Abstract
In this paper we present a novel knowledge-based approach that aims at helping scientists to face and resolve a large number of proteomics problem. The system architecture is based on an ontology to model the knowledge base, a reasoner that starting from the user’s request and a set of rules builds the workflow of tasks to be done, and an executor that runs the algorithms and software scheduled by the reasoner. The system can interact with the user showing him intermediate results and several options in order to refine the workflow and supporting him to choose among different forks. Thanks to the presence of the knowledge base and the modularity provided by the ontology, the system can be enriched with new expertise in order to deal with other proteomic or bioinformatics issues. Two possible application scenarios are presented.
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References
Cios, K.J., Shin, I., Wedding II, D.K.: Bayesian Approach to Dealing with Uncertainties for Detection of Coronary Artery Stenosis Using a Knowledge Based System. IEEE Engineering in Medicine and Biology 8(4), 53–58 (1989)
Lhotska, L., Marik, V., Vlcek, T.: Medical applications of enhanced rule-based expert systems. International Journal of Medical Informatics 63(1), 61–75 (2001)
Lin, H.N., Chang, J.M., Wu, K.P., Sung, T.Y., Hsu, W.L.: HYPROSP II: a knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence. Bioinformatics 21(15), 3227–3233 (2005)
Wu, L.C., Lee, J.X., Huang, H.D., Liu, B.J., Horng, J.T.: An expert system to predict protein thermostability using decision tree. Expert Systems with Applications 36(5), 9007–9014 (2009)
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)
Bartocci, E., Corradini, F., Merelli, E., Schortichini, L.: BioWMS: a Web-based Workflow Management System for Bioinformatics. BMC Bioinformatics 8(1) (2007)
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)
Larranaga, P., Calvo, B., Santana, R., Bielza, C., Galdiano, J., Inza, I., Lozano, J.A., Armananzas, R., Santafe, G., Perez, A., Robles, V.: Machine learning in bioinformatics. Briefing in bioinformatics 7(1), 86–112 (2005)
Robles, V., Larraaga, P., Pea, J.M., Menasalvas, E., Prez, M.S., Herves, V.: Bayesian networks as consensed voting system in the construction of a multi-classifier for protein secondary structure prediction. Artificial Intelligence in Medicine 31, 117–136 (2004)
Yamakawa, H., Maruhashi, K., Nakao, Y.: Predicting Types of Protein-Protein Interactions Using a Multiple-Instance Learning Model. In: Washio, T., Satoh, K., Takeda, H., Inokuchi, A. (eds.) JSAI 2006. LNCS (LNAI), vol. 4384, pp. 42–53. Springer, Heidelberg (2007)
Hanisch, D., Fundel, K., Mevissen, H.T., Zimmer, R., Fluck, J.: ProMiner: rule-based protein and gene entity recognition. BMC Bioinformatics 6(suppl. 1), S14 (2005)
Whisstock, J.C., Lesk, A.M.: Prediction of protein function from protein sequence and structure. Quarterly Reviews of Biophysics 36(3), 307–340 (2003)
Su, E.C., Chiu, H.S., Lo, A., Hwang, J.K., Sung, T.Y., Hsu, W.L.: Protein subcellular localization prediction based on compartment-specific features and structure conservation. BMC Bioinformatics 8 (2007)
CASP: Critical Assessment of Techniques for Protein Structure Prediction, http://predictioncenter.org/index.cgi
Zemla, A.: LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Research 31(13), 3370–3374 (2003)
Zhang, Y., Skolnick, J.: Scoring function for automated assessment of protein structure template quality. Proteins 57, 702–710 (2004)
Altschul, S.F., et al.: Gapped Blast and PSI-Blast: a new generation of protein database search programs. Nucleic Acids Research 25(17), 3389–3402 (1997)
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/
Eriksson, H.: Using JessTab to integrate Protegé and Jess. IEEE Intelligent Systems 18(2), 43–50 (2003)
Murzin, A.G., Brenner, S.E., Hubbard, T., Chothia, C.: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536–540 (1995)
Orengo, C.A., Michie, A.D., Jones, D.T., Swindells, M.B., Thornton, J.M.: CATH: A Hierarchic Classification of Protein Domain Structures. Structure 5, 1093–1108 (1997)
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data Bank. Nucleic Acids Research 28, 235–242 (2000), http://www.pdb.org
Natale, D.A., Arighi, C.N., Barker, W.C., Blake, J., Chang, T., Hu, Z., Liu, H., Smith, B., Wu, C.H.: Framework for a Protein Ontology. BMC Bioinformatics 8(suppl. 9), S1 (2007)
Bairoch, A., Boeckmann, B., Ferro, S., Gasteiger, E.: Swiss-Prot: Juggling between evolution and stability. Brief. Bioinformatics 5, 39–55 (2004)
The UniProt Consortium: The Universal Protein Resource (UniProt). Nucleic Acids Res. 36, D190–D195 (2008)
Wiederstein, M., Sippl, M.J.: ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research 35, W407–W410 (2007)
Wang, Z., Tegge, A.N., Cheng, J.: Evaluating the absolute quality of a single protein model using structural features and support vector machines. Proteins 75, 638–645 (2009)
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Fiannaca, A., Gaglio, S., La Rosa, M., Peri, D., Rizzo, R., Urso, A. (2010). A Proposed Knowledge Based Approach for Solving Proteomics Issues. In: Masulli, F., Peterson, L.E., Tagliaferri, R. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2009. Lecture Notes in Computer Science(), vol 6160. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-14571-1_23
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DOI: https://doi.org/10.1007/978-3-642-14571-1_23
Publisher Name: Springer, Berlin, Heidelberg
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