Time & Date

9:00am–5:00pm EDT on May 9, 2019


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.


Image of Presenters, Organizers and CCF UI Development Team
Click to open event photos


Luddy Hall, Rm 3006
700 N. Woodlawn Ave.
Bloomington, IN 47408


Portrait: Katy Börner

Katy Börner

Indiana University

Portrait: Jeffrey Spraggins

Jeffrey Spraggins

Vanderbilt University

Portrait: Sanjay Jain

Sanjay Jain

Washington University, St. Louis

Local Organizers

Portrait: Lisel Record

Lisel Record

Indiana University

Portrait: Matt Martindale

Matt Martindale

Indiana University


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
    • Paul Macklin et al., IU; Kidney Metadata and Ontology Design (HuBMAP) (video) (slides)
    • Bernard de Bono, U of Auckland; Kidney Anatomical Knowledge and Metadata (SPARC) (video) (slides)
  • 10:40amCoffee Break
  • 11:10am Metadata
    • Matthias Kretzler and Becky Steck, U of Washington; The Kidney Precision Medicine Project Overview of KPMP Metadata (KPMP) (video) (slides)
  • 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
    • Katy Börner, IU; Multi-Level, Multi-Modal CCF UI for Data Providers and Users (HuBMAP) (video) (slides)
    • Becky Steck, U Mich; KPMP’s User-Centered Approach to User Interfaces and Data Visualization (KPMP) (video) (slides)
    • Peter Hunter, U of Auckland; 3D Scaffolds (SPARC) (video) (slides)
  • 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.


Portrait: Olivier Bodenreider

Olivier Bodenreider


Portrait: Katy Börner

Katy Börner

Indiana University

Portrait: Bernard de Bono

Bernard de Bono

University of Auckland

Portrait: Zorina Galis

Zorina Galis


Portrait: Yongqun He

Yongqun "Oliver" He

University of Michigan Medical School

Portrait: Peter Hunter

Peter Hunter

University of Auckland

Portrait: Matthias Kretzler

Matthias Kretzler

University of Michigan

Portrait: Paul Macklin

Paul Macklin

Indiana University

Portrait: Jonathan Silverstein

Jonathan Silverstein

University of Pittsburgh
Graphing UMLS

Portrait: James (Jim) Sluka

Jim Sluka

Indiana University

Portrait: Becky Steck

Becky Steck

University of Michigan

Portrait: Simon Watkins

Simon Watkins

University of Pittsburgh

Portrait: Alan Watson

Alan Watson

University of Pittsburgh

Portrait: Seth Winfree

Seth Winfree

Indiana University School of Medicine


  • Ulysses Balis
    University of Michigan
  • Olivier Bodenreider
    National Library of Medicine
  • Katy Börner
    Indiana University
  • Kasia Bourcier
  • Todd Brusko
    University of Florida
  • Marc Charette
  • Richard Conroy
  • Bernard de Bono
    University of Auckland
  • Samuel Friedman
    Opto-Knowledge Systems, Inc.
  • Zorina Galis
  • Daniel Gossett
  • Matthew Green
  • 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
  • Lucy Hsu
  • Peter Hunter
    University of Auckland
  • Sanjay Jain
    Washington University School of Medicine, St. Louis
  • Marda Jorgensen
    University of Florida
  • Chris Ketchum
  • Matthias Kretzler
    University of Michigan
  • Furkan Kurtoglu
    Indiana University
  • Shin Lin
    University of Washington
  • Jerry Li
  • 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
  • Ajay Pillai
  • Dena Procaccini
  • Gloria Pryhuber
    University of Rochester Medical Center / UCSD TMC
  • Ellen Quardokus
    Indiana University
  • Ellen Roufs
    USC - CC
  • Cindy Roy
  • Bill Shirey
    University of Pittsburgh
  • Jonathan Silverstein
    University of Pittsburgh
  • James Sluka
    Indiana University
  • Jeff Spraggins
  • Victoria Spruance
  • 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
  • Yafei Wang
    Indiana University
  • Clive Wasserfall
    University of Florida
  • Simon Watkins
    University of Pittsburgh
  • Alan Watson
    University of Pittsburgh
  • Dani Welter
  • Seth Winfree
    Indiana University School of Medicine
  • Dan Xi
    National Cancer Institute


The work was funded by NIH Awards OT2OD026671, U54DK120058, and U54HL145608.