Abstract
Research in life sciences faces increasing amounts of cross-domain data, also kown as “big data”. This has notable effects on IT-departments and the dry lab desk alike. In this paper, we report on experiences from a decade of data management in a plant research institute. We explain the switch from personally managed files and heterogeneous information systems towards a centrally organised storage management. In particular, we discuss lessons that were learned within the last decade of productive research, data generation and software development from the perspective of a modern plant research institute and present the results of a strategic realignment of the data management infrastructure. Finally, we summarise the challenges which were solved and the questions which are still open.
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
Preview
Unable to display preview. Download preview PDF.
References
Arend, D., Lange, M., Colmsee, C., Flemming, S., Chen, J., Scholz, U.: The e!DAL JAVA-API: Store, Share and Cite Primary Data in Life Sciences. In: IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Philadelphia, U.S.A., October 4-7, pp. 511–515 (2012)
Colmsee, C., Mascher, M., Czauderna, T., Hartmann, A., Schlüter, U., Zellerhoff, N., Schmitz, J., Bräutigam, A., Pick, T.R., Alter, P., Gahrtz, M., Witt, S., Fernie, A., Börnke, F., Fahnenstich, H., Bucher, M., Dresselhaus, T., Weber, A.P.M., Schreiber, F., Scholz, U., Sonnewald, U.: OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize. BMC Plant Biology 12(1), e245 (2012)
Colmsee, C., Keller, E.R.J., Zanke, C., Senula, A., Funke, T., Oppermann, M., Weise, S., Scholz, U.: The Garlic and Shallot Core Collection image database of IPK presenting two vegetatively maintained crops in the Federal ex situ Genebank for Agricultural and Horticultural Crops at Gatersleben, Germany. Genetic Resources and Crop Evolution 59(7), 1407–1415 (2012)
DataCite Consortium: DataCite, http://datacite.org/ (accessed January 2014)
Grbavac, I., Koepler, O., Dohmeyer-Fischer, S., Fels, G., Sens, I., Brase, J.: Embedded infrastructure for primary data in chemistry. Journal of Cheminformatics 2(suppl. 1), P8 (2010)
Knüpffer, H., Ochsmann, J., Biermann, N.: The “Mansfeld Database” in its national and international context. Schriften zu Genetischen Ressourcen 22, 32–34 (2003)
Kuenne, C., Grosse, I., Matthies, I., Scholz, U., Sretenovic-Rajicic, T., Stein, N., Stephanik, A., Steuernagel, B., Weise, S.: Using Data Warehouse Technology in Crop Plant Bioinformatics. Journal of Integrative Bioinformatics 4(1), e88 (2007)
Künne, C., Lange, M., Funke, T., Miehe, H., Grosse, I., Scholz, U.: CR–EST: a resource for crop ESTs. Nucleic Acids Research 33(suppl.1), D619–D621 (2005)
Neuroth, H., Oßwald, A., Scheffel, R., Strathmann, S., Huth, K.: nestor Handbuch: Eine kleine Enzyklopädie der digitalen Langzeitarchivierung, Version 2.3 (2010), http://nestor.sub.uni-goettingen.de/handbuch/index.php (accessed January 2014)
Schadt, E.E., Linderman, M.D., Sorenson, J., Lee, L., Nolan, G.P.: Computational solutions to large-scale data management and analysis. Nature Reviews Genetics 11(9), 647–657 (2010)
Schreiber, F., Colmsee, C., Czauderna, T., Grafahrend-Belau, E., Hartmann, A., Junker, A., Junker, B.H., Klapperstück, M., Scholz, U., Weise, S.: MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Research 40(D1), D1173–D1177 (2012)
Swedlow, J.R., Zanetti, G., Best, C.: Channeling the data deluge. Nat. Methods 8(6), 463–465 (2011)
Thaller, M.: Das Digitale Archiv NRW in der Praxis. Verlag Dr. Kovac (2013)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer International Publishing Switzerland
About this paper
Cite this paper
Arend, D. et al. (2014). Data Management Experiences and Best Practices from the Perspective of a Plant Research Institute. In: Galhardas, H., Rahm, E. (eds) Data Integration in the Life Sciences. DILS 2014. Lecture Notes in Computer Science(), vol 8574. Springer, Cham. https://doi.org/10.1007/978-3-319-08590-6_4
Download citation
DOI: https://doi.org/10.1007/978-3-319-08590-6_4
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-08589-0
Online ISBN: 978-3-319-08590-6
eBook Packages: Computer ScienceComputer Science (R0)