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.
Opportunity Hooks
Phage, Mobile Elements, and Defense
Why This Lens Exists
Tenant and database boundaries do not match how scientists or agents plan analyses. This data-type lens groups collections by the kind of evidence they provide and the questions they make easier to ask.
Collections In This Lens
phagefoundry_acinetobacter_genome_browserphagefoundry_klebsiella_genome_browser_genomedepotphagefoundry_paeruginosa_genome_browserphagefoundry_pviridiflava_genome_browserphagefoundry_strain_modellingprotect_genomedepot
Best Uses
Use this lens to find reusable source data before choosing a specific collection. It is especially useful for agents that need to identify complementary data, select join keys, or explain why a derived product is reusable across projects.
Recent project use: prophage_amr_comobilization uses pangenome AMR and prophage markers to make prophage burden a covariate for resistance ecology, while t4ss_cazy_environmental_hgt uses environmental MAGs to connect T4SS neighborhoods, CAZy HGT, and metal-resistance enrichment.
Metrics To Watch
- Evidence traces: which projects already used these collections.
- Reuse: whether derived products exist beyond a single project.
- Under-explored combinations: collection pairs with obvious scientific value but few projects.
- Caveat load: schema gaps, identifier mismatches, sampling bias, and staging status.
- Mechanism partitioning: whether a signal is prophage, plasmid, ICE/IME, T4SS, or generic genome openness.
Caveats
Do not treat collection co-membership as proof that a join is valid. A join recipe should name stable identifiers, filtering rules, and failure modes before it supports a claim.