extracting-clinical-entities SKILL.md skillA
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- SKILL.md skill
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- maziyarpanahi/openmed
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skills/extracting-clinical-entities/SKILL.md- Versions recorded
- 1
- Latest version
- v1.0, committed Jul 20, 2026
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- License
- Apache-2.0
Run clinical and biomedical named-entity recognition on medical text with OpenMed's analyze_text. Use when the user wants to extract diseases, drugs, anatomy, genes, or other biomedical entities from notes; needs NER output as dict/json/html/csv; wants to filter by confidence, group entities, toggle sentence detection, or save spans to JSONL; or wants the openmed analyze CLI. Pairs with loading-openmed-models and choosing-openmed-models, and runs after deidentifying-clinical-text in a…
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What the file says
# Extracting Clinical Entities
`openmed.analyze_text` runs a token-classification model over medical text and
returns structured entities with character offsets and confidence scores. It runs
**on-device** after a one-time model download.
## When to use
- Pull diseases, medications, anatomy, genes, proteins, etc. out of clinical text.
- You need exact **character spans** (start/end) plus **confidence** per entity.
- You want output as objects, JSON, an HTML highlight view, or CSV.
- You are building the "extract entities" stage of a clinical NLP pipeline.
To choose a model, see `choosing-openmed-models`. To load it once and reuse it,
see `loading-openmed-models`. **In a PHI workflow, de-identify first** (see
`deidentifying-clinical-text`), then run NER on the redacted text.
## Install
```bash
pip install "openmed[hf]"
```
## Quick start
```python
import openmed
note = (
"Patient prescribed 500 mg metformin for type 2 diabetes mellitus. "
"Reports intermittent chest pain; ruled out myocardial infarction."
)
result = openmed.analyze_text(
note,
model_name="disease_detection_superclinical", # registry key, HF id, or local path
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How to install
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The registry has recorded 1 version of this file, committed on Jul 20, 2026.
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Source
maziyarpanahi/openmed · 5,784 stars · license Apache-2.0 · pushed 2026-11-07 · branch master
API
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