Ontology and Imaging Informatics: Difference between revisions

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*Workshop: June 24-25, 2014  
*Workshop: June 24-25, 2014  


*Venue: [http://www.ramadahotelamherst.com/ Ramada Inn Hotel and Conference Center, Amherst, NY 14068]. For logistics details, including access to special hotel room rate, please contact [mailto:sgsmith2@buffalo.edu Sandra Smith].
*Venue: [http://www.ramadahotelamherst.com/ Ramada Hotel & Conference Center, Amherst, NY 14068].  
 
_______________________________________________________________________________________________________________
 
'''THIS MEETING IS NOW CLOSED TO FURTHER PARTICIPANTS'''
 
---------------------------------------------------------------------------------------------------------------
 


==Goals==  
==Goals==  
Line 17: Line 10:
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 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 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 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.
- 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.


== '''Schedule: Tutorial''' ==
== '''Tutorial: Monday, June 23'''==


<u>Monday, June 23</u>
:10:00 Registration


'''Tutorial'''
:10:30 [http://www.ccmb.med.umich.edu/node/192 '''Ulysses Balis]: [http://ncor.buffalo.edu/images/Introduction%20to%20Imaging%20Informatics_Balis.pptx 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


10:00 Registration
:12:30 Lunch Buffet


10:30 [http://www.ccmb.med.umich.edu/node/192 Ulysses Balis] (Michigan): Introduction to Imaging Informatics: The Problem of Image Data Interoperability
:13:30 [http://ontology.buffalo.edu/smith '''Barry Smith]: [http://ncor.buffalo.edu/images/Introduction_to_Biomedical_Ontology.ppt 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


12:30 Lunch
:15:00 Refreshment Break


13:30 [http://ontology.buffalo.edu/smith Barry Smith] (Buffalo): Introduction to Ontology for Imaging Informatics
:15:30 [http://ontolog.cim3.net/cgi-bin/wiki.pl?BillHogan '''William Hogan]: [http://ncor.buffalo.edu/images/hogan_ctsa_ontology_ws_buffalo.pptx 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


15:00 Break
== '''Workshop - Day 1: Tuesday, June 24'''==
 
15:30 [http://dbmi.uams.edu/faculty/william-r-hogan-m-d/ William Hogan] (Arkansas): Ontology in the CTSA Consortium
 
== '''Schedule: Workshop''' ==
 
<u>Tuesday, June 24</u>


<u> Morning </u>
<u> Morning </u>


:8:30 Breakfast and Registration
:8:30 Registration and Continental Breakfast


:9:00 Participant Introductions
:9:00 Participant Introductions


:9:15 Keynote Address: [http://www.stanford.edu/~rubin/ '''Daniel Rubin]: Imaging Big Data'''
:9:15 Keynote Address: [http://www.stanford.edu/~rubin/ '''Daniel Rubin]: [http://ncor.buffalo.edu/images/Rubin.pdf 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]]
::[[Abstract]]


:10:15 Break
:10:15 Refreshment Break


:10:30 '''[http://www.dbmi.pitt.edu/person/michael-j-becich-md-phd Michael J. Becich]: An Overview of Standards and Initiatives in Digital Pathology'''
:10:30 '''[http://www.dbmi.pitt.edu/person/michael-j-becich-md-phd Michael J. Becich]: [http://ncor.buffalo.edu/images/Digital_Path_Standards_Ontology_Becich.pptx An Overview of Standards and Initiatives in Digital Pathology]'''


:11:15 '''[http://www.mcw.edu/radiology/faculty/CharlesKahn.htm Charles Kahn]: Radiology Gamuts Ontology: Differential Diagnosis in Radiology'''
:11:15 '''[http://www.mcw.edu/radiology/faculty/CharlesKahn.htm Charles Kahn]: [http://ncor.buffalo.edu/images/Kahn_Gamuts_ontology.pdf Radiology Gamuts Ontology: Differential Diagnosis in Radiology]'''  
::On Gamuts see [http://ncorwiki.buffalo.edu/index.php/Gamuts here]


