Cargando…
BacDive in 2022: the knowledge base for standardized bacterial and archaeal data
The bacterial metadatabase BacDive (https://bacdive.dsmz.de) has developed into a leading database for standardized prokaryotic data on strain level. With its current release (07/2021) the database offers information for 82 892 bacterial and archaeal strains covering taxonomy, morphology, cultivatio...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728306/ https://www.ncbi.nlm.nih.gov/pubmed/34718743 http://dx.doi.org/10.1093/nar/gkab961 |
_version_ | 1784626710394699776 |
---|---|
author | Reimer, Lorenz Christian Sardà Carbasse, Joaquim Koblitz, Julia Ebeling, Christian Podstawka, Adam Overmann, Jörg |
author_facet | Reimer, Lorenz Christian Sardà Carbasse, Joaquim Koblitz, Julia Ebeling, Christian Podstawka, Adam Overmann, Jörg |
author_sort | Reimer, Lorenz Christian |
collection | PubMed |
description | The bacterial metadatabase BacDive (https://bacdive.dsmz.de) has developed into a leading database for standardized prokaryotic data on strain level. With its current release (07/2021) the database offers information for 82 892 bacterial and archaeal strains covering taxonomy, morphology, cultivation, metabolism, origin, and sequence information within 1048 data fields. By integrating high-quality data from additional culture collections as well as detailed information from species descriptions, the amount of data provided has increased by 30% over the past three years. A newly developed query builder tool in the advanced search now allows complex database queries. Thereby bacterial strains can be systematically searched based on combinations of their attributes, e.g. growth and metabolic features for biotechnological applications or to identify gaps in the present knowledge about bacteria. A new interactive dashboard provides a statistic overview over the most important data fields. Additional new features are improved genomic sequence data, integrated NCBI TaxIDs and links to BacMedia, the new sister database on cultivation media. To improve the findability and interpretation of data through search engines, data in BacDive are annotated with bioschemas.org terms. |
format | Online Article Text |
id | pubmed-8728306 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-87283062022-01-05 BacDive in 2022: the knowledge base for standardized bacterial and archaeal data Reimer, Lorenz Christian Sardà Carbasse, Joaquim Koblitz, Julia Ebeling, Christian Podstawka, Adam Overmann, Jörg Nucleic Acids Res Database Issue The bacterial metadatabase BacDive (https://bacdive.dsmz.de) has developed into a leading database for standardized prokaryotic data on strain level. With its current release (07/2021) the database offers information for 82 892 bacterial and archaeal strains covering taxonomy, morphology, cultivation, metabolism, origin, and sequence information within 1048 data fields. By integrating high-quality data from additional culture collections as well as detailed information from species descriptions, the amount of data provided has increased by 30% over the past three years. A newly developed query builder tool in the advanced search now allows complex database queries. Thereby bacterial strains can be systematically searched based on combinations of their attributes, e.g. growth and metabolic features for biotechnological applications or to identify gaps in the present knowledge about bacteria. A new interactive dashboard provides a statistic overview over the most important data fields. Additional new features are improved genomic sequence data, integrated NCBI TaxIDs and links to BacMedia, the new sister database on cultivation media. To improve the findability and interpretation of data through search engines, data in BacDive are annotated with bioschemas.org terms. Oxford University Press 2021-10-29 /pmc/articles/PMC8728306/ /pubmed/34718743 http://dx.doi.org/10.1093/nar/gkab961 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Database Issue Reimer, Lorenz Christian Sardà Carbasse, Joaquim Koblitz, Julia Ebeling, Christian Podstawka, Adam Overmann, Jörg BacDive in 2022: the knowledge base for standardized bacterial and archaeal data |
title | BacDive in 2022: the knowledge base for standardized bacterial and archaeal data |
title_full | BacDive in 2022: the knowledge base for standardized bacterial and archaeal data |
title_fullStr | BacDive in 2022: the knowledge base for standardized bacterial and archaeal data |
title_full_unstemmed | BacDive in 2022: the knowledge base for standardized bacterial and archaeal data |
title_short | BacDive in 2022: the knowledge base for standardized bacterial and archaeal data |
title_sort | bacdive in 2022: the knowledge base for standardized bacterial and archaeal data |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728306/ https://www.ncbi.nlm.nih.gov/pubmed/34718743 http://dx.doi.org/10.1093/nar/gkab961 |
work_keys_str_mv | AT reimerlorenzchristian bacdivein2022theknowledgebaseforstandardizedbacterialandarchaealdata AT sardacarbassejoaquim bacdivein2022theknowledgebaseforstandardizedbacterialandarchaealdata AT koblitzjulia bacdivein2022theknowledgebaseforstandardizedbacterialandarchaealdata AT ebelingchristian bacdivein2022theknowledgebaseforstandardizedbacterialandarchaealdata AT podstawkaadam bacdivein2022theknowledgebaseforstandardizedbacterialandarchaealdata AT overmannjorg bacdivein2022theknowledgebaseforstandardizedbacterialandarchaealdata |