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Bacterial Diversity Metadatabase

Abbreviation:BacDive

General Information

BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. BacDive contains entries for over 63,000 strains and provides information on their taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.

Homepage https://bacdive.dsmz.de/

Countries that developed this resource Germany

Created in 2012

Taxonomic range

Archaea

Bacteria

Knowledge Domains

Subjects

User-defined Tags

Metadata standardization

Species-environment interaction

How to cite this record FAIRsharing.org: BacDive; Bacterial Diversity Metadatabase; DOI: https://doi.org/10.25504/FAIRsharing.aSszvY; Last edited: June 22, 2021, noon; Last accessed: Jul 31 2021 10:13 p.m.

Publication for citation BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis. Reimer LC,Vetcininova A,Carbasse JS,Sohngen C,Gleim D,Ebeling C,Overmann J; Nucleic Acids Res ; 2018; 10.1093/nar/gky879;

This record is maintained by lorenz.reimer ORCID

Record added: Sept. 5, 2018, 3:25 p.m.
Record updated: June 11, 2021, 5:09 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.aSszvY' by 'The FAIRsharing Team' at 17:09, 11 Jun 2021 (approved):

	'licences' has been modified:
		Before:
			BacDive Privacy Policy, Terms of use & Copyright|https://bacdive.dsmz.de/about|Data
		After:
			BacDive Privacy Policy, Terms of use & Copyright|https://bacdive.dsmz.de/about|Data
			Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)|https://creativecommons.org/licenses/by-nc/4.0/|Data
		Added:
			Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)|https://creativecommons.org/licenses/by-nc/4.0/|Data
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.aSszvY' by 'The FAIRsharing Team' at 17:09, 11 Jun 2021 (approved):

	'licences' has been modified:
		Before:
			BacDive Privacy Policy, Terms of use & Copyright|https://bacdive.dsmz.de/about|Data
			Creative Commons Attribution-NonCommercial 4.0 International License|https://creativecommons.org/licenses/by-nc/4.0/|Data
		After:
			BacDive Privacy Policy, Terms of use & Copyright|https://bacdive.dsmz.de/about|Data
		Added:
		Removed:
			Creative Commons Attribution-NonCommercial 4.0 International License|https://creativecommons.org/licenses/by-nc/4.0/|Data

Edits to 'https://fairsharing.org/FAIRsharing.aSszvY' by 'The FAIRsharing Team' at 11:31, 20 Apr 2021 (approved):

	'licences' has been modified:
		Before:
			Free for non-commercial use||Data
			Free for academic use||Data
			Attribution required||Data
			Permission required for commercial use||Data
			Permission required for redistribution||Data
		After:
			BacDive Free for non-commercial use|https://bacdive.dsmz.de/about|Data
			BacDive Free for academic use|https://bacdive.dsmz.de/about|Data
			BacDive Attribution required|https://bacdive.dsmz.de/about|Data
			BacDive Permission required for commercial use|https://bacdive.dsmz.de/about|Data
			BacDive Permission required for redistribution||Data
			Creative Commons Attribution-NonCommercial 4.0 International License|https://creativecommons.org/licenses/by-nc/4.0/|Data
		Added:
			BacDive Free for non-commercial use|https://bacdive.dsmz.de/about|Data
			BacDive Free for academic use|https://bacdive.dsmz.de/about|Data
			BacDive Attribution required|https://bacdive.dsmz.de/about|Data
			BacDive Permission required for commercial use|https://bacdive.dsmz.de/about|Data
			BacDive Permission required for redistribution||Data
			Creative Commons Attribution-NonCommercial 4.0 International License|https://creativecommons.org/licenses/by-nc/4.0/|Data
		Removed:
			Free for non-commercial use||Data
			Free for academic use||Data
			Attribution required||Data
			Permission required for commercial use||Data
			Permission required for redistribution||Data

Edits to 'https://fairsharing.org/FAIRsharing.aSszvY' by 'The FAIRsharing Team' at 14:57, 16 Oct 2018 (approved):

	'domains' has been modified:
		Before:
			Antimicrobial
			Biodiversity
			Life Science
			Metadata standardization
			Microbiology
			Phenotype
			Resource metadata
		After:
			Antimicrobial
			Biodiversity
			Life Science
			Metadata standardization
			Microbiology
			Morphology
			Phenotype
			Resource metadata
			Species-environment interaction
		Added:
			Morphology
			Species-environment interaction
		Removed:

	'description' has been modified:
		Before: BacDive?the Bacterial Diversity Metadatabase
(http://bacdive.dsmz.de) merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. Currently (release
7/2018), BacDive contains entries for 63,669  strains
and provides information on their taxonomy,
morphology, physiology, sampling and concomitant
environmental conditions as well as molecular
biology.
		After: BacDive?the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.  BacDive contains entries for over 63,000  strains and provides information on their taxonomy, morphology, physiology, sampling and concomitant
environmental conditions as well as molecular biology.

