BacDiveR: A Programmatic Interface For BacDive

BacDiveR provides programmatic access to the BacDive bacterial diversity metadatabase (DSMZ), enabling retrieval of organism-linked metadata for bacterial and archaeal strains including taxonomic classification, morphology, physiology, cultivation, natural habitat, geographic origin, application, and interactions for downstream analysis.

Key Features:

• Programmatic access: Query BacDive and retrieve structured records of taxonomy, morphology, physiology, cultivation, habitat, geographic origin, application, and interactions for bacterial and archaeal strains.
• Data download: Download BacDive records for offline analysis and integration into computational workflows.
• Reproducibility: Document and script searches and downloads in .R and .Rmd files to support reproducible data analysis pipelines.
• R integration: Expose BacDive data via an R package interface for direct use within R analysis environments.

Scientific Applications:

• Taxonomic and comparative analyses: Retrieve taxonomic metadata and organism attributes to compare strains across taxa.
• Phenotypic and physiological trait analysis: Use morphology and physiology records to analyse trait distributions and correlations.
• Cultivation and experimental design: Use cultivation and growth-condition data to inform laboratory culture conditions and experimental setups.
• Biogeography and ecology: Use natural habitat and geographic origin metadata to study strain distributions and ecological patterns.
• Applied microbiology and interactions: Link strains to applications and recorded interactions for biotechnological or ecological investigations.
• Reproducible data pipelines: Incorporate scripted searches and downloads in .R/.Rmd to produce reproducible datasets for downstream analysis.

Methodology:

Provide programmatic functions to query BacDive, retrieve and download structured strain records, and document searches and downloads in .R and .Rmd scripts.