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BacDive

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BacDive
Content
DescriptionThe Bacterial Diversity Database
Contact
Research centerLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH
Primary citationPMID 39470737
Release date2012
Access
Websitehttp://bacdive.dsmz.de/
Web service URLhttps://api.bacdive.dsmz.de/
Sparql endpointhttps://sparql.dsmz.de/bacdive/

BacDive (The Bacterial Diversity Database) is the worldwide largest database for standardized bacterial and archaeal strain-level information.

It is a comprehensive resource containing diverse data on bacterial and archaeal strains, including taxonomy, morphology, physiology, sampling and environmental data and sequence information.[1][2] The database is built on a base of curated data from culture collections. In 2024 BacDive contains information on 97,334 strains, including 20,060 type strains.[3] The database is hosted by the Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH and is part of the integrated DSMZ Digital Diversity infrastructure. The database is a member of de.NBI - the German Network for Bioinformatics Infrastructure, as well as ELIXIR. The Global Biodata Coalition designated BacDive a Global Core Biodata Resource (GCBR) in 2022.[4] In 2023, BacDive was additionally named as an ELIXIR Core Data Resource.[5]

Database content

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BacDive was initially released in April 2012 to standardize and make publicly available strain data of culture collections, other compendia, and publications. The first release, contained 89,758 entries for 18,157 strains and 179 different used data fields. [6] Today (as of December 2023), the database encompassed over 1000 different data fields. The database now comprises 2,675,988 entries for 97,334 strains. Each entry is linked to a reference.[7] Data for each strain is divided into the categories "Name and taxonomic classification", "Morphology", "Culture and growth conditions, "Physiology and metabolism", "Isolation, sampling and environmental information." "Safety information", "Sequence information". [8] Since 2023 high-quality predicted data produced using machine learning models trained on curated BacDive data can be found in an additional section titled "Genome-based predictions". [9]

Data access

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Data can be accessed either via a GUI or via the RESTful web service. [10] Using the GUI the user can choose between a simple search for searching strains by name, Culture collection number, NCBI Tax ID or INSDC sequence accession number, 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 RESTful web service portal BacDive content can be accessed automatically (a free registration is needed).To support the use of the API, software clients in Python and R are available.

Other databases

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For data that are outside the focus of BacDive, links to other databases are provided.

Other databases within the DSMZ Digital Diversity infrastructure:

External databases:

References

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  1. ^ Abu-Jamous, Basel; Fa, Rui; Nandi, Asoke K. (2015). Integrative Cluster Analysis in Bioinformatics. John Wiley & Sons. p. 448. ISBN 9781118906552.
  2. ^ Reimer, LC; Sardà Carbasse, J; Koblitz, J; Ebeling, C; Podstawka, A; Overmann, J (January 7, 2022). "BacDive in 2022: the knowledge base for standardized bacterial and archaeal data". Nucleic Acids Research. 50 (Database issue): D741–D746. doi:10.1093/nar/gkab961. PMC 8728306. PMID 34718743.
  3. ^ Schober, I; Koblitz, J; Sardà Carbasse, J; Ebeling, C; Schmidt, ML; Podstawka, A; Gupta, R; Ilangovan, V; Chamanara, J; Overmann, J; Reimer, LC (29 October 2024). "BacDive in 2025: the core database for prokaryotic strain data". Nucleic Acids Research. doi:10.1093/nar/gkae959. PMID 39470737.
  4. ^ "Database from Braunschweig is essential for global bacteria research". dsmz.de. Retrieved 14 November 2024.
  5. ^ "ELIXIR announces new Core Data Resources and Recommended Interoperability Resources". elixir-europe.org. 14 December 2023. Retrieved 14 November 2024.
  6. ^ 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.
  7. ^ "BacDive News". December 21, 2023.
  8. ^ 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.
  9. ^ Schober, I; Koblitz, J; Sardà Carbasse, J; Ebeling, C; Schmidt, ML; Podstawka, A; Gupta, R; Ilangovan, V; Chamanara, J; Overmann, J; Reimer, LC (29 October 2024). "BacDive in 2025: the core database for prokaryotic strain data". Nucleic Acids Research. doi:10.1093/nar/gkae959. PMID 39470737.
  10. ^ 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.
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