# Exporting To Fhir

Convert OpenMed NER output (entities from openmed.analyze_text) into FHIR R4 resources...

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

## Description

Convert OpenMed NER output (entities from openmed.analyze_text) into FHIR R4 resources, Condition, MedicationStatement, Observation, using OpenMed's built-in FHIR R4 export helpers in openmed.clinical.exporters. Covers the verified CodeableConcept builder (coding, codeable_concept, system_uri), deterministic fullUrl references, and OperationOutcome reporting. Use after running OpenMed NER when the user wants standards-conformant FHIR JSON, mentions FHIR, Condition/Observation/MedicationStatement, CodeableConcept, RxNorm/LOINC/ICD-10/SNOMED coding, or interoperability with an EHR. Pairs after extracting-clinical-entities; feeds assembling-fhir-bundles and validating-us-core.

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

# Exporting to FHIR

OpenMed's NER (`openmed.analyze_text`) returns spans, text, label, offsets,
confidence. To make those spans interoperable you wrap each clinically relevant
span in a **FHIR R4 resource** (`Condition`, `MedicationStatement`,
`Observation`, ...) carrying a coded `CodeableConcept`. OpenMed ships the
**mechanical** R4 export helpers for this in `openmed.clinical.exporters`; you
own the small amount of clinical mapping (which span becomes which resource).

## When to use

Use this after NER, when the consumer is a FHIR system (an EHR, a registry, a
data lake on FHIR). Reach for it when the user says "export to FHIR", "make a
Condition/Observation", "build a CodeableConcept", or needs RxNorm/LOINC/ICD-10/
SNOMED-coded resources. For packaging many resources into one transaction
Bundle, hand off to `assembling-fhir-bundles`. To check the result against US
Core, hand off to `validating-us-core`.

## What OpenMed gives you (verified API)

OpenMed deliberately ships the *purely mechanical* pieces and leaves clinical
judgement to you. The verified entry points:

```python
# CodeableConcept builder, openmed/clinical/exporters/codeable_concept_simple.py
from openmed.clinical.exporters.codeable_concept_simple import (
    system_uri,        # vocab id -> canonical HL7 system URI
    coding,            # (system, code, display) -> Coding dict
    codeable_concept,  # [Coding, ...] -> CodeableConcept dict (deterministic order)
)

# Bundle + reference + OperationOutcome, openmed/clinical/exporters/fhir/
from openmed.clinical.exporters.fhir import (
    to_bundle,                 # [resource, ...] -> R4 transaction Bundle
    deterministic_fullurl,     # (doc_id, index) -> stable urn:uuid
    OperationOutcomeIssue,     # issue dataclass
    to_operation_outcome,      # [issue, ...] -> OperationOutcome
    from_validation_result,    # validator result -> OperationOutcome
)
```

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