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Introduction

The German Human Genome-Phenome Archive (GHGA) is funded by the German Research Foundation (DFG) within the framework of the National Research Data Infrastructure (NFDI).

The main goal of GHGA is to address the needs for establishing a national genome archive for human genome data while tackling challenges in data access, sharing, and privacy. GHGA aims to provide a national infrastructure for secure and safe storage,access management, dissemination, and analysis of human omics data under a coherent ethical-legal framework.

This repository aims to serve as the source of truth for the metadata schema used by the German Human Genome-Phenome Archive.

The schema is modeled using LinkML and exists as a YAML, which can be found in src/schema/.

Using the YAML, and the LinkML framework, we autogenerate vendor/technology specific artifacts like:

  • JSON Schema
    • JSON Schema definitions of all classes and properties
  • Python Dataclasses
    • Python Dataclasses for each defined class
  • SQL DDL
    • SQL Data Definition Language to create SQL tables for all classes
  • SQLAlchemy classes
    • SQLAlchemy classes to map SQL tables and columns to each defined class and slot, respectively
  • GraphQL
    • GraphQL types for each defined class
  • ShEx
    • Shape Expressions for each defined class
  • RDF
    • The model represented as RDF Turtle (TTL)
  • OWL
    • The model in Web Ontology Language (OWL), serialized as RDF Turtle (TTL)
  • CSV
    • A CSV summary of the model and its classes
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