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A systematic approach to modeling, capturing, and disseminating proteomics experimental data

Abstract

Both the generation and the analysis of proteome data are becoming increasingly widespread, and the field of proteomics is moving incrementally toward high-throughput approaches. Techniques are also increasing in complexity as the relevant technologies evolve. A standard representation of both the methods used and the data generated in proteomics experiments, analogous to that of the MIAME (minimum information about a microarray experiment) guidelines for transcriptomics, and the associated MAGE (microarray gene expression) object model and XML (extensible markup language) implementation, has yet to emerge. This hinders the handling, exchange, and dissemination of proteomics data. Here, we present a UML (unified modeling language) approach to proteomics experimental data, describe XML and SQL (structured query language) implementations of that model, and discuss capture, storage, and dissemination strategies. These make explicit what data might be most usefully captured about proteomics experiments and provide complementary routes toward the implementation of a proteome repository.

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Figure 1: Examples of the types of data generated by proteomics experiments.
Figure 2: The PEDRo UML class diagram provides a conceptual model of proteomics experiment data, which form the basis for the XML and relational schemas.
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Acknowledgements

Special thanks go to Francesco Brancia, Jenny Ho, and Sandy Yates for their critical appraisal of the Schema at various stages. This work was supported by a grant from the Investigating Gene Function (IGF) Initiative of the Biotechnology & Biological Sciences Research Council to S.G.O., N.W.P., A.B., S.G., S.H., P.C., and A.J.P.B. for the COGEME (Consortium for the Functional Genomics of Microbial Eukaryotes) program. D.B.K. thanks the BBSRC for financial support, also under the IGF initiative. K.L.G. is supported by the North West Regional e-Science centre (ESNW), within the UK eScience Programme. Many people have contributed their advice and expertise to the design of PEDRo, at various meetings formal and otherwise, notably attendees at the 2002 Proteomics Standards Initiative meeting of the Human Proteome Organisation at the European Bioinformatics Institute.

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Correspondence to Stephen G. Oliver.

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Taylor, C., Paton, N., Garwood, K. et al. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol 21, 247–254 (2003). https://doi.org/10.1038/nbt0303-247

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