# Fetching Fhir Resources

Fetches and pages FHIR R4 resources (Patient, DocumentReference, DiagnosticReport...

- Repository: https://github.com/maziyarpanahi/openmed (5755 stars)
- Category: Engineering
- License: Apache-2.0
- Last updated: 2026-10-31
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add maziyarpanahi/openmed --skill fetching-fhir-resources -g -a claude-code -y`
Codex: `npx skills add maziyarpanahi/openmed --skill fetching-fhir-resources -g -a codex -y`
Cursor: `npx skills add maziyarpanahi/openmed --skill fetching-fhir-resources -g -a cursor -y`
Gemini CLI: `npx skills add maziyarpanahi/openmed --skill fetching-fhir-resources -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add maziyarpanahi/openmed`

## Description

Fetches and pages FHIR R4 resources (Patient, DocumentReference, DiagnosticReport, Observation, Condition) from a FHIR REST server, decodes base64 attachments, and extracts clinical narrative for OpenMed. Use before OpenMed processing when pulling charts from an EHR FHIR API (Epic, Cerner/Oracle, HAPI, or any US Core server) and you need the note text de-identified and analyzed, then results rejoined by patient. Hand narrative to openmed.deidentify and openmed.analyze_text; openmed.interop.fhir_operations implements a $de-identify operation over Bundles. Trigger keywords: FHIR, R4, US Core, DocumentReference, DiagnosticReport, Bundle, _revinclude, presentedForm, base64, EHR API.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# Fetching FHIR R4 Resources for OpenMed

FHIR R4 is the modern EHR API: a RESTful, JSON-or-XML interface over resources
like `Patient`, `Encounter`, `Condition`, `Observation`, `DiagnosticReport`,
and `DocumentReference`. The unstructured clinical text you want for NLP lives
in **`DocumentReference.content.attachment`** and
**`DiagnosticReport.presentedForm`**, usually **base64-encoded** PDF, RTF, or
plain text. This skill pulls those resources, pages through results, decodes the
attachments, and hands the narrative to OpenMed.

## When to use

- You have FHIR R4 access to an EHR (Epic, Oracle Health/Cerner, HAPI, Medplum,
  Azure/Google/AWS HealthLake) and want note text for de-id and NER.
- You need to page a large search result set safely (`Bundle.link[next]`).
- You want to pull a patient's documents/reports and rejoin NLP output by
  patient and encounter.

## FHIR REST in one minute

Search is `GET [base]/[Type]?param=value`. Results come back as a
**searchset `Bundle`**; the next page is the URL in `Bundle.link` where
`relation == "next"`. Use `_count` to size pages, `_revinclude` to pull related
resources in one round trip, and `_since`/`_lastUpdated` for incremental sync.

```
GET /Patient?identifier=http://hospital.org/mrn|12345
GET /DocumentReference?patient=Patient/abc&category=clinical-note&_count=50
GET /DiagnosticReport?patient=Patient/abc&_revinclude=Observation:related
```

## Quick start

Page a search, decode attachments, hand narrative to OpenMed:

```python
import base64
import requests
import openmed

BASE = "https://fhir.example.org/r4"
HEADERS = {"Accept": "application/fhir+json", "Authorization": "Bearer <token>"}

The rest: https://github.com/maziyarpanahi/openmed/blob/HEAD/skills/fetching-fhir-resources/SKILL.md