Time & Date

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


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.


Extended Vascular Table
Vessel to Body Part
Vasculature Literature Review


• 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


Virtual, zoom links will be provided.


Portrait: Katy Börner

Griffin M Weber, MD, PhD

Associate Professor of Medicine and Biomedical Informatics, Harvard Medical School

Portrait: James Gee

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.

Portrait: Katy Börner

Katy Börner

Director, CNS, Intelligent Systems Engineering, Indiana University

Portrait: Lisel Record

Lisel Record

CNS Associate Director, Intelligent Systems Engineering, Indiana University

Portrait: Matthew Martindale

Matthew Martindale

CNS Center Assistant, Intelligent Systems Engineering, Indiana University

Portrait: Medina Sydykanova

Medina Sydykanova

CNS Project Support Specialist, Intelligent Systems Engineering, Indiana University


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


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

Contact Us

Matthew Martindale
Cyberinfrastructure for Network Science (CNS) Center Assistant
Luddy School of Informatics, Computing, and Engineering,
Indiana University
812-855-9930 masmarti@iu.edu

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