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.