What this entity is
Canonical name: PROTECT Genome Depot. 1
Known aliases: protect_genomedepot; PROTECT. 1
Stable external identifier: No stable external identifier is specified in the source document. 1
PROTECT Genome Depot is a dataset catalog used for pathogen-genome data within the KBase Data Lakehouse inventory. 1
Key facts
The BERDL Data Atlas reports that the PROTECT tenant contains 4% of the inventoried tables, appears in 2 of 66 audited BERIL projects, and covers 6 biological topics. 1
PROTECT has a topic-coverage entropy of 2.37 in the atlas comparison. 1
The atlas recommends PROTECT Genome Depot for pathogen-genome data. 1
The cf formulation study supports this pathogen-genome recommendation by analyzing 643 annotated PROTECT genomes: 304 (47%) were PAO1-like, 48 (7%) were PA14-like, and 291 (45%) were intermediate; among classifiable isolates, 86% were PAO1-like. 2
The study further refines the dataset’s pathogen-diversity context: PROTECT isolates were distributed across the broader lung-PA diversity in a Pfam-based tree of 165 genomes rather than clustering in one lineage. 2
The proposed UC4 bridge between NMDC and PROTECT had 10 shared schema-level join keys and zero realized use at audit time; the proposed use was to study environmental distributions of clinically relevant pathogens and associated biogeochemistry. 1
The UC4 bridge remains a proposal rather than a validated integration because the atlas sample-validated only UC1; UC4 requires live-cluster execution to establish value-space overlap. 1
The dataset is therefore relevant to environmental-resistome, particularly analyses connecting environmental samples with pathogen genomes and resistance-associated context. 1
The dataset is also part of the cross-tenant integration opportunities described in BERDL Data Atlas — Inventory, Topic Map, and Cross-Reference Synergies. 1
The new formulation analysis is documented in Rational Design of Protective Microbiome Formulations for Competitive Exclusion of *Pseudomonas aeruginosa* in Cystic Fibrosis Airways. 2