Agent skill

Extract Clinical Entities To Fhir

by maziyarpanahi in maziyarpanahi/openmed

Extract clinical entities from synthetic or already de-identified text with OpenMed and map them into deterministic FHIR R4 resources and a Bundle.

Apache-2.0Auto-check passedResearch & Science

Install Extract Clinical Entities To Fhir

skills CLI

$ npx skills add maziyarpanahi/openmed --skill extract-clinical-entities-to-fhir -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install maziyarpanahi/openmed extract-clinical-entities-to-fhir --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/extract-clinical-entities-to-fhir .claude/skills/extract-clinical-entities-to-fhir && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "extract-clinical-entities-to-fhir" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/extract-clinical-entities-to-fhir into .claude/skills/extract-clinical-entities-to-fhir/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "extract-clinical-entities-to-fhir", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/maziyarpanahi/openmed/tree/master/skills/extract-clinical-entities-to-fhir

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add maziyarpanahi/openmed --skill extract-clinical-entities-to-fhir -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install maziyarpanahi/openmed extract-clinical-entities-to-fhir --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/extract-clinical-entities-to-fhir .agents/skills/extract-clinical-entities-to-fhir && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "extract-clinical-entities-to-fhir" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/extract-clinical-entities-to-fhir into .agents/skills/extract-clinical-entities-to-fhir/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "extract-clinical-entities-to-fhir", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add maziyarpanahi/openmed --skill extract-clinical-entities-to-fhir -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install maziyarpanahi/openmed extract-clinical-entities-to-fhir --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/extract-clinical-entities-to-fhir .cursor/skills/extract-clinical-entities-to-fhir && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "extract-clinical-entities-to-fhir" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/extract-clinical-entities-to-fhir into .cursor/skills/extract-clinical-entities-to-fhir/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "extract-clinical-entities-to-fhir", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/maziyarpanahi/openmed.git --path skills/extract-clinical-entities-to-fhir

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add maziyarpanahi/openmed --skill extract-clinical-entities-to-fhir -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install maziyarpanahi/openmed extract-clinical-entities-to-fhir --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/extract-clinical-entities-to-fhir .gemini/skills/extract-clinical-entities-to-fhir && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "extract-clinical-entities-to-fhir" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/extract-clinical-entities-to-fhir into .gemini/skills/extract-clinical-entities-to-fhir/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "extract-clinical-entities-to-fhir", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install maziyarpanahi/openmed extract-clinical-entities-to-fhir

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add maziyarpanahi/openmed --skill extract-clinical-entities-to-fhir -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/extract-clinical-entities-to-fhir .github/skills/extract-clinical-entities-to-fhir && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "extract-clinical-entities-to-fhir" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/extract-clinical-entities-to-fhir into .github/skills/extract-clinical-entities-to-fhir/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "extract-clinical-entities-to-fhir", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add maziyarpanahi/openmed --skill extract-clinical-entities-to-fhir -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install maziyarpanahi/openmed extract-clinical-entities-to-fhir --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/extract-clinical-entities-to-fhir .opencode/skills/extract-clinical-entities-to-fhir && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "extract-clinical-entities-to-fhir" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/extract-clinical-entities-to-fhir into .opencode/skills/extract-clinical-entities-to-fhir/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "extract-clinical-entities-to-fhir", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: extract-clinical-entities-to-fhir
GitHub stars: 5.5k
Token cost: ~940 tokens
SKILL.md length: 206 words
Files: 1
Skills in repo: 74
Repo updated: Oct 11, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

Extract clinical entities from synthetic or already de-identified text with OpenMed and map them into deterministic FHIR R4 resources and a Bundle.

Works in 6 steps: Keep the source synthetic, or… → Run openmed.analyze_text with the… → Filter predictions by label and… → …
An agent must turn local clinical NER output into Conditions
SKILL.md covers Procedure, Runnable synthetic example, Safety checks and Repository example
Calls python; reaches terminology.hl7.org

What it does

Extract Clinical Entities To Fhir is an agent skill from maziyarpanahi/openmed. Extract clinical entities from synthetic or already de-identified text with OpenMed and map them into deterministic FHIR R4 resources and a Bundle. Use when an agent must turn local clinical NER output into Conditions, MedicationStatements, Observations, or other FHIR resources without inventing terminology codes.

Its SKILL.md is about 940 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Clinical and healthcare research. The repository describes itself as: Local-first healthcare AI: clinical NER and HIPAA PII de-identification on hardware you control. 2,200+ medical models, 35 model-backed PII languages, and Python, MLX, Android… The licence is Apache-2.0.

