Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas

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 Börner

doi:10.1038/s41597-023-01993-8

Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas

Sci Data. 2023 Mar 27;10(1):171. doi: 10.1038/s41597-023-01993-8.

Authors

Affiliations

¹ Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.
² Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, 94305, USA.
³ Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA. abueckle@iu.edu.
⁴ Department of Computer Science, Stony Brook University, Stony Brook, NY, 11794, USA.
⁵ Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, 11794, USA.
⁶ European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
⁷ Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA. katy@indiana.edu.

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.

Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas

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Abstract

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