April 1994.
- N. Aizenbud-Reshef, B. T. Nolan, J. Rubin, and Y. Shaham-Gafni, “Model traceability,” IBM Systems Journal, vol. 45, no. 3, pp. 515–526, 2006.
- A. Shaban-Nejad and V. Haarslev, “Incremental biomedical ontology change management through learning agents,” in Proceedings of the 2nd KES International Symposium on Agent and Multi-Agent Systems (KES-AMSTA '08), vol. 4953, pp. 526–535, Incheon, Korea, March 2008.
- E. D. Krasovec, Limber Labs, 2007, http://www.starlims.com/ICT_Autumn_2007.pdf.
- C. J. O. Baker, A. Shaban-Nejad, X. Su, V. Haarslev, and G. Butler, “Semantic web infrastructure for fungal enzyme biotechnologists,” Web Semantics: Science, Services and Agents on the World Wide Web, vol. 4, no. 3, pp. 168–180, 2006.
- C. J. O. Baker and R. Witte, “Mutation mining—a prospector's tale,” Information Systems Frontiers, vol. 8, no. 1, pp. 47–57, 2006.
- D. Jackson and A. Fergus, “Gene expression informatics,” PharmaGenomics, pp. 24–26, November-December 2002.
- Microarray and Gene Expression Data-MGED, http://www.mged.org/index.html.
- Minimum Information about a Microarray Experiment, http://www.mged.org/Workgroups/MIAME/miame.html.
- MAGE-ML: MicroArray Gene Expression Markup Language, http://xml.coverpages.org/MAGEdescription2.pdf.
- G. Kotonya and I. Sommerville, Requirements Engineering: Processes and Techniques, John Wiley & Sons, New York, NY, USA, 1998.
- M. J. Healy and T. P. Caudell, “Ontologies and worlds in category theory: implications for neural systems,” Axiomathes, vol. 16, no. 1-2, pp. 165–214, 2006.
- A. I. MacFarlane, “Dynamic structure theory: a structural approach to social and biological systems,” Bulletin of Mathematical Biology, vol. 43, no. 5, pp. 579–591, 1981.
- J. Adamek, H. Herrlich, and G. E. Strecker, Abstract and Concrete Categories: The Joy of Cats, John Wiley & Sons, New York, NY, USA, 1990.
- A. C. Ehresmann and J.-P. Vanbremeersch, “The memory evolutive systems as a model of Rosen's organisms-(metabolic, replication) systems,” Axiomathes, vol. 16, no. 1-2, pp. 137–154, 2006.
- A. Shaban-Nejad and V. Haarslev, “Categorical representation of evolving structure of an ontology for clinical fungus,” in Proceedings of the 11th Conference on Artificial Intelligence in Medicine (AIME '07), pp. 277–286, Amsterdam, The Netherlands, July 2007.
- I. Rahwan, S. D. Ramchurn, N. R. Jennings, P. McBurney, S. Parsons, and L. Sonenberg, “Argumentation-based negotiation,” Knowledge Engineering Review, vol. 18, no. 4, pp. 343–375, 2003.
- N. R. Jennings, S. Parsons, P. Noriega, and C. Sierra, “On argumentation-based negotiation,” in Proceedings of the International Workshop on Multi-Agent Systems (IWMA'S '98), Boston, Mass, USA, July 1998.
- R. Ashri, I. Rahwan, and M. Luck, “Architectures for negotiating agents,” in Proceedings of the 3rd International Central and Eastern European Conference on Multi-Agent Systems and Applications(CEEMAS '03), pp. 136–146, Prague, Czech Republic, June 2003.
- M. Capobianco, C. I. Chesñevar, and G. R. Simari, “Argumentation and the dynamics of warranted beliefs in changing environments,” Autonomous Agents and Multi-Agent Systems, vol. 11, no. 2, pp. 127–151, 2005.
- S. A. Whitmire, Object Oriented Design Measurement, John Wiley & Sons, New York, NY, USA, 1997.
- J. L. Fiadeiro, Categories for Software Engineering, Springer, Berlin, Germany, 1st edition, 2004.
