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<title>HuBMAP: CCF Portal</title>
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<a class="dropdown-item" href="pages/ccf-anatomical-structures.html">CCF Anatomical Structures, Cell
Types and Biomarkers (ASCT+B) Tables</a>
<a class="dropdown-item" href="pages/ccf-3d-reference-library.html">CCF 3D Reference Object Library</a>
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<a class="dropdown-item" href="https://hubmap-ccf-ui.netlify.app/rui/" title="Opens external website" target="_blank">CCF Registration User Interface (RUI)</a>
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<a class="dropdown-item" href="https://expand.iu.edu/browse/sice/cns/courses/hubmap-visible-human-mooc" title="Opens external website" target="_blank">Visible Human MOOC</a>
<a class="dropdown-item" href="https://portal.hubmapconsortium.org/" title="Opens external website" target="_blank">HuBMAP Data Portal</a>
<a class="dropdown-item" href="pages/kaggle.html" title="Opens external website">Kaggle #1: HuBMAP - Hacking the Kidney</a>
<a class="dropdown-item" href="pages/kaggle2.html" title="Opens external website">Kaggle #2: HuBMAP + HPA - Hacking the Human Body</a>
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<h1 class="row"><span class="col-12 col-sm-2 text-center"><img
style="max-width: 140px; width: 100%; max-height: 140px; height: auto; margin-bottom: 1rem;"
src="img/logo-hubmap-body-color.svg" alt="HuBMAP Body" /></span><span
class="col-sm-10">The Human Reference Atlas: High-Resolution, Functional Mapping of
Voxel,
Vector, and Meta Datasets <br><strong class="lead">MC-IU team within the HuBMAP
HIVE</strong></span></h1>
<p class="mt-5">The ultimate goal of the HIVE Mapping effort is to develop a common coordinate framework (CCF) for the healthy human body. This framework will support cataloging different types of individual cells, understanding the functions of and relationships between those cell types, and modeling their individual and collective function. During the initial three years of HuBMAP, the MC-IU team has built many elements of the CCF. We co-organized the construction of ASCT+B Tables and implemented a CCF Ontology. We collaborated with NIAID at NIH on the design of a 3D Reference Object Library. Lastly, we developed three interactive user interfaces. The CCF ASCT+B Reporter supports the authoring and interactive review of ASCT+B Tables. The CCF Registration User Interface (RUI) supports uniform tissue data registration across organs and labs. The CCF Exploration User Interface (EUI) supports exploration of semantically and spatially explicit data—from the whole body to the single cell level. For an introduction to HuBMAP goals, data, and code visit the Visible Human MOOC (VHMOOC).
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<p class="card-title">CCF Anatomical Structures, Cell Types and
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<a href="pages/ccf-ontology.html" title="Link to CCF Ontology page">
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<a href="pages/ccf-3d-reference-library.html"
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<a href="pages/ccf-2d-reference-library.html"
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<p class="card-title">Organ Mapping Antibody Panels (OMAPs)</p>
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<div class="col-12 col-md-6 mb-3">
<a href="https://hubmapconsortium.github.io/ccf-ui/rui/"
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<div class="col-12 col-md-6 mb-3">
<a href="pages/asctb-azimuth-data-comparison.html"
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<a href="https://portal.hubmapconsortium.org/ccf-eui
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<div class="col-12 col-md-6 mb-3">
<a href="https://expand.iu.edu/browse/sice/cns/courses/hubmap-visible-human-mooc"
