WHONET Export

WHONET and GLASS Export#

Overview#

Laboratory data stored as FHIR resources can be exported to flat-file formats for use with WHONET or submission to WHO GLASS (Global Antimicrobial Resistance and Use Surveillance System).

The $export-whonet operation on DiagnosticReport flattens the FHIR resource hierarchy into one row per isolate, with a column per antibiotic for S/I/R interpretation and MIC values.

Operation#

POST [base]/DiagnosticReport/$export-whonet

Parameters

Parameter	Type	Description
`start`	date	Specimen collection date range start
`end`	date	Specimen collection date range end
`facility`	string	Filter by facility name
`format`	code	`whonet` (pipe-delimited) or `glass` (GLASS CSV)

Output

A Binary resource with contentType: text/csv containing the flattened data.

How It Works#

Query DiagnosticReports matching the date range and facility filters
For each report, resolve the Encounter (ward type, admission date), Patient (demographics), and Specimen (type, collection date)
For each OrganismObservation in result[organism], create one row
Pivot each SusceptibilityObservation under that organism into columns
Output as pipe-delimited text or GLASS batch CSV

GLASS Classification#

The Encounter profile captures data needed for GLASS origin classification:

Ward type (Encounter.class): Inpatient, outpatient, ICU, or emergency
Admission date (Encounter.period.start): A specimen collected ≥ 2 calendar days after admission is classified as hospital-acquired
Facility (Encounter.serviceProvider): Maps to the GLASS laboratory/institution identifier

Workflow#

Flutter app → FHIR server → $export-whonet → WHONET / GLASS
    │                              │
    │  captures AMR data           │  generates flat files
    │  stores as FHIR resources    │  on demand
    └──────────────────────────────┘

ConceptMaps are used server-side during export to translate FHIR terminology codes to WHONET-native codes. The Flutter application does not need the ConceptMaps — it works with standard FHIR terminologies.

`bw_amr_export` Dart Package#

The export logic is implemented as a standalone Dart package (export/ in the bw-amr-ig repository). It can be used from a FHIR server, a web application, or a CLI tool.

Components

Class	Purpose
`ConceptMapIndex`	Builds reverse lookup tables from ConceptMap JSON (LOINC→WHONET, SNOMED→WHONET, WHONET→ATC)
`ResourceResolver`	Walks DiagnosticReport→OrganismObservation→SusceptibilityObservation and produces `IsolateRow` s
`WhonetExporter`	Generates WHONET pipe-delimited output with dynamic antibiotic columns
`GlassExporter`	Generates WHO GLASS CSV with ATC codes and HA/CO origin classification
`IsolateRow`	Data model for a single flattened isolate row

Usage

import 'dart:io';
import 'package:bw_amr_export/bw_amr_export.dart';
import 'package:fhir_r4/fhir_r4.dart';

// 1. Build the ConceptMap index from JSON files
final index = ConceptMapIndex.fromJson(
  antibioticToLoincJson: File('ConceptMap-whonet-antibiotic-to-loinc.json').readAsStringSync(),
  antibioticToAtcJson: File('ConceptMap-whonet-antibiotic-to-atc.json').readAsStringSync(),
  organismToSnomedJson: File('ConceptMap-whonet-organism-to-snomed.json').readAsStringSync(),
);

// 2. Resolve FHIR resources into flat isolate rows
final resolver = ResourceResolver(index: index);
final rows = resolver.resolve(bundleResources); // List<Resource>

// 3. Export as WHONET pipe-delimited or GLASS CSV
final whonetOutput = WhonetExporter().export(rows);
final glassOutput = GlassExporter(index: index).export(rows);

Installation

dependencies:
  bw_amr_export:
    git:
      url: https://github.com/Dokotela/bw-amr-ig.git
      path: export