Difference between revisions of "Workshop on Ontology of Images"

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[[Agenda]]
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[[Presentations|Imaging Workshop Slides]]
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[[Hotel]]
 
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[[#Participants|Participants]]  
 
  
 
[[#Some Relevant Links|Some Relevant Links]]  
 
[[#Some Relevant Links|Some Relevant Links]]  
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== Background ==
 
== Background ==
  
−
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the ontology of (biomedical) images and imaging. The workshop will take place on March 24-25, 2006 in Stanford.  
+
The [https://www.bioontology.org/ National Center for Biomedical Ontology] will host a two-day workshop focused on the ontology of (biomedical) images and imaging. The workshop will take place on March 24-25, 2006 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford.  
  
 
The goal of the workshop is to promote interoperability of biomedical image and imaging ontologies through the application of principles of sound ontology construction and through the coordination of current ontology development efforts in the imaging domain. One subsidiary goal is to ensure compatibility of image ontologies with ontologies of those biomedical entities which images represent. The workshop will include hands-on experiments directed towards building a biomedical image ontology on the basis of sample ontologies submitted by participants in advance.
 
The goal of the workshop is to promote interoperability of biomedical image and imaging ontologies through the application of principles of sound ontology construction and through the coordination of current ontology development efforts in the imaging domain. One subsidiary goal is to ensure compatibility of image ontologies with ontologies of those biomedical entities which images represent. The workshop will include hands-on experiments directed towards building a biomedical image ontology on the basis of sample ontologies submitted by participants in advance.
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- building an ontology of imaging tools and data, including issues related to the classification of imaging algorithms and to the potential uses of a tools ontology in supporting interoperability of bioinformatics software (in conjunction with the [http://na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group Software and Data Integration Working Group] of the NIH Roadmap National Centers for Biomedical Computing).
 
- building an ontology of imaging tools and data, including issues related to the classification of imaging algorithms and to the potential uses of a tools ontology in supporting interoperability of bioinformatics software (in conjunction with the [http://na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group Software and Data Integration Working Group] of the NIH Roadmap National Centers for Biomedical Computing).
  
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The workshop is designed to be of value to all those involved in biocomputing in the imaging domain, including representatives of those NCBCs who use or develop imaging technologies. It has been made possible by financial support from GlaxoSmithKline (GSK) and Language & Computing (L&C).  
+
The workshop is designed to be of value to all those involved in biocomputing in the imaging domain, including representatives of those NCBCs who use or develop imaging technologies.  
  
−
An [[agenda]] is provided here. [[Hotel]] and related information is provided here.
+
This workshop was funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. Additional support has been provided by GlaxoSmithKline (GSK), Language & Computing (L&C) and Agfa.
 +
 
 +
== Workgroups and Mailing List ==
 +
 
 +
At the conclusion of the workshop, many participants expressed interest in continuing the discussions and undertaking the work related to imaging ontology. A mailing list for these discussions was set up (https://www.neuroinformatics.org/mailman/listinfo/image-ontology)
 +
 
 +
In addition, a Wiki to host materials related to a working group in imaging ontology was created (http://www.neuroinformatics.org:8080/xwiki/bin/view/ImageOntology/Main). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.
 +
 
 +
== Agenda ==
 +
 
 +
(See [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images#Webcast Webcast] for videos of all sessions.)
 +
 
 +
'''Session I: How to Build an Ontology''' Barry Smith (Moderator)
 +
 
 +
9:00am Introduction
 +
 
 +
-- What this Meeting is For
 +
 
 +
-- Basic Principles of Ontology Design
 +
 
 +
-- The OBO Foundry Project
 +
 
 +
-- The OBO Relation Ontology
 +
 
 +
10:30am Coffee
 +
 
 +
11:00am Towards an Ontology for the Imaging Domain
 +
 
 +
-- BIRNLex and RadLex Case Studies
 +
 
 +
12:15pm Kaustubh Supekar: An Overview of the Groups Represented at this Meeting
 +
 
