Ontology and Imaging Informatics

Third Clinical and Translational Science Ontology Workshop

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

• Venue: Ramada Hotel & Conference Center, Amherst, NY 14068.

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 1 will consist in a tutorial providing an introduction to biomedical imaging ontology.

- Day 2 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 3 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: Introduction to Imaging Informatics: The Problem of Image Data Interoperability

• A brief history of digital imaging, digital annotation, markup and metadata encoding
• Primer on image data encoding concepts and requirements
• Primer on Image storage data formats
• Primer on DICOM
• Primer on image metadata concepts
• Exploration of OME as a representative image metadata lexicon
• Case studies in image metadata challenges, as created by a contemporary lack of a single common framework

12:30 Lunch Buffet

13:30 Barry Smith: Introduction to Ontology for Imaging Informatics

• The Special Role of the Gene Ontology
• Open Biomedical Ontologies (OBO) Foundry
• The Semantic Web
• Principles for good ontology development
• Basic Formal Ontology (BFO)
• The Foundational Model of Anatomy (FMA) Ontology
• The Information Artifact Ontology (IAO)
• Images as Information Artifacts

15:00 Refreshment Break

15:30 William Hogan: Ontology in the CTSA Consortium

• Why ontology is important to clinical and translational science
• How ontology is being used in clinical and translational science
• The Clinical and Translational Science Ontology Group

Workshop - Day 1: 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 Heiner Oberkampf and James A. Overton: 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 (on the Ramada Hotel's Ellicott Patio) sponsored by the University at Buffalo Department of Biomedical Informatics (No-Host Bar)

Workshop - Day 2: Wednesday, June 25

Morning

8:30 Continental 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].

Metin N. Gurcan: Histopathological Image Analysis (HIMA) and Ontology: Part 1

John Tomaszewski: Histopathological Image Analysis (HIMA) and Ontology: Part 2

10:30-10:45 Refreshment 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 Buffet

Afternoon

13:00: Anant Madabhushi: Histopathological Image Analysis (HIMA) and Ontology: Part 3

13:15 Hackathon: Building an Ontology for Digital Pathology

Facilitators: James Overton and Barry Smith

Topics:

• QIBO -- and the issue of permanence
• Aristotelian definitions
• 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.

15:40 ICBO 2014

15:45 Further discussion of imaging ontology white paper

16:00 Close of Workshop

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. Post-workshop paper now published in Journal of Pathology Informatics: “Biomedical Imaging Ontologies: A Survey and Proposal for Future Work”

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 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 (University at Buffalo)

William Hogan (University of Florida)

John Tomaszewski (University at Buffalo)

Participants

Sivaram Arabandi (Ontopro)

Ulysses J. Balis (University of Michigan, Ann Arbor)

Carol Bean (NCBO / Stanford University)

Michael Becich (University of Pittsburgh)

Andrew H. Beck (Harvard Medical School)

Tanja Bekhuis (University of Pittsburgh)

Talapady N. Bhat (NIST)

Jonathan Bona (University at Buffalo)

Erich Bremer (Stony Brook Medicine)

Mathias Brochhausen (University of Arkansas for Medical Sciences)

Wiam Bshara (Roswell Park Cancer Institute)

Michael Calhoun (Sinq Systems)

Werner Ceusters (University at Buffalo)

Paolo Ciccarese (Harvard Medical School)

Alexander Cox (University at Buffalo)

Chris Crowner (University at Buffalo)

Alexander Diehl (University at Buffalo)

William Duncan (University at Buffalo)

Michael Dwyer (University at Buffalo)

Peter Elkin (University Buffalo)

Gilberto Fragoso (NCI / NIH)

Carmelo Gaudioso (Roswell Park Cancer Institute)

Nancy Gertrudez (CUDI / Mexican Universities Research Network)

Bernard Gibaud (LTSI, Rennes)

Allan S. Goldberg (Touro University, California)

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

Metin Gurcan (State University of Ohio)

William Hogan (University of Florida)

Mark Jensen (University at Buffalo)

Charles E. Kahn (Medical College of Wisconsin, Milwaukee)

Venkat N. Krovi (University at Buffalo)

Anant Madabhushi (Case Western Reserve University)

Tatiana Malyuta (CUNY)

Anna Maria Masci (Duke University)

Kevin Mitchell (University of Pittsburgh)

Heiner Oberkampf (Siemens, Munich / University of Augsburg)

James A. Overton (Knocean, Toronto)

Patrick Ray (University at Buffalo)

Michael Riben, MD (MD Anderson Cancer Center, Houston)

Daniel Rubin (Stanford University)

Alan Ruttenberg (University at Buffalo)

András Sablauer (St Jude Children's Research Hospital, Memphis)

Yonatan Schreiber (University at Buffalo / CUBRC)

Ferdinand Schweser (University at Buffalo)

Selja Seppala (University at Buffalo)

Barry Smith (University at Buffalo)

Dagobert Soergel (University at Buffalo)

Jose Luis Tapia (University at Buffalo)

John Tomaszewski (University at Buffalo)

Eugene Tseytlin (University of Pittsburgh)

Marc van Driel (Philips Research, The Netherlands)

Amber Worral (Roswell Park Cancer Institute)