Abstract
In this paper, we present a new Decision Support System for Bioinformatics and System Biology issues. Our system is based on a Knowledge base, representing the expertise about the application domain, and a Reasoner. The Reasoner, consulting the Knowledge base and according to the user’s request, is able to suggest one or more strategies in order to resolve the selected problem. Moreover, the system can build, at different abstraction layers, a workflow for the current problem on the basis of the user’s choices, freeing the user from implementation details and assisting him in the correct configuration of the algorithms. Two possible application scenarios will be introduced: the analysis of protein-protein interaction networks and the inference of gene regulatory networks.
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References
Jauch, R., Yeo, H.C., Kolatkar, P.R., Clarke, N.D.: Assessment of CASP7 structure predictions for template free targets. Proteins: Structure, Function, and Bioinformatics 69, 57–67 (2007)
Power, D.J.: Brief History of Decision Support Systems. DSSResources.COM, http://DSSResources.COM/history/dsshistory.html
Keen, P.G., Scott Morton, M.S.: Decision support systems: an organizational perspective. Addison-Wesley Pub. Co., Reading (1978)
Moore, J.H., Chang, M.G.: Design of Decision Support System. Database 12, 8–14 (1980)
Parker, B.J.: Decision support systems: the reality that seems hard to accept. Omega 14, 135–143 (1986)
Buchanan, B.G., Shortliffe, E.H. (eds.): Rule-Based Expert Systems: The MYCIN Experiments of the Stanford Heuristic Programming Project. AAAI, Menlo Park (1984)
Shortliffe, E.H., Scott, A.C., Bischoff, M.B., et al.: ONCOCIN: an expert system for oncology protocol management. In: International Joint Conference on Artificial Intelligence, pp. 876–881 (1981)
Ceccarelli, M., Donatiello, A., Vitale, D.: KON3: a Clinical Decision Support System, in oncology environment, based on knowledge management. In: IEEE International Conference on Tools with Artificial Intelligence, vol. 2, pp. 206–210 (2008)
Hollinsworth, D.: The Workflow Reference Model. Tech. Rep. TC00-Workflow Management Coalition (1994)
Hull, D., Wolstencroft, K., Stevens, R., Goble, C., Pocock, M.R., Li, P., Oinn, T.: Taverna: a tool for building and running workflows of services. Nucleic Acids Res. 34 (2006)
Romano, P., Bartocci, E., Bertolini, G., De Paoli, F., Marra, D., Mauri, G., Merelli, E., Milanesi, L.: Biowep: a workflow enactment portal for bioinformatics applications. BMC Bioinformatics 8 (2007)
Johnson, B., Shneiderman, B.: Tree-maps: a space-filling approach to the visualization of hierarchical information structures. In: Proceedings of IEEE Conference on Visualization, pp. 284–291 (1991)
The Protege Ontology Editor and Knowledge Acquisition System, http://protege.stanford.edu
Sandia National Laboratories: Jess: The rule engine for the JavaTM platform (2003), http://herzberg.ca.sandia.gov/jess/
Xenarios, I., Rice, D.W., Salwinski, L., Baron, M.K., Marcotte, E.M., Eisenberg, D.: DIP: the database of interacting proteins. Nucleic Acids Research 28, 289–291 (2000)
Pagel, P., Kovac, S., Oesterheld, M., Brauner, B., Dunger-Kaltenbach, I., Frishman, G., Montrone, C., Mark, P., Stümpflen, V., Mewes, H.W., Ruepp, A., Frishman, D.: The MIPS mammalian protein-protein interaction database. Bioinformatics 21, 832–834 (2005)
Sabidussi, G.: The centrality index of a graph. Psychometrika 31, 581–603 (1966)
Freeman, L.C.: A set of measures of centrality based on betweenness. Sociometry 40, 35–41 (1977)
Yu, H., Paccanaro, A., Trifonov, V., Gerstein, M.: Predicting interactions in protein networks by completing defective cliques. Bioinformatics 22, 823–829 (2006)
Chen, K., Rajewsky, N.: The evolution of gene regulation by transcription factors and microRNAs. Nat. Rev. Genet. 8, 93–103 (2007)
Huang, Y., Tienda-Luna, I., Wang, Y.: Reverse engineering gene regulatory networks. IEEE Signal Processing Magazine 26, 76–97 (2009)
Cho, K.H., Choo, S.M., Jung, S.H., Kim, J.R., Choi, H.S., Kim, J.: Reverse engineering of gene regulatory networks. Systems Biology, 149–163 (2007)
Hecker, M., Lambeck, S., Toepfer, S., van Someren, E., Guthke, R.: Gene regulatory network inference: Data integration in dynamic models–A review. Biosystems 96, 86–103 (2009)
Zou, M., Conzen, S.D.: A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data. Bioinformatics 21, 71–79 (2005)
Kim, S.Y., Imoto, S., Miyano, S.: Inferring gene networks from time series microarray data using dynamic Bayesian networks. Briefings in Bioinformatics 4, 228–235 (2003)
Gat-Viks, I., Tanay, A., Raijman, D., Shamir, R.: A probabilistic methodology for integrating knowledge and experiments on biological networks. J. Comput. Biol. 13, 165–181 (2006)
Lahdesmaki, H., Hautaniemi, S., Shmulevich, I., Yli-Harja, O.: Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. Signal Process. 86, 814–834 (2006)
Margolin, A., Nemenman, I., Basso, K., Wiggins, C., Stolovitzky, G., Favera, R., Califano, R.A.: ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinform. 7 (2006)
Gardner, T.S., di Bernardo, D., Lorenz, D., Collins, J.J.: Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301, 102–105 (2003)
di Bernardo, D., Thompson, M., Gardner, T., Chobot, S., Eastwood, E., Wojtovich, A., Elliott, S., Schaus, S., Collins, J.: Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat. Biotechnol. 23, 377–383 (2005)
MacQueen, J.B.: Some Methods for classification and Analysis of Multivariate Observations. In: Proceedings of 5th Berkeley Symposium on Mathematical Statistics and Probability, pp. 281–297 (1967)
Gansner, E.R., North, S.C.: An open graph visualization system and its applications to software engineering. Softw. Pract. Exper. (1999)
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Fiannaca, A., Gaglio, S., La Rosa, M., Peri, D., Rizzo, R., Urso, A. (2011). A Knowledge Based Decision Support System for Bioinformatics and System Biology. In: Rizzo, R., Lisboa, P.J.G. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2010. Lecture Notes in Computer Science(), vol 6685. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21946-7_17
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DOI: https://doi.org/10.1007/978-3-642-21946-7_17
Publisher Name: Springer, Berlin, Heidelberg
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