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, 42 (Database issue), D592-9

BacDive--the Bacterial Diversity Metadatabase

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BacDive--the Bacterial Diversity Metadatabase

Carola Söhngen et al. Nucleic Acids Res.

Abstract

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 9/2013), BacDive contains entries for 23 458 strains and provides information on their taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology. Where available, links to access the respective biological resources are given. The majority of the BacDive data is manually annotated and curated. The BacDive portal offers an easy-to-use simple search and in addition powerful advanced search functionalities allowing to combine more than 30 search fields for text and numerical data. The user can compile individual sets of strains to a download selection that can easily be imported into nearly all spreadsheet applications.

Figures

Figure 1.
Figure 1.
Simple search. BacDive portal entrance (a) with a clear user interface provides quick access through its navigation bar on the top of the site (b) to simple search (SEARCH), ADVANCED SEARCH and DOWNLOAD SELECTION. Also at the navigation bar the FAQ/HELP, NEWS and IMPRINT/CONTACT can be called anytime. A free text search is activated by selecting the check box right to the simple search query field (c).
Figure 2.
Figure 2.
Advanced search. All search fields feature short tool tips containing compact explanations of the scope of the search fields, which are displayed on mouse-over. The query pattern (search terms highlighted in yellow) shown retrieves all strains with their species name containing ‘Pseudomonas OR Clostridium OR *bacillus’, having assigned the biosafety level 1, growing at a temperature higher than 50°C, on media containing ‘Peptone’, GC-content <65 mol% and being sampled in Europe. This query retrieves 15 strains.
Figure 3.
Figure 3.
Strain detail view. The sections ‘Culture and Growth conditions’, ‘Isolation, sampling and environmental information’ as well as ‘Application and Interaction’ are hidden in this view for better clarity. A grey ‘*’ symbol besides the reference identification number indicates content derived from text mining.
Figure 4.
Figure 4.
Results page and export panel. After submitting a query, a result set is generated and displayed as a list (a). Strains can be selected using checkboxes besides the list (a) or via the export panel (b) integrated in the strain detail view.

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