Ontology and Imaging Informatics

Ontology and the Future of Laboratory Information

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.

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. The meeting will include community breakout groups addressing specific communities, including the CTSA consortium.

- 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 consist of a number of breakout groups addressing specific goals of their respective communities. One such group will focus on a draft Digital Pathology Image Ontology, which will be distributed to interested participants in advance. Another group will address the role of ontology in the coordination of research across the CTSA consortium.

The meeting will conclude with reports from the breakout groups and with a session devoted to future plans.

Examples of the types of subtopics to be addressed include:

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)

• Space for this meeting is limited and intending participants are encouraged to write to Barry Smith as soon as possible.

Draft 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

Draft Schedule: Workshop

Tuesday, June 24

8:30 Breakfast and Registration

9:15 Participant Introductions

9:30 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

10:30 Break

11:00 Michael J. Becich: An Overview of Standards and Initiatives in Digital Pathology

12:00 Lunch

13:00 Charles Kahn: Radiology Gamuts Ontology: Differential Diagnosis in Radiology

14:00 Metin N. Gurcan, Anant Madabhushi and John Tomaszewski: Histopathological Image Analysis (HIMA) and Ontology

15:00 Break

15:30

James Overton and Heiner Overkamp: Expressing Medical Image Measurements using the Ontology for Biomedical Investigations

Andrew H. Beck: Imaging Informatics and Ontologies for the Development and Dissemination of Integrative Cancer Diagnostics

Paolo Ciccarese: Interoperable Biomedical Image Annotations. Describing and Linking Biomedical Images through Open Annotation and Domain Ontologies

Alexander Diehl: The NIF / ImmPort Antibody Registries

Wednesday, June 25

8:30 Breakfast

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

12:00 Lunch

13:00 Group Meetings

1. Hackathon: Building an Ontology for Digital Pathology

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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Organizing Committee

Barry Smith (Buffalo)

William Hogan (Arkansas)

John Tomaszewski (Buffalo)

Participants will include

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)

Werner Ceusters (Buffalo)

Paolo Ciccarese (Harvard)

Chris Crowner (Buffalo)

Alexander Diehl (Buffalo)

Michael Dwyer (Buffalo)

Peter Elkin (Buffalo)

Carmelo Gaudioso (Buffalo)

Bernard Gibaud (LTSI, Rennes)

Allan S. Goldberg (Touro University, California)

Metin Gurcan (Ohio)

William Hogan (Arkansas)

Charles E. Kahn (Milwaukee)

Venkat N. Krovi (Buffalo)

Anant Madabhushi (Case)

Anna Maria Masci (Duke)

Heiner Overkamp (Siemens)

James A. Overton (Knocean, Toronto)

Daniel Rubin (Stanford)

Alan Ruttenberg (Buffalo)

Ferdinand Schweser (Buffalo)

Barry Smith (Buffalo)

Jose Luis Tapia (Buffalo)

John Tomaszewski (Buffalo)

Amber Worral (Buffalo)