Time & Date
9:00am–5:00pm EDT on May 9, 2019
Goals
HuBMAP will develop a common reference map or coordinate system called the Common Coordinate Framework (CCF). As stated in the Common Coordinate Framework Meeting (CCFM) document, a CCF makes it possible to uniquely and effectively define and name any location in the human body. A set of robust origin points (serving as landmarks) make it possible to reference organs, tissues, cells over different anatomical scales, tolerate human variability and function across lifespan and disease, and help integrate heterogeneous data layers and a wide range of reference maps such as whole body spatial maps, genetic variant maps, and coordinate systems that align with vascular pathways.
This CCF workshop will focus on a kidney-specific CCF and atlas but also discuss other relevant CCF/atlas efforts. It will feature presentations and discussions on:
- CCF metadata—what data are currently captured, how can they be unified across tissue mapping centers (TMCs), what additional data are needed to meet stakeholder (research) needs.
- CCF ontologies—what ontologies exist and are used in what part of the data pipeline; what ‘desirable properties’ and ‘success criteria’ exist?
- CCF mapping and numerical construction—including dealing with human variation and using CCF user interfaces as a means to properly register data and review data completeness.
- General principles and processes that can inform CCF design for other organs and continuous adaptation of CCF to emerging technologies and ever changing user requirements.
The ultimate goal is a set of draft guidelines for TMCs detailing what data to provide in which formats to maximize CCF mapping accuracy and data utility.
Photos
Location
Luddy Hall, Rm 3006
700 N. Woodlawn Ave.
Bloomington, IN 47408
Organizers
Katy Börner
MC-IU
Indiana University
Jeffrey Spraggins
TMC-Vanderbilt
Vanderbilt University
Sanjay Jain
TMC-UCSD
Washington University, St. Louis
Local Organizers
Lisel Record
MC-IU
Indiana University
Matt Martindale
MC-IU
Indiana University
Agenda
All times are in Eastern Daylight Time (UTC-4)
- 9:00amWelcome by Organizers and Richard Conroy, NIH (video)
- 9:05amBrief Introductions by Participants
- 9:30amHuBMAP Overview by
Organizers (video)
- 10:00amMetadata — Sanjay
Jain
- 10:40amCoffee Break
- 11:10am Metadata
- 11:30amOntologies — Katy
Bӧrner
- Jonathan Silverstein, U Pitt; Graphing UMLS (HuBMAP) (video)
- Yongqun "Oliver" He, U Michigan Medical School; Integrative Ontology Development to Support Precision Medicine and Molecular Atlas Research (KPMP) (video) (slides)
- Olivier Bodenreider, NLM/NIH; Anatomical Ontologies: How many of them do we need? (video) (slides)
- 12:30pmCatered Lunch
- 1:30pmAnatomical Mapping —
Jeffrey Spraggins
- Zorina Galis, NIH/NHLBI; Using the Vasculature for CCF (NIH) (video) (slides)
- Simon Watkins & Alan Watson, U Pitt; Ribbon Scanning Confocal for High-Speed High-Resolution Volume Imaging(video)
- Seth Winfree, IU School of Medicine; Bi-directional Interrogation of Image Volumes and Segmented Cells With 3D Tissue Cytometry (KPMP) (video) (slides)
- 2:30pmCoffee Break
- 3:00pmCCF User Interfaces —
Jim Sluka
- 4:00pmDiscussion of challenges and
(collaboration) opportunities (video)
HuBMAP Common Coordinate Framework: Challenges and Opportunities Workshop Discussion Log is available upon request. Contact Matthew Martindale (masmarti@iu.edu). - 5:00pmAdjourn
- 5:30pmDinner at FARMbloomington
Restaurant
Due to federal funding policy, participants will be responsible for their individual dinner expenses.
Presenters
Olivier Bodenreider
NLM/NIH
Katy Börner
Indiana University
MC-IU
Bernard de Bono
University of Auckland
SPARC
Zorina Galis
NIH/NHLBI
Yongqun "Oliver" He
University of Michigan Medical School
KPMP
Peter Hunter
University of Auckland
SPARC
Matthias Kretzler
University of Michigan
KPMP
Paul Macklin
Indiana University
MC-IU
Jonathan Silverstein
University of Pittsburgh
Graphing UMLS
Jim Sluka
Indiana University
MC-IU
Becky Steck
University of Michigan
KPMP
Simon Watkins
University of Pittsburgh
Alan Watson
University of Pittsburgh
Seth Winfree
Indiana University School of Medicine
Participants
- Ulysses Balis
University of Michigan - Olivier Bodenreider
National Library of Medicine - Katy Börner
Indiana University - Kasia Bourcier
NIAID - Todd Brusko
University of Florida - Marc Charette
NHLBI - Richard Conroy
NIH - Bernard de Bono
University of Auckland - Samuel Friedman
Opto-Knowledge Systems, Inc. - Zorina Galis
NIH - Daniel Gossett
NIDDK - Matthew Green
EBI - Raymond Harris
Vanderbilt University Medical Center - Yongqun "Oliver" He
University of Michigan - Randy Heiland
Indiana University - Bruce Herr
Indiana University - Jonathan Himmelfarb
University of Washington - Deborah Hoshizaki
NIH/NIDDK - Lucy Hsu
NHLBI - Peter Hunter
University of Auckland - Sanjay Jain
Washington University School of Medicine, St. Louis - Marda Jorgensen
University of Florida - Chris Ketchum
NIH/NIDDK/KUH - Matthias Kretzler
University of Michigan - Furkan Kurtoglu
Indiana University - Shin Lin
University of Washington - Jerry Li
NCI/NIH - Paula Mabee
University of South Dakota - Paul Macklin
Indiana University - Chuck McCallum
Harvard Medical School - John Metzcar
Indiana University - Josh Moore
Open Microscopy Environment (OME) / University of Dundee - Kousaku Okubo
National Institute of Genetics, Japan - Zina Perova
EMBL-EBI - Ajay Pillai
NIH - Dena Procaccini
NIH - Gloria Pryhuber
University of Rochester Medical Center / UCSD TMC - Ellen Quardokus
Indiana University - Ellen Roufs
USC - CC - Cindy Roy
NIH/NIDDK - Bill Shirey
University of Pittsburgh - Jonathan Silverstein
University of Pittsburgh - James Sluka
Indiana University - Jeff Spraggins
Vanderbilt - Victoria Spruance
NIDDK - Becky Steck
University of Michigan - Hongsuda Tangmunarunkit
USC Information Sciences Institute - M. Todd Valerius
Brigham and Women's Hospital - Raf Van de Plas
Delft University of Technology - Patrick Wall
Indiana University - Wendy Wang
NCI - Yafei Wang
Indiana University - Clive Wasserfall
University of Florida - Simon Watkins
University of Pittsburgh - Alan Watson
University of Pittsburgh - Dani Welter
EMBL-EBI - Seth Winfree
Indiana University School of Medicine - Dan Xi
National Cancer Institute
Acknowledgements
The work was funded by NIH Awards OT2OD026671, U54DK120058, and U54HL145608.