The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database
Identifieur interne : 000213 ( Main/Exploration ); précédent : 000212; suivant : 000214The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database
Auteurs : Okba Selama [Algérie] ; Phillip James [Royaume-Uni] ; Farida Nateche [Algérie] ; Elizabeth M. H. Wellington [Royaume-Uni] ; Hocine Hacène [Algérie]Source :
- BioMed Research International [ 2314-6133 ] ; 2013.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- genetics : Bacteria.
- Biodiversity, Databases, Nucleic Acid, Phylogeography, Search Engine.
Abstract
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
Url:
DOI: 10.1155/2013/240175
PubMed: 24228241
PubMed Central: 3818805
Affiliations:
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Le document en format XML
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H." last="Wellington">Elizabeth M. H. Wellington</name><affiliation wicri:level="1"><nlm:aff id="I2">Environmental Microbiology, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Environmental Microbiology, School of Life Sciences, University of Warwick, Coventry CV4 7AL</wicri:regionArea></affiliation></author><author><name sortKey="Hacene, Hocine" sort="Hacene, Hocine" uniqKey="Hacene H" first="Hocine" last="Hacène">Hocine Hacène</name><affiliation wicri:level="1"><nlm:aff id="I1">Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, BP 32, EL ALIA, Bab Ezzouar, Algiers, Algeria</nlm:aff><country xml:lang="fr">Algérie</country><wicri:regionArea>Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, BP 32, EL ALIA, Bab Ezzouar, Algiers</wicri:regionArea></affiliation></author></analytic><series><title level="j">BioMed Research International</title><idno type="ISSN">2314-6133</idno><idno type="eISSN">2314-6141</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacteria (genetics)</term><term>Biodiversity (MeSH)</term><term>Databases, Nucleic Acid (MeSH)</term><term>Phylogeography (MeSH)</term><term>Search Engine (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bactéries (génétique)</term><term>Bases de données d'acides nucléiques (MeSH)</term><term>Biodiversité (MeSH)</term><term>Moteur de recherche (MeSH)</term><term>Phylogéographie (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Bactéries</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biodiversity</term><term>Databases, Nucleic Acid</term><term>Phylogeography</term><term>Search Engine</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données d'acides nucléiques</term><term>Biodiversité</term><term>Moteur de recherche</term><term>Phylogéographie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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 <italic>E-utilities</italic> and <italic>Python</italic> 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 <italic>Proteobacteria</italic> are the most abundant and widely distributed phylum within both databases.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Martiny, Jbh" uniqKey="Martiny J">JBH Martiny</name></author><author><name sortKey="Bohannan, Bjm" uniqKey="Bohannan B">BJM Bohannan</name></author><author><name sortKey="Brown, Jh" uniqKey="Brown J">JH Brown</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cox, Cb" uniqKey="Cox C">CB Cox</name></author><author><name sortKey="Moore, Pd" uniqKey="Moore P">PD Moore</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brown, Jh" uniqKey="Brown J">JH Brown</name></author><author><name sortKey="Riddle, Br" uniqKey="Riddle B">BR Riddle</name></author><author><name sortKey="Lomolino, 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Cottenie</name></author><author><name sortKey="Muylaert, K" uniqKey="Muylaert K">K Muylaert</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Horner Devine, Mc" uniqKey="Horner Devine M">MC Horner-Devine</name></author><author><name sortKey="Silver, Jm" uniqKey="Silver J">JM Silver</name></author><author><name sortKey="Leibold, Ma" uniqKey="Leibold M">MA Leibold</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Remsen, D" uniqKey="Remsen D">D Remsen</name></author><author><name sortKey="Ko, B" uniqKey="Ko B">B Ko</name></author><author><name sortKey="Chavan, V" uniqKey="Chavan V">V Chavan</name></author><author><name sortKey="Raymond, M" uniqKey="Raymond M">M Raymond</name></author></analytic></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Algérie</li><li>Royaume-Uni</li></country></list><tree><country name="Algérie"><noRegion><name sortKey="Selama, Okba" sort="Selama, Okba" uniqKey="Selama O" first="Okba" last="Selama">Okba Selama</name></noRegion><name sortKey="Hacene, Hocine" sort="Hacene, Hocine" uniqKey="Hacene H" first="Hocine" last="Hacène">Hocine Hacène</name><name sortKey="Nateche, Farida" sort="Nateche, Farida" uniqKey="Nateche F" first="Farida" last="Nateche">Farida Nateche</name></country><country name="Royaume-Uni"><noRegion><name sortKey="James, Phillip" sort="James, Phillip" uniqKey="James P" first="Phillip" last="James">Phillip James</name></noRegion><name sortKey="Wellington, Elizabeth M H" sort="Wellington, Elizabeth M H" uniqKey="Wellington E" first="Elizabeth M. H." last="Wellington">Elizabeth M. H. Wellington</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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