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<div class="card-body">
<p class="card-title">Visible Human MOOC (VHMOOC)</p>
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</div>
</div>
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<div class="col-12 col-md-6 mb-3">
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title="Link to the Kaggle Competition">
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<p class="card-title">Kaggle #1: HuBMAP - Hacking the Kidney</p>
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</div>
</div>
</div>
</a>
</div>
<div class="col-12 col-md-6 mb-3">
<a href="pages/kaggle2.html"
title="Link to the Kaggle Competition">
<div class="card h-100 card-kaggle-blue h-card">
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<div class="col-3 col-lg-2 bg-kaggle-blue align-middle text-center px-1 py-1">
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<div class="col-9 col-lg-10">
<div class="card-body">
<p class="card-title">Kaggle #2: HuBMAP + HPA - Hacking the Human Body</p>
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</div>
</div>
</div>
</a>
</div>
<div class="col-12 col-md-6 mb-3">
<a href="https://hubmapconsortium.github.io/hra-millitome/"
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<div class="col-9 col-lg-10">
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<p class="card-title">HRA Millitome</p>
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</div>
</div>
</div>
</a>
</div>
<div class="col-12 col-md-6 mb-3">
<a href="pages/ccf-gallery.html"
title="Link to the CCF Organ VR Gallery">
<div class="card h-100 card-burnt-orange h-card">
<div class="row no-gutters h-100">
<div class="col-3 col-lg-2 bg-burnt-orange align-middle text-center px-1 py-1">
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<div class="card-body">
<p class="card-title">CCF Organ VR Gallery</p>
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</a>
</div>
</div>
<h3 class="mt-5">References</h3>
<ul class="list-unstyled">
<li class="mb-3">Börner, Katy, Andreas D. Bueckle, and Michael Ginda. 2019. "<a href="https://cns.iu.edu/docs/publications/2019-borner-pnas.pdf" title="Download paper (PDF)" target="_blank">Data Visualization Literacy: Definitions, Conceptual Frameworks, Exercises, and Assessments</a>." <span class="font-italic">PNAS</span>116 (6): 1857-1864. doi:10.1073/pnas.1807180116.</li>
<li class="mb-3">Börner, Katy, Ellen M. Quardokus, Bruce W. Herr II, Leonard E. Cross, Elizabeth G. Record, Yingnan Ju, Andreas D. Bueckle, James P. Sluka, Jonathan C. Silverstein, Kristen M. Browne, Sanjay Jain, Clive H. Wasserfall, Marda L. Jorgensen, Jeffrey M. Spraggins, Nathan H. Patterson, Mark A. Musen, and Griffin M. Weber. 2020. "<a href="https://arxiv.org/abs/2007.14474" title="View on arXiv.org" target="_blank">Construction and Usage of a Human Body Common Coordinate Framework Comprising Clinical, Semantic, and Spatial Ontologies</a>." arXiv:2007.14474v1.</li>
<li class="mb-3">Börner, Katy, Sarah A Teichmann, Ellen M Quardokus, James Gee, Kristen Browne, David Osumi-Sutherland, Bruce W Herr II, Andreas Bueckle, Hrishikesh Paul, Muzlifah A Haniffa, Laura Jardine, Amy Bernard, Song-Lin Ding, Jeremy A Miller, Shin Lin, Marc Halushka, Avinash Boppana, Teri A Longacre, John Hickey, Yiing Lin, M Todd Valerius, Yongqun He, Gloria Pryhuber, Xin Sun, Marda Jorgensen, Andrea J Radtke, Clive Wasserfall, Fiona Ginty, Jonhan Ho, Joel Sunshine, Rebecca T Beuschel, Maigan Brusko, Sujin Lee, Rajeev Malhotra, Sanjay Jain, and Griffin Weber. 2021. "<a href="https://cns.iu.edu/docs/publications/2021-Borner-ASCT+B_of_the_HRA.pdf" title="Download paper (PDF)" target="_blank">Anatomical structures, cell types and biomarkers of the Human Reference Atlas</a>." <span class="font-italic">Nature Cell Biology</span> 23: 1117-1128. doi: 10.1038/s41556-021-00788-6. </li>
