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BacDive

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BacDive
Content
Descriptioninformation about bacterial and archaeal strains
Data types
captured		metadata
Contact
Research centerLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH
Primary citationPMID 26424852
Release date2012
Access
Websitehttp://bacdive.dsmz.de/
Web service URLhttp://bacdive.dsmz.de/api/

BacDive is a bacterial metadatabase that provides strain-linked information about bacterial and archael biodiversity.

Introduction

BacDive is a resource for different kind of metadata like taxonomy, morphology, physiology, environment and molecular-biology. [1] [2] [3] [4] [5] The majority of data is manually annotated and curated. With the release in September 2015 BacDive offers information for 53,978 strains.[6] 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 September 2015 release of the database encompassed 233 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 293,145 entries, linked to the according strain and reference.[6] 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 35 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 mulitple 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:

References

  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.
  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. doi:10.1093/nar/gkt1282.
  3. ^ Cohan lab (October 23, 2015). "DSMZ's BacDive Bacterial Diversity Database".{{cite web}}: CS1 maint: date and year (link)
  4. ^ Abu-Jamous, Basel; Fa, Rui; Nandi, Asoke K. (2015). Integrative Cluster Analysis in Bioinformatics. John Wiley & Sons. p. 448.
  5. ^ Zhulin, I. B. (August 1, 2015). "Databases for Microbiologists". Journal of Bacteriology. 197 (15). doi:10.1128/JB.00330-15.
  6. ^ a b 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.


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