 +
12:30pm Lunch
 +
 
 +
'''Session II: Imaging Terms and Relations'''
 +
Daniel Rubin (Moderator)
 +
 
 +
1:30pm Participant self-introductions
 +
 
 +
2:00pm Ontologies and Terminologies in Radiology and Biological Imaging
 +
 
 +
-- Curt Langlotz: RadLex
 +
 
 +
-- Maryann Martone: BIRNLex
 +
 
 +
-- Anand Kumar: DICOM
 +
 
 +
3:30pm Coffee
 +
 
 +
4:00pm Relations and Reasoning in Image Ontologies
 +
 
 +
-- Dirk Marwede: Relations in Image Ontologies and Anatomy Ontologies
 +
 
 +
-- Mariana Casella dos Santos: Bootstrapping an Image Ontology
 +
 
 +
-- Helen Chen: Building Real-World Applications and Reasoning in Radiology
 +
 
 +
'''Session III: Image Ontologies'''
 +
Suzanna Lewis (Moderatrix)
 +
 
 +
9:00am Examples
 +
 
 +
-- Matthew Fielding: From RadLex to RadiO
 +
 
 +
-- C. Forbes Dewey: Experibase
 +
 
 +
10:30am Coffee
 +
 
 +
11:00am Reasoning with Image Ontologies
 +
 
 +
-- W. Lorensen: Engineering Beyond Pixels
 +
 
 +
-- William Bug: BIRN's Image Ontology Requirements
 +
 
 +
-- Louis Goldberg: On Reasoning with Images
 +
 
 +
12:30pm Lunch
 +
 
 +
'''Session IV: Imaging Tools and Data'''
 +
Ivo Dinov and Barry Smith (Moderators)
 +
 
 +
1:30pm Towards an Ontology of Imaging Tools and Data
 +
 
 +
-- David Kennedy: The Internet Analysis Tools Registry
 +
 
 +
-- Barry Smith: What Should an Ontology of Tools and Data Look Like?
 +
 
 +
-- Ontology vs. Yellow Pages: Concluding Debate between Ivo Dinov, Peter Lyster, Suzanna Lewis and Bill Lorensen
 +
 
 +
3:30pm Coffee
 +
 
 +
-- Strategy Session: How to Build an Image Ontology
  
 
== Participants ==
 
== Participants ==
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James A Butler (GlaxoSmithKline)
 
James A Butler (GlaxoSmithKline)
  
−
John Carrino (Partners)
+
David Channin (NMH)
  
−
Werner Ceusters (Buffalo)
+
Helen Chen (Agfa)
  
−
David Clunie (RadPharm, Princeton)
+
Beverly Collins (Radlex)  
  
−
Beverly Collins (Radlex)  
+
Sherri de Coronado (NCI)
  
 
C. Forbes Dewey (MIT)
 
C. Forbes Dewey (MIT)
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Keith Dreyer (Harvard)
 
Keith Dreyer (Harvard)
 +
 +
Matthew Fielding (IFOMIS)
 +
 +
Daniel Gardner (Cornell)
  
 
Christine Golbreich (Rennes)
 
Christine Golbreich (Rennes)
 +
 +
Louis Goldberg (Buffalo)
  
 
Jeff Grethe (BIRN)
 
Jeff Grethe (BIRN)
  
−
Donald Harrington (NIBIB)  
+
Ammar Halawa (FujiFilm Medical Systems)
  
−
Frank Hartel (NCI)
+
Donald Harrington (NIBIB)
  
−
Dave Helman (L&C)
+
David Hellman (L&C)  
  
 
Peter Hunter (Aukland)
 
Peter Hunter (Aukland)
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William Lorensen (General Electric)
 
William Lorensen (General Electric)
−
 
−
Yves Lussier (Columbia)
 
  
 
Peter F. Lyster (NIH/NIGMS)
 
Peter F. Lyster (NIH/NIGMS)
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Maryann Martone (BIRN)
 
Maryann Martone (BIRN)
  
−
Dirk Marwede (IFOMIS)
+
Dirk Marwede (IFOMIS / Department of Radiology, University of Leipzig)
  
−
Robin A. McEntire (GlaxoSmithKline)
+
Jose L. Mejino, Jr. (Foundational Model of Anatomy)
 +
 
 +
John Michon (Duke)
  
 
Chris Mungall (Berkeley)
 
Chris Mungall (Berkeley)
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Dianne Reeves (NCI)
 
Dianne Reeves (NCI)
 +
 +
Jens Rittscher (GE)
  
 
Daniel Rubin (Stanford)
 
Daniel Rubin (Stanford)
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Nigam Shah (Stanford)
 
Nigam Shah (Stanford)
 +
 +
Ken Shastri (FujiMed)
 +
 +
Barry Smith (Buffalo)
  
 
Kaushtubh Supekar (Stanford)
 
Kaushtubh Supekar (Stanford)
  
−
Barry Smith (Buffalo)
+
== Webcast ==
 +
 
 +
Session I
 +
Barry Smith (Moderator)
 +
 
 +
'''How to Build an Ontology'''
 +
 
 +
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram
 +
 
 +
'''Towards an Ontology for the Imaging Domain'''
 +
 
 +
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram
 +
 
 +
 
 +
Session II
 +
Daniel Rubin (Moderator)
 +
 
 +
'''Imaging Terms and Relations'''
 +
 
 +
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-1330.ram
 +
 
 +
'''Relations and Reasoning in Image Ontologies'''
 +
 
 +
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-1600.ram
 +
 
 +
 
 +
Session III
 +
Suzanna Lewis (Moderatrix)
 +
 
 +
'''Image Ontologies'''
 +
 
 +
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-09.ram
 +
 
 +
'''Reasoning with Image Ontologies'''
 +
 
 +
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-11.ram
 +
 
 +
 
 +
Session IV
 +
Ivo Dinov and Barry Smith (Moderators)
 +
 
 +
'''Imaging Tools and Data'''
 +
 
 +
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-1330.ram
 +
 
 +
'''Ontology vs. Yellow Pages'''
 +
 
 +
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-1600.ram
  
 
== Some Relevant Links ==
 
== Some Relevant Links ==
Line 119: Line 264:
  
