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Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph.

Andreas Bueckle1, Bruce W Herr2, Josef Hardi3

  • 1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA. abueckle@iu.edu.

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Summary
This summary is machine-generated.

The Human Reference Atlas Knowledge Graph integrates anatomical structures, cell types, and biomarkers for the healthy adult body. This resource enables complex biological queries across multiple scales, advancing biomedical research.

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Area of Science:

  • Biomedical informatics
  • Human anatomy and cell biology
  • Data science

Background:

  • The Human Reference Atlas (HRA) aims to standardize descriptions of the healthy adult human body.
  • Existing data lacks standardized terminologies and spatial referencing, hindering cross-scale biological analysis.

Purpose of the Study:

  • Introduce the Human Reference Atlas Knowledge Graph (HRA KG) as a central data resource.
  • Facilitate cross-scale biological queries using Resource Description Framework (RDF) graphs and SPARQL.
  • Provide data, code, and methods for HRA KG construction and deployment.

Main Methods:

  • Developed the HRA KG, integrating anatomical structures (ASs), cell types (CTs), and biomarkers (Bs) with spatial information.
  • Utilized the Common Coordinate Framework Ontology to standardize 13 types of Digital Objects (DOs).
  • Deployed the HRA KG as Linked Open Data, accessible via APIs and user interfaces.

Main Results:

  • HRA KG v2.2 (May 2025) covers 71 organs, 5,800 ASs, 2,268 CTs, and 2,531 Bs.
  • The KG contains over 10 million nodes and 171 million edges, with a size of 125.84 GB.
  • Data and code for KG construction and deployment are publicly available.

Conclusions:

  • The HRA KG serves as a foundational resource for standardized, cross-scale biological data integration.
  • The KG supports advanced querying and data exploration for human biology research.
  • This work facilitates the development of comprehensive digital atlases for the human body.