Orient and bootstrap any project that uses OpenMed, the on-device clinical and biomedical NLP library, for named-entity recognition, PHI de-identification, FHIR export, and evaluation.
$ npx skills add maziyarpanahi/openmed --skill building-with-openmed -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install maziyarpanahi/openmed building-with-openmed --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/building-with-openmed .claude/skills/building-with-openmed && rm -rf skills-srcUse ~/.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/
Install the "building-with-openmed" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/building-with-openmed into .claude/skills/building-with-openmed/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "building-with-openmed", 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 install https://github.com/maziyarpanahi/openmed/tree/master/skills/building-with-openmedType 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.
$ npx skills add maziyarpanahi/openmed --skill building-with-openmed -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install maziyarpanahi/openmed building-with-openmed --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/building-with-openmed .agents/skills/building-with-openmed && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "building-with-openmed" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/building-with-openmed into .agents/skills/building-with-openmed/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "building-with-openmed", 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.
$ npx skills add maziyarpanahi/openmed --skill building-with-openmed -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install maziyarpanahi/openmed building-with-openmed --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/building-with-openmed .cursor/skills/building-with-openmed && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "building-with-openmed" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/building-with-openmed into .cursor/skills/building-with-openmed/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "building-with-openmed", 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 https://github.com/maziyarpanahi/openmed.git --path skills/building-with-openmed--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add maziyarpanahi/openmed --skill building-with-openmed -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install maziyarpanahi/openmed building-with-openmed --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/building-with-openmed .gemini/skills/building-with-openmed && rm -rf skills-srcUse ~/.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/
Install the "building-with-openmed" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/building-with-openmed into .gemini/skills/building-with-openmed/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "building-with-openmed", 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.
$ gh skill install maziyarpanahi/openmed building-with-openmedInstalls 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).
$ npx skills add maziyarpanahi/openmed --skill building-with-openmed -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/building-with-openmed .github/skills/building-with-openmed && rm -rf skills-srcUse ~/.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/
Install the "building-with-openmed" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/building-with-openmed into .github/skills/building-with-openmed/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "building-with-openmed", 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.
$ npx skills add maziyarpanahi/openmed --skill building-with-openmed -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install maziyarpanahi/openmed building-with-openmed --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/building-with-openmed .opencode/skills/building-with-openmed && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "building-with-openmed" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/building-with-openmed into .opencode/skills/building-with-openmed/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "building-with-openmed", 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.
building-with-openmedOrient and bootstrap any project that uses OpenMed, the on-device clinical and biomedical NLP library, for named-entity recognition, PHI de-identification, FHIR export, and evaluation.
Building With Openmed is an agent skill from maziyarpanahi/openmed. Orient and bootstrap any project that uses OpenMed, the on-device clinical and biomedical NLP library, for named-entity recognition, PHI de-identification, FHIR export, and evaluation. Use when the user mentions OpenMed, wants to install it, asks which OpenMed capability or model fits a task, or is starting to build a clinical/medical text pipeline and needs the right entry point.
Its SKILL.md is about 1.4k 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 AI & LLM Engineering, covering Natural language processing and Clinical and healthcare research. It works with Model Context Protocol. 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.
Read from SKILL.md and the folder at commit 34d7b8c. It shows what the files ask for, not the result of running them.
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.
Shell commands in SKILL.md call:
pipFrom the folder's file list and the shell code blocks in SKILL.md.
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
From URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Building With Openmed loads about 1.4k tokens when it runs. Until then it costs about 101 tokens; SKILL.md has 398 words of instructions outside code blocks.
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.
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.
The full file from maziyarpanahi/openmed at commit 34d7b8c, republished under its Apache-2.0 licence (© maziyarpanahi). 398 words, ~1,443 tokens.
.claude/skills/building-with-openmed/SKILL.md (or your agent's skills folder).OpenMed is an Apache-2.0, local-first Python library for clinical and biomedical NLP. Models download once from the Hugging Face Hub and then run fully on-device — no network calls, no telemetry, no raw PHI in logs, caches, or temp files. This skill is the map: it tells you what OpenMed can do and which focused skill (or API) to reach for next.
