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Tissue Registration and Exploration User Interfaces in support of a Human Reference Atlas

View ORCID ProfileKaty Börner, View ORCID ProfileAndreas Bueckle, View ORCID ProfileBruce W. Herr II, View ORCID ProfileLeonard E. Cross, View ORCID ProfileEllen M. Quardokus, View ORCID ProfileElizabeth G. Record, View ORCID ProfileYingnan Ju, View ORCID ProfileJonathan C. Silverstein, View ORCID ProfileKristen M. Browne, View ORCID ProfileSanjay Jain, View ORCID ProfileClive H. Wasserfall, View ORCID ProfileMarda L. Jorgensen, View ORCID ProfileJeffrey M. Spraggins, View ORCID ProfileNathan H. Patterson, View ORCID ProfileGriffin M. Weber
doi: https://doi.org/10.1101/2021.12.30.474265
Katy Börner
1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
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  • For correspondence: katy@indiana.edu abueckle@iu.edu
Andreas Bueckle
1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
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  • For correspondence: katy@indiana.edu abueckle@iu.edu
Bruce W. Herr II
1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
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Leonard E. Cross
1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
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Ellen M. Quardokus
1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
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Elizabeth G. Record
1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
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Yingnan Ju
1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA
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Jonathan C. Silverstein
2Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Kristen M. Browne
3Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Sanjay Jain
4Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA
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Clive H. Wasserfall
5Departments of Pathology and Pediatrics, University of Florida, Gainesville, Florida, USA
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Marda L. Jorgensen
5Departments of Pathology and Pediatrics, University of Florida, Gainesville, Florida, USA
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Jeffrey M. Spraggins
6Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
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Nathan H. Patterson
6Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
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Griffin M. Weber
7Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
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Abstract

Several international consortia are collaborating to construct a human reference atlas, which is a comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body. Laboratories around the world are collecting tissue specimens from donors varying in sex, age, ethnicity, and body mass index. However, integrating and harmonizing tissue data across 20+ organs and more than 15 bulk and spatial single-cell assay types poses diverse challenges. Here we present the software tools and user interfaces developed to annotate (“register”) and explore the collected tissue data. A key part of these tools is a common coordinate framework, which provides standard terminologies and data structures for describing specimens, biological structures, and spatial positions linked to existing ontologies. As of December 2021, the “registration” user interface has been used to harmonize and make publicly available data on 6,178 tissue sections from 2,698 tissue blocks collected by the Human Biomolecular Atlas Program, the Stimulating Peripheral Activity to Relieve Conditions program, the Human Cell Atlas, the Kidney Precision Medicine Project, and the Genotype Tissue Expression project. The second “exploration” user interface enables consortia to evaluate data quality and coverage, explore tissue data in the context of the human body, and guide data acquisition.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted December 30, 2021.
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Tissue Registration and Exploration User Interfaces in support of a Human Reference Atlas
Katy Börner, Andreas Bueckle, Bruce W. Herr II, Leonard E. Cross, Ellen M. Quardokus, Elizabeth G. Record, Yingnan Ju, Jonathan C. Silverstein, Kristen M. Browne, Sanjay Jain, Clive H. Wasserfall, Marda L. Jorgensen, Jeffrey M. Spraggins, Nathan H. Patterson, Griffin M. Weber
bioRxiv 2021.12.30.474265; doi: https://doi.org/10.1101/2021.12.30.474265
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Tissue Registration and Exploration User Interfaces in support of a Human Reference Atlas
Katy Börner, Andreas Bueckle, Bruce W. Herr II, Leonard E. Cross, Ellen M. Quardokus, Elizabeth G. Record, Yingnan Ju, Jonathan C. Silverstein, Kristen M. Browne, Sanjay Jain, Clive H. Wasserfall, Marda L. Jorgensen, Jeffrey M. Spraggins, Nathan H. Patterson, Griffin M. Weber
bioRxiv 2021.12.30.474265; doi: https://doi.org/10.1101/2021.12.30.474265

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