AMRnet: Data Architecture & Platform Overview

A comprehensive platform for antimicrobial resistance genomic surveillance

1
Data Sources & Automated Ingestion
Public Genomic Databases
PW
Pathogenwatch
S. Typhi, K. pneumoniae, N. gonorrhoeae data with AMR predictions
EB
Enterobase
E. coli, Shigella, Salmonella with hierarchical clustering
Automated Data Harvesting
🕷️
Spyder Robot
Automated web scraping tool for genomic data extraction
API
Data Ingestion APIs
Custom APIs for automated data retrieval and processing
2
Data Lake & Harmonization
Raw Data Storage
DB
MongoDB Atlas
Raw data store with version control and organism-specific collections
S3
AWS S3 Storage
Backup storage and direct data access buckets
Data Processing & QC
⚙️
Data Harmonization
Country names, regions, date formats, spurious value cleanup
🔍
Quality Control
Validation, deduplication, and metadata standardization
3
MERN Application & Deployment
Frontend (React)
⚛️
Interactive Dashboard
Maps, trends, heatmaps with multi-language support
📊
Data Visualizations
D3.js charts, geographic maps, temporal analysis
Backend & Deployment
🔧
Node.js/Express API
RESTful endpoints with rate limiting and authentication
🚀
Heroku Deployment
Auto-scaling with Fixie proxy for secure DB connections
4
Multi-Modal Data Access
Web Interface
🌐
AMRnet Dashboard
Interactive web application at amrnet.org
📱
Responsive Design
Mobile-friendly with accessibility features
Programmatic Access
🔌
RESTful API
Comprehensive API with 10,000+ req/hour capacity
📁
Direct Downloads
AWS S3 bucket access for bulk data retrieval
8
Pathogen Species
500K+
Genomic Records
75+
Countries
4
Languages
Supported Organisms & Data Sources
Salmonella Typhi
Pathogenwatch
Klebsiella pneumoniae
Pathogenwatch
Neisseria gonorrhoeae
Pathogenwatch
Escherichia coli
Enterobase
Diarrheagenic E. coli
Enterobase
Shigella spp.
Enterobase
Salmonella enterica
Enterobase
Invasive Salmonella
Enterobase
Platform Capabilities & Performance
⚡
70-87% Faster
Load time improvements with optimization
🗜️
90% Compression
Payload size reduction techniques
🔄
Real-time Updates
Automated data synchronization
🌍
Global Coverage
Multi-regional AMR surveillance
📊
Interactive Analytics
Maps, trends, heatmaps, comparisons
🔓
Open Access
Free platform with comprehensive API