BacDive-News

News 

last updated: 01.09.2017

New BacDive Major Release (01.09.2017)

The new BacDive major release is online since September 2017 with some new features and new data content.
The overall data content has increased by 30 %. Currently we offer metadata on 56,420 strains.
 

BacDive Section
 Release 09/2013
Release 09/2014 Release 09/2015  Release 09/2016  Release 09/2017  2016-2017 increase
Name and taxonomic classification* 23,458 104,922 106,952 108,226  111,832 3%
Morphology and physiology* 11,521 23,928 39,087 54,129 126,992 135%
Culture and growth conditions* 21,605 23,696 24,280 58,206 77,471 33%
Isolation, sampling and environmental information* 20,769 21,873 22,448 23,077 25,509 11%
Application and interaction* 14,639 15,637 15,680 15,873 18,863 19%
Molecular biology* 14,591 16,168 17,668 20,029 23,349 17%
Strain availability* 18,459 62,888 66,832
68,798 68,853 0.1%
 overall entries* 125,042 269,112 292,947 373,628 452,869 30%
*) Denotes the distinct combination of strain, reference, data entry


Besides the increase of data content, we offer some new features in the BacDive Webportal:

API test finder:
API-test finderThe API test finder is a new tool to find matching API tests within the database.

Antibiotic susceptibility tests 
Antibiotic susceptibility test
Data on antibiotic susceptibility tests is now available. Inhibition zone diameters can be queried via the advanced search.
Digital Object identifier (DOI) and PDF archiving system 
DOI/PDF archive
The PDF archive for each strain and the according DOIs can be found under "PDF archive" in the strain detail view (upper right corner).

Video tutorials online (02.03.2017)

BacDive now offers short video tutorials on the usage of the BacDive GUI. These tutorials deal with the topics "basic functions", "advanced search" and "export functions" and can be found in the tutorial section.

New BacDive Minor Release (27.02.2017)

The new BacDive minor release is online since February 2017. This update includes some smaller database changes and additional data content, including extracted data from 523 initial strain descriptions published in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). This data set comprises predominantly data on the morphology and physiology of strains and in consequence the data content of this section has increased by 74 %.  Due to optimization of data structures the content for Culture and growth conditions has slightly decreased. Overall the data content has increased by 11 % and BacDive now offers metadata on 55.687 strains.
 

BacDive Section
 Release 09/2013
Release 09/2014 Release 09/2015  Release 09/2016  Release 02/2017  2016-2017 increase
Name and taxonomic classification* 23,458 104,922 106,952 108,226  110,385 2%
Morphology and physiology* 11,521 23,928 39,087 54,129 94,158 74%
Culture and growth conditions* 21,605 23,696 24,280 83,496 74,024 -11%
Isolation, sampling and environmental information* 20,769 21,873 22,448 23,077 24,648 7%
Application and interaction* 14,639 15,637 15,680 15,873 18,766 18%
Molecular biology* 14,591 16,168 17,668 20,029 22,565 13%
Strain availability* 18,459 62,888 66,832
68,798 68,991 0.3%
 overall entries* 125,042 269,112 292,947 373,628 413,537 11%
*) Denotes the distinct combination of strain, reference, data entry


Downtime due to server maintenance at 10./11.12

Due to a server maintenance, BacDive will be temporarily unavailable during the 10./11.12.

User satisfaction survey

BacDive is a part of the German Network for Bioinformatics Infrastructure de.NBI.

de.NBI-logo  

To evaluate and improve the quality of our service we need your feedback.
Please help us by participating in this short survey.

Training for the use of BacDive on 2nd of November 2016

In the course of the de.NBI training sessions there will be a training for the database BacDive. The training comprises an introduction, a detailed presentation of the utilization possibilities and comprehensive exercises. Please find detailed information in this flyer or at the de.NBI page.
The training is free of charge. However the participants have to cover their travelling and hotel expenses. The application is open to all though de.NBI members will be preferred.

Location:               
DSMZ-Building at the HZI-Campus Braunschweig
Inhoffenstraße 7B  38124 Braunschweig

Date:          
2. November 2016, 10 a.m. to 4 p.m.

Please register at training@bacdive.de


New BacDive Major Release (06.09.2016)

The new BacDive major release is online since September 2016 with a refurbished Webportal and some new features. Additionally the data content has increased by 23%. Currently we offer metadata on 54,610 strains.
 

