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 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.

Tutorial: Monday, June 23

10:00 Registration

10:30 Ulysses Balis (Michigan): Introduction to Imaging Informatics: The Problem of Image Data Interoperability

12:30 Lunch Buffet

13:30 Barry Smith (Buffalo): Introduction to Ontology for Imaging Informatics

15:00 Refreshment Break

15:30 William Hogan (Arkansas): Ontology in the CTSA Consortium

Workshop: Tuesday, June 24

Morning

8:30 Registration and Continental Breakfast

9:00 Participant Introductions

9:15 Keynote Address: Daniel Rubin: Imaging Big Data

Abstract

10:15 Refreshment 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 (On Gamuts see here.)

12:00 Buffet Lunch

Afternoon

13:00 Michael Calhoun and Ilya Goldberg: Image Language Processing and Encoding

Abstract on the Open Microscopy Environment

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 Refreshment 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 (No-Host Bar)

Workshop: 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

The goal of this session is to sketch a framework which will allow us to assess progress in building an imaging ontology by providing a list of the types of questions which the ontology will allow us to answer. These should be questions for which you think your data suffice to provide answers, but which cannot be effectively asked with current approaches. Questions sent in advance are welcome; please send to [1].

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 and Mathias Brochhausen: 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

Facilitators: James Overton and Barry Smith

First draft image ontology based on the Ontology for Biomedical Investigations (OBI):

OWL File

XSL File

The scope of the ontology will be the entire domain of biomedical imaging, including Radiology, Neuro-imaging, and Histopathology; it should also include a branch relating to image-processing algorithms. However, we will focus primarily on populating the branch devoted to (quantitative) histopathology.

Possible starting points for ontology development

1. Quantitative Imaging Biomarker Ontology (QIBO)

Unfortunately QIBO contains no definitions. Suggested top-level mappings from QIBO to OBI/OBO are:

- Acquisition Device -> OBI:device

- Biological Intervention -> OBI:material processing

- Biological Target -> use relations instead of classes

- Biomarker Use -> ~IAO:objective specifications

- Imaging Agent -> ChEBI

- Imaging Agent Source of Emitted Energy -> energy terms need to be added to OBO

- Imaging Subject -> use relations instead of classes

- Imaging Technique -> OBI:assay

- Indicated Biology

- Biological Process -> GO

- Disease -> https://code.google.com/p/ogms/ OGMS], DOID

- Post-processing Algorithm -> OBI:data transformation

- Quantitative Imaging Biomarker -> ~OBI:measurement datum

2. OME Data Model

3. TBD

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

• 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.

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

Sivaram Arabandi (Houston)

Ulysses J. Balis (Ann Arbor)

Carol Bean (NCBO / Stanford)

Michael Becich (Pittsburgh)

Andrew H. Beck (Harvard)

Tanja Bekhuis (Pittsburgh)

Erich Bremer (Stony Brook)

Mathias Brochhausen (Arkansas)

Wiam Bshara (Buffalo)

Michael Calhoun (Sinq Systems)

Alexander Cox (Buffalo)

Gilberto Fragoso (NCI / NIH)

Ilya Goldberg (Open Microscopy Initiative / NIH National Institute on Aging)

Werner Ceusters (Buffalo)

Paolo Ciccarese (Harvard)

Chris Crowner (Buffalo)

Alexander Diehl (Buffalo)

Marc van Driel (Philips, Netherlands)

William Duncan (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)