Modeling and Storing Scientific Protocols

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.

[1]  Matthew R. Pocock,et al.  Taverna: a tool for the composition and enactment of bioinformatics workflows , 2004, Bioinform..

[2]  Yong Zhao,et al.  Chimera: a virtual data system for representing, querying, and automating data derivation , 2002, Proceedings 14th International Conference on Scientific and Statistical Database Management.

[3]  Anton E. Lawson.  Studying for biology , 1997 .

[4]  Ricardo da Silva Torres,et al.  WOODSS and the Web: annotating and reusing scientific workflows , 2005, SGMD.

[5]  David J. DeWitt,et al.  Integrating databases and workflow systems , 2005, SGMD.

[6]  Sung Lee,et al.  Abstracting Workflows: Unifying Bioinformatics Task Conceptualization and Specification Through Semantic Web Services , 2004 .

[7]  Maria-Esther Vidal,et al.  Path-based Systems to Guide Scientists in the Maze of Biological Data Sources , 2006, J. Bioinform. Comput. Biol..

[8]  Edward A. Lee,et al.  Scientific workflow management and the Kepler system , 2006, Concurr. Comput. Pract. Exp..

[9]  Carole A. Goble,et al.  A classification of tasks in bioinformatics , 2001, Bioinform..

[10]  Elaine Toms,et al.  Developing a protocol for bioinformatics analysis: An integrated information behavior and task analysis approach , 2005, J. Assoc. Inf. Sci. Technol..

[11]  Elaine G. Toms,et al.  Developing a protocol for bioinformatics analysis: An integrated information behavior and task analysis approach: Research Articles , 2005 .

[12]  Yong Zhao,et al.  A notation and system for expressing and executing cleanly typed workflows on messy scientific data , 2005, SGMD.

[13]  I-Min A Chen,et al.  An Overview of the Object-Protocol Model (OPM) and OPM Data Management Tools , 1995, Inf. Syst..

[14]  Anastasia Ailamaki,et al.  Scientific workflow management by database management , 1998, Proceedings. Tenth International Conference on Scientific and Statistical Database Management (Cat. No.98TB100243).

[15]  Alvaro A. A. Fernandes,et al.  A language for comprehensively supporting the in vitro experimental process in silico , 2004, Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering.

[16]  Bertram Ludäscher,et al.  Compiling abstract scientific workflows into Web service workflows , 2003, 15th International Conference on Scientific and Statistical Database Management, 2003..

[17]  Jacek Sroka,et al.  Petri Net + Nested Relational Calculus = Dataflow , 2005, OTM Conferences.