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Phagefoundry Paeruginosa Genome Browser

phagefoundry_paeruginosa_genome_browser

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

Domain

Schema status

discovered

Curation status

discovered

Source

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

Citation & Attribution

Provider: PhageFoundry

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_contig

Column Type Description

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...

Atlas Pages

claim

Ecotype analyses need rigor gates before translation

Ecotype-derived target lists can collapse under leakage, confound, and independent-evidence checks, so translation requires explicit gates.

 conflict

Ecotype labels versus translational leakage

Ecotype labels are reusable stratification products, but translational target lists can collapse when labels and outcomes share leaked or confounded features.

 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

Ecotype Assignments

Reusable within-species or community ecotype labels that support environmental validation, microbiome stratification, and downstream hypothesis tests.

 data collection

P. aeruginosa

P. aeruginosa genome browser

 hypothesis

Cross-cohort metabolite ecotypes require batch correction

Absolute-intensity metabolite ecotypes are dominated by cohort batch effects unless corrected before clustering.

 topic

Host Microbiome Translation

Synthesis of IBD phage targeting, formulation design, metabolomics caveats, patient stratification, and intervention cost accounting.

 topic

Mobile Elements, Phage, and Genome Plasticity

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

Atlas Reuse

label_set

Ecotype Assignments

promoted · 2 downstream projects

 partially resolved

Ecotype labels versus translational leakage

Ecotype labels are reusable stratification products, but translational target lists can collapse when labels and outcomes share leaked or confounded features.

Start Exploring

Access the full Phagefoundry Paeruginosa Genome Browser data through BERDL JupyterHub.

Open JupyterHub