Abstract
Cross-Omics studies aimed at characterizing a specific phenotype on multiple levels are entering the scientific literature, and merging e.g. transcriptomics and proteomics data clearly promises to improve Omics data interpretation. Also for Systems Biology the integration of multi-level Omics profiles (also across species) is considered as central element. Due to the complexity of each specific Omics technique, specialization of experimental and bioinformatics research groups have become necessary, in turn demanding collaborative efforts for effectively implementing cross-Omics. This setting imposes specific emphasis on data sharing platforms for Omics data integration and cross-Omics data analysis and interpretation. Here we describe a software concept and methodology fostering Omics data sharing in a distributed team setting which next to the data management component also provides hypothesis generation via inference, semantic search, and community functions. Investigators are supported in data workflow management and interpretation, supporting the transition from a collection of heterogeneous Omics profiles into an integrated body of knowledge.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Sagotsky, J. A., Zhang, L., Wang, Z., Martin, S., and Deisboeck, T. S. (2008) Life Sciences and the web: a new era for collaboration. Mol Syst Biol 4, 201.
Waldrop, M. (2008) Big data: Wikiomics. Nature 455, 22–25.
Ruttenberg, A., Clark, T., Bug, W., Samwald, M., Bodenreider, O., Chen, H., Doherty, D., Forsberg, K., Gao, Y., Kashyap, V., Kinoshita, J., Luciano, J., Marshall, M. S., Ogbuji, C., Rees, J., Stephens, S., Wong, G. T., Wu, E., Zaccagnini, D., Hongsermeier, T., Neumann, E., Herman, I., and Cheung, K. (2007) Advancing translational research with the Semantic Web. BMC Bioinformatics 8 Suppl 3, S2.
Stein, L. D. (2008) Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges. Nat Rev Genet 9, 678–88.
Disis, M. L., and Slattery, J. T. (2010) The road we must take: multidisciplinary team science. Sci Transl Med 2, 22–9.
Nelson, B. (2009) Data sharing: empty archives. Nature 461, 160–3.
Moore, R. (2000) Data management systems for scientific applications. IFIP Conf Proc 188, 273–84.
Bian, X., Gurses, L., Miller, S., Boal, T., Mason, W., Misquitta, L., Kokotov, D., Swan, D., Duncan, M., Wysong, R., Klink, A., Johnson, A., Klemm, J., Fontenay, G., Basu, A., Colbert, M., Liu, J., Hadfield, J., Komatsoulis, G., Duvall, P., Srinivasa, R., and Parnell, T. (2009) Data submission and curation for caArray, a standard based microarray data repository system. Nat Proc doi:10.1038/npre.2009.3138.1.
Edgar, R., Domrachev, M., and Lash, A. E. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30, 207–10.
Parkinson, H., Kapushesky, M., Kolesnikov, N., Rustici, G., Shojatalab, M., Abeygunawardena, N., Berube, H., Dylag, M., Emam, I., Farne, A., Holloway, E., Lukk, M., Malone, J., Mani, R., Pilicheva, E., Rayner, T. F., Rezwan, F., Sharma, A., Williams, E., Bradley, X. Z., Adamusiak, T., Brandizi, M., Burdett, T., Coulson, R., Krestyaninova, M., Kurnosov, P., Maguire, E., Neogi, S. G., Rocca-Serra, P., Sansone, S., Sklyar, N., Zhao, M., Sarkans, U., and Brazma, A. (2009) ArrayExpress update – from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res 37, D868–72.
Hubble, J., Demeter, J., Jin, H., Mao, M., Nitzberg, M., Reddy, T. B. K., Wymore, F., Zachariah, Z. K., Sherlock, G., and Ball, C. A. (2009) Implementation of GenePattern within the Stanford Microarray Database. Nucleic Acids Res 37, D898–901.
Gray, J., Liu, D. T., Nieto-Santisteban, M., Szalay, A., DeWitt, D. J., and Heber, G. (2005) Scientific data management in the coming decade. ACM SIGMOD Record 34, 34–41.
National Information Standards Organization (U.S.). (2004) Understanding metadata. NISO Press, Bethesda, MD.
Wuchty, S., Jones, B. F., and Uzzi, B. (2007) The increasing dominance of teams in production of knowledge. Science 316, 1036–39.
Gray, N. S. (2006) Drug discovery through industry-academic partnerships. Nat Chem Biol 2, 649–53.
Project Management Institute (2008). A Guide to the Project Management Body of Knowledge: PMBoK Guide, Fourth Edition, PMI.
Bodenreider, O. (2004) The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res 32, D267–70.
Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L. J., Eilbeck, K., Ireland, A., Mungall, C. J., Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S., Scheuermann, R. H., Shah, N., Whetzel, P. L., and Lewis, S. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25, 1251–55.
Das, S., Girard, L., Green, T., Weitzman, L., Lewis-Bowen, A., and Clark, T. (2009) Building biomedical web communities using a semantically aware content management system. Brief Bioinformatics 10, 129–38.
Acknowledgments
The research leading to these results has received funding from the European Community’s Seventh Framework Programme under grant agreement n° HEALTH-F5-2008-202222.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Wiesinger, M. et al. (2011). Data and Knowledge Management in Cross-Omics Research Projects. In: Mayer, B. (eds) Bioinformatics for Omics Data. Methods in Molecular Biology, vol 719. Humana Press. https://doi.org/10.1007/978-1-61779-027-0_4
Download citation
DOI: https://doi.org/10.1007/978-1-61779-027-0_4
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-026-3
Online ISBN: 978-1-61779-027-0
eBook Packages: Springer Protocols