When your agent uses it

An agent must turn local clinical NER output into Conditions
MedicationStatements
Other FHIR resources without inventing terminology codes

Example prompts

“/extract-clinical-entities-to-fhir”

Requirements

Python 3

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

Keep the source synthetic, or de-identify it inside the trusted boundary
Run openmed.analyze_text with the task-appropriate clinical model.
Filter predictions by label and confidence; preserve offsets in a
Map each accepted span to the correct FHIR resource type.
Add terminology codes only from a user-approved mapping or terminology
Assemble resources with to_bundle and validate against the target profile.

What it can do on your machine

Read from SKILL.md and the folder at commit 34d7b8c. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
- python
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
- terminology.hl7.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Extract Clinical Entities To Fhir loads about 940 tokens when it runs. Until then it costs about 87 tokens; SKILL.md has 206 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~87
When it runs · the whole SKILL.md, loaded when a task matches: ~940

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from maziyarpanahi/openmed at commit 34d7b8c, republished under its Apache-2.0 licence (© maziyarpanahi). 206 words, ~940 tokens.

Download SKILL.mdSave it as .claude/skills/extract-clinical-entities-to-fhir/SKILL.md (or your agent's skills folder).

name: extract-clinical-entities-to-fhir
description: Extract clinical entities from synthetic or already de-identified text with OpenMed and map them into deterministic FHIR R4 resources and a Bundle. Use when an agent must turn local clinical NER output into Conditions, MedicationStatements, Observations, or other FHIR resources without inventing terminology codes.

Extract clinical entities to FHIR

Separate extraction from clinical coding. OpenMed finds spans and supplies the mechanical FHIR builders; the application decides which resource type and status are clinically appropriate.

Procedure

Keep the source synthetic, or de-identify it inside the trusted boundary before extraction.
Run openmed.analyze_text with the task-appropriate clinical model.
Filter predictions by label and confidence; preserve offsets in a PHI-safe audit record.
Map each accepted span to the correct FHIR resource type.
Add terminology codes only from a user-approved mapping or terminology service. Never invent a code.
Assemble resources with to_bundle and validate against the target profile.

Runnable synthetic example

Install the model runtime first with python -m pip install "openmed[hf]".

python

import json

from openmed import analyze_text
from openmed.clinical.exporters.fhir import to_bundle

note = "Assessment: type 2 diabetes mellitus is stable on metformin."
result = analyze_text(
    note,
    model_name="disease_detection_superclinical",
    confidence_threshold=0.5,
)

resources = [{"resourceType": "Patient", "id": "synthetic-patient"}]
for index, entity in enumerate(result.entities, start=1):
    if entity.label.upper() not in {"CONDITION", "DIAGNOSIS", "DISEASE"}:
        continue
    resources.append(
        {
            "resourceType": "Condition",
            "id": f"condition-{index}",
            "clinicalStatus": {
                "coding": [
                    {
                        "system": (
                            "http://terminology.hl7.org/CodeSystem/"
                            "condition-clinical"
                        ),
                        "code": "active",
                    }
                ]
            },
            "verificationStatus": {
                "coding": [
                    {
                        "system": (
                            "http://terminology.hl7.org/CodeSystem/"
                            "condition-ver-status"
                        ),
                        "code": "confirmed",
                    }
                ]
            },
            # A text-only CodeableConcept is preferable to an invented code.
            "code": {"text": entity.text},
            "subject": {"reference": "Patient/synthetic-patient"},
        }
    )

if len(resources) == 1:
    raise RuntimeError("No condition spans met the label and confidence rules")

bundle = to_bundle(resources, doc_id="synthetic-note-001")
print(json.dumps(bundle, indent=2))

Safety checks

Do not put raw identifiers, source text, or reversible mappings in logs, OperationOutcome.diagnostics, or trace metadata.
Keep a patient identity service separate from extracted clinical facts.
Preserve negation, temporality, and experiencer context before asserting a resource as active or confirmed.
Use a text-only CodeableConcept when no approved code is available.
Validate the Bundle against the receiver's FHIR and profile requirements.
Do not bundle restricted terminologies; use the user's licensed service.

Repository example

Read and run the redaction-to-FHIR walkthrough for an offline-friendly pipeline with deterministic extraction.

Files

Just SKILL.md in skills/extract-clinical-entities-to-fhir of maziyarpanahi/openmed.

