---
name: openmed-b8dd93ba5580
description: "Production-ready medical NLP toolkit (maziyarpanahi/openmed). Entity extraction, assertion detection, PII de-identification, batch processing, REST API, and multilingual support. Covers installation, all model families, configuration, and deployment."
tags: [medical-nlp, clinical-text, entity-extraction, deidentification, pii, icd10, healthcare, zorai, openmed]
---

# OpenMed

**OpenMed** transforms clinical text into structured insights. It bundles curated biomedical NER models, HIPAA-compliant de-identification, batch processing, a Dockerized REST API, and Apple Silicon acceleration — all behind a single `analyze_text()` call.

## When to Use

| Scenario | Start with |
|---|---|
| Extract diseases, drugs, anatomy from clinical notes | `references/entity-extraction` |
| Remove PHI/PII before sharing or storing data | `references/pii-deidentification` |
| Run NER on hundreds of clinical documents | `references/batch-processing` |
| Serve OpenMed behind a REST API | `references/rest-service` |
| Set up on Apple Silicon, Docker, or Swift | `references/installation` |
| Configure profiles, pick the right model | `references/configuration` |
| PII in French, German, Spanish, Portuguese, etc. | `references/multilingual-pii` |
| Privacy Filter (OpenAI / Nemotron) families | `references/privacy-filter` |

## Quick Start

```bash
git clone https://github.com/maziyarpanahi/openmed.git
cd openmed
uv pip install -e ".[hf]"
```

```python
from openmed import analyze_text

result = analyze_text(
    "Patient started imatinib for chronic myeloid leukemia.",
    model_name="disease_detection_superclinical",
)
for entity in result.entities:
    print(f"{entity.label:<12} {entity.text:<35} {entity.confidence:.2f}")
# DISEASE      chronic myeloid leukemia          0.98
# DRUG         imatinib                           0.95
```

## Model Registry (12+ Models)

| Model | Entity Types |
|---|---|
| `disease_detection_superclinical` | DISEASE, CONDITION, DIAGNOSIS |
| `pharma_detection_superclinical` | DRUG, MEDICATION, TREATMENT |
| `pii_detection_superclinical` | NAME, DATE, SSN, PHONE, EMAIL, ADDRESS |
| `anatomy_detection_electramed` | ANATOMY, ORGAN, BODY_PART |
| `gene_detection_genecorpus` | GENE, PROTEIN |

Browse the full catalog: `openmed.life/docs/model-registry`

## Key Concepts

- **analyze_text()** — single-call inference with configurable model, aggregation, format, and confidence threshold
- **BatchProcessor** — multi-text and multi-file workflows with progress tracking
- **extract_pii()** / **deidentify()** — HIPAA-compliant PII detection and redaction
- **Configuration Profiles** — `dev`, `prod`, `test`, `fast` presets via YAML or env vars
- **REST API** — FastAPI endpoints: `/health`, `/analyze`, `/pii/extract`, `/pii/deidentify`

## References

- [OpenMed docs](https://openmed.life/docs/)
- [OpenMed arXiv paper](https://arxiv.org/abs/2508.01630)
- [OpenMed GitHub](https://github.com/maziyarpanahi/openmed)
- `references/installation.md` — cross-platform install, Docker, Swift
- `references/entity-extraction.md` — disease, drug, anatomy, gene models
- `references/pii-deidentification.md` — HIPAA compliance, smart merging, anonymization
- `references/batch-processing.md` — BatchProcessor API
- `references/rest-service.md` — FastAPI endpoints, Docker
- `references/configuration.md` — profiles, model registry, profiling
- `references/multilingual-pii.md` — 9-language PII support
- `references/privacy-filter.md` — OpenAI Privacy Filter, Nemotron, MLX


---
Source attribution: mkurman
Original project: https://github.com/mkurman/zorai/blob/d06ee7597049567dab92db22d41b2764cf89094a/skills/scientific-skills/openmed/SKILL.md
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Mega AI Hub.

## Upstream license notice

MIT License

Copyright (c) 2026 zorai contributors

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Mega AI Hub resource metadata

Creator / publisher: mkurman
Original project: https://github.com/mkurman/zorai/blob/d06ee7597049567dab92db22d41b2764cf89094a/skills/scientific-skills/openmed/SKILL.md
Attribution basis: Source repository record

Fields of work: Data & Analytics, Development & Engineering, Healthcare & Life Sciences, Product Management
Roles: Clinical Research, Data Scientist, ML / AI Engineer, Product Manager
Specialties: API, Backend
Tools: Docker, GitHub
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: 95ec931f5a201193d7cbe114c5bd96c16e80204325afcacc6b2d042f1e22a2a2