This paper describes the construction and usage of the Human Reference Atlas (HRA) v2.0, which integrates multiscale data across 36 organs and provides tools for analysis and visualization.

Nature Methods · Mar 13, 2025Peer-reviewedBioinformatics

The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics

Nicolas Matentzoglu, Susan M. Bello, Ray Stefancsik, Sarah M. Alghamdi, Anna V. Anagnostopoulos, James P. Balhoff, Meghan A. Balk, Yvonne M. Bradford, Yasemin Bridges, Tiffany J. Callahan, Harry Caufield, Alayne Cuzick, Leigh Carmody, Anita R. Caron, Vinícius de Souza, , David Osumi-Sutherland

The paper introduces uPheno, a framework for cross-species phenomics integration by harmonizing phenotype data across species and ontologies.

Genetics · Mar 1, 2025Peer-reviewedBioinformatics

The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences

Ray Stefancsik, James P. Balhoff, Meghan A. Balk, Robyn L. Ball, Susan M. Bello, Anita R. Caron, Elissa J. Chesler, Vinícius de Souza, Sarah A. Gehrke, Melissa Anne Haendel, Laura Wiseman Harris, Nomi L. Harris, Arwa Ibrahim, Sebastian Koehler, Nicolas Matentzoglu, , David Osumi-Sutherland

This paper introduces OBA, a formalized ontology for biological attributes to facilitate data integration across phenotypic, genetic, and environmental data.

Mammalian Genome · Apr 19, 2023Peer-reviewedBioinformatics

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

Bruce W. Herr, Josef Hardi, Ellen M. Quardokus, Andreas Bueckle, Lu Chen, Fusheng Wang, Anita R. Caron, David Osumi-Sutherland, Mark A. Musen, Katy Börner

This paper introduces the Common Coordinate Framework Ontology (CCFO) v2.0.1 to integrate specimen, biological structure, and spatial data for the Human Reference Atlas, enabling interoperability and programmatic access.

Scientific Data · Mar 27, 2023Peer-reviewedBioinformatics