Difference between revisions of "Workshop on Ontology of Images"

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[[Presentations|Imaging Workshop Slides]]
  
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[[#Some Relevant Links|Some Relevant Links]]
  
 
== Background ==
 
== Background ==
  
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the ontology of (biomedical) images. The goal of the workshop, which will take place on March 24-25, 2006 in Stanford, is to coordinate current efforts towards the development of a biomedical image/imaging ontology. The following topics will be addressed:
+
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.  
  
        * basic principles of sound ontologies
+
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.
  
        * steps towards coordination and integration of ontologies in the imaging domain
+
The following topics will be addressed:
  
        * hands-on experiments directed towards building a biomedical image ontology (dealing with: images and image-classification, image features, interpretations, relation of images to reality, the role of a reference ontology such as the FMA)
+
- coordination and integration of ontologies in the imaging domain
  
        * preliminary discussions directed towards 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
+
- ontologies for classification of images, image features, interpretations,  
  
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.
+
- the role of a reference ontology such as the [http://sig.biostr.washington.edu/projects/fm/AboutFM.html FMA]
  
    Participants will include Yasser alSafadi (Philips Research), Carol Bean (NCRR), Bruce Bray (Utah), James A Butler (GlaxoSmithKline), John Carrino (Partners), Werner Ceusters (IFOMIS), David Clunie (RadPharm, Princeton), C. Forbes Dewey (MIT), Ivo Dinov (UCLA), Keith Dreyer (Harvard), Donald Harrington (NIBIB), Frank Hartel (NCI), Dave Helman (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), Yves Lussier (Columbia), Peter F. Lyster (NIH/NIGMS), Dirk Marwede (IFOMIS), Robin A. McEntire (GlaxoSmithKline), Robert Murphy (CMU), Mark Musen (Stanford), Dianne Reeves (NCI), Daniel Rubin (Stanford), Mariana Casella Dos Santos (L&C, Belgium), Barry Smith (Buffalo).
+
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]), including relations among images, features, interpretations, and the underlying reality
  
    Sessions will be scheduled from 9am to 5.30pm on each of the two days.
+
- use of ontologies in reasoning
  
    We gratefully acknowledge the financial support of GlaxoSmithKline (GSK) and Language & Computing (L&C).
+
- 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).
  
    Barry Smith
+
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.  
    http://ontology.buffalo.edu/smith
 
  
   
+
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.
  
    Draft Agenda
+
== Workgroups and Mailing List ==
  
    Friday March 24 2006
+
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)
    Session I: Barry Smith (Moderator)
 
    9am Basic Principles of Ontology Design
 
    10.30pm Coffee
 
    11am Towards an Ontology for the Imaging Domain
 
  
    12.30pm Lunch
+
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.
  
    Session II: Daniel Rubin (Moderator)
+
== Agenda ==
    2pm RadLex, Ontologies and Terminologies in Radiology
 
    (with brief presentations from RadLex and DICOM)
 
    3.30pm Coffee
 
    4pm Ontologies and Reasoning with Radiological Image Data
 
  
    Saturday March 25 2006
+
(See [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images#Webcast Webcast] for videos of all sessions.)
    Session III: Werner Ceusters and Suzanna Lewis (Moderators)
 
    9am Towards Interoperability of Ontologies: Presentations from Image Ontology groups
 
    10.30-11am Coffee
 
    11am How to Align Image Ontologies
 
  
    12.30pm Lunch
+
'''Session I: How to Build an Ontology''' Barry Smith (Moderator)
  
    Session IV: Ivo Dinov and Barry Smith (Moderators)
+
9:00am Introduction
    2pm Towards an Ontology of Imaging Tools and Data
 
    Presentations from NCBC Image Groups on Available Resources and Needs for Tool/Data Registry
 
    3.30 Coffee
 
    4pm How to Realize Identified Needs: Ontology vs. Yellow Pages
 
   
 
  
    Some Relevant Links
+
-- What this Meeting is For
  
    The Open Microscopy Environment (OME) Data Model
+
-- Basic Principles of Ontology Design
  
    OBO Biological Imaging Methods
+
-- The OBO Foundry Project
  
    RadLex: A Lexicon for Uniform Indexing and Retrieval of Radiology Information Resources
+
-- The OBO Relation Ontology
  
    DICOM
+
10:30am Coffee
  
    David Clunie's Medical Image Format Site
+
11:00am Towards an Ontology for the Imaging Domain
  
    Medical Image Databases
+
-- BIRNLex and RadLex Case Studies
  
    Pathbase (Mutant Mouse Images)
+
12:15pm Kaustubh Supekar: An Overview of the Groups Represented at this Meeting
  
    Foundational Model of Anatomy
+
12:30pm Lunch
  
    Structured Reporting
+
'''Session II: Imaging Terms and Relations'''
 +
Daniel Rubin (Moderator)
  
    IATR Registry of Image Analysis Tools
+
1:30pm Participant self-introductions
  
    Murphy Lab Image Services
+
2:00pm Ontologies and Terminologies in Radiology and Biological Imaging
  
    In Vivo Imaging
+
-- Curt Langlotz: RadLex
  
    A Taxonomy of Diagram Taxonomies
+
-- Maryann Martone: BIRNLex
  
   
+
-- Anand Kumar: DICOM
  
    Recommended Hotel: http://www.stanford.edu/dept/hds/SLAC/
+
3:30pm Coffee
    Standard room with full-sized bed: $65 +10% occupancy tax
 
    Larger room with a queen-sized bed: $80 +10% occupancy tax
 
    Larger room with two full-sized beds: $95 +10% occupancy tax
 
   
 
    Participants can book online at https://webbooking.pegs.com/default.aspx?pcode=SLACG&rateplan=medctr
 
    or by calling 650-926-2800; please mention in comment field:
 
   
 
    Group number = #232246
 
    Group name = "Image Ontology Workshop."
 
  
    Other Hotels
+
4:00pm Relations and Reasoning in Image Ontologies
  
    Directions
+
-- 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 ==
 +
 
 +
[http://genomebiology.com/2005/6/5/R47 The Open Microscopy Environment (OME) Data Model]
 +
 
 +
[http://obo.sourceforge.net/cgi-bin/detail.cgi?image OBO Biological Imaging Methods]
 +
 
 +
[http://www.rsna.org/Radlex/index.cfm RadLex: A Lexicon for Uniform Indexing and Retrieval of Radiology Information Resources]
 +
 
 +
[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.library.uthscsa.edu/internet/ImageDatabases.cfm Medical Image Databases]
 +
 
 +
[http://www.pathbase.net/Pathbase/ Mutant Mouse Images]
 +
 
 +
[http://sig.biostr.washington.edu/projects/fm/AboutFM.html Foundational Model of Anatomy]
 +
 
 +
[http://www.structuredreporting.com/ Structured Reporting]
 +
 
 +
[http://murphylab.web.cmu.edu/services/ Murphy Lab Image Services]
 +
 
 +
[https://cabig.nci.nih.gov/workspaces/Imaging In Vivo Imaging]
 +
 
 +
[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