 
[http://medical.nema.org/ DICOM]
 
[http://medical.nema.org/ DICOM]
 +
 +
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]
  
 
[http://www.dclunie.com/ David Clunie's Medical Image Format Site]
 
[http://www.dclunie.com/ David Clunie's Medical Image Format Site]
Line 129: Line 276:
  
 
[http://www.structuredreporting.com/ Structured Reporting]
 
[http://www.structuredreporting.com/ Structured Reporting]
−
 
−
[http://www.cma.mgh.harvard.edu/iatr/ Registry of Image Analysis Tools]
 
  
 
[http://murphylab.web.cmu.edu/services/ Murphy Lab Image Services]
 
[http://murphylab.web.cmu.edu/services/ Murphy Lab Image Services]
Line 137: Line 282:
  
 
[http://www.cl.cam.ac.uk/%7Eafb21/publications/TwD98.html A Taxonomy of Diagram Taxonomies]
 
[http://www.cl.cam.ac.uk/%7Eafb21/publications/TwD98.html A Taxonomy of Diagram Taxonomies]
 +
 +
[http://www.bioimage.org/ Bioimage Database]
 +
 +
[http://www.brainmap.org/ BrainMap:A Functional Neuroimaging Database]
 +
 +
 +
== Tool Registries ==
 +
 +
[http://www.cma.mgh.harvard.edu/iatr/ Registry of Image Analysis Tools]
 +
 +
[http://www.brc-central.org/tdb/prok_manatee/brc-central/software.shtml BRC Central Bioinformatics Resource Center]
 +
 +
 +
----
 +
 +
[[Hotel]]
 +
 +
[[Venue]]

Latest revision as of 19:32, 1 March 2018

Imaging Workshop Slides

Some Relevant Links

Background

The National Center for Biomedical Ontology will host a two-day workshop focused on the ontology of (biomedical) images and imaging. The workshop will take place on March 24-25, 2006 in Room M-112 of the Lane Medical Library in Stanford.

The goal of the workshop is to promote interoperability of biomedical image and imaging ontologies through the application of principles of sound ontology construction and through the coordination of current ontology development efforts in the imaging domain. One subsidiary goal is to ensure compatibility of image ontologies with ontologies of those biomedical entities which images represent. The workshop will include hands-on experiments directed towards building a biomedical image ontology on the basis of sample ontologies submitted by participants in advance.

The following topics will be addressed:

- coordination and integration of ontologies in the imaging domain

- ontologies for classification of images, image features, interpretations,

- the role of a reference ontology such as the FMA

- the use of common relations (along the lines advanced in the OBO Relation Ontology), including relations among images, features, interpretations, and the underlying reality

- use of ontologies in reasoning

- building an ontology of imaging tools and data, including issues related to the classification of imaging algorithms and to the potential uses of a tools ontology in supporting interoperability of bioinformatics software (in conjunction with the Software and Data Integration Working Group of the NIH Roadmap National Centers for Biomedical Computing).

The workshop is designed to be of value to all those involved in biocomputing in the imaging domain, including representatives of those NCBCs who use or develop imaging technologies.

This workshop was funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at http://nihroadmap.nih.gov/bioinformatics. Additional support has been provided by GlaxoSmithKline (GSK), Language & Computing (L&C) and Agfa.

Workgroups and Mailing List

At the conclusion of the workshop, many participants expressed interest in continuing the discussions and undertaking the work related to imaging ontology. A mailing list for these discussions was set up (https://www.neuroinformatics.org/mailman/listinfo/image-ontology)

In addition, a Wiki to host materials related to a working group in imaging ontology was created (http://www.neuroinformatics.org:8080/xwiki/bin/view/ImageOntology/Main). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.

Agenda

(See Webcast for videos of all sessions.)