Use it to scope a task and pick an entry point. For the actual work, hand off to the focused OpenMed skills (each is grounded in the real API):
| Task | Skill / API |
|---|---|
| Find and load a model | loading-openmed-models, choosing-openmed-models |
| Run clinical/biomedical NER | extracting-clinical-entities (openmed.analyze_text) |
| Zero-shot NER (no fine-tune) | running-zeroshot-ner (openmed zero) |
| Remove / mask PHI | deidentifying-clinical-text (openmed.deidentify) |
| Detect PHI spans only | extracting-pii-entities (openmed.extract_pii) |
| Restore masked PHI | reidentifying-text (openmed.reidentify) |
| Pick a privacy policy | configuring-privacy-policies (7 bundled profiles) |
| Non-English PHI | deidentifying-multilingual-text |
| Signed, no-PHI audit | auditing-deidentification-runs (audit=True) |
| Negation / temporality | resolving-clinical-context (openmed.clinical) |
| Evaluate with leakage gates | evaluating-with-leakage-gates (openmed.eval) |
| FHIR R4 export | exporting-to-fhir (openmed.interop) |
| Serve REST / MCP | serving-openmed-rest-api, deploying-openmed-mcp |
| Run on Apple Silicon / edge | running-openmed-ondevice (MLX / CoreML / ONNX) |
pip install openmed # core: NER + de-identification
pip install "openmed[hf]" # add Hugging Face model downloads
pip install "openmed[mcp]" # Model Context Protocol server
pip install "openmed[service]" # FastAPI REST service
pip install "openmed[mlx]" # Apple Silicon acceleration
pip install "openmed[presidio]" # Microsoft Presidio bridgeExtras map to capabilities: cli, mcp, service, presidio, spacy,
langchain, gliner (zero-shot), multimodal/ocr-paddle (document intake),
mlx/coreml/onnx (on-device backends), hf (model hub), dev (tests/lint).
import openmed
# 1) Named-entity recognition (token classification)
result = openmed.analyze_text(
"Patient prescribed 500 mg metformin for type 2 diabetes.",
model_name="disease_detection_superclinical", # registry key, HF id, or local path
output_format="dict", # dict | json | html | csv
)
# 2) De-identify PHI (mask | remove | replace | hash | shift_dates)
deid = openmed.deidentify(
"John Doe (MRN 12345) seen on 2024-03-02.",
method="replace",
policy="hipaa_safe_harbor", # bundled policy profile
)
print(deid.deidentified_text) # PHI removed; deid.pii_entities lists the spans
# 3) Detect PHI spans without changing the text
pii = openmed.extract_pii("Call Dr. Smith at 617-555-0123.") # PredictionResult
spans = pii.entities # the PHI spansanalyze_text and deidentify are the workhorses. Everything else
(multilingual, audit, policies, FHIR, eval) layers on top of these.
Never hardcode model lists or language counts — query them:
import openmed
openmed.list_model_categories() # e.g. Privacy, Disease, Oncology, Genomics ...
openmed.get_models_by_category("Disease")
openmed.get_pii_models_by_language("es")
from openmed.core.pii_i18n import SUPPORTED_LANGUAGES # de-id language setCLI equivalents: openmed models list, openmed models info <key>,
openmed analyze --text "<text>" --model <key> --format json. MCP/REST expose
the same surface as tools (openmed_analyze_text, openmed_deidentify,
openmed_list_models, …).
audit=True for tamper-evident, no-PHI audit output.openmed.eval, not on F1 alone (see evaluating-with-leakage-gates).ingest (HL7v2 / FHIR / C-CDA / OCR)
→ de-identify (openmed.deidentify, policy=…)
→ extract entities (openmed.analyze_text)
→ ground to terminology (out-of-process: RxNorm / LOINC / SNOMED)
→ assemble FHIR (openmed.interop)
→ evaluate (openmed.eval leakage gates)Each stage has a companion skill in this directory. Start here, then jump to the stage you need.
© maziyarpanahi, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Just SKILL.md in skills/building-with-openmed of maziyarpanahi/openmed.
