Specimen, Biological Structure, and Spatial Ontologies in Support of a Human Reference Atlas

Overview

Journal Sci Data

Specialty Science

Date 2023 Mar 27

PMID 36973309

Authors

Bruce W Herr 2nd

Josef Hardi

Ellen M Quardokus

Andreas Bueckle

Lu Chen

Fusheng Wang

Anita R Caron

David Osumi-Sutherland

Mark A Musen

Katy Borner

Affiliations

Soon will be listed here.

Abstract

The Human Reference Atlas (HRA) is defined as a comprehensive, three-dimensional (3D) atlas of all the cells in the healthy human body. It is compiled by an international team of experts who develop standard terminologies that they link to 3D reference objects, describing anatomical structures. The third HRA release (v1.2) covers spatial reference data and ontology annotations for 26 organs. Experts access the HRA annotations via spreadsheets and view reference object models in 3D editing tools. This paper introduces the Common Coordinate Framework (CCF) Ontology v2.0.1 that interlinks specimen, biological structure, and spatial data, together with the CCF API that makes the HRA programmatically accessible and interoperable with Linked Open Data (LOD). We detail how real-world user needs and experimental data guide CCF Ontology design and implementation, present CCF Ontology classes and properties together with exemplary usage, and report on validation methods. The CCF Ontology graph database and API are used in the HuBMAP portal, HRA Organ Gallery, and other applications that support data queries across multiple, heterogeneous sources.

Citing Articles

Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage.

Borner K, Blood P, Silverstein J, Ruffalo M, Satija R, Teichmann S Nat Methods. 2025; .

PMID: 40082611 DOI: 10.1038/s41592-024-02563-5.

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

Bueckle A, Herr B, Herr 2nd B, Hardi J, Quardokus E, Musen M bioRxiv. 2025; .

PMID: 39764040 PMC: 11703146. DOI: 10.1101/2024.12.22.630006.

A general strategy for generating expert-guided, simplified views of ontologies.

Caron A, Puig-Barbe A, Quardokus E, Balhoff J, Belfiore J, Chipampe N bioRxiv. 2025; .

PMID: 39763856 PMC: 11702530. DOI: 10.1101/2024.12.13.628309.

Publication, funding, and experimental data in support of Human Reference Atlas construction and usage.

Kong Y, Borner K Sci Data. 2024; 11(1):574.

PMID: 38834597 PMC: 11150433. DOI: 10.1038/s41597-024-03416-8.

Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage.

Borner K, Blood P, Silverstein J, Ruffalo M, Satija R, Teichmann S bioRxiv. 2024; .

PMID: 38826261 PMC: 11142047. DOI: 10.1101/2024.03.27.587041.

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