Open the folder on GitHubat commit 34d7b8c

Compare with similar skills

Extract Clinical Entities To Fhir next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Extract Clinical Entities To Fhir compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Extract Clinical Entities To Fhir this skillmaziyarpanahi/openmed	5.5k	—	~940	Automated safety check: Pass	Apache-2.0	today
Clinical Trials Databasegoogle-deepmind/science-skills	3.2k	2 repos	~3.2k	Automated safety check: Pass	Apache-2.0	yesterday
CHARLS Paper Reproduction Guidexjtulyc/MedgeClaw	617	1 repos	~1.8k	Automated safety check: Pass	None	7 mo ago
Biomedical Analysis Dispatchxjtulyc/MedgeClaw	617	1 repos	~2k	Automated safety check: Pass	None	7 mo ago
Research Paperluwill/research-skills	862	—	~1.9k	Automated safety check: Pass	None	yesterday
Research Proposalluwill/research-skills	862	—	~4.5k	Automated safety check: Notes	None	yesterday

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Questions about Extract Clinical Entities To Fhir

What does Extract Clinical Entities To Fhir do?

Extract clinical entities from synthetic or already de-identified text with OpenMed and map them into deterministic FHIR R4 resources and a Bundle. Extract Clinical Entities To Fhir is an agent skill from maziyarpanahi/openmed. Extract clinical entities from synthetic or already de-identified text with OpenMed and map them into deterministic FHIR R4 resources and a Bundle.

When should I use Extract Clinical Entities To Fhir?

Extract Clinical Entities To Fhir fits situations like: an agent must turn local clinical NER output into Conditions; medicationStatements; other FHIR resources without inventing terminology codes.

How do I install Extract Clinical Entities To Fhir in Claude Code?

Run `npx skills add maziyarpanahi/openmed --skill extract-clinical-entities-to-fhir -a claude-code`. Or copy the skill folder (skills/extract-clinical-entities-to-fhir in maziyarpanahi/openmed) into .claude/skills/extract-clinical-entities-to-fhir in your project. Claude Code loads it when a task matches its description.

How do I install Extract Clinical Entities To Fhir in Codex?

Run `npx skills add maziyarpanahi/openmed --skill extract-clinical-entities-to-fhir -a codex`. Or copy the skill folder (skills/extract-clinical-entities-to-fhir in maziyarpanahi/openmed) into .agents/skills/extract-clinical-entities-to-fhir in your project. Codex loads it when a task matches its description.

Can I use Extract Clinical Entities To Fhir in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add maziyarpanahi/openmed --skill extract-clinical-entities-to-fhir -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/extract-clinical-entities-to-fhir, .gemini/skills/extract-clinical-entities-to-fhir, .github/skills/extract-clinical-entities-to-fhir and .opencode/skills/extract-clinical-entities-to-fhir in your project.

What does Extract Clinical Entities To Fhir need to run?

Going by SKILL.md and its folder, Extract Clinical Entities To Fhir needs the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Extract Clinical Entities To Fhir access the network?

SKILL.md names 1 domain. In commands or code: terminology.hl7.org; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.

Is Extract Clinical Entities To Fhir safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Extract Clinical Entities To Fhir use?

Extract Clinical Entities To Fhir is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Extract Clinical Entities To Fhir use?

About 940 tokens (SKILL.md is roughly 3.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Extract Clinical Entities To Fhir?

Skills that share tags, products or a category with Extract Clinical Entities To Fhir: Clinical Trials Database (google-deepmind/science-skills, 3.2k stars), CHARLS Paper Reproduction Guide (xjtulyc/MedgeClaw, 617 stars), Biomedical Analysis Dispatch (xjtulyc/MedgeClaw, 617 stars) and Research Paper (luwill/research-skills, 862 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Extract Clinical Entities To Fhir?

maziyarpanahi (a GitHub user) maintains it in maziyarpanahi/openmed, which has 5,506 GitHub stars. The repository holds 74 skills in this directory. The repository was last updated on October 11, 2026.

Source: maziyarpanahi/openmed on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Extract Clinical Entities To Fhir

Install Extract Clinical Entities To Fhir

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Extract clinical entities to FHIR

Procedure

Runnable synthetic example

Safety checks

Repository example

Files

Compare with similar skills

Similar skills

Clinical Trials Database

CHARLS Paper Reproduction Guide

Biomedical Analysis Dispatch

Research Paper

Research Proposal

Medical Imaging Review

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Questions about Extract Clinical Entities To Fhir

Install Extract Clinical Entities To Fhir

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Extract clinical entities to FHIR

Procedure

Runnable synthetic example

Safety checks

Repository example

Files

Compare with similar skills

Similar skills

More from maziyarpanahi/openmed

Related

Questions about Extract Clinical Entities To Fhir