Data access¶

AMRnet data can be accessed in three ways: (1) directly from the dashboard via the Download button at the bottom of each organism page, (2) as flat files from the public S3 bucket, and (3) programmatically through the public REST API at api.amrnet.org.

1. Download via the dashboard¶

Every organism page in the dashboard has a Download database (TSV format) button at the bottom. This returns the full sample-level dataset for the currently-selected organism, including all curated metadata and AMR determinant fields. No registration is required.

2. Download via the public S3 bucket¶

Up-to-date compressed CSV snapshots of the whole database are published weekly to a public AWS S3 bucket. Choose the organism from the table below and append its key to https://amrnet.s3.amazonaws.com/amrnet-latest/.

Organism	S3 key
Salmonella Typhi	`amrnetdb-Salmonella_Typhi.csv.gz`
Salmonella (non-typhoidal)	`amrnetdb-Salmonella_enterica_nontyphoidal.csv.gz`
Salmonella (invasive non-typhoidal)	`amrnetdb-Salmonella_enterica_invasive_nontyphoidal.csv.gz`
Klebsiella pneumoniae	`amrnetdb-Klebsiella_pneumoniae.csv.gz`
Neisseria gonorrhoeae	`amrnetdb-Neisseria_gonorrhoeae.csv.gz`
Escherichia coli	`amrnetdb-Escherichia_coli.csv.gz`
Escherichia coli (diarrheagenic)	`amrnetdb-Escherichia_coli_diarrheagenic.csv.gz`
Shigella + EIEC	`amrnetdb-Shigella_EIEC.csv.gz`

Example — browser or curl:

# Download the S. Typhi snapshot
curl -O https://amrnet.s3.amazonaws.com/amrnet-latest/amrnetdb-Salmonella_Typhi.csv.gz

# List every file in the bucket (XML response)
curl -s https://amrnet.s3.amazonaws.com/

Example — s3cmd (unauthenticated; the bucket is public-read):

s3cmd --no-check-certificate get s3://amrnet/amrnet-latest/amrnetdb-Salmonella_Typhi.csv.gz

3. Programmatic access: AMRnet REST API¶

The public REST API at https://api.amrnet.org exposes the same curated dataset that powers the dashboard. It replaces the earlier MongoDB Atlas Data API described in previous versions of this document.

3.1 Get an API key¶

Register a key at https://api.amrnet.org/api-register. Registration is free; a key is emailed to you. All endpoints require the key passed either as:

HTTP header — X-API-Key: YOUR_KEY (recommended)
Query parameter — ?api_key=YOUR_KEY

3.2 Interactive docs (Swagger / OpenAPI)¶

Full interactive documentation lives at https://api.amrnet.org/api-docs. Every endpoint has a Try it out button that issues a live request — paste your key into the “Authorize” dialog and the built-in server selector already targets the production host.

The OpenAPI 3.0 spec is available at https://api.amrnet.org/api-docs.json if you want to generate a client library with openapi-generator.

3.3 Endpoints¶

3.4 Quick start — `curl`¶

API_KEY="your-registered-api-key"

# List every organism with its current genome count
curl -H "X-API-Key: $API_KEY" https://api.amrnet.org/api/v1/organisms

# Resistance prevalence for S. enterica in Brazil
curl -H "X-API-Key: $API_KEY" \
  "https://api.amrnet.org/api/v1/organisms/senterica/resistance?country=Brazil"

# Per-country summary for E. coli
curl -H "X-API-Key: $API_KEY" https://api.amrnet.org/api/v1/organisms/ecoli/countries

# Full CSV export for S. Typhi
curl -H "X-API-Key: $API_KEY" \
  "https://api.amrnet.org/api/v1/organisms/styphi/download?format=csv" \
  -o styphi.csv

3.5 Quick start — Python¶

import requests
import pandas as pd

BASE = "https://api.amrnet.org/api/v1"
HEADERS = {"X-API-Key": "your-registered-api-key"}

# Organism list
orgs = requests.get(f"{BASE}/organisms", headers=HEADERS).json()

# Resistance prevalence for S. Typhi
r = requests.get(
    f"{BASE}/organisms/styphi/resistance",
    headers=HEADERS,
    params={"country": "India", "year_from": 2018, "year_to": 2023},
).json()

df = pd.DataFrame(r["data"])

3.6 Quick start — R¶

library(httr)
library(jsonlite)

base <- "https://api.amrnet.org/api/v1"
key  <- "your-registered-api-key"

r <- GET(
  paste0(base, "/organisms/kpneumo/resistance"),
  add_headers(`X-API-Key` = key),
  query = list(country = "Pakistan")
)
df <- fromJSON(content(r, "text"))$data

3.7 Rate limits¶

/api/v1/* — 30 requests / second per IP, bursts of 50
/api/v1/organisms/*/download — 2 requests / second per IP, bursts of 5

These limits are enforced by nginx upstream of the Node application. If you need a bulk export, the S3 snapshots in section 2 are the recommended source — no key, no rate limit, and the file is already compressed.

Citation¶

If you use AMRnet data in published work, please cite:

Cerdeira LT, Dyson ZA, Sharma V, et al. AMRnet: a data visualization platform to interactively explore pathogen variants and antimicrobial resistance. Nucleic Acids Res. 2025. doi: 10.1093/nar/gkaf1101.

Please also cite the upstream data sources relevant to the organism(s) you queried — these are listed on each pathogen page and under Source data & tools.