The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database
Databases are an essential tool and resource within the field of bioinformatics. The primary aim of this study was to generate an overview of global bacterial biodiversity and biogeography using available data from the two largest public online databases, NCBI Nucleotide and GBIF. The secondary aim...
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ftdoajarticles:oai:doaj.org/article:14966a4a86134594921516d1fc6973a5 2023-05-15T13:34:44+02:00 The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database Okba Selama Phillip James Farida Nateche Elizabeth M. H. Wellington Hocine Hacène 2013-01-01T00:00:00Z https://doi.org/10.1155/2013/240175 https://doaj.org/article/14966a4a86134594921516d1fc6973a5 EN eng Hindawi Limited http://dx.doi.org/10.1155/2013/240175 https://doaj.org/toc/2314-6133 https://doaj.org/toc/2314-6141 2314-6133 2314-6141 doi:10.1155/2013/240175 https://doaj.org/article/14966a4a86134594921516d1fc6973a5 BioMed Research International, Vol 2013 (2013) Medicine R article 2013 ftdoajarticles https://doi.org/10.1155/2013/240175 2022-12-31T04:02:55Z Databases are an essential tool and resource within the field of bioinformatics. The primary aim of this study was to generate an overview of global bacterial biodiversity and biogeography using available data from the two largest public online databases, NCBI Nucleotide and GBIF. The secondary aim was to highlight the contribution each geographic area has to each database. The basis for data analysis of this study was the metadata provided by both databases, mainly, the taxonomy and the geographical area origin of isolation of the microorganism (record). These were directly obtained from GBIF through the online interface, while E-utilities and Python were used in combination with a programmatic web service access to obtain data from the NCBI Nucleotide Database. Results indicate that the American continent, and more specifically the USA, is the top contributor, while Africa and Antarctica are less well represented. This highlights the imbalance of exploration within these areas rather than any reduction in biodiversity. This study describes a novel approach to generating global scale patterns of bacterial biodiversity and biogeography and indicates that the Proteobacteria are the most abundant and widely distributed phylum within both databases. Article in Journal/Newspaper Antarc* Antarctica Directory of Open Access Journals: DOAJ Articles BioMed Research International 2013 1 11 |
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English |
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Medicine R |
spellingShingle |
Medicine R Okba Selama Phillip James Farida Nateche Elizabeth M. H. Wellington Hocine Hacène The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database |
topic_facet |
Medicine R |
description |
Databases are an essential tool and resource within the field of bioinformatics. The primary aim of this study was to generate an overview of global bacterial biodiversity and biogeography using available data from the two largest public online databases, NCBI Nucleotide and GBIF. The secondary aim was to highlight the contribution each geographic area has to each database. The basis for data analysis of this study was the metadata provided by both databases, mainly, the taxonomy and the geographical area origin of isolation of the microorganism (record). These were directly obtained from GBIF through the online interface, while E-utilities and Python were used in combination with a programmatic web service access to obtain data from the NCBI Nucleotide Database. Results indicate that the American continent, and more specifically the USA, is the top contributor, while Africa and Antarctica are less well represented. This highlights the imbalance of exploration within these areas rather than any reduction in biodiversity. This study describes a novel approach to generating global scale patterns of bacterial biodiversity and biogeography and indicates that the Proteobacteria are the most abundant and widely distributed phylum within both databases. |
format |
Article in Journal/Newspaper |
author |
Okba Selama Phillip James Farida Nateche Elizabeth M. H. Wellington Hocine Hacène |
author_facet |
Okba Selama Phillip James Farida Nateche Elizabeth M. H. Wellington Hocine Hacène |
author_sort |
Okba Selama |
title |
The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database |
title_short |
The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database |
title_full |
The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database |
title_fullStr |
The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database |
title_full_unstemmed |
The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database |
title_sort |
world bacterial biogeography and biodiversity through databases: a case study of ncbi nucleotide database and gbif database |
publisher |
Hindawi Limited |
publishDate |
2013 |
url |
https://doi.org/10.1155/2013/240175 https://doaj.org/article/14966a4a86134594921516d1fc6973a5 |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_source |
BioMed Research International, Vol 2013 (2013) |
op_relation |
http://dx.doi.org/10.1155/2013/240175 https://doaj.org/toc/2314-6133 https://doaj.org/toc/2314-6141 2314-6133 2314-6141 doi:10.1155/2013/240175 https://doaj.org/article/14966a4a86134594921516d1fc6973a5 |
op_doi |
https://doi.org/10.1155/2013/240175 |
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BioMed Research International |
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2013 |
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1 |
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11 |
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1766056808105902080 |