:12:00 Lunch
:12:00 Buffet Lunch


<u> Afternoon </u>
<u> Afternoon </u>


:13:00 '''[https://www.linkedin.com/pub/michael-calhoun/19/36a/567 Michael Calhoun] and [http://www.irp.nia.nih.gov/branches/irp/igoldberg.htm Ilya Goldberg]: Image Language Processing and Encoding'''
:13:00 '''[https://www.linkedin.com/pub/michael-calhoun/19/36a/567 Michael Calhoun] and [http://www.irp.nia.nih.gov/branches/irp/igoldberg.htm Ilya Goldberg]: [http://ncor.buffalo.edu/images/Goldberg_Calhoun.pdf Image Language Processing and Encoding]'''
::[[Abstract on the Open Microscopy Environment]]


:13:40 '''[https://medicis.univ-rennes1.fr/members/bernard.gibaud/index Bernard Gibaud]: Ontology of Imaging Datasets as a Prerequisite for Ontologies of Imaging Biomarkers'''  
:13:40 '''[https://medicis.univ-rennes1.fr/members/bernard.gibaud/index Bernard Gibaud]: [http://ncor.buffalo.edu/images/Bernard-Gibaud.ppt Ontology of Imaging Datasets as a Prerequisite for Ontologies of Imaging Biomarkers]'''  


:14:20 :'''[http://knocean.com/ James Overton] and Heiner Overkampf: Expressing Medical Image Measurements using the Ontology for Biomedical Investigations'''
:14:20 '''[http://www.informatik.uni-augsburg.de/en/chairs/swt/ds/staff/oberkampf/ Heiner Oberkampf] and [http://knocean.com James A. Overton]: [http://ncor.buffalo.edu/images/OBI_Image_Measurements.pdf Expressing Medical Image Measurements using the Ontology for Biomedical Investigations]'''
   
   
:15:00 Break
:15:00 Refreshment Break


:15:20 '''[http://www.becklab.org Andrew H. Beck]: Imaging Informatics and Ontologies for the Development and Dissemination of Integrative Cancer Diagnostics'''
:15:20 '''[http://www.becklab.org Andrew H. Beck]: [http://ncor.buffalo.edu/images/Beck_C-Path_Ontology.pptx Imaging Informatics and Ontologies for the Development and Dissemination of Integrative Cancer Diagnostics]'''


:16:00 '''[http://www.hcklab.org/ Paolo Ciccarese]: Interoperable Biomedical Image Annotations. Describing and Linking Biomedical Images through Open Annotation and Domain Ontologies'''
:16:00 '''[http://www.hcklab.org/ Paolo Ciccarese]: [http://www.slideshare.net/paolociccarese/integrating-open-annotation-with-any-domain-ontology Interoperable Biomedical Image Annotations. Describing and Linking Biomedical Images through Open Annotation and Domain Ontologies]'''


:16:40 '''[https://www.linkedin.com/pub/anna-maria-masci/11/a74/a55 Anna Maria Masci]: Immunological Images and the ImmPort Database and Analysis Portal'''
:16:40 '''[https://www.linkedin.com/pub/anna-maria-masci/11/a74/a55 Anna Maria Masci]: [http://ncor.buffalo.edu/images/Masci.pptx Immunological Images and the ImmPort Database and Analysis Portal]'''


:17:20 '''[http://medicine.buffalo.edu/faculty/profile.html?ubit=addiehl Alexander Diehl]: The NIF / ImmPort Antibody Registries: Benefits of Consistent Naming'''
:17:20 '''[http://medicine.buffalo.edu/faculty/profile.html?ubit=addiehl Alexander Diehl]: The NIF / ImmPort Antibody Registries: Benefits of Consistent Naming'''


:18:00 '''Reception and Dinner''' sponsored by the University at Buffalo [http://wings.buffalo.edu/smbs/biomedicalinformatics/ Department of Biomedical Informatics]
:18:00 '''Reception and Dinner (on the Ramada Hotel's Ellicott Patio)''' sponsored by the University at Buffalo [http://wings.buffalo.edu/smbs/biomedicalinformatics/ Department of Biomedical Informatics] (No-Host Bar)


<u>Wednesday, June 25</u>
== '''Workshop - Day 2: Wednesday, June 25'''==


<u> Morning </u>
<u> Morning </u>


:8:30 Breakfast
: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
: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
Line 98: Line 102:
::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 [mailto:alanruttenberg@gmail.com].
::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 [mailto:alanruttenberg@gmail.com].