BacDive Section
 Release 09/2013
Release 09/2014 Release 09/2015  Release 09/2016  2015-2016 increase
Name and taxonomic classification* 23,458 104,922 106,952 108,226  4%
Morphology and physiology* 11,521 23,928 39,087 54,129 28%
Culture and growth conditions* 21,605 23,696 24,280 83,496 71%
Isolation, sampling and environmental information* 20,769 21,873 22,448 23,077 3%
Application and interaction* 14,639 15,637 15,680 15,873 1%
Molecular biology* 14,591 16,168 17,668 20,029 13%
Strain availability* 18,459 62,888 66,832
68,798 3%
? overall entries* 125,042 269,112 292,947 373,628 23%
*) Denotes the distinct combination of strain, reference, data entry

Besides the increase of data content, we offer some new features in the BacDive Webportal:

TAXplorer:

TAXplorer »
The TAXplorer offers the opportunity to filter all available strains by their taxonomic classification. Thereby you are able to browse through taxonomy and narrow down the list until you received the desired strain(s).
API-test data

API-test data
» The section morphology and physiology offers a substantially increased amount of API-test data, that can be viewed by clicking the expand button.
Custom CSV export:

custom CSV export » With the custom export function the data that should be exported can be chosen by clicking the according check boxes. This function is especially useful, if the export of all data is too complex.
 

 

Publication out now (30.09.2015)

The latest Publication on BacDive is now available.

BacDive - the Bacterial Diversity Metadatabase in 2016
Söhngen C., Bunk B., Podstawka A., Gleim D., Vetcininova A., Reimer L.C., Overmann J.
Nucleic Acids Res. 2015. doi: 10.1093/nar/gkv983. Epub 2015 Sep 30.
PMID:  26424852

Please cite BacDive and results obtained by the use of the BacDive database.
 

New BacDive Major Release (04.09.2015)

The new BacDive major release is online since September 2015 with a substantially increase of content. Currently we offer metadata on 53,978 strains.
These data is derived out of 22,033 source references


BacDive Section  Release 09/2013 Release 09/2014 Release 09/2015  2014-2015 increase  2013-2015 increase
Name and taxonomic classification* 23,458 104,922 106,952 2%  356%
Morphology and physiology* 11,521 23,928 39,087 63% 239%
Culture and growth conditions* 21,605 23,696 24,280 2% 12%
Isolation, sampling and environmental information* 20,769 21,873 22,448 3% 8%
Application and interaction* 14,639 15,637 15,680 - 7%
Molecular biology* 14,591 16,168 17,668 9% 21%
Strain availability* 18,459 62,888 66,832
6% 262%
? overall entries* 125,042 269,112 292,947 9% 134%
*) Denotes the distinct combination of strain, reference, data entry

Besides the increase of data content, we offer some new features of the BacDive Webportal:

Search for species in external web resources:

»
Search for information on refering species in external web resources, e.g. BRaunschweig ENzyme DAtabase (BRENDA), Global Biodiversity Information Facility (GBIF), PANGAEA, StrainInfo
 Enhancement of the section molecular biology:

» The section molecular biology offers some more data fields: BacDive strain entries with International Nucleotide Sequence Database Collaboration (INSDC) accession numbers are now complemented by the brief sequence accession description and the associated ID of the NCBI Taxonomy. Additionally we annotated accession numbers of completed genomes of 654 strains.
Additional fields in the advanced search:

» In order to search for gene names, plasmids or 16S rRNA in BacDive  use the advanced search to query the field sequence accession description. The BacDive advanced search is now also capable to retreive entries by a given ID of the NCBI Taxonomy.
 

 

Training for the use of the databases BacDive and BRENDA in October 2015 (26.08.2015)

In the course of the de.NBI training sessions there will be a training for the databases BacDive and BRENDA. The goals of this training are to introduce the databases and to give detailed information on the scope, the organization, the content, and how to work with the tools. The training is open to all, but de.NBI members will be given preference.

Please find more detailed information about the program and the registration in this flyer. The training is free of charge. However the participants have to cover their traveling and hotel expenses.

