ARGminer

ARGminer facilitates curation and validation of antibiotic resistance genes (ARGs) by combining sequence alignment evidence and crowdsourced annotations to produce comprehensive, validated ARG annotations.

Key Features:

• Multi-Level Annotation: Supports annotation at gene name, antibiotic category, resistance mechanism, and evidence for mobility and occurrence in clinically-important bacterial strains.
• Sequence-alignment Evidence Aggregation: Aggregates evidence from sequence alignment and multiple sources to inform annotations.
• Crowdsourcing Strategy: Employs crowdsourcing to expand curation capacity and generate community curator annotations.
• Trust Validation Filter: Applies a trust validation filter to reject confounding or spam inputs and improve reliability of curated data.
• Validation against Expert Curation: Validated across multiple curator cohorts, achieving annotation accuracy greater than 90% compared with expert annotation.
• Comparative Efficiency: Demonstrated to be more cost-effective and less time-consuming than traditional expert curation while maintaining high accuracy.

Scientific Applications:

• ARG Database Curation: Curation and validation of comprehensive ARG databases using aggregated evidence and crowdsourced annotations.
• ARG Attribute Annotation: Annotation of gene name, antibiotic category, resistance mechanism, mobility evidence, and occurrence in clinically-important bacterial strains.
• Annotation Benchmarking: Comparison of crowdsourced annotations to expert curation to assess and quantify annotation accuracy.

Methodology:

Combines sequence alignment and aggregation of evidence from multiple sources, crowdsourced curator annotations, a trust validation filter to reject confounding inputs, and validation against expert curation cohorts.