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atlas-designer

Design declarative YAML schemas for Homeobox biomedical atlases.

7|Updated Feb 21, 2026
Search Tags:#schema validation#biomedical research#multimodal data#homeobox#atlas schema#yaml code generation#feature registries
One-click install
npx skills add https://github.com/epiblastai/homeobox --skill atlas-designer
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: atlas-designer
Source: https://github.com/epiblastai/homeobox/tree/main/packages/polycomb/skills/atlas-designer
Command: npx skills add https://github.com/epiblastai/homeobox --skill atlas-designer

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires homeobox, polycomb, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill helps design robust Homeobox atlas schemas without hand-writing complex Python schema definitions or ingestion logic.

Core Features & Use Cases

  • Declarative Schema Design: Creates YAML schema intermediate representations for observations, datasets, feature registries, foreign-key registries, enums, and auxiliary tables.
  • Rich Schema Semantics: Supports feature-space pointers, stable identifiers, registry references, polymorphic relationships, ontology and database mappings, summaries, constraints, computed fields, and presence flags.
  • Validation and Code Generation: Checks registry markers, validates pointer and enum compatibility, generates deterministic schema.py code, and builds a temporary atlas to verify the resulting schema.
  • Use Case: Design a multimodal single-cell atlas supporting gene expression, protein abundance, image features, donor metadata, and perturbation records, then validate the complete schema before ingestion.

Quick Start

Ask the atlas-designer skill to create and validate a YAML schema IR for your proposed Homeobox atlas, including its observation rows, feature spaces, registries, relationships, and biological metadata.

Frequently Asked Questions about atlas-designer

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

FAQPage Schema
How do I create a validated YAML schema for a multimodal single-cell biomedical atlas?▼

Designing a declarative YAML schema intermediate representation for a multimodal single-cell atlas involves defining observations, feature registries, and metadata, followed by generating schema.py code and building a temporary atlas to validate the structure.

What is a Homeobox schema IR and when do I need it for biomedical research data?▼

A Homeobox schema IR is a declarative YAML intermediate representation for modeling heterogeneous biomedical atlases. You need it to structure multimodal single-cell, imaging, and perturbation data alongside feature registries and biological metadata.

Can I define polymorphic relationships and ontology mappings in a single atlas schema?▼

Yes, you can define polymorphic relationships, database and ontology mappings, stable identifiers, and feature-space pointers within a single declarative YAML schema, which then validates registry markers and generates deterministic schema.py code.

Does atlas schema design require manual Python ingestion logic for feature registries?▼

No, designing atlas schemas requires valid Homeobox schema IR rather than manual Python ingestion logic, as the process validates registry markers and generates deterministic schema.py code directly from the declarative YAML structure.

How do I validate feature-space pointers and cross-references in a biomedical atlas schema?▼

You validate feature-space pointers and cross-references by checking registry markers and enum compatibility within the YAML schema IR, then building a temporary atlas to verify the generated deterministic schema.py code.

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