<li class="mb-3">Börner, Katy, William Rouse, Paul Trunfio, and H. Eugene Stanley. 2018. "<a href="https://cns.iu.edu/docs/publications/2018-borner-forecasting-innovations.pdf" title="Download paper (PDF)" target="_blank">Forecasting Innovations in Science, Technology, and Education</a>." <span class="font-italic">PNAS</span> 115 (50): 12573-12581. doi:10.1073/pnas.1818750115.</li>
<li class="mb-3">Bueckle, Andreas, Kilian Buehling, Patrick C. Shih, and Katy Börner. 2021. "<a href="https://arxiv.org/abs/2102.12030" title="View on arXiv.org" target="_blank">Comparing Completion Time, Accuracy, and Satisfaction in Virtual Reality vs. Desktop Implementation of the Common Coordinate Framework (CCF RUI)</a>." arXiv:2101.12030v1.</li>
<li class="mb-3">Ginda, Michael, Michael C. Richey, Mark Cousino, and Katy Börner. 2019. "<a href="https://cns.iu.edu/docs/publications/2019-journal.pone.0215964.pdf" title="Download paper (PDF)" target="_blank">Visualizing Learner Engagement, Performance, and Trajectories to Evaluate and Optimize Online Course Design</a>." <span class="font-italic">PLOS One</span> 14 (5): e0215964. doi:10.1371/journal.pone.0215964.</li>
<li class="mb-3">Snyder, Michael P., Shin Lin, Amanda Posgai, Mark Atkinson, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Leslie Gaffney, Anna Hupalowska, Rahul Satija, Nils Gehlenborg, Jay Shendure, Julia Laskin, Pehr Harbury, Nicholas A. Nystrom, Jonathan C. Silverstein, Ziv Bar-Joseph, Kun Zhang, Katy Börner, Yiing Lin, Richard Conroy, Dena Procaccini, Ananda L. Roy, Ajay Pillai, Marishka Brown, and Zorina S. Galis. 2019. "<a href="https://cns.iu.edu/docs/publications/2019-Snyder-HuBMAP.pdf" title="Download paper (PDF)" target="_blank">The Human Body at Cellular Resolution: The NIH Human Biomolecular Atlas Program</a>." <span class="font-italic">Nature</span> 574: 187-192. doi:10.1038/s41586-019-1629-x.</li>
<li class="mb-3">Weber, Griffin M, Yingnan Ju, and Katy Börner. 2020. "<a href="https://cns.iu.edu/docs/publications/2020-Weber-Considerations.pdf" title="Download paper (PDF)" target="_blank">Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body</a>." <span class="font-italic">Frontiers in Cardiovascular Medicine</span> 7 (29). doi:10.3389/fcvm.2020.00029.</li>
</ul>
<h3 class="mt-5">Presentations</h3>
<ul class="list-unstyled">
<li class="mb-3">November 18, 2020: <a href="dld/2020.11.18-CZI-Borner.pdf"
title="Download poster (PDF)" target="_blank"><span class="font-italic">Human Reference Atlas: Anatomical Structures, Cell Types & Biomarkers</span></a> at <a href="https://chanzuckerberg.com/science/programs-resources/single-cell-biology/seednetworks/" title="Links to external website">Chan Zuckerberg Initiative (CZI) Seed Networks 2020 Annual Meeting</a>, Virtual Event.</li>
<li class="mb-3">May 19, 2020: <a href="dld/2020.05.19-Borner-HuBMAPposter.pdf"
title="Download poster (PDF)" target="_blank"><span class="font-italic">The Human Body Atlas:
High-Resolution, Functional Mapping of Voxel, Vector, and Meta
Datasets</span></a> at HuBMAP Virtual Annual Meeting, Washington, DC.</li>
<li>March 17, 2020: <a href="dld/2020.03.17-MC-IU.KPMP-Talk.pdf"
title="Download talk (PDF)" target="_blank"><span class="font-italic">Harmonizing KPMP/HuBMAP
Data:
Developing Novel Common Coordinate Framework User Interfaces</span></a> at
KPMP Virtual Meeting, Washington, DC.</li>
</ul>
<h3 class="mt-5">Acknowledgements</h3>
<p>We deeply value close collaborations with the HuBMAP TMCs and other HIVE teams. This research has been funded in part by the NIH Common Fund OTA 20-005 under award OT2 OD030545 and through the Office of Strategic Coordination/Office of the NIH Director under award OT2OD026671, by the NIDDK Kidney Precision Medicine Project grant U2CDK114886, and the NIH NIAID, Department of Health and Human Services under BCBB Support Services Contract HHSN316201300006W/HHSN27200002. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the NIH.</p>
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