building-gold-corpus

Builds synthetic OpenMed annotation corpora for clinical NER and de-identification evaluation.

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

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill helps teams create trustworthy evaluation data for OpenMed clinical NER and de-identification models without committing real patient information or licensed clinical corpora.

Core Features & Use Cases

  • Label Schema Design: Define canonical entity labels, boundary rules, examples, and edge-case decisions.
  • Annotation Project Setup: Create annotation guidelines and configure BRAT or Label Studio workflows.
  • Synthetic Gold Fixtures: Generate validated, character-offset annotations with disciplined document-level train, development, and test splits.
  • Use Case: Build a synthetic held-out corpus for measuring model quality, checking subgroup performance, and enforcing CI release gates while keeping sensitive datasets outside the repository.

Quick Start

Use the building-gold-corpus skill to create a synthetic OpenMed annotation project with a label schema, guidelines, tool configuration, and disjoint train, development, and test fixtures.

Frequently Asked Questions about building-gold-corpus

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

FAQPage Schema
How do I create synthetic clinical evaluation data for de-identification models?

Synthetic gold-standard corpora provide fabricated clinical text with character-offset validated annotations, enabling trustworthy evaluation of named-entity recognition and de-identification models without risking patient privacy or committing licensed clinical corpora to your repository.

How do I set up an annotation project in Label Studio for clinical NER?

Configure Label Studio by defining canonical OpenMed entity labels, establishing boundary rules and edge-case decisions, and applying strict annotation guidelines to ensure consistent clinical named-entity recognition tagging across annotators.

What is a gold corpus in clinical named-entity recognition evaluation?

A gold corpus is a validated set of annotated clinical text with canonical OpenMed labels and character-offset validation, used to measure named-entity recognition model quality, check subgroup performance, and enforce CI release gates without using licensed external corpora.

Can I use BRAT configuration for clinical de-identification annotation workflows?

Yes, BRAT configuration supports clinical de-identification annotation workflows by applying canonical OpenMed label schemas, character-offset validation, and annotation guidelines to generate synthetic gold-standard evaluation fixtures for de-identification models.

How do I split synthetic clinical data into train development and test fixtures safely?

Split synthetic clinical data safely by enforcing strict document-level partitioning to create disjoint train, development, and test fixtures. This leakage-safe separation keeps committed synthetic data strictly distinct from licensed external corpora during evaluation.

What are the limitations of using synthetic data for clinical NER evaluation fixtures?

Synthetic clinical NER evaluation fixtures require canonical OpenMed labels and character-offset validation, and cannot substitute for licensed external corpora in training. They serve strictly as committed synthetic data for measuring model quality and enforcing CI release gates.