GELI: A data model for the representation of a gel electrophoresis experiment

Background: The numerous methods and techniques employed in proteomics investigations generate vast quantities of heterogeneous data, both results and provenance. A standard representation of proteomics data and techniques is urgently required in order to document a proteomics investigation. A standard representation will facilitate data exchange, verification and further analysis, and provide a standard repository format for proteomics. Gel electrophoresis can form an integral component of a proteomic investigation, and to date the is not a model or markup language that provides a structure to accurately record a complete gel electrophore experiment from sample application through to image acquisition and image analysis. Results: We propose a data model to represent a gel electrophoresis experiment. The Gel ELectrophoresis Information (GELI) model captures the data associated with a gel electrophoresis experiment. GELI models the electrophoresis techniques of onedimensional, two-dimensional and difference-gel electrophoresis; from sample application and image acquisition through to image analysis. We have designed an implementation independent Unified Modelling Language (UML) model of GELI. An eXtensible Markup Language (XML) schema has been derived from the UML model to facilitate data exchange. Conclusions: The proposed GELI-UML and GELI XML-schema (GELI-ML) models represent and facilitate the transmission of the information generated in gel electrophoresis experiments. The models are available at http://bioinf.ncl.ac.uk/proteomics/geli/ and can be easily extended to represent further electrophoresis techniques. © 2005 University of Newcastle upon Tyne. Printed and published by the University of Newcastle upon Tyne, Computing Science, Claremont Tower, Claremont Road, Newcastle upon Tyne, NE1 7RU, England. Bibliographical details GIBSON, F., WIPAT, A., POCOCK, M., MORRIS, N.. GELI: A data model for the representation of a gel electrophoresis experiment [By] F. Gibson, A. Wipat, M. Pocock and N. Morris Newcastle upon Tyne: University of Newcastle upon Tyne: Computing Science, 2005. (University of Newcastle upon Tyne, Computing Science, Technical Report Series, No. CS-TR-942) Added entries UNIVERSITY OF NEWCASTLE UPON TYNE Computing Science. Technical Report Series. CS-TR-942 Abstract Background: The numerous methods and techniques employed in proteomics investigations generate vast quantities of heterogeneous data, both results and provenance. A standard representation of proteomics data and techniques is urgently required in order to document a proteomics investigation. A standard representation will facilitate data exchange, verification and further analysis, and provide a standard repository format for proteomics. Gel electrophoresis can form an integral component of a proteomic investigation, and to date the is not a model or markup language that provides a structure to accurately record a complete gel electrophore experiment from sample application through to image acquisition and image analysis. Results: We propose a data model to represent a gel electrophoresis experiment. The Gel ELectrophoresis Information (GELI) model captures the data associated with a gel electrophoresis experiment. GELI models the electrophoresis techniques of one-dimensional, two-dimensional and difference-gel electrophoresis; from sample application and image acquisition through to image analysis. We have designed an implementation independent Unified Modelling Language (UML) model of GELI. An eXtensible Markup Language (XML) schema has been derived from the UML model to facilitate data exchange. Conclusions: The proposed GELI-UML and GELI XML-schema (GELI-ML) models represent and facilitate the transmission of the information generated in gel electrophoresis experiments. The models are available at http://bioinf.ncl.ac.uk/proteomics/geli/ and can be easily extended to represent further electrophoresis techniques.Background: The numerous methods and techniques employed in proteomics investigations generate vast quantities of heterogeneous data, both results and provenance. A standard representation of proteomics data and techniques is urgently required in order to document a proteomics investigation. A standard representation will facilitate data exchange, verification and further analysis, and provide a standard repository format for proteomics. Gel electrophoresis can form an integral component of a proteomic investigation, and to date the is not a model or markup language that provides a structure to accurately record a complete gel electrophore experiment from sample application through to image acquisition and image analysis. Results: We propose a data model to represent a gel electrophoresis experiment. The Gel ELectrophoresis Information (GELI) model captures the data associated with a gel electrophoresis experiment. GELI models the electrophoresis techniques of one-dimensional, two-dimensional and difference-gel electrophoresis; from sample application and image acquisition through to image analysis. We have designed an implementation independent Unified Modelling Language (UML) model of GELI. An eXtensible Markup Language (XML) schema has been derived from the UML model to facilitate data exchange. Conclusions: The proposed GELI-UML and GELI XML-schema (GELI-ML) models represent and facilitate the transmission of the information generated in gel electrophoresis experiments. The models are available at http://bioinf.ncl.ac.uk/proteomics/geli/ and can be easily extended to represent further electrophoresis techniques. About the author Frank Gibson is a PhD student at the School of Computing Science, University of Newcastle. Anil Wipat joined the School of Computing Science in 2001 as a Lecturer in Bioinformatics. Anil is the degree programme director for the recently established MRes in Bioinformatics at Newcastle University. Matthew Pocock is a Research Associate for the School of Computing Science at the University of Newcastle. Suggested keywords DATA MODEL, GEL ELECTROPHORESIS, UML, XML, PROTEOMICS, DATA STANDARDS, DATA FORMAT GELI: A data model for the representation of a gel electrophoresis experiment Frank Gibson, Anil Wipat , Matthew Pocock and Nicholas J Morris Institute for Cell and Molecular Biosciences, The Medical School, University of Newcastle, Framlington Place, Newcastle upon Tyne NE2 4HH, UK School of Computing Science, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK Email: Frank Gibson [email protected]; Anil Wipat [email protected]; Matthew Pocock [email protected]; Nicholas J [email protected]; ∗Corresponding author