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
Location
Virtual, zoom links will be provided.
Organizers
![Portrait: Katy Börner](./images/people/griffin_weber.jpg)
Griffin M Weber, MD, PhD
Associate Professor of Medicine and Biomedical Informatics, Harvard Medical School
![Portrait: James Gee](./images/people/avinash_boppana.jpg)
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](./images/people/katyborner.png)
Katy Börner
Director, CNS, Intelligent Systems Engineering, Indiana University
![Portrait: Lisel Record](./images/people/lisel_record.png)
Lisel Record
CNS Associate Director, Intelligent Systems Engineering, Indiana University
![Portrait: Matthew Martindale](./images/people/matthew_martindale.png)
Matthew Martindale
CNS Center Assistant, Intelligent Systems Engineering, Indiana University
![Portrait: Medina Sydykanova](./images/people/medina_sydykanova.png)
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.
Prior CCF Workshops
NIH-Hubmap Common Coordinate Framework Workshop, 2019
Contact Us
Matthew MartindaleCyberinfrastructure for Network Science (CNS) Center Assistant
Luddy School of Informatics, Computing, and Engineering,
Indiana University
812-855-9930 masmarti@iu.edu
Social Media
HuBMAP twitter feed: @_hubmap
Share on TwitterHashtag: #HuBMAP