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.

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THIS MEETING IS NOW CLOSED TO FURTHER PARTICIPANTS

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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 Digital Pathology Image Ontology and to explore how ontology can contribute to the coordination of research across the CTSA consortium.

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

18:00 Reception and Dinner sponsored by the University at Buffalo Department of Biomedical Informatics

Wednesday, June 25

Morning

8:30 Breakfast

9:00 Digital Pathology: Practical sessions devoted to creating a strategy to promote interoperability of digital pathology data and systems

10:30-10:45 Break

12:00 Lunch

Afternoon

13:00 Group Meetings

1. Hackathon: Building an Ontology for Digital Pathology

Metin N. Gurcan, Anant Madabhushi and John Tomaszewski: Histopathological Image Analysis (HIMA) and Ontology

2. CTS Ontology Affinity Group

Topics to be addressed will include:

• The Ontology for Medically Relevant Social Entities (OMRSE),
• Biobanking
• Referent Tracking

Other breakout sessions will be organized according to demand

16:00 Close

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Sponsors

• Department of Biomedical Informatics, University at Buffalo

• Department of Pathology and Anatomy, School of Medicine and Biomedical Sciences, University at Buffalo

• Clinical and Translational Science Ontology Affinity Group.

• National Center for Biomedical Ontology (NCBO)

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.

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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)

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)