running-zeroshot-ner

Extract custom biomedical entities from text using local GLiNER checkpoints.

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

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill extracts custom biomedical and clinical entities from text without requiring labeled training data or fine-tuning, while keeping inference local and on-device.

Core Features & Use Cases

  • Custom Entity Extraction: Define arbitrary labels such as Drug, Device, Disease, Symptom, or Procedure at inference time.
  • GLiNER Support: Run GLiNER and GLiNER2 models through OpenMed's zero-shot NER workflow.
  • Index and Infer Workflow: Build a local model index, select a checkpoint by model ID, and return entities with labels, offsets, and confidence scores.
  • Use Case: Extract medications, implanted devices, and diseases from clinical notes when the required schema is new, evolving, or not covered by a fine-tuned model.

Quick Start

Use the running-zeroshot-ner skill to index your local GLiNER models and extract custom Drug, Device, and Disease entities from a clinical sentence.

Frequently Asked Questions about running-zeroshot-ner

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

FAQPage Schema
How do I extract custom biomedical entities from text without labeled training data?

You can extract custom biomedical entities without training data by using zero-shot NER to define arbitrary labels like Drug or Disease at inference time. This approach applies GLiNER models to identify clinical text entities without fine-tuning.

Can I define custom labels for clinical text extraction on-device?

Yes, you can define custom labels for clinical text extraction on-device. The process uses local GLiNER checkpoints to keep inference local, allowing you to extract medications, devices, and diseases without sending data externally.

How do I run zero-shot NER with GLiNER for evolving clinical schemas?

To run zero-shot NER with GLiNER for evolving schemas, build a local model index, select a checkpoint by model ID, and input your custom labels. The workflow returns extracted entities with labels, offsets, and confidence scores.

Do I need local GLiNER checkpoints to extract diseases and procedures from clinical notes?

Yes, you need local GLiNER or GLiNER2 checkpoints and an OpenMed model index to extract diseases and procedures. These local dependencies enable on-device inference for custom biomedical entity extraction.

What is the best way to extract medical devices and drugs when the required schema is new?

The best way to extract medical devices and drugs from new schemas is zero-shot NER. It allows dynamic label definition at inference time, bypassing the need for fine-tuned models when dealing with evolving or uncovered clinical categories.

Why use zero-shot NER instead of fine-tuned models for biomedical entity extraction?

Use zero-shot NER instead of fine-tuned models when your extraction schema is new, evolving, or uncovered. It allows dynamic label assignment at inference time, avoiding the time and data requirements of training specialized models.