Ontology and Imaging Informatics

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Third Clinical and Translational Science Ontology Workshop

  • Tutorial: June 23, 2014
  • Workshop: June 24-25, 2014

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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

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

Histopathological Image Analysis
Cell Image Ontologies; see also here.
Qualitative Imaging Biomarker Ontology
The Open Microscopy Environment (OME)
The Radiology Gamuts Ontology
Aperio ePathology
Ontology for Biomedical Investigations (OBI)

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)