BacDive
 | |
| Content | |
|---|---|
| Description | information aboutbacterialandarchaealstrains |
| Data types captured | metadata |
| Contact | |
| Research center | Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH |
| Primary citation | PMID34718743 |
| Release date | 2012 |
| Access | |
| Website | http://bacdive.dsmz.de/ |
| Web serviceURL | https://api.bacdive.dsmz.de/ |
BacDive(the Bacterial Diversity Metadatabase) is a bacterialmetadatabasethat provides strain-linked information aboutbacterialandarchaealbiodiversity.
Introduction
[edit]BacDiveis a resource for different kind of metadata like taxonomy, morphology, physiology, environment and molecular-biology. [1][2][3][4][5][6][7][8] The majority of data is manually annotated and curated. With the release in December 2022 BacDiveoffers information for 93,254 strains, including 19,313 type strains. The database is hosted by theLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbHand is part ofde.NBIthe German Network for Bioinformatics Infrastructure, as well asElixirthe European Network for Bioinformatics. In December 2022 BacDivewas selected by theGlobal Biodata Coalitionas a Global Core Biodata Resource (GCBR). GCBRs are considered critical data resources for the global research endeavour in life sciences and biomedicine.
Content and Features
[edit]Database
[edit]The December release of the database encompassed over 1000 different data fields, 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 "and" Strain availability ". The database comprised 1,922,166 entries, linked to the according strain and reference.[9] The data are retrieved from internal descriptions of culture collections, expert-compiled compendia and primary scientific literature like species descriptions.
Data access
[edit]Data can be accessed either via aGUIor via the RESTfulweb service.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 inPDFformat (for single strains) or inCSVformat for larger data sets (for multiple strains). Via theRESTful web service portalBacDivecontent can be accessed automatically (a free registration is needed).To support the use of the API,software clientsin Python and R are available.
Other databases
[edit]For data that are outside the focus of BacDive,links to other databases are provided that deliver strain-associated data:
- SILVA
- BRENDA
- List of Prokaryotic names with Standing in Nomenclature
- Straininfo.net
- EBI
- NCBI
- MicrobeAtlas
References
[edit]- ^ 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.PMC3965005.PMID24214959.
- ^ 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.PMC3965027.PMID24316579.
- ^Cohan lab (October 23, 2015)."DSMZ's BacDive Bacterial Diversity Database".Archivedfrom the original on May 7, 2019.RetrievedMay 6,2016.
- ^ Abu-Jamous, Basel; Fa, Rui; Nandi, Asoke K. (2015).Integrative Cluster Analysis in Bioinformatics.John Wiley & Sons. p. 448.ISBN9781118906552.
- ^ Zhulin, I. B. (August 1, 2015)."Databases for Microbiologists".Journal of Bacteriology.197(15): 2458–2467.doi:10.1128/JB.00330-15.PMC4505447.PMID26013493.
- ^ 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.PMC4702946.PMID26424852.
- ^ Reimer, LC; Vetcininova, A; Sardà Carbasse, J; Söhngen, C; Gleim, D; Ebeling, C; Overmann, J (September 17, 2018)."BacDivein 2019: bacterial phenotypic data for High-throughput biodiversity analysis ".Nucleic Acids Research.47(Database issue): D631–D636.doi:10.1093/nar/gky879.PMC6323973.PMID30256983.
- ^ Reimer, LC; Sardà Carbasse, J; Koblitz, J; Ebeling, C; Podstawka, A; Overmann, J (January 7, 2022)."BacDivein 2022: the knowledge base for standardized bacterial and archaeal data ".Nucleic Acids Research.50(Database issue): D741–D746.doi:10.1093/nar/gkab961.PMC8728306.PMID34718743.
- ^"DSMZ's BacDive Bacterial Diversity Database".December 22, 2022.Archivedfrom the original on July 16, 2024.RetrievedJuly 16,2024.
External links
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