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:

import base64
import requests
import openmed

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