building-with-openmed

Guide developers in building local-first clinical NLP pipelines with OpenMed.

5.0k|615|Updated Oct 4, 2025
One-click install
npx skills add https://github.com/maziyarpanahi/openmed --skill building-with-openmed
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: building-with-openmed
Source: https://github.com/maziyarpanahi/openmed/tree/main/skills/building-with-openmed
Command: npx skills add https://github.com/maziyarpanahi/openmed --skill building-with-openmed

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill helps developers quickly scope, install, and bootstrap OpenMed projects for privacy-preserving clinical and biomedical NLP without sending patient data to the cloud.

Core Features & Use Cases

  • Capability Guidance: Select the right OpenMed entry point for entity extraction, PHI detection and de-identification, multilingual processing, clinical context, FHIR export, evaluation, or API serving.
  • Local-First Setup: Choose the appropriate package extras and on-device backend for Python, Hugging Face, Apple Silicon, Android, REST, or MCP deployments.
  • Safe Pipeline Design: Apply privacy policies, avoid raw PHI in artifacts, use leakage-gated evaluation, and preserve permissive licensing and clinical safety boundaries.
  • Use Case: Start with clinical notes, de-identify them locally, extract biomedical entities, assemble interoperable FHIR output, and evaluate the workflow for residual information leakage.

Quick Start

Ask the skill to recommend and bootstrap an OpenMed pipeline for locally de-identifying clinical notes and extracting biomedical entities.

Frequently Asked Questions about building-with-openmed

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I de-identify PHI in clinical notes locally without sending data to the cloud?

You can de-identify PHI in clinical notes locally by building an on-device NLP pipeline that processes text without cloud transmission. This approach uses runtime-discovered models to detect and remove protected health information while preserving clinical context.

What's the best way to extract biomedical entities and export them to FHIR format?

The best way to extract biomedical entities and export to FHIR is through a local-first clinical NLP pipeline. This workflow performs named-entity recognition on clinical text, then assembles the extracted entities into interoperable FHIR output artifacts.

Can I run clinical NLP models on Apple Silicon or Android for on-device processing?

Yes, you can run clinical NLP models on Apple Silicon or Android by selecting appropriate package extras and on-device backends. The setup supports Python, Hugging Face, REST, and MCP deployments for local execution across these platforms.

How do I evaluate clinical NLP pipelines for residual information leakage?

You evaluate clinical NLP pipelines for information leakage using leakage-gated validation. This process assesses de-identified outputs to ensure privacy policies are enforced and raw PHI is avoided in artifacts, validating that residual data exposure meets safety boundaries.

Does multilingual clinical text processing work for biomedical entity extraction?

Yes, multilingual clinical text processing works for biomedical entity extraction through runtime-discovered models. The workflow applies multilingual processing capabilities to extract entities and resolve clinical context across different languages.

What are the limitations of on-device clinical NLP for de-identifying patient records?

Limitations of on-device clinical NLP include dependency on runtime-discovered models and the need for permissive assets to maintain clinical safety boundaries. You must apply privacy policies and leakage-aware validation to ensure de-identified artifacts do not expose residual PHI.