BERIL Knowledge Wiki

Dataset

PROTECT Gold

Corroborated. AI-generated wiki from AI-conducted research reports. Partially reviewed by scientists. See About This Wiki.

Sources cited
1 project report and 1 cross-project digest, listed in the margin
Linked from
1 page

PROTECT Gold (stored at ~/protect/gold/) is a named data collection of 23 tables (30.5M rows). It covers an isolate catalog, inhibition assays, carbon utilization, growth kinetics, patient metagenomics and pairwise interactions. 1

Data-quality caveat

Two PROTECT Gold tables, fact_pairwise_interaction and fact_carbon_utilization, contain identical values (correlation = 1.0, mean difference = 0.0). This was flagged in the cf_formulation_design project. The endpoint optical-density (OD) data therefore does not capture co-culture metabolic interactions. Only the RFU-based (relative fluorescence unit) competition assay provides pairwise interaction effects. Analyses that need pairwise effects should not treat fact_pairwise_interaction as an independent measurement. 2

Sources cited

  1. Rational Design of Protective Microbiome Formulations for Competitive Exclusion of *Pseudomonas aeruginosa* in Cystic Fibrosis Airwayscf_formulation_design · cited 1×
  2. KBase Data Lakehouse: Common Pitfalls & Gotchaspitfalls · cited 1× · cross-project digest