Ontology and Imaging Informatics
Third Clinical and Translational Science Ontology Workshop
- Tutorial: June 23, 2014
- Workshop: June 24-25, 2014
- Venue: Ramada Inn Hotel and Conference Center, Amherst, NY 14068. For logistics details, including access to special hotel room rate, please contact Sandra Smith.
_______________________________________________________________________________________________________________
THIS MEETING IS NOW CLOSED TO FURTHER PARTICIPANTS
Goals
The goal of this meeting is to advance discoverability, interoperability and combinability of biomedical imaging data. It consists of a tutorial providing an introduction to imaging ontology, followed by two days of presentation and discussion of major contributions to biomedical imaging in radiology and digital pathology.
- Day 0 of the workshop will consist in a tutorial providing an introduction to biomedical imaging ontology.
- Day 1 of the workshop will consist in an overview of major contributions to biomedical imaging in radiology and digital pathology with a view towards coordination and exchange of ideas.
- Day 2 will focus on the creation and review of a draft Biomedical Image Ontology and explore how ontology can contribute to the coordination of research across the CTSA consortium with a special reference to digital histopathology imaging.
Schedule: Tutorial
Monday, June 23
Tutorial
10:00 Registration
10:30 Ulysses Balis (Michigan): Introduction to Imaging Informatics: The Problem of Image Data Interoperability
12:30 Lunch
13:30 Barry Smith (Buffalo): Introduction to Ontology for Imaging Informatics
15:00 Break
15:30 William Hogan (Arkansas): Ontology in the CTSA Consortium
Schedule: Workshop
Tuesday, June 24
Morning
- 8:30 Breakfast and Registration
- 9:00 Participant Introductions
- 9:15 Keynote Address: Daniel Rubin: Imaging Big Data
- Driving use cases for imaging in the era of Big Data
- The central role of imaging ontology
- Example projects using ontologies
- Abstract
- 10:15 Break
- 10:30 Michael J. Becich: An Overview of Standards and Initiatives in Digital Pathology
- 11:15 Charles Kahn: Radiology Gamuts Ontology: Differential Diagnosis in Radiology
- 12:00 Lunch
Afternoon
- 13:00 Michael Calhoun and Ilya Goldberg: Image Language Processing and Encoding
- 13:40 Bernard Gibaud: Ontology of Imaging Datasets as a Prerequisite for Ontologies of Imaging Biomarkers
- 14:20 :James Overton and Heiner Overkampf: Expressing Medical Image Measurements using the Ontology for Biomedical Investigations
- 15:00 Break
- 15:20 Andrew H. Beck: Imaging Informatics and Ontologies for the Development and Dissemination of Integrative Cancer Diagnostics
- 16:00 Paolo Ciccarese: Interoperable Biomedical Image Annotations. Describing and Linking Biomedical Images through Open Annotation and Domain Ontologies
- 16:40 Anna Maria Masci: Immunological Images and the ImmPort Database and Analysis Portal
- 17:20 Alexander Diehl: The NIF / ImmPort Antibody Registries: Benefits of Consistent Naming
- 18:00 Reception and Dinner sponsored by the University at Buffalo Department of Biomedical Informatics
Wednesday, June 25
Morning
- 8:30 Breakfast
- 9:00 Practical sessions devoted to creating a strategy to promote comparability and queryability of biomedical image data in general and digital pathology imaging data in particular
Sessions will include:
- Alan Ruttenberg: Queryathon This session is targeted to participants with imaging data. The goal is to develop a set of competency questions to help assess progress on a imaging ontology. If we don't document the purpose for which we are building an ontology then we won't be able to assess whether what we've built is fit for purpose. The competency questions we will be looking for will be questions participants want to be able to ask of their data for which they think the data suffice to answer the questions but which can't be effectively asked with current approaches to image representation.
- Barry Smith: An Ontology Framework for Biomedical Imaging
- Metin N. Gurcan, Anant Madabhushi and John Tomaszewski: Histopathological Image Analysis (HIMA) and Ontology
- 10:30-10:45 Break
- William Hogan: Biobanking and Digital Pathology: How to Make Ontologies that Work Together
- Werner Ceusters: Referent Tracking: How to Use Ontologies to Deal with Instance Data
- 12:00 Lunch
Afternoon
- 13:00 Hackathon: Building an Ontology for Digital Pathology
16:00 Close
Sponsors
- Department of Biomedical Informatics, University at Buffalo
- Department of Pathology and Anatomy, School of Medicine and Biomedical Sciences, University at Buffalo
- This meeting forms part of a series of ontology workshops sponsored by the NCBO. A precursor event in this series, devoted to the ontology of images, was held in 2006.
Background
Organizing Committee
- Barry Smith (Buffalo)
- William Hogan (Arkansas)
- John Tomaszewski (Buffalo)
Participants
Travis Allen (Buffalo)
Sivaram Arabandi (Houston)
Ulysses J. Balis (Ann Arbor)
Carol Bean (NCBO / Stanford)
Michael Becich (Pittsburgh)
Andrew H. Beck (Harvard)
Tanja Bekhuis (Pittsburgh)
Mathias Brochhausen (Arkansas)
Wiam Bshara (Buffalo)
Michael Calhoun (Sinq Systems)
Alexander Cox (Buffalo)
Ilya Goldberg (Open Microscopy Initiative / NIH National Institute on Aging)
Werner Ceusters (Buffalo)
Paolo Ciccarese (Harvard)
Chris Crowner (Buffalo)
Alexander Diehl (Buffalo)
Michael Dwyer (Buffalo)
Peter Elkin (Buffalo)
Carmelo Gaudioso (Buffalo)
Nancy Gertrudiz (@CARES, Mexico City)
Bernard Gibaud (LTSI, Rennes)
Allan S. Goldberg (Touro University, California)
Metin Gurcan (Ohio)
William Hogan (Arkansas)
Mark Jensen (Buffalo)
Charles E. Kahn (Milwaukee)
Warren A. Kibbe (National Cancer Institute)
Venkat N. Krovi (Buffalo)
Anant Madabhushi (Case)
Tatiana Malyuta (CUNY)
Anna Maria Masci (Duke)
Kevin Mitchell (Pittsburgh)
Heiner Oberkampf (Siemens, Munich)
James A. Overton (Knocean, Toronto)
Patrick Ray (Buffalo)
Michael Riben, MD (MD Anderson Cancer Center, Houston)
Daniel Rubin (Stanford)
Alan Ruttenberg (Buffalo)
András Sablauer (Memphis)
Ferdinand Schweser (Buffalo)
Barry Smith (Buffalo)
Jose Luis Tapia (Buffalo)
John Tomaszewski (Buffalo)
Eugene Tseytlin (Pittsburgh)
Amber Worral (Buffalo)
