Sample database of the Centre for Polar Ecology - Database design and data management

Vol.4,No.2(2014)

Abstract

The increasing number of observations and samples led to development of systems for data storage and management. In this paper, design and experience with data manage-ment of the Sample database (SampleDTB) used in the Centre for Polar Ecology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic, is presented. The SampleDTB was designed for microbiological, phycological or hydro-biological data. The SampleDTB consists of data tables including defined lists of cli-matic zones, habitats, communities and taxons, specific queries for datasets determina-tion and searches, forms for filling in samples and reports. The data tables contain detailed information on site, its environment, types of habitats and communities, in-cluding data on taxonomic diversity. The queries provide source data for reports or serve for searches for specific taxon, sample etc. Forms are used primarily for data entry or modifications. The reports provide summaries and charts for export, either for whole data set or for specific datasets. Data management resulted in system of sample numbering, site specification, and system for photographs storage. Possible future development will be focused on on-line data access, biovolume and diversity indices calculation, laboratory sample processing, and connection to culture collection database.


Keywords:
database; species diversity; ecology
References

Benson, D., Lipman, D. J. and Ostell, J. (1993): GenBank. Nucleic Acids Research, 21: 2963-2965

Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T., Garrity, G. M. and Tiedje, J. M. (2009): The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Research, 37: D141-D145.

Ettl, H., Gärtner, G. (2014): Syllabus der Boden-, Luft- und Flechtenalgen. Springer, Berlin Heidelberg, 773 p. 2nd edition.

Hoham, R. W., Mullet, J. E. (1978): Chloromonas nivalis (Chod.) Hoh. & Mull. comb. spec. nov., and additional comments on the snow alga, Scotiella. Phycologia, 17: 106-107.

Jones, M. B., Schildhauer, M. P., Reichman, O. J. and Bowers, S. (2006): The new bioinformatics: integrating ecological data from the gene to the biosphere. Annual Review of Ecology, Evolution, and Systematics, 37: 519-544.

Khalsa, S. J. S., Yarmey, L. (2014): Data management challenges in polar ecology. In: Kavan, J. and Bernardová, A. (eds.): Polar Ecology Conference 2014. Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, pp. 70.

Klimešová, J., De Bello, F. (2009): CLOPLA: the database of clonal and bud bank traits of Central European flora. Journal of Vegetation Science, 20: 511-516.

Kol, E. (1968): Kryobiologie. Biologie und Limnologie des Schnees und Eises I. Cryovegetation. E. Schweizerbart'sche Verlagbuchhandlung, Stuttgart, 220 p.

Komárek, J., Anagnostidis, K. (1999): Süßwasserflora von Mitteleuropa 19/1. Cyanoprokaryota. 1.Teil: Chroococcales. Gustav Fischer Verlag, Jena, 548 p.

Komárek, J., Anagnostidis, K. (2005): Süßwasserflora von Mitteleuropa 19/2. Cyanoprokaryota. 2.Teil: Oscillatoriales. Elsevier/Spektrum, Heidelberg, 759 p.

Komárek, J. (2013): Süßwasserflora von Mitteleuropa 19/3. Cyanoprokaryota. 3.Teil: Heterocytous genera. Springer, Heildelberg, 1131 p.

Kvíderová, J., Elster, J. (2013): Standardized algal growth potential and/or algal primary production rates of maritime Antarctic stream waters (King George Island, South Shetlands). Polar Research, 32: 11191, 17p. DOI: 10.3402/polar.v32i0.11191.

Magurran, A. E. (1988): Ecological diversity and its measurement. Springer-Science+Business Media, B.Y., 179 p.

Peet, R. K., Lee, M. T., Jennings, M. D. and Faber-Langendoen, D. (2012): VegBank: a permanent, open-access archive for vegetation plot data. Biodiversity & Ecology, 4: 233-241.

Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., Sahl, J. W., Stres, B., Thallinger, G. G., Van Horn, D. J. and Weber, C. F. (2009): Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Applied and Environmental Microbiology, 75: 7537-7541.

Sun, J., Liu, D. (2003): Geometric models for calculating cell biovolume and surface area for phytoplankton. Journal of Plankton Research, 25: 1331-1346.

Ter Braak, C. J. F., Šmilauer, P. (2012): Canoco reference manual and user's guide: software for ordination, version 5.0. Microcomputer Power, Ithaca, USA, 496 p.

Watanabe, M., Shimizu, A. and Satake, K. (1992): NIES-Microbial Culture Collection at the National Institute of Environmental Studies: Cryopreservation and database of culture strains of microalgae. Proceedings of Symposium on Culture Collection of Algae. NIES, Tsukuba, Japan, pp. 33-41.

Žáková, Z. (1980): Trofický potenciál a jeho aplikace ve vodním hospodářství [Trophic potential and its application in water management]. VÚV, Praha, 116 p.,

Metrics

0


175

Views

21

PDF views