:'''[http://ontology.buffalo.edu/smith Barry Smith]: An Ontology Framework for Biomedical Imaging'''
:'''[http://medicine.osu.edu/bmi/people/metin_gurcan/pages/index.aspx Metin N. Gurcan]: [http://ncor.buffalo.edu/images/Gurcan.pdf Histopathological Image Analysis (HIMA) and Ontology: Part 1]'''


:'''[http://medicine.osu.edu/bmi/people/metin_gurcan/pages/index.aspx Metin N. Gurcan], [http://engineering.case.edu/centers/ccipd/ Anant Madabhushi] and [http://medicine.buffalo.edu/faculty/profile.html?ubit=johntoma John Tomaszewski]: Histopathological Image Analysis (HIMA) and Ontology'''
:'''[http://medicine.buffalo.edu/faculty/profile.html?ubit=johntoma John Tomaszewski]: [http://ncor.buffalo.edu/images/Tomaszewski.pptx Histopathological Image Analysis (HIMA) and Ontology: Part 2]'''


:10:30-10:45 Break
:10:30-10:45 Refreshment Break


:'''[https://www.linkedin.com/profile/view?id=106844090&authType=NAME_SEARCH&authToken=byF1&locale=en_US&srchid=27153661400790133689&srchindex=1&srchtotal=387&trk=vsrp_people_res_name&trkInfo=VSRPsearchId%3A27153661400790133689%2CVSRPtargetId%3A106844090%2CVSRPcmpt%3Aprimary William Hogan]: Biobanking and Digital Pathology: How to Make Ontologies that Work Together'''
:'''[https://www.linkedin.com/profile/view?id=106844090&authType=NAME_SEARCH&authToken=byF1&locale=en_US&srchid=27153661400790133689&srchindex=1&srchtotal=387&trk=vsrp_people_res_name&trkInfo=VSRPsearchId%3A27153661400790133689%2CVSRPtargetId%3A106844090%2CVSRPcmpt%3Aprimary William Hogan and Mathias Brochhausen]: [http://ncor.buffalo.edu/images/Hogan_Brochhausen.pptx Biobanking and Digital Pathology: How to Make Ontologies that Work Together]'''


:'''[http://www.referent-tracking.com/RTU/?page=ceusters_vita Werner Ceusters]: Referent Tracking: How to Use Ontologies to Deal with Instance Data'''
:'''[http://www.referent-tracking.com/RTU/?page=ceusters_vita Werner Ceusters]: [http://ncor.buffalo.edu/images/Ceusters.pptx Referent Tracking: How to Use Ontologies to Deal with Instance Data]'''
   
   
:12:00 Lunch
:12:00 Lunch Buffet


<u> Afternoon </u>
<u> Afternoon </u>


:13:00 Hackathon: Building an Ontology for Digital Pathology'''
13:00: '''[http://engineering.case.edu/centers/ccipd/ Anant Madabhushi]: [http://ncor.buffalo.edu/images/Madabhushi.pdf Histopathological Image Analysis (HIMA) and Ontology: Part 3]'''


:First draft image ontology based on the [http://obi-ontology.org/page/Main_Page Ontology for Biomedical Investigations (OBI)]:
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 [http://obi-ontology.org/page/Main_Page Ontology for Biomedical Investigations (OBI)]:
::[http://ncor.buffalo.edu/images/image-draft.owl OWL File]
::[http://ncor.buffalo.edu/images/image-draft.owl OWL File]
::[http://ncor.buffalo.edu/images/image-draft.xslx XSL File]
::[http://ncor.buffalo.edu/images/image-draft.xslx 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 [http://icbo14.com/ ICBO 2014]
15:45 Further discussion of [[imaging ontology white paper]]
:16:00 Close of Workshop
=='''Possible starting points for ontology development''' ==
:1. [http://bioportal.bioontology.org/ontologies/QIBO Quantitative Imaging Biomarker Ontology (QIBO)]
::Unfortunately QIBO contains no definitions. Suggested top-level mappings from QIBO to OBI/OBO are:
::- Acquisition Device -> [http://obi-ontology.org/page/Main_Page OBI]:device
::- Biological Intervention -> OBI:material processing
::- Biological Target -> use [http://obofoundry.org/ro/ relations] instead of classes
::- Biomarker Use -> ~[https://code.google.com/p/information-artifact-ontology/ 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 -> [http://www.geneontology.org/ GO]
::  - Disease -> https://code.google.com/p/ogms/ OGMS], [http://disease-ontology.org/ DOID]
::- Post-processing Algorithm -> OBI:data transformation
::- Quantitative Imaging Biomarker -> ~OBI:measurement datum


