NCOR Wiki - User contributions [en]

2014 ICBO OBO Workshop

2014-09-03T18:59:05Z

James Overton: Added some a link for the 2014 ICBO OBO Workshop

A workshop at the [http://icbo14.com 5th International Conference on Biomedial Ontologies] in Houston, October 6-9 2014.

* [http://icbo14.com/sessions/obo-technical-workshop-hands-on-with-open-biological-and-biomedical-ontologies/ ICBO 2014 conference page]

== Hands-On with Open Biological and Biomedical Ontologies ==

OBO developers use online development workflows every day, but there is no substitute for face-to-face communication. This participant-driven workshop is open to developers and users of any OBO project. We will focus on technical problems we are facing, aiming for concrete solutions that we can begin to implement during the session. The primary topic will be improving OBO development workflows, but participants will be invited to suggest their own topics and benefit from the collective experience of the workshop attendees.

== Summary ==

The Open Biological and Biomedical Ontologies (OBO) embrace open source development practices and the online tools that support them, including public mailing lists, issue trackers, wikis, teleconferences, etc. Despite all these tools, there is no substitute for face-to-face meetings and the rich communication they allow. The OBO Technical Workshop is an opportunity for developers and users of any OBO project to meet face-to-face, discuss technical problems, and start solving them. By sharing experience, advice, code, and best practices with a group of like-minded developers, we aim to generate small breakthroughs that push projects forward, and to build foundations for future collaboration.

The agenda for this workshop will be driven by the participants. While we hope to have both experts and beginners present, we expect all attendees to be active participants in the workshop. Proposed topics will be shared in advance and goals will be set at the beginning of the workshop. The focus will be on problems (1) with a technical element, and (2) for which we can make concrete progress during the session. By the end of the session we will have deliverables such as requirement documents, new code, new or enhanced ontologies, tracker items, etc.

The primary topic for the workshop is improving development workflows for OBO projects. The outcome will be a list of requirements and a plan for improvements. We will also discuss and create tracker items for current tools. Other topics may include:

* getting started with a new application ontology
* improving reasoner or query performance for an ontology project
* improving domain modelling using OBO ontologies
* improving OBO tools, such as OWLTools
* improving OBO infrastructure
* debugging software installation and configuration problems
* tackling tricky tracker items

== Organizers ==

=== Mélanie Courtot ===

:BC Cancer Agency
:mcourtot@gmail.com
Mélanie Courtot is a PhD Candidate whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. She has actively contributed to several biomedical ontologies, including the Ontology for Biomedical Investigations (OBI), the Information Artifact Ontology (IAO), the Vaccine Ontology (VO) and the Influenza Ontology. She co-developed the Minimum Information to Reference an External Ontology Term (MIREOT), increasing their interoperability. She co-founded and organized the Semantic Web Meetup group in Vancouver, which currently counts more than 140 members. She is an elected steering committee member of the OWL Experiences and Directions (OWLED) workshop series since 2008, and chaired the OWLED 2011 workshop. She chaired the workshop session at ICBO 2012 and co-organized the OBO tutorial at ICBO 2013.

=== Melissa Haendel ===

:Department of Medical Informatics and Epidemiology, Oregon Health and Science University
:haendel@ohsu.edu
Melissa Haendel has led several previous ontology workshops and has participated in development of a number of other Open Bio-Ontology (OBO) standards for anatomy (CARO, Uberon, VAO, ZFA), phenotype (PATO), and biomedical resource ontologies (OBI, ERO). Her interest is in using ontologies for translational research to link human diseases to model organism data, and to infer experimental details relating to the use of organismally derived research resources.

=== James A. Overton ===

:[http://knocean.com Knocean.com], Toronto, Canada
:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He is also the release manager for the Ontology for Biomedical Investigations (OBI) and contributor to several other OBO ontologies. James has built ontology testing and release tools for OBI and contributed to OWLTools development. His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications.

=== Bjoern Peters ===

:La Jolla Institute for Allergy and Immunology
:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is Principal Investigator or Co-Investigator on multiple projects ranging from leading the bioinformatics component of the Immune Epitope Database to designing and analyzing clinical and basic studies of immune responses in the context of allergy, Dengue fever, Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO foundry, and is actively contributing to several other ontologies. He has led several workshops for users of the IEDB.

