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BioMed Research International
Volume 2013 (2013), Article ID 240175, 11 pages
http://dx.doi.org/10.1155/2013/240175
Review Article

The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database

1Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, BP 32, EL ALIA, Bab Ezzouar, Algiers, Algeria
2Environmental Microbiology, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK

Received 14 March 2013; Revised 11 July 2013; Accepted 13 August 2013

Academic Editor: Konstantinos Mavrommatis

Copyright © 2013 Okba Selama et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

The zipped file may be extracted in any directory in the computer but all files and the two folders should be extracted in the same directory so the scripts would function correctly. The scripts had been tested on Windows environment. Python 2.7 and Biopython 1.6 should be installed before running the scripts. To extract data from NCBI Nucleotide you should run “NCBI_Nucleotide_Tracker.py” for countries exception handling, run “NCBI_Nucleotide_Exception.py”. For the GBIF Database, only three countries are provided as an example in the folder “GBIF_Plus” for additional countries you may download them from GBIF website, the only data that should be extracted are these of taxonomy, no need for other metadata (Dataset, Geospatial) as described in the paper. Once all countries of interest are downloaded you may run “GBIF_Filter.py” to filter data. The results of this study are presented in: “country_all.txt” for NCBI Nucleotide Database, “gbif_Classification_2000_Plus.txt”, “absent_taxa_Classification_2000_Plus.txt”, and absent_taxa_Classification_2000_Plus_ex_All.txt” for GBIF Database. The final results are presented in “NCBI_GBIF_overall_data.xlsx”. Some errors that may occur during the script execution are presented in “error.txt” file.

  1. Supplementary Materials