Exporting Bulk Fhir
Kick off and harvest a FHIR Bulk Data $export (system-, group-, or patient-level) and...
Install
npx skills add maziyarpanahi/openmed --skill exporting-bulk-fhir -g -a claude-code -y- Repository
- maziyarpanahi/openmed5.8k
- Category
- Writing
- Updated
- 4d ago
- License
- Apache-2.0
- Context cost
- Mediumabout 1,694 tokens
- Runs scripts
- No, instructions only
What it does
Kick off and harvest a FHIR Bulk Data $export (system-, group-, or patient-level) and stream the resulting NDJSON into a batch OpenMed de-identification + NER pipeline at cohort scale. Covers the async kickoff (Prefer respond-async) -> poll Content-Location -> download NDJSON flow, the Bulk Data Access IG, _type/_since filters, and feeding DocumentReference/DiagnosticReport notes into openmed.deidentify in batch. Use when the user needs population-scale note extraction from an EHR or data warehouse to feed OpenMed, mentions bulk export, $export, NDJSON, Flat FHIR, or cohort de-identification. Pairs before the OpenMed de-id/NER pipeline.
Exporting Bulk FHIR
When you need cohort-scale clinical text, not one patient in a UI, you use
the FHIR Bulk Data Access ($export) operation: an async job that emits
NDJSON files of resources you then stream into OpenMed for batch
de-identification and NER. This skill sits before the OpenMed pipeline: it is
how the notes arrive.
When to use
Reach for it when the source is an EHR or FHIR data warehouse and the volume is
a population/group (thousands of patients), the workload is headless (no
clinician UI), and the goal is to batch-feed openmed.deidentify /
openmed.analyze_text. Triggers: "bulk export", "$export", "NDJSON", "Flat
FHIR", "cohort de-identification", "export all notes". For a single in-chart
patient with a UI, use scaffolding-smart-on-fhir instead.
Three export levels
- System,
GET [base]/$export, everything the client is authorized for. - Group,
GET [base]/Group/[id]/$export, a defined cohort (most common). - Patient,
GET [base]/Patient/$export, all patients in scope.
Bulk export uses SMART Backend Services auth (a system/*.read-scoped
client-credentials token via a signed JWT assertion), not an interactive launch.
Quick start: kickoff → poll → download
# 1) Kickoff (async). Ask for clinical-note-bearing resource types.
curl -s -X GET \
'https://ehr.example/fhir/Group/cohort-42/$export?_type=DocumentReference,DiagnosticReport&_since=2024-01-01T00:00:00Z' \
-H 'Authorization: Bearer <backend-services-token>' \
-H 'Accept: application/fhir+json' \
-H 'Prefer: respond-async' -D -
# -> 202 Accepted
# Content-Location: https://ehr.example/fhir/bulkstatus/JOB123
