clinical-nlp-extractor

by FreedomIntelligence

Install this Skill

curl -fsSL -o clinical-nlp-extractor.zip https://skill.seembox.com/api/v1/skills/clinical-nlp-extractor/download && unzip clinical-nlp-extractor.zip

Download clinical-nlp-extractor.zip

SKILL.md About

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# COPYRIGHT NOTICE
# This file is part of the "Universal Biomedical Skills" project.
# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
# All Rights Reserved.
#
# This code is proprietary and confidential.
# Unauthorized copying of this file, via any medium is strictly prohibited.
#
# Provenance: Authenticated by MD BABU MIA

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---
name: 'clinical-nlp-extractor'
description: 'Extracts medical entities (Diseases, Medications, Procedures) from unstructured clinical text using regex and simple rules (or LLM wrappers).'
measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.
allowed-tools:
  - read_file
  - run_shell_command
---

# Clinical NLP Entity Extractor

The **Clinical NLP Skill** converts free-text clinical notes into structured data. It identifies key medical entities like problems/diagnoses, medications, and procedures.

## When to Use This Skill

*   When analyzing unstructured EHR notes.
*   To populate a patient's problem list or medication reconciliation.
*   To de-identify text (phi-removal) - *Basic version*.

## Core Capabilities

1.  **NER (Named Entity Recognition)**: Extracts Problems, Drugs, Procedures.
2.  **Negation Detection**: (Basic) Checks if a finding is denied ("No fever").
3.  **Structuring**: Returns JSON format compatible with FHIR/USDL.

## Workflow

1.  **Input**: A string of clinical text or a text file.
2.  **Process**: Tokenizes and matches against patterns/dictionaries.
3.  **Output**: JSON list of entities with spans and types.

## Example Usage

**User**: "Extract entities from this note."

**Agent Action**:
```bash
python3 Skills/Clinical/Clinical_NLP/entity_extractor.py \
    --text "Patient has diabetes type 2. Prescribed Metformin 500mg. No chest pain." \
    --output entities.json
```

```