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Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph for Linked Open Data.

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The Human Reference Atlas Knowledge Graph organizes healthy human body data, enabling complex biological queries across anatomical structures, cell types, and biomarkers. This resource facilitates standardized data integration and accessibility for researchers worldwide.

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Area of Science:

  • Human anatomy and cell biology
  • Bioinformatics and data science
  • Computational biology

Background:

  • The Human Reference Atlas (HRA) is an international effort to create a comprehensive map of the healthy adult human body.
  • Standardized terminologies and data structures are crucial for integrating diverse biological datasets.
  • Existing resources often lack comprehensive spatial and cross-scale integration of anatomical, cellular, and molecular data.

Purpose of the Study:

  • To introduce the Human Reference Atlas Knowledge Graph (HRA KG) as a central data resource for HRA v2.2.
  • To enable cross-scale biological queries using Resource Description Framework (RDF) graphs and SPARQL.
  • To provide a standardized framework for describing specimens, biological structures, cell types, and biomarkers within a common coordinate system.

Main Methods:

  • Development of the HRA KG using Linked Open Data principles.
  • Integration of 13 types of Digital Objects (DOs) standardized by the Common Coordinate Framework Ontology.
  • Utilizing SPARQL for querying the RDF graph data.

Main Results:

  • The HRA KG v2.2 covers 71 organs, including 5,800 anatomical structures, 2,268 cell types, and 2,531 biomarkers.
  • The graph contains over 10 million nodes and 171 million edges, with a total size of 125.84 GB.
  • Data and code for KG construction, deployment, and usage via APIs and UIs are provided.

Conclusions:

  • The HRA KG serves as a foundational resource for standardized, integrated, and queryable human biological data.
  • It supports advanced cross-scale biological research by linking diverse datasets within a unified framework.
  • The KG promotes data accessibility and reusability, accelerating discoveries in human health and disease.