Abstract
We propose an abstract model for scientific protocols, where several atomic operators are proposed for protocol composition. We distinguish two different layers associated with scientific protocols: design and implementation, and discuss the mapping between them. We illustrate our approach with a representative example and describe ProtocolDB, a scientific protocol repository currently in development. Our approach benefits scientists by allowing the archiving of scientific protocols with the collected data sets to constitute a scientific portfolio for the laboratory to query, compare and revise protocols.
An erratum to this chapter can be found at http://dx.doi.org/10.1007/11915034_125.
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References
Lawson, A.: Studying for Biology. Addison-Wesley, Reading (1995)
Stevens, R., Goble, C.A., Baker, P.G., Brass, A.: A classification of tasks in bioinformatics. Bioinformatics 17(1), 180–188 (2001)
Bartlett, J.C., Toms, E.G.: Developing a Protocol for Bioinformatics Analysis: An Integrated Information Behavior and Task Analysis Approach. Journal of the American Society for Information Science and Technology 56(5), 469–482 (2005)
Tröger, A., Fernandes, A.: A language for comprehensively supporting the in vitro experimental process in silico. In: Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2004), pp. 47–56 (2004)
Chen, I.M.A., Markowitz, V.M.: An overview of the object protocol model (opm) and the opm data management tools. Inf. Syst. 20(5), 393–418 (1995)
Ailamaki, A., Ioannidis, Y.E., Livny, M.: Scientific workflow management by database management. In: SSDBM, pp. 190–199 (1998)
Shankar, S., Kini, A., DeWitt, D.J., Naughton, J.: Integrating databases and workflow systems. SIGMOD Rec. 34(3), 5–11 (2005)
Oinn, T., Addis, M., Ferris, J., Marvin, D., Senger, M., Greenwood, M., Carver, T., Glover, K., Pocock, M.R., Wipat, A., Li, P.: Taverna: A tool for the composition and enactment of bioinformatics workflows. Bioinformatics Journal 20(17), 3045–3054 (2004)
Ludäscher, B., Altintas, I., Berkley, C., Higgins, D., Jaeger-Frank, E., Jones, M., Lee, E., Tao, J., Zhao, Y.: Scientific Workflow Management and the Kepler System. Concurrency and Computation: Practice & Experience, Special Issue on Scientific Workflows (to appear, 2005)
Ludäscher, B., Altintas, I., Gupta, A.: Compiling abstract scientific workflows into web service workflows. In: SSDBM, pp. 251–254. IEEE Computer Society, Los Alamitos (2003)
Medeiros, C., Alcazar, J., Digiampietri, L., Pastorello, G., Santanche, A., Torres, R., Madeira, E.: WOODSS and the Web: annotating and reusing scientific workflows. SIGMOD Record 34(3), 18–23 (2005)
Hashmi, N., Lee, S., Cummings, M.: Abstracting Workflows: Unifying Bioinformatics Task Conceptualization and Specification Through Semantic Web Services. In: W3C Semantic Web for Life Sciences position paper (2004)
Foster, I., Voeckler, J., Wilde, M., Zhao, Y.: Chimera: a virtual data system for representing, querying and automating data derivation. In: SSDBM, p. 37 (2002)
Zhao, Y., Dobson, J., Foster, I., Moreau, L., Wilde, M.: A notation and system for expressing and executing cleanly typed workflows on messy scientific data. ACM SIGMOD Record 34, 37–43 (2005)
Hidders, J., Kwasnikowska, N., Sroka, J., Tyszkiewicz, J., Van den Bussche, J.: Petri net + nested relational calculus = dataflow. Technical Report TR UA 2006-04, University of Antwerp, Belgium (2006)
Cohen-Boulakia, S., Davidson, S., Froidevaux, C., Lacroix, Z., Vidal, M.E.: Path-based systems to guide scientists in the maze of biological data sources. Journal of Bioinformatics and Computational Biology (to appear, 2006)
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Kwasnikowska, N., Chen, Y., Lacroix, Z. (2006). Modeling and Storing Scientific Protocols. In: Meersman, R., Tari, Z., Herrero, P. (eds) On the Move to Meaningful Internet Systems 2006: OTM 2006 Workshops. OTM 2006. Lecture Notes in Computer Science, vol 4277. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11915034_97
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DOI: https://doi.org/10.1007/11915034_97
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