=== Alan Ruttenberg ===

:University at Buffalo School of Dental Medicine
:alanruttenberg@gmail.com
Alan Ruttenberg's research interest is in structuring and using biological and clinical knowledge to enable computational interpretation of clinical and experimental data, and the scope of his current work spans technical, medical, and organizational aspects of improving access to essential knowledge. In that context, he has been an active member in a number of open biomedical ontology efforts, including: the Ontology for Biomedical Investigations (OBI), the Basic Formal Ontology (BFO) that forms the upper level ontology for the OBO Foundry, of which he is a coordinating editor, the Infectious Disease Ontology (IDO), the Program on Ontologies of Neural Structures (PONS), and the Information Artifact Ontology (IAO). He has been an active participant in W3C Semantic Web activities, and was chair of the OWL working group, developing the Neurocommons project as a prototype of how to deploy biomedical knowledge using Semantic Web technologies.

=== Jie Zheng ===

:Department of Genetics, Perelman School of Medicine, University of Pennsylvania
:jiezheng@upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical metadata analysis and biomedical data integration including ontology development and data modeling. She has contributed to the development of several ontologies such as the Ontology for Biomedical Investigations (OBI), the Ontology of Biological and Clinical Statistics (OBCS) and application ontologies based on OBI (Beta Cell Genomics Ontology (BCGO) and biobank ontology). She has taken responsibility for making releases of several ontologies, such as OBI, OBCS, and BCGO. She has been involved in the development of ontology subset extraction and Basic Formal Ontology version conversion tools. She is currently working on biosample metadata standardization and biomedical data integration from different resources with various representations and annotations based on OBI semantic framework.

2014 ICBO OBO Tutorial

2014-09-03T18:58:04Z

James Overton: Added some links for the 2014 ICBO OBO Tutorial

A tutorial at the [http://icbo14.com 5th International Conference on Biomedial Ontologies] in Houston, October 6-9 2014.

* [http://icbo14.com/sessions/obo-tutorial-getting-things-done-with-open-biological-and-biomedical-ontologies/ ICBO 2014 conference page]
* online tutorial with supporting materials: https://github.com/jamesaoverton/obo-tutorial

== Getting Things Done with Open Biological and Biomedical Ontologies ==

In this hands-on tutorial participants will learn about the tools, techniques, and best practices available for developing and working with OBO projects. We will cover three main topics: the use and reuse of ontologies; processing data with ontologies; and development workflows, including updates, testing, and managing releases. Participants will work with us through a range of real-world examples using OBO Foundry and Library ontologies.

== Summary ==

The Open Biological and Biomedical Ontologies (OBO) provide a suite of interoperable ontologies for biology and medicine. Close collaboration between diverse projects brings many benefits to ontology users, but it also requires commitment to standards and disciplined development practices. In this hands-on half-day tutorial we will cover a wide range of best practices for using and contributing to OBO projects. Participants will be asked to bring their laptops and work with us through a series of real-world examples of ontology development focused on OBO Foundry and Library ontologies, covering these topics:

* A brief introduction to the OBO Library and to the OBO Foundry
* Using and Reusing Ontologies
** assessing ontologies for reuse
** importing single terms with MIREOT
** importing sets of terms using OntoFox
** importing lists of terms with Quick Term Templates
** importing full ontologies in Protégé
** extracting and importing ontology modules
* Processing Data with Ontologies
** converting relational data to RDF
** using SPARQL with OWL ontologies
** converting instance data to OWL
** querying instance data with DL Query and SPARQL
** best practises for reasoning over large data sets
* Updating, Testing, and Releasing Ontologies
** tracking changes with ontology diff tools
** filing effective term requests and bug reports with issue trackers and TermGenie
** best practices for committing changes to an ontology
** quality checking for ontologies
** unit testing for ontologies
** continuous integration with Jenkins
** release workflows with OWLTools
** publishing ontologies
** managing PURLs

== Organizers ==

=== Mélanie Courtot ===

:BC Cancer Agency
:mcourtot@gmail.com
Mélanie Courtot is a PhD Candidate whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. She has actively contributed to several biomedical ontologies, including the Ontology for Biomedical Investigations (OBI), the Information Artifact Ontology (IAO), the Vaccine Ontology (VO) and the Influenza Ontology. She co-developed the Minimum Information to Reference an External Ontology Term (MIREOT), increasing their interoperability. She co-founded and organized the Semantic Web Meetup group in Vancouver, which currently counts more than 140 members. She is an elected steering committee member of the OWL Experiences and Directions (OWLED) workshop series since 2008, and chaired the OWLED 2011 workshop. She chaired the workshop session at ICBO 2012 and co-organized the OBO tutorial at ICBO 2013.

=== Melissa Haendel ===

:Department of Medical Informatics and Epidemiology, Oregon Health and Science University
:haendel@ohsu.edu
Melissa Haendel has led several previous ontology workshops and has participated in development of a number of other Open Bio-Ontology (OBO) standards for anatomy (CARO