BacDive

BacDive provides standardized strain-level information on bacterial and archaeal species to support research into taxonomy, morphology, physiology, sampling conditions, environmental context, and molecular biology.

Key Features:

• Comprehensive Data Integration: Integrates datasets from culture collections, primary literature, and unpublished lab notes to centralize strain-level information.
• Data Types Covered: Contains detailed records on taxonomy, morphology, physiology, sampling conditions, environmental contexts, molecular biology, strain isolation sources, and cultivation conditions.
• Manual Curation and Annotation: Includes manually annotated and curated entries to enhance data accuracy and reliability.
• Advanced Querying: Supports combination queries across over 30 fields, including text and numerical data, for precise data retrieval.
• Data Accessibility and Interoperability: Provides RESTful web services delivering machine-readable XML and JSON output for integration with other tools.
• Linkage to External Resources: Links entries to external life science resources to provide additional context and cross-references.

Scientific Applications:

• Microbial diversity and taxonomy: Enables analysis of strain-level diversity and taxonomic classification of bacteria and archaea.
• Physiology and phenotype characterization: Supports studies of morphology, physiological traits, and cultivation-related phenotypes.
• Environmental microbiology and ecology: Facilitates investigation of sampling conditions, environmental contexts, and ecological roles of microorganisms.
• Evolutionary biology and interactions: Provides data useful for studying microbial interactions and evolutionary relationships among strains.

Methodology:

Digitization and text mining of sources such as typewritten index cards from culture collections and paper forms containing Analytical Profile Index (API) tests, plus metadata extraction from new species descriptions in scientific journals.