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PROTECT Pathogen Browser

protect_genomedepot

Domain

Philosophy

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

Data sources: PROTECT

Scale

6
tables

Schema Browser

Tables (2)

browser_genome browser_gene_sampled

browser_gene_sampled

## Pitfalls

Column Type Description
id string **Primary Key**
name string Gene name
locus_tag string Locus tag
type string Feature type
start string Start position
end string End position
strand string Strand
function string Gene function
contig_id string FK -> contig
genome_id string FK -> `browser_genome`
operon_id string Operon identifier
protein_id string Protein identifier

Sample Queries

Get pathogen genomes

SELECT *
FROM protect_genomedepot.browser_genome
LIMIT 20

Projects Using This Collection

CF Protective Microbiome Formulation Design

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

Start Exploring

Access the full PROTECT Pathogen Browser data through BERDL JupyterHub.

Open JupyterHub