BacDive API

BacDive API provides programmatic access to strain-linked metadata on bacterial and archaeal biodiversity, delivering taxonomy, morphology, physiology, sampling, cultivation, and molecular biology data in machine-readable formats such as JSON and XML for computational analyses.

Key Features:

• Extensive Data Coverage: As of 9/2015 the database contains records for 53,978 strains including taxonomy, morphology, physiology, sampling conditions, environmental contexts, and molecular biology.
• Data Formats and Access: The BacDive WS API returns data in machine-readable JSON and XML formats for programmatic retrieval.
• Advanced Search Capabilities: Supports simple and advanced queries combining over 30 fields with text and numerical filters and specific fields such as gene names, plasmids, and 16S rRNA sequences.
• Manual Annotation: The majority of data entries are manually annotated to increase accuracy and reliability of metadata.
• Integration of Diverse Data Sources: Metadata are integrated from culture collections, typewritten index cards (including the Reichenbach myxobacteria collection), paper forms, and new species descriptions in the scientific literature.
• Interoperability with External Resources: Strain records include links to external life science web resources to enable cross-database integration.

Scientific Applications:

• Comparative studies: Enables comparative analyses of phenotype and taxonomy across thousands of bacterial and archaeal strains.
• Ecological assessments: Provides sampling and environmental metadata to support assessments of habitat distribution and ecological context.
• Evolutionary analyses: Supplies taxonomic and molecular biology data to inform phylogenetic and evolutionary investigations.
• Systems biology and metagenomics integration: Supplies curated strain-linked metadata that can be integrated with genomic and metagenomic datasets for systems-level analyses.

Methodology:

Digitization of scattered microbial records, text mining and integration of metadata from culture collections and literature, with data exposed via the BacDive WS API in JSON and XML formats.