Location:               
Technische Universität Braunschweig, Braunschweig, Germany
Date:          
13.+14. October 2015
Registration deadline:
15.09.2015 for partners of the de.NBI Network
1.10.2015 for all others

 

Assembling the microbial diversity jigsaw puzzle  - 5 demonstrators for data mobilization (24.08.2015)

BacDive strives for more manually annotated content derived out of publications. The limited scope of five bacterial strains have been in the focus of this mobilization pilot project. Although a biological resource might be of crucial importance for the environmental state of a certain biotope, it is still laborious to screen and compare certain properties of candidate strains.This holds also true if a strain is already deposited within a culture collection and has become a research object with published data. The information about the strain is scattered in publications and data bases around the world.

The data mobilization of five bacterial strains demonstrates the valuable and comprehensive data sources represented by culture collection data base content and the related research results and publications. For this mobilization demonstrators the taxon-related descriptive information has been manually annotated out of the referring publications and added to BacDive. In this attempt an average of 276 (180-319) data points per strain could be mobilized.

The ecological and environmental relevance of these strains is given by their participation in nitrogen and carbon cycles (significant exoenzyme activity) within their particular habitat. The detailed documented metabolic and physiologic profile of each strain indicates their significant adaptation to the soils of different climates. Hence, these strains are important biotic components of their environment.

The detailed descriptions in BacDive:








Beta-Tests completed  (31.07.2015)

We thank all those who have tested our web services and gave us feedback on their optimization. The BacDive web services are available to all interested BacDive users. If you like to obtain an account, you simply need to register (Registration forms BacDive, PNU).

Beta-Testers Wanted!  (01.03.2015)

We are providing the new BacDive web service as beta release. All endpoints are comprehensively documented. The content can be retrieved in machine readable XML and JSON format. If you are interested in becoming a beta tester, please apply via the provided registration forms.

Additional information on more than 1000 strains available (17.02.2015)

The Compendium of Actinobacteria is an comprehensive electronic PDF manual including the descriptions of the important bacterial calls of Actinobacteria compiled by PD Dr. Joachim Wink ( HZI-Helmholtz-Centre for Infection Research, Braunschweig). The descriptions of morphology and physiology are now available as structured database content within BacDive. Here some representative links:




New BacDive Major Release (30.09.2014)

The new BacDive major release is online since September 2014 with a substantially increase of content. Currently we offer metadata on 53,588 strains. These data is derived out of  21,222 source references.

BacDive Section  Release 09/2012
  Release 09/2013
Release 09/2014  2013-2014 increase 
Name and taxonomic classification* 18,157 23,458 104,922 347% 
Morphology and physiology* 4,053 11,521 23,928 108%
Culture and growth conditions* 20,634 21,605 23,696 10%
Isolation, sampling and environmental information* 15,449 20,769 21,873 5%
Application and interaction* - 14,639 15,637 7%
Molecular biology* 13,609 14,591 16,168 11%
Strain availability* 17,856 18,459 62,888 241%
? overall entries* 89,758 125,042 266,718 241%
*) Denotes the distinct combination of strain, reference, data entry

Besides the increase of data content, we offer some new features of the BacDive Webportal.

Publication out now (11.11.2013)

The Publication on BacDive is now available.

BacDive - the Bacterial Diversity Metadatabase
Söhngen C., Bunk B., Podstawka A., Gleim D., Overmann J.
Nucleic Acids Res. 2014 Jan 1;42(1):D592-9. doi: 10.1093/nar/gkt1058. Epub 2013 Nov 7.
PMID:  24214959

Please cite BacDive and results obtained by the use of the BacDive database.

New BacDive Major Release (02.09.2013)

The new  BacDive major release is online since September 2013 with a substantially increase of content.

BacDive Section  Release 09/2012     Release 09/2013    2012-2013 increase 
Name and taxonomic classification* 18,157 23,458 29% 
Morphology and physiology* 4,053 11,521 184%
Culture and growth conditions* 20,634 21,605 5%
Isolation, sampling and environmental information* 15,449 20,769 34%
Application and interaction* 0 14,639 100%
Molecular biology* 13,609 14,591 7%
Strain availability* 17,856 18,459 3%
? overall entries* 89,758 125,042 39%
*) Denotes the distinct combination of strain, reference, data entry

Besides the increase of data content, we have added and enhanced some features of the BacDive Webportal.
  • The BacDive advanced search has been adapted and offers now large-scale queries functionality by combining more than 30 data fields for your individual comparative analyses of a multitude of strains.
  • We added Help and FAQ that provide you with a quick and easy introduction to the use of the BacDive features and functionalities.