BacDive

BacDive
Content
Description	information about bacterial and archaeal strains
Data types; captured	metadata
Contact
Research center	Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH
Primary citation	PMID 26424852
Release date	2012
Access
Website	http://bacdive.dsmz.de/
Web service URL	http://bacdive.dsmz.de/api/

BacDive (the Bacterial Diversity Metadatabase) is a bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity.

Introduction

BacDive is a resource for different kind of metadata like taxonomy, morphology, physiology, environment and molecular-biology. [1][2][3][4][5][6] The majority of data is manually annotated and curated. With the release in July 2018 BacDive offers information for 63,669 strains.[7] The database is hosted by the Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH and is part of de.NBI the German Network for Bioinformatics Infrastructure.

Content and Features

Database

The July 2018 release of the database encompassed over 600 different data fields, divided into the categories "Name and taxonomic classification", "Morphology and physiology", "Culture and growth conditions," "Isolation, sampling and environmental information." "Application and interaction", "Molecular biology" and "Strain availability". The database comprised 712,958 entries, linked to the according strain and reference.[7] The data are retrieved from internal descriptions of culture collections, expert-compiled compendia on strains and primary scientific literature.

Data access

Data can be accessed either via a GUI or via the RESTful web service. Using the GUI the user can choose between a simple search for searching the main fields like taxonomy or strain ID, or the user can use the advanced search, which enables the search in 130 data fields and gives the opportunity of complex queries by combining several fields. Data can be downloaded in PDF format (for single strains) or in CSV format for larger data sets (for multiple strains). Via the web service portal not only BacDive content, but also the taxon reference list Prokaryotic Nomenclature Up-To-Date can be accessed.

Other databases

For data that are outside the focus of BacDive, links to other databases are provided that deliver strain-associated data:

SILVA
BRENDA
PANGAEA
Straininfo.net
GBIF
EBI
NCBI

References

Söhngen, C; Boyke, B; Podstawka, A; Gleim, D; Overmann, J (October 13, 2013). "BacDive - The Bacterial Diversity Metadatabase". Nucleic Acids Research. 42 (Database issue): D592–D599. doi:10.1093/nar/gkt1058. PMC 3965005. PMID 24214959.
Fernández-Suárez, X. M.; Rigden, D. J.; Galperin, M. Y. (December 5, 2013). "The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection". Nucleic Acids Research. 42 (Database issue): D1–D6. doi:10.1093/nar/gkt1282. PMC 3965027. PMID 24316579.
Cohan lab (October 23, 2015). "DSMZ's BacDive Bacterial Diversity Database".
Abu-Jamous, Basel; Fa, Rui; Nandi, Asoke K. (2015). Integrative Cluster Analysis in Bioinformatics. John Wiley & Sons. p. 448. ISBN 9781118906552.
Zhulin, I. B. (August 1, 2015). "Databases for Microbiologists". Journal of Bacteriology. 197 (15): 2458–2467. doi:10.1128/JB.00330-15. PMC 4505447. PMID 26013493.
Söhngen, C; Podstawka, A; Boyke, B; Gleim, D; Vetcininova, A; Reimer, LC; Ebeling, C; Pendarovski, C; Overmann, J (September 30, 2015). "BacDive - The Bacterial Diversity Metadatabase in 2016". Nucleic Acids Research. 44 (Database issue): D581–D585. doi:10.1093/nar/gkv983. PMC 4702946. PMID 26424852.
Reimer, LC; Vetcininova, A; Sardà Carbasse, J; Söhngen, C; Gleim, D; Ebeling, C; Overmann, J (September 17, 2018). "BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis". Nucleic Acids Research. 47 (Database issue): D631–D636. doi:10.1093/nar/gky879. PMC 6323973. PMID 30256983.

External links

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[1] Söhngen, C; Boyke, B; Podstawka, A; Gleim, D; Overmann, J (October 13, 2013). "BacDive - The Bacterial Diversity Metadatabase". Nucleic Acids Research. 42 (Database issue): D592–D599. doi:10.1093/nar/gkt1058. PMC 3965005. PMID 24214959.

[2] Fernández-Suárez, X. M.; Rigden, D. J.; Galperin, M. Y. (December 5, 2013). "The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection". Nucleic Acids Research. 42 (Database issue): D1–D6. doi:10.1093/nar/gkt1282. PMC 3965027. PMID 24316579.

[3] Cohan lab (October 23, 2015). "DSMZ's BacDive Bacterial Diversity Database".

[4] Abu-Jamous, Basel; Fa, Rui; Nandi, Asoke K. (2015). Integrative Cluster Analysis in Bioinformatics. John Wiley & Sons. p. 448. ISBN 9781118906552.

[5] Zhulin, I. B. (August 1, 2015). "Databases for Microbiologists". Journal of Bacteriology. 197 (15): 2458–2467. doi:10.1128/JB.00330-15. PMC 4505447. PMID 26013493.

[6] Söhngen, C; Podstawka, A; Boyke, B; Gleim, D; Vetcininova, A; Reimer, LC; Ebeling, C; Pendarovski, C; Overmann, J (September 30, 2015). "BacDive - The Bacterial Diversity Metadatabase in 2016". Nucleic Acids Research. 44 (Database issue): D581–D585. doi:10.1093/nar/gkv983. PMC 4702946. PMID 26424852.

[BacDive2019-7] Reimer, LC; Vetcininova, A; Sardà Carbasse, J; Söhngen, C; Gleim, D; Ebeling, C; Overmann, J (September 17, 2018). "BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis". Nucleic Acids Research. 47 (Database issue): D631–D636. doi:10.1093/nar/gky879. PMC 6323973. PMID 30256983.