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

Abstract

The Human Reference Atlas (HRA) for the healthy, adult body is being developed by a team of international, interdisciplinary experts across 20+ consortia. It provides standard terminologies and data structures for describing specimens, biological structures, and spatial positions of experimental datasets and ontology-linked reference anatomical structures (AS), cell types (CT), and biomarkers (B). We introduce the HRA Knowledge Graph (KG) as central data resource for HRA v2.2, supporting cross-scale, biological queries to Resource Description Framework graphs using SPARQL. In February 2025, the HRA KG covered 71 organs with 5,800 AS, 2,268 CT, 2,531 B; it had 10,064,033 nodes, 171,250,177 edges, and a size of 125.84 GB. The HRA KG comprises 13 types of Digital Objects (DOs) using the Common Coordinate Framework Ontology to standardize core concepts and relationships across DOs. We (1) provide data and code for HRA KG construction; (2) detail HRA KG deployment by Linked Open Data principles; and (3) illustrate HRA KG usage via application programming interfaces, user interfaces, data products. A companion website is at https://cns-iu.github.io/hra-kg-supporting-information.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

* The paper was re-formatted into another type of publication. To support this, a Technical Validation section was added.

* https://github.com/hubmapconsortium/hra-kg

* https://cns-iu.github.io/hra-kg-supporting-information/

* https://github.com/hubmapconsortium/hra-do-processor

* https://github.com/x-atlas-consortia/hra-api

* https://github.com/x-atlas-consortia/hra-ubkg-exporter

* https://github.com/hubmapconsortium/ccf-grlc

* https://cdn.humanatlas.io/hra-kg-releases/hra-kg.v2.2.tar.xz