Time & Date

March 29, 2021, 10:00am - 12:00pm EST

Summary

Several ongoing international efforts are developing methods of localizing single cells within organs or mapping the entire human body at the single cell level. A major challenge is combining heterogeneous tissue samples into a reference map that will enable multiscale, multidimensional Google Maps-like exploration of the human body. Key to making alignment of tissue samples work is identifying and using a coordinate system called a Common Coordinate Framework (CCF), which defines the positions, or "addresses," in a reference body, from whole organs down to functional tissue units and individual cells. The Vascular Common Coordinate Framework (VCCF) is a proposed approach, which uses the vasculature as a coordinate system in locating position in the body. This workshop will review work we have done on the VCCF, including constructing an ASCT+B table of the vasculature, pointing out limitations and challenges, and discussing next steps with an emphasis on reviewing related literature.

References:

• Extended Vascular Table
• Vessel to Body Part
• Vasculature Literature Review

Goals

• Make sure we are aligned on what a "vasculature coordinate system" means
• Review how vasculature is represented in the ASCT+B tables and 3D models
• Confirm initial list of cell types and biomarkers
• Discuss limitations, challenges and next steps

Organizers

Griffin M Weber, MD, PhD

Associate Professor of Medicine and Biomedical Informatics, Harvard Medical School

Avinash Boppana

Undergraduate Student, Princeton

Local Organizers

Members of the Cyberinfrastructure for Network Science Center (CNS) at the Luddy School of Informatics, Computing, and Engineering, Indiana University.

Katy Börner

Director, CNS, Intelligent Systems Engineering, Indiana University

Lisel Record

CNS Associate Director, Intelligent Systems Engineering, Indiana University

Matthew Martindale

CNS Center Assistant, Intelligent Systems Engineering, Indiana University

Medina Sydykanova

CNS Project Support Specialist, Intelligent Systems Engineering, Indiana University

Agenda

All times are in Eastern Daylight Time (UTC-4)

March 29, 2021

• 10:00amIntroductions
• 10:10amVCCF Vision
• 10:30amVasculature ASCT+B Table
• 10:40amExtended VCCF Table
• 10:50amDifferences with UBERON and FMA
• 11:00amCell types and biomarkers
• 11:10amVariants
• 11:20amLiterature review
• 11:40amDiscussion
• 12:00amAdjourn

Acknowledgements

We thank Zorina S. Galis from the National Institutes of Health for helping develop the idea of a vascular-based coordinate system; Sujin Lee, Rajeev Malhotra, and Marc Halushka as domain experts who reviewed and contributed to the vasculature ASCT+B table; and Ellen Quardokus, Kristen Browne, and other ASCT+B table authors for linking vasculature structures to organs and 3D models.

Social Media

HuBMAP twitter feed: @_hubmap
Hashtag: #HuBMAP

Prior CCF Workshops

NIH-Hubmap Common Coordinate Framework Workshop, 2019

NIH-HCA Common Coordinate Framework Session, 2020

Hubmap Common Framework ASCT+B Table Workshop, 2021

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