:16:00 Close
:2. [http://www.openmicroscopy.org/site/support/ome-model/developers/model-overview.html OME Data Model]
 
:3. Post-workshop paper now published in Journal of Pathology Informatics: “[http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2015;volume=6;issue=1;spage=37;epage=37;aulast=Smith Biomedical Imaging Ontologies: A Survey and Proposal for Future Work]”


== Sponsors ==
== Sponsors ==
Line 126: Line 162:
*[http://www.smbs.buffalo.edu/path/index.htm Department of Pathology and Anatomy], School of Medicine and Biomedical Sciences, University at Buffalo
*[http://www.smbs.buffalo.edu/path/index.htm Department of Pathology and Anatomy], School of Medicine and Biomedical Sciences, University at Buffalo


*[https://www.ctsacentral.org/committee/ikfc-clinical-and-translational-science-affinity-group-ctso-ag Clinical and Translational Science Ontology Affinity Group].  
*[[Clinical and Translational Science Ontology Group]].  


*[http://bioontologies.org National Center for Biomedical Ontology (NCBO)]
*[http://bioontologies.org National Center for Biomedical Ontology (NCBO)]
Line 133: Line 169:
== Background ==
== Background ==


::[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2910932/ Histopathological Image Analysis]
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2910932/ Histopathological Image Analysis]
::[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293096/ Cell Image Ontologies]; see also [http://sbd.nist.gov/image/cell_image.html here].
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293096/ Cell Image Ontologies]; see also [http://sbd.nist.gov/image/cell_image.html here].
::[http://www.ncbi.nlm.nih.gov/pubmed/23589184 Qualitative Imaging Biomarker Ontology]
*[http://www.ncbi.nlm.nih.gov/pubmed/23589184 Qualitative Imaging Biomarker Ontology]
::[http://www.openmicroscopy.org/ The Open Microscopy Environment] (OME)
*[http://www.openmicroscopy.org/ The Open Microscopy Environment] (OME)
::[[Gamuts | The Radiology Gamuts Ontology]]
*[[Gamuts | The Radiology Gamuts Ontology]]
::[http://www.aperio.com/healthcare/eslide Aperio ePathology]
*[http://www.aperio.com/healthcare/eslide Aperio ePathology]
::[http://obi-ontology.org/page/Main_Page Ontology for Biomedical Investigations] (OBI)
*[http://obi-ontology.org/page/Main_Page Ontology for Biomedical Investigations] (OBI)


== Organizing Committee ==
== Organizing Committee ==


:Barry Smith (Buffalo)
Barry Smith (University at Buffalo)
:William Hogan (Arkansas)
 
:John Tomaszewski (Buffalo)
William Hogan (University of Florida)
 
John Tomaszewski (University at Buffalo)


== Participants ==
== Participants ==


Travis Allen (Buffalo)
Sivaram Arabandi (Ontopro)


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


Ulysses J. Balis (Ann Arbor)
Carol Bean (NCBO / Stanford University)


Carol Bean (NCBO / Stanford)
Michael Becich (University of Pittsburgh)


Michael Becich (Pittsburgh)
Andrew H. Beck (Harvard Medical School)


Andrew H. Beck (Harvard)
Tanja Bekhuis (University of Pittsburgh)


Tanja Bekhuis (Pittsburgh)
Talapady N. Bhat (NIST)


