Third Clinical and Translational Science Ontology Workshop, Amherst, NY, June 24-25, 2014

| May 19, 2014

Thanks to a loyal reader for sharing news of the Third Clinical and Translational Ontology Workshop from The National Center for Ontological Research (NCOR). Details about the meeting later next month are available on the NCOR Ontology and Informatics Workshop Wiki. My first experience with seeing a meeting program in the form of a Wiki and a “Day 0” of the conference.

Information below.  Links will take you to Wiki. All of the information is arranged in a complicated ontology with emphasis on digital pathology and cancer diagnostics.

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

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
9:00 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
13:00 Metin N. GurcanAnant Madabhushi and John Tomaszewski: Histopathological Image Analysis (HIMA) and Ontology
13:45 Bernard Gibaud: Ontology of Imaging Datasets as a Prerequisite for Ontologies of Imaging Biomarkers
14:30 :James Overton and Heiner Overkampf: Expressing Medical Image Measurements using the Ontology for Biomedical Investigations
15:00 Break
15:30 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
16:30 Alexander Diehl: The NIF / ImmPort Antibody Registries
17:00 Anna Maria Masci: Immunological Images and the ImmPort Database and Analysis Portal
18:00 Conference Dinner sponsored by the University at Buffalo Department of Biomedical Informatics

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:

Other breakout sessions will be organized according to demand

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.

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)

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)

Nancy Gertrudiz (@CARES, Mexico City)

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)

Kevin Mitchell (Pittsburgh)

Heiner Oberkampf (Siemens, Munich)

James A. Overton (Knocean, Toronto)

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)

About NCOR

The National Center for Ontological Research (NCOR) was established in Buffalo in 2005 with the goal of advancing the quality of ontological research and development and of establishing tools and measures for ontology evaluation and quality assurance. NCOR draws on the expertise of ontologists associated with the University at Buffalo and of their collaborators in scientific, commercial and government institutions throughout the world.

NCOR serves as a vehicle to coordinate, enhance, publicize, and seek funding for ontological research activities. It provides coordination, infrastructure, and independent review to organizations employing ontologies in fields such as defense and intelligence, management, healthcare and biomedical sciences.

It provides researchers working in ontology-related areas with specialized support in seeking external funding and in assembling collaborative, interdisciplinary teams both nationally and internationally. It provides consultant services for ontology projects especially in the defense and security fields and in health care and biomedical informatics. NCOR also engages in training and outreach endeavors that are designed to broaden the range of institutions and individuals accepting the goals of high quality ontology in both theory and practice.

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