Edits to 'https://fairsharing.org/FAIRsharing.aSszvY' by 'lorenz.reimer' at 06:58, 08 Oct 2018 (approved):

	'publications' has been modified:
		Before:
			BacDive--the Bacterial Diversity Metadatabase.|Sohngen C,Bunk B,Podstawka A,Gleim D,Overmann J|Nucleic Acids Res|2013
			BacDive--The Bacterial Diversity Metadatabase in 2016.|Sohngen C,Podstawka A,Bunk B,Gleim D,Vetcininova A,Reimer LC,Ebeling C,Pendarovski C,Overmann J|Nucleic Acids Res|2015
			Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase.|Reimer LC,Sohngen C,Vetcininova A,Overmann J|J Biotechnol|2017
		After:
			BacDive--the Bacterial Diversity Metadatabase.|Sohngen C,Bunk B,Podstawka A,Gleim D,Overmann J|Nucleic Acids Res|2013
			BacDive--The Bacterial Diversity Metadatabase in 2016.|Sohngen C,Podstawka A,Bunk B,Gleim D,Vetcininova A,Reimer LC,Ebeling C,Pendarovski C,Overmann J|Nucleic Acids Res|2015
			Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase.|Reimer LC,Sohngen C,Vetcininova A,Overmann J|J Biotechnol|2017
			BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis.|Reimer LC,Vetcininova A,Carbasse JS,Sohngen C,Gleim D,Ebeling C,Overmann J|Nucleic Acids Res|2018
		Added:
			BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis.|Reimer LC,Vetcininova A,Carbasse JS,Sohngen C,Gleim D,Ebeling C,Overmann J|Nucleic Acids Res|2018
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.aSszvY' by 'lorenz.reimer' at 06:54, 13 Sep 2018 (approved):

	'miriam_id' has been modified:
		Before: 
		After: MIR:00000676

Edits to 'https://fairsharing.org/FAIRsharing.aSszvY' by 'The FAIRsharing Team' at 11:32, 06 Sep 2018 (approved):

	'licences' has been modified:
		Before:
		After:
			Free for non-commercial use||Data
			Free for academic use||Data
			Attribution required||Data
			Permission required for commercial use||Data
			Permission required for redistribution||Data
		Added:
			Free for non-commercial use||Data
			Free for academic use||Data
			Attribution required||Data
			Permission required for commercial use||Data
			Permission required for redistribution||Data
		Removed:

	'supportLinks' has been modified:
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		After:
			help|https://youtu.be/n1aw3iEGxbA
			help|https://youtu.be/YQ66nz4h_5I
			help|https://bacdive.dsmz.de/help
			help|https://youtu.be/aqpUiDEIcn4
			online documentation|https://bacdive.dsmz.de/contact
			online documentation|https://bacdive.dsmz.de/news
			online documentation|https://bacdive.dsmz.de/about
		Added:
			help|https://youtu.be/n1aw3iEGxbA
			help|https://youtu.be/YQ66nz4h_5I
			help|https://bacdive.dsmz.de/help
			help|https://youtu.be/aqpUiDEIcn4
			online documentation|https://bacdive.dsmz.de/contact
			online documentation|https://bacdive.dsmz.de/news
			online documentation|https://bacdive.dsmz.de/about
		Removed:

	'accessPoints' has been modified:
		Before:
			REST|https://bacdive.dsmz.de/api/bacdive/|Access do data of the Bacterial Diversity Metadata
			REST|https://bacdive.dsmz.de/api/pnu/|Access do data of the Prokaryotic Nomenclature Up-to-date database
		After:
			REST|https://bacdive.dsmz.de/api/bacdive/|Access data from the Bacterial Diversity Metadata
			REST|https://bacdive.dsmz.de/api/pnu/|Access data from the Prokaryotic Nomenclature Up-to-date database
		Added:
			REST|https://bacdive.dsmz.de/api/bacdive/|Access data from the Bacterial Diversity Metadata
			REST|https://bacdive.dsmz.de/api/pnu/|Access data from the Prokaryotic Nomenclature Up-to-date database
		Removed:
			REST|https://bacdive.dsmz.de/api/bacdive/|Access do data of the Bacterial Diversity Metadata
			REST|https://bacdive.dsmz.de/api/pnu/|Access do data of the Prokaryotic Nomenclature Up-to-date database

	'tools' has been modified:
		Before:
		After:
			API Test Finder||https://bacdive.dsmz.de/api-test-finder
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			API Test Finder||https://bacdive.dsmz.de/api-test-finder
		Removed:

	'dataProcesses' has been modified:
		Before:
		After:
			Browse by Taxonomy
			Advanced Search
			Microbial Isolation Sources Search
		Added:
			Browse by Taxonomy
			Advanced Search
			Microbial Isolation Sources Search
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.aSszvY' by 'lorenz.reimer' at 16:05, 05 Sep 2018 (approved):

