Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph
Abstract The Human Reference Atlas (HRA) for the healthy, adult body is being developed by a team of international, interdisciplinary experts across 25+ consortia. It provides standard terminologies and data structures for describing specimens, biological structures, and spatial positions of experim...
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| Format: | Article |
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Nature Portfolio
2025-07-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-05183-6 |
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| author | Andreas Bueckle Bruce W. Herr Josef Hardi Ellen M. Quardokus Mark A. Musen Katy Börner |
| author_facet | Andreas Bueckle Bruce W. Herr Josef Hardi Ellen M. Quardokus Mark A. Musen Katy Börner |
| author_sort | Andreas Bueckle |
| collection | DOAJ |
| description | Abstract The Human Reference Atlas (HRA) for the healthy, adult body is being developed by a team of international, interdisciplinary experts across 25+ 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 (ASs), cell types (CTs), and biomarkers (Bs). This paper introduces the HRA Knowledge Graph (KG) as central data resource for the HRA, supporting cross-scale, biological queries to Resource Description Framework graphs using SPARQL. In May 2025, the HRA KG v2.2 covers 71 organs with 5,800 ASs, 2,268 CTs, 2,531 Bs; it has 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. This work (1) provides data and code for HRA KG construction; (2) details HRA KG deployment as Linked Open Data; and (3) illustrates HRA KG usage via application programming interfaces, user interfaces, and data products. A companion website is at cns-iu.github.io/hra-kg-supporting-information . |
| format | Article |
| id | doaj-art-ecb0414b31974ef889552a33a8e8754b |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-ecb0414b31974ef889552a33a8e8754b2025-08-20T03:37:19ZengNature PortfolioScientific Data2052-44632025-07-0112111810.1038/s41597-025-05183-6Construction, Deployment, and Usage of the Human Reference Atlas Knowledge GraphAndreas Bueckle0Bruce W. Herr1Josef Hardi2Ellen M. Quardokus3Mark A. Musen4Katy Börner5Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana UniversityDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana UniversityStanford Center for Biomedical Informatics Research, Stanford UniversityDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana UniversityStanford Center for Biomedical Informatics Research, Stanford UniversityDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana UniversityAbstract The Human Reference Atlas (HRA) for the healthy, adult body is being developed by a team of international, interdisciplinary experts across 25+ 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 (ASs), cell types (CTs), and biomarkers (Bs). This paper introduces the HRA Knowledge Graph (KG) as central data resource for the HRA, supporting cross-scale, biological queries to Resource Description Framework graphs using SPARQL. In May 2025, the HRA KG v2.2 covers 71 organs with 5,800 ASs, 2,268 CTs, 2,531 Bs; it has 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. This work (1) provides data and code for HRA KG construction; (2) details HRA KG deployment as Linked Open Data; and (3) illustrates HRA KG usage via application programming interfaces, user interfaces, and data products. A companion website is at cns-iu.github.io/hra-kg-supporting-information .https://doi.org/10.1038/s41597-025-05183-6 |
| spellingShingle | Andreas Bueckle Bruce W. Herr Josef Hardi Ellen M. Quardokus Mark A. Musen Katy Börner Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph Scientific Data |
| title | Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph |
| title_full | Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph |
| title_fullStr | Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph |
| title_full_unstemmed | Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph |
| title_short | Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph |
| title_sort | construction deployment and usage of the human reference atlas knowledge graph |
| url | https://doi.org/10.1038/s41597-025-05183-6 |
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