- S. Easterbrook, “Category theory for beginners,” in Proceedings of the 3rd IEEE International High-Assurance Systems Engineering Symposium (HASE '98), Honolulu, Hawaii, USA, October 1998.
- P. Hitzler, M. Krötzsch, M. Ehrig, and Y. Sure, “What is ontology merging?—a category-theoretical perspective using pushouts,” in Proceedings of the 1st International Workshop on Contexts and Ontologies (C&O '05), pp. 104–107, Pittsburgh, Pa, USA, July 2005.
- A. Zimmermann, M. Krötzsch, J. Euzenat, and P. Hitzler, “Formalizing ontology alignment and its operations with category theory,” in Proceedings of International Conference on Formal Ontology in Information Systems (FOIS '06), pp. 277–288, Baltimore, Maryland, USA, November 2006.
- G. Resconi and L. C. Jain, Intelligent Agents: Theory and Applications, vol. 155 of Studies in Fuzziness and Soft Computing, Springer, Berlin, Germany, 2004.
- G. Resconi and G. Hill, “The language of general systems logical theory: a categorical view,” in Proceedings of the 3rd European Congress on Systems Science, pp. 1091–1096, Rome, Italy, October 1996.
- M. W. Johnson, T. Miller, and P. McBurney, “Modelling multi-agent interaction protocols using categories enriched over pointed sets,” Tech. Rep. ULCS-07-009, University of Liverpool, Liverpool, UK, 2007.
- E. Yanenko, “Evolving categories: consistent framework for representation of data and algorithms,” http://arxiv.org/abs/cs/0412089.
- V. Haarslev and R. Möller, “Description logics for the semantic web: racer as a basis for building agent systems,” Künstliche Intelligenz, vol. 17, no. 3, pp. 10–15, 2003.
- A. Poigné, “Elements of categorical reasoning: products and coproducts and some other (Co-) limits,” in Proceedings of the International Workshop on Category Theory and Computer Programming (CTCS '85), pp. 16–42, Guildford, UK, September 1986.
- D. Kozen, C. Kreitz, and E. Richter, “Automating proofs in category theory,” in Proceedings of the 3rd International Joint Conference Automated Reasoning (IJCAR '06), pp. 392–407, Seattle, Wash, USA, August 2006.
- B. Mazur, “When is one thing equal to some other thing?” June 2007, http://www.math.harvard.edu/~mazur/preprints/when_is_one.pdf.
- J. J. Cimino and P. D. Clayton, “Coping with changing controlled vocabularies,” in Proceedings of the Annual Symposium on Computer Applications in Medical Care, pp. 135–139, Washington, DC, USA, November 1994.
- D. E. Oliver, Y. Shahar, E. H. Shortliffe, and M. A. Musen, “Representation of change in controlled medical terminologies,” Artificial Intelligence in Medicine, vol. 15, no. 1, pp. 53–76, 1999.
- N. F. Noy, A. Chugh, W. Liu, and M. A. Musen, “A framework for ontology evolution in collaborative environments,” in Proceedings of the 5th International Semantic Web Conference (ISWC '06), pp. 544–558, Athens, Ga, USA, November 2006.
- M. C. A. Klein and N. F. Noy, “A component-based framework for ontology evolution,” in Proceedings of the 18th International Joint Conferences on Artificial Intelligence (IJCAI '03), vol. 71, CEUR-WS, Acapulco, Mexico, August 2003.
- J. E. Hopcroft, R. Motwani, and J. D. Ullman, Introduction to Automata Theory, Languages, and Computation, Addison-Wesley, Reading, Mass, USA, 2nd edition, 2001.
- R. Rosen, “The representation of biological systems from the standpoint of the theory of categories,” The Bulletin of Mathematical Biophysics, vol. 20, no. 4, pp. 317–341, 1958.
- V. Wiels and S. Easterbrook, “Management of evolving specifications using category theory,” in Proceedings of the 13th IEEE International Conference on Automated Software Engineering, pp. 12–21, Honolulu, Hawaii, USA, October 1998.
- T. Mens, “A formal foundation for object-oriented software evolution,” in Proceedings of IEEE International Conference on Software Maintenance (ICSM '01), pp. 549–552, Florence, Italy, November 2001.