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PROTECT Pathogen Browser

protect_genomedepot

Tenant: PROTECT · Snapshot 2026-04-29T21:35:53.838483+00:00

Domain

Schema status

discovered

Curation status

curated

Source

berdl-spark-connect://metrics.berdl.kbase.us:443

Philosophy

Support pathogen surveillance research. Catalog pathogen genomes, track strain variation, and enable comparative genomic analysis for public health applications.

Data sources: PROTECT

Citation & Attribution

Provider: PROTECT

Scale

6
tables

Schema Browser

Tables (37)

browser_annotation browser_cazy_family browser_cog_class browser_contig browser_ec_number browser_eggnog_description browser_gene browser_genome browser_genome_tags browser_go_term browser_kegg_ortholog browser_kegg_pathway browser_kegg_reaction browser_operon browser_ortholog_group browser_protein browser_protein_cazy_families browser_protein_cog_classes browser_protein_ec_numbers browser_protein_go_terms browser_protein_kegg_orthologs browser_protein_kegg_pathways browser_protein_kegg_reactions browser_protein_ortholog_groups browser_protein_tc_families browser_regulon browser_regulon_regulators browser_sample browser_sample_metadata browser_site browser_site_genes browser_site_operons browser_strain browser_strain_metadata browser_tag browser_taxon browser_tc_family

browser_protein_kegg_orthologs

Column Type Description

Sample Queries

Get pathogen genomes

SELECT *
FROM protect_genomedepot.browser_genome
LIMIT 20

Projects Using This Collection

BERDL Data Atlas — Inventory, Topic Map, and Cross-Reference Synergies

What data is available in BERDL (across tenants, agencies, and programs), what biological topics does it cover, and wher...

Metagenome-Prioritized Phage Cocktails for Crohn's Disease and IBD

Which bacterial pathobionts are **enriched, ubiquitous, and non-protective** in IBD, UC, and Crohn's disease patients — ...

CF Protective Microbiome Formulation Design

Can we build a multi-criterion framework that explains measured *P. aeruginosa* PA14 inhibition from metabolic competiti...

Atlas Pages

data type

Phage, Mobile Elements, and Defense

Host-specific phage browsers, pathogen genome views, and mobile-element signals used to reason about host range, defense, resistance, and engineered interventions.

 data type

Host, Clinical, Pathogen, and Isolate Data

Collections organized around host-associated samples, pathogen isolates, clinical context, or strain-level interpretation.

 derived product

CF Formulation Scores

Reusable formulation scoring outputs for CF airway community design and Pseudomonas competition analysis.

 data collection

PROTECT

Pathogen genome browser (GenomeDepot format)

 topic

Mobile Elements, Phage, and Genome Plasticity

Synthesis of phage ecology, prophage signals, defense systems, mobile-element gene flow, and intervention relevance.

Atlas Reuse

ranking

CF Formulation Scores

candidate · 0 downstream projects

Start Exploring

Access the full PROTECT Pathogen Browser data through BERDL JupyterHub.

Open JupyterHub