Session I: How to Build an Ontology Barry Smith (Moderator)

9:00am Introduction

-- What this Meeting is For

-- Basic Principles of Ontology Design

-- The OBO Foundry Project

-- The OBO Relation Ontology

10:30am Coffee

11:00am Towards an Ontology for the Imaging Domain

-- BIRNLex and RadLex Case Studies

12:15pm Kaustubh Supekar: An Overview of the Groups Represented at this Meeting

12:30pm Lunch

Session II: Imaging Terms and Relations Daniel Rubin (Moderator)

1:30pm Participant self-introductions

2:00pm Ontologies and Terminologies in Radiology and Biological Imaging

-- Curt Langlotz: RadLex

-- Maryann Martone: BIRNLex

-- Anand Kumar: DICOM

3:30pm Coffee

4:00pm Relations and Reasoning in Image Ontologies

-- Dirk Marwede: Relations in Image Ontologies and Anatomy Ontologies

-- Mariana Casella dos Santos: Bootstrapping an Image Ontology

-- Helen Chen: Building Real-World Applications and Reasoning in Radiology

Session III: Image Ontologies Suzanna Lewis (Moderatrix)

9:00am Examples

-- Matthew Fielding: From RadLex to RadiO

-- C. Forbes Dewey: Experibase

10:30am Coffee

11:00am Reasoning with Image Ontologies

-- W. Lorensen: Engineering Beyond Pixels

-- William Bug: BIRN's Image Ontology Requirements

-- Louis Goldberg: On Reasoning with Images

12:30pm Lunch

Session IV: Imaging Tools and Data Ivo Dinov and Barry Smith (Moderators)

1:30pm Towards an Ontology of Imaging Tools and Data

-- David Kennedy: The Internet Analysis Tools Registry

-- Barry Smith: What Should an Ontology of Tools and Data Look Like?

-- Ontology vs. Yellow Pages: Concluding Debate between Ivo Dinov, Peter Lyster, Suzanna Lewis and Bill Lorensen

3:30pm Coffee

-- Strategy Session: How to Build an Image Ontology

Participants

Yasser alSafadi (Philips Research)

Carol Bean (NCRR)

Bruce Bray (Utah)

William Bug (BIRN)

James A Butler (GlaxoSmithKline)

David Channin (NMH)

Helen Chen (Agfa)

Beverly Collins (Radlex)

Sherri de Coronado (NCI)

C. Forbes Dewey (MIT)

Ivo Dinov (UCLA)

Keith Dreyer (Harvard)

Matthew Fielding (IFOMIS)

Daniel Gardner (Cornell)

Christine Golbreich (Rennes)

Louis Goldberg (Buffalo)

Jeff Grethe (BIRN)

Ammar Halawa (FujiFilm Medical Systems)

Donald Harrington (NIBIB)

David Hellman (L&C)

Peter Hunter (Aukland)

David Kennedy (Harvard)

Richard I. Kitney (Imperial College, London)

Anand Kumar (IFOMIS)

Curtis Langlotz (University of Pennsylvania)

Suzanna Lewis (Berkeley)

William Lorensen (General Electric)

Peter F. Lyster (NIH/NIGMS)

Maryann Martone (BIRN)

Dirk Marwede (IFOMIS / Department of Radiology, University of Leipzig)

Jose L. Mejino, Jr. (Foundational Model of Anatomy)

John Michon (Duke)

Chris Mungall (Berkeley)

Robert Murphy (CMU)

Mark Musen (Stanford)

Dianne Reeves (NCI)

Jens Rittscher (GE)

Daniel Rubin (Stanford)

Mariana Casella Dos Santos (L&C, Belgium)

Nigam Shah (Stanford)

Ken Shastri (FujiMed)

Barry Smith (Buffalo)

Kaushtubh Supekar (Stanford)

Webcast

Session I Barry Smith (Moderator)

How to Build an Ontology

http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram

Towards an Ontology for the Imaging Domain

http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram


Session II Daniel Rubin (Moderator)

Imaging Terms and Relations

http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-1330.ram

Relations and Reasoning in Image Ontologies

http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-1600.ram


Session III Suzanna Lewis (Moderatrix)

Image Ontologies

http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-09.ram

Reasoning with Image Ontologies

http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-11.ram


Session IV Ivo Dinov and Barry Smith (Moderators)

Imaging Tools and Data

http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-1330.ram

Ontology vs. Yellow Pages

http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-1600.ram

Some Relevant Links

The Open Microscopy Environment (OME) Data Model

OBO Biological Imaging Methods

RadLex: A Lexicon for Uniform Indexing and Retrieval of Radiology Information Resources

DICOM

Neuroimaging Informatics Technology Initiative

David Clunie's Medical Image Format Site

Medical Image Databases

Mutant Mouse Images

Foundational Model of Anatomy

Structured Reporting

Murphy Lab Image Services

In Vivo Imaging

A Taxonomy of Diagram Taxonomies

Bioimage Database

BrainMap:A Functional Neuroimaging Database


Tool Registries

Registry of Image Analysis Tools

BRC Central Bioinformatics Resource Center


Hotel

Venue

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