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.

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

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

15:00 Break

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

Workshop: Tuesday, June 24

Morning

8:30 Breakfast and Registration
9:00 Participant Introductions
9:15 Keynote Address: Daniel Rubin: Imaging Big Data
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

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: 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. However, we will focus primarily on populating the branch devoted to (quantitative) histopathology.
Possible starting points for term-population:
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


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

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)

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

Werner Ceusters (Buffalo)

Paolo Ciccarese (Harvard)

Chris Crowner (Buffalo)

Alexander Diehl (Buffalo)

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)