Open the folder on GitHubat commit 34d7b8c
Building With Openmed 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Building With Openmed this skillmaziyarpanahi/openmed | 5.5k | — | ~1.4k | Automated safety check: Pass | Apache-2.0 | |
| Hcls Build Agentaws-samples/amazon-bedrock-agents-healthcare-lifesciences | 274 | — | ~885 | Automated safety check: Pass | MIT-0 | |
| Find AI Consultancyjeremylongshore/tons-of-skills-marketplace | 2.8k | — | ~4k | Automated safety check: Notes | MIT | |
| Local RAG Searchnkapila6/mcp-local-rag | 134 | 1 repos | ~1.6k | Automated safety check: Pass | MIT | |
| Medical Imaging ReviewLeonChaoX/qinyan-academic-skills | 944 | 3 repos | ~1.1k | Automated safety check: Notes | MIT | |
| Sciverseopendatalab/Sciverse-Agent-Tools | 120 | — | ~3k | Automated safety check: Pass | Custom licence |
aws-samples/amazon-bedrock-agents-healthcare-lifesciences
A skill your agent uses when a developer wants to build a new healthcare or life sciences agent, structure tools and system prompts for an HCLS workflow, or create a Strands agent with…
jeremylongshore/tons-of-skills-marketplace
A skill your agent uses whenever the user wants to find, shortlist, vet, or enrich US AI/ML/data consulting firms (consultancies) — AI/ML development, MLOps, generative AI / LLM apps (RAG, chatbots…
nkapila6/mcp-local-rag
Efficiently perform web searches using the mcp-local-rag server with semantic similarity ranking.
LeonChaoX/qinyan-academic-skills
Write comprehensive literature reviews for medical imaging AI research.
opendatalab/Sciverse-Agent-Tools
A skill your agent uses when the user needs academic paper retrieval — searching scientific literature by author/year/journal, finding paper chunks for RAG-style citations, or expanding original…
lyonzin/knowledge-rag
Every technical claim drawn from the local corpus must ship with a source citation formatted as path:line or path:section.
maziyarpanahi/openmed
Checks OpenMed de-identified clinical text against the 18 HIPAA Safe Harbor identifier categories and reports gaps and residual re-identification risk.
maziyarpanahi/openmed
Fills in a model card for an OpenMed clinical NER or de-identification model from its evaluation reports: intended use, metrics, subgroups and limitations.
maziyarpanahi/openmed
Walks a data pipeline against the HIPAA Privacy and Security Rule checklist and produces a gap report before it processes patient data.
maziyarpanahi/openmed
Suggests candidate ICD-10-CM diagnosis and ICD-10-PCS procedure codes for clinical text extracted by OpenMed, with rationale for a certified coder to review.
maziyarpanahi/openmed
Maps OpenMed-extracted, terminology-coded conditions, drugs and measurements into OMOP CDM v5.4 tables for OHDSI and ATLAS analytics.
maziyarpanahi/openmed
Finds social risks such as housing instability or food insecurity in clinical notes and proposes matching ICD-10-CM Z-codes for a coder to confirm.
Works with
Categories
Orient and bootstrap any project that uses OpenMed, the on-device clinical and biomedical NLP library, for named-entity recognition, PHI de-identification, FHIR export, and evaluation. Building With Openmed is an agent skill from maziyarpanahi/openmed. Orient and bootstrap any project that uses OpenMed, the on-device clinical and biomedical NLP library, for named-entity recognition, PHI de-identification, FHIR export, and evaluation.
Building With Openmed fits situations like: the user mentions OpenMed; wants to install it; asks which OpenMed capability; model fits a task.
Run `npx skills add maziyarpanahi/openmed --skill building-with-openmed -a claude-code`. Or copy the skill folder (skills/building-with-openmed in maziyarpanahi/openmed) into .claude/skills/building-with-openmed in your project. Claude Code loads it when a task matches its description.
Run `npx skills add maziyarpanahi/openmed --skill building-with-openmed -a codex`. Or copy the skill folder (skills/building-with-openmed in maziyarpanahi/openmed) into .agents/skills/building-with-openmed in your project. Codex loads it when a task matches its description.
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add maziyarpanahi/openmed --skill building-with-openmed -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/building-with-openmed, .gemini/skills/building-with-openmed, .github/skills/building-with-openmed and .opencode/skills/building-with-openmed in your project.
Going by SKILL.md and its folder, Building With Openmed needs the command-line tools its instructions call (pip). Our summary lists: Python 3.
SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
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.
Building With Openmed is published under the Apache-2.0 licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
About 1.4k tokens (SKILL.md is roughly 5.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
Skills that share tags, products or a category with Building With Openmed: Hcls Build Agent (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars), Find AI Consultancy (jeremylongshore/tons-of-skills-marketplace, 2.8k stars), Local RAG Search (nkapila6/mcp-local-rag, 134 stars) and Medical Imaging Review (LeonChaoX/qinyan-academic-skills, 944 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
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.
