BERIL Knowledge Wiki

Dataset in Translational Microbiome and Phage Therapeutics

PhageFoundry

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Sources cited
3 project reports and 1 cross-project digest, listed in the margin
Relations
supports 2refines 1
Linked from
8 pages4 topics

Identity

Canonical name: PhageFoundry. 1

Known aliases: No aliases are specified in the source document. 1

Stable external identifier: No stable external identifier is specified in the source document. 1

PhageFoundry is a KBase Data Lakehouse dataset and tenant containing phage, mobile-element, and strain-modelling records. 1

Key Facts

PhageFoundry accounts for 14% of the KBase Data Lakehouse tables, and the mobile_phage topic is 96% owned by PhageFoundry. 1 The inventory contains 15,677,623 IMG/VR viral sequence records and 933,103 PhageFoundry strain-modelling gene records. 1

Among 66 audited BERIL projects, PhageFoundry appears in 5 projects, despite containing 14% of the KBase Data Lakehouse tables. 1 The atlas recommends PhageFoundry catalogs for phage and mobile-element data. 1

The discoveries log refines the strain-modelling inventory with a database-level example: PhageFoundry contained 17,672 binary infection outcomes from 188 Escherichia coli strains and 96 phages, supporting its use for strain–phage susceptibility modelling; an ML model achieved AUC=0.883. 2 Lambda infected 1/188 strains (0.5%), compared with 43.4% for Myoviridae, illustrating strong phage-specific variation in the recorded outcomes. 2

The new IBD phage-targeting analysis supports this strain–phage modelling use: its PhageFoundry subset contained 96 phages, 188 Escherichia coli strains, and 17,672 experimentally tested susceptibility pairs, including 3,929 susceptible pairs and a 22 % susceptibility rate. 3 A greedy minimum-set-cover design selected five phages covering 94.7 % of the 188 strains, while an eight-phage design reached 98.4 % coverage. 3 These coverage results refine the atlas-level recommendation by showing a concrete cocktail-design application, but they apply to tested E. coli strains rather than UC Davis patient isolates and do not establish in-vivo efficacy. 3

The discoveries log also supports PhageFoundry as a source for defense-system and mobile-element analyses: the SNIPE defense system occurred in 4,572 gene clusters across 1,696 species and 33 phyla, with 86.7% accessory or singleton. 2 The SNIPE analysis supports and refines this role by linking PhageFoundry’s strain–phage records to a corrected SNIPE architecture and reporting DUF4041 in Klebsiella but not in Acinetobacter, P. aeruginosa, or P. viridiflava in the four-species comparison. 4 It also reports 188 E. coli strains, 96 phages, and 17,672 possible binary infection outcomes, of which 3,929 were positive and 13,743 negative; the model achieved AUC = 0.883 and accuracy = 84.3%. 4 These findings refine rather than replace the atlas’s inventory-level recommendation: database presence and schema compatibility still do not establish complete value-space overlap or biological comparability. 1,2

The atlas identifies an unused UC2 bridge between ENIGMA and PhageFoundry with 11 shared keys for studying subsurface prophages, metal resistance, and the Oak Ridge contamination gradient. 1 UC2 had zero realized use at the time of the audit and requires live-cluster execution because schema-level key compatibility does not establish value-space overlap. 1

Sources cited

  1. BERDL Data Atlas — Inventory, Topic Map, and Cross-Reference Synergiesberdl_data_atlas · cited 11× · primary source · supports · refines
  2. Discoveries Logdiscoveries · cited 4× · cross-project digest · supports · refines
  3. Metagenome-Prioritized Phage Cocktails for Crohn's Disease and IBDibd_phage_targeting · cited 3× · supports
  4. SNIPE Defense System in the KBase Data Lakehouse Pangenomesnipe_defense_system · cited 2× · supports · refines