	'domains' has been modified:
		Before:
			Antimicrobial
			Biodiversity
			Life Science
			Metadata standardization
			Microbiology
			Resource metadata
		After:
			Antimicrobial
			Biodiversity
			Life Science
			Metadata standardization
			Microbiology
			Phenotype
			Resource metadata
		Added:
			Phenotype
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.aSszvY' by 'lorenz.reimer' at 15:51, 05 Sep 2018 (approved):

	'description' has been modified:
		Before: BacDive?the Bacterial Diversity Metadatabase
(http://bacdive.dsmz.de) merges detailed strain-
linked information on the different aspects of bac-
terial and archaeal biodiversity. Currently (release
7/2018), BacDive contains entries for63,669  strains
and provides information on their taxonomy,
morphology, physiology, sampling and concomitant
environmental conditions as well as molecular
biology.
		After: BacDive?the Bacterial Diversity Metadatabase
(http://bacdive.dsmz.de) merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. Currently (release
7/2018), BacDive contains entries for 63,669  strains
and provides information on their taxonomy,
morphology, physiology, sampling and concomitant
environmental conditions as well as molecular
biology.

Edits to 'https://fairsharing.org/FAIRsharing.aSszvY' by 'lorenz.reimer' at 15:35, 05 Sep 2018 (approved):

	'domains' has been modified:
		Before:
			Experiment metadata
			Resource metadata
		After:
			Antimicrobial
			Biodiversity
			Life Science
			Metadata standardization
			Microbiology
			Resource metadata
		Added:
			Antimicrobial
			Biodiversity
			Life Science
			Metadata standardization
			Microbiology
		Removed:
			Experiment metadata

	'standardsImplemented' has been modified:
		Before:
			Chemical Entities of Biological Interest
		After:
			Chemical Entities of Biological Interest
			INSD sequence record XML
		Added:
			INSD sequence record XML
		Removed:

	'related_databases' has been modified:
		Before:
			BRENDA
			Pangaea - Data Publisher for Earth and Environmental Science
		After:
			BRENDA
			Pangaea - Data Publisher for Earth and Environmental Science
			SILVA
		Added:
			SILVA
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.aSszvY' by 'lorenz.reimer' at 15:28, 05 Sep 2018 (approved):

	'domains' has been modified:
		Before:
			Resource metadata
		After:
			Experiment metadata
			Resource metadata
		Added:
			Experiment metadata
		Removed:

	'related_databases' has been modified:
		Before:
		After:
			BRENDA
			Pangaea - Data Publisher for Earth and Environmental Science
			SILVA
		Added:
			BRENDA
			Pangaea - Data Publisher for Earth and Environmental Science
			SILVA
		Removed:

Support

General

help	Advanced Search Video Tutorial
help	BacDive API Strip Test Finder Video Tuto ...
help	Help Pages
help	Quickstart Video Tutorial
online documentation	Contact Form
online documentation	News
online documentation	About BacDive

Additional Information

Contact

Lorenz Reimer ORCID

Tools

API Test Finder

https://bacdive.dsmz.de/api-test-finder

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Access

Browse by Taxonomy	https://bacdive.dsmz.de/taxplorer
Advanced Search	https://bacdive.dsmz.de/advsearch
Microbial Isolation Sources Search	https://bacdive.dsmz.de/isolation-sources

REST Web Services

Access data from the Bacterial Diversity Metadata	https://bacdive.dsmz.de/api/bacdive/
Access data from the Prokaryotic Nomenclature Up-to-date database	https://bacdive.dsmz.de/api/pnu/

Publications

BacDive--the Bacterial Diversity Metadatabase.

Sohngen C,Bunk B,Podstawka A,Gleim D,Overmann J
Nucleic Acids Res 2013

View Paper (PubMed) View Publication

BacDive--The Bacterial Diversity Metadatabase in 2016.

Sohngen C,Podstawka A,Bunk B,Gleim D,Vetcininova A,Reimer LC,Ebeling C,Pendarovski C,Overmann J
Nucleic Acids Res 2015

View Paper (PubMed) View Publication

Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase.

Reimer LC,Sohngen C,Vetcininova A,Overmann J
J Biotechnol 2017

View Paper (PubMed) View Publication

BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis.

Reimer LC,Vetcininova A,Carbasse JS,Sohngen C,Gleim D,Ebeling C,Overmann J
Nucleic Acids Res 2018

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Chemical Entities of Biological Interest

Models and Formats

INSD sequence record XML

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by lorenz.reimer ORCID

Funds

German Network for Bioinformatics Infrastructure (de.NBI), Germany (Consortium)

Maintains

Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Germany (Research institute) Lead

Bacterial Diversity Metadatabase

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