Erich Bremer (Stony Brook)
Jonathan Bona (University at Buffalo)


Mathias Brochhausen (Arkansas)
Erich Bremer (Stony Brook Medicine)


Wiam Bshara (Buffalo)
Mathias Brochhausen (University of Arkansas for Medical Sciences)
 
Wiam Bshara (Roswell Park Cancer Institute)


Michael Calhoun (Sinq Systems)
Michael Calhoun (Sinq Systems)


Alexander Cox (Buffalo)
Werner Ceusters (University at Buffalo)


Ilya Goldberg (Open Microscopy Initiative / NIH National Institute on Aging)
Paolo Ciccarese (Harvard Medical School)


Werner Ceusters (Buffalo)
Alexander Cox (University at Buffalo)


Paolo Ciccarese (Harvard)
Chris Crowner (University at Buffalo)


Chris Crowner (Buffalo)
Alexander Diehl (University at Buffalo)


Alexander Diehl (Buffalo)
William Duncan (University at Buffalo)


William Duncan (Buffalo)
Michael Dwyer (University at Buffalo)


Michael Dwyer (Buffalo)
Peter Elkin (University Buffalo)


Peter Elkin (Buffalo)
Gilberto Fragoso (NCI / NIH)


Carmelo Gaudioso (Buffalo)
Carmelo Gaudioso (Roswell Park Cancer Institute)


Nancy Gertrudiz (@CARES, Mexico City)
Nancy Gertrudez (CUDI / Mexican Universities Research Network)


Bernard Gibaud ([http://www.ltsi.univ-rennes1.fr/?q=en/node/269 LTSI], Rennes)
Bernard Gibaud ([http://www.ltsi.univ-rennes1.fr/?q=en/node/269 LTSI], Rennes)
Line 197: Line 237:
Allan S. Goldberg (Touro University, California)
Allan S. Goldberg (Touro University, California)


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


William Hogan (Arkansas)
Metin Gurcan (State University of Ohio)


Mark Jensen (Buffalo)
William Hogan (University of Florida)


Charles E. Kahn (Milwaukee)
Mark Jensen (University at Buffalo)


Warren A. Kibbe (National Cancer Institute)
Charles E. Kahn (Medical College of Wisconsin, Milwaukee)


Venkat N. Krovi (Buffalo)
Venkat N. Krovi (University at Buffalo)


Anant Madabhushi (Case)
Anant Madabhushi (Case Western Reserve University)


Tatiana Malyuta (CUNY)
Tatiana Malyuta (CUNY)


Anna Maria Masci (Duke)
Anna Maria Masci (Duke University)


Kevin Mitchell (Pittsburgh)
Kevin Mitchell (University of Pittsburgh)


Heiner Oberkampf (Siemens, Munich)
Heiner Oberkampf (Siemens, Munich / University of Augsburg)


James A. Overton ([http://Knocean.com Knocean], Toronto)
James A. Overton ([http://Knocean.com Knocean], Toronto)


Patrick Ray (Buffalo)
Patrick Ray (University at Buffalo)


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


Daniel Rubin (Stanford)
Daniel Rubin (Stanford University)


Alan Ruttenberg (Buffalo)
Alan Ruttenberg (University at Buffalo)


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


Ferdinand Schweser (Buffalo)
Yonatan Schreiber (University at Buffalo / CUBRC)


Barry Smith (Buffalo)
Ferdinand Schweser (University at Buffalo)


Jose Luis Tapia (Buffalo)
Selja Seppala (University at Buffalo)


John Tomaszewski (Buffalo)
Barry Smith (University at Buffalo)


Eugene Tseytlin (Pittsburgh)
Dagobert Soergel (University at Buffalo)
 
Jose Luis Tapia (University at Buffalo)
 
John Tomaszewski (University at Buffalo)
 
Eugene Tseytlin (University of Pittsburgh)
   
   
Amber Worral (Buffalo)
Marc van Driel (Philips Research, The Netherlands)
 
Amber Worral (Roswell Park Cancer Institute)

Latest revision as of 13:06, 23 July 2015

Third Clinical and Translational Science Ontology Workshop

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

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:
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

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

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)

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