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Database Overview

PBI-Scope stores metadata and sequence assets in complementary layers.

Database Reports

For a quick visual overview of all PhageScope tables and data quality, see the Database Validation Report and Phage Metadata Report.

Current Statistics

Metric Value
Phages in DB 1,350,644
Proteins in DB 71,971,209
Hosts in DB 5,529
Phage-Host Associations 1,241,301
Phage sequences 1,327,915
Protein sequences 71,969,191
Host sequences 5,517

Core structure

  • DuckDB: phage-centric star schema for analytical metadata queries
  • Indexed FASTA files: phage/protein sequences and host genomes
  • Link/mapping files: host and private-source resolution paths

Schema (DuckDB)

                     dim_proteins -------------------+
                  dim_terminators -------------------+
                  dim_anti_crispr -------------------+
             dim_virulent_factors -------------------+
       dim_transmembrane_proteins -------------------+--> fact_phages
                   dim_trna_tmrna -------------------+
dim_antimicrobial_resistance_genes ------------------+
                  dim_crispr_array ------------------+
               dataset_provenance -------------------+
          pipeline_run_provenance -------------------+

Host data is not a DuckDB dimension table. Host sequences are stored as FASTA files and linked via mapping files.

  • phage_host_candidates.csv
  • phage_host_assemblies.csv
  • phage_host_links.csv
  • host_metadata.csv
  • host_fasta_mapping.json
  • private_phage_mapping.json (if private sources are enabled)
  • public_data_manifest.json/.csv
  • pipeline_run_provenance.json/.csv

Data sources

  • Public phage data via PhageScope
  • Optional private source folders from private_data/
  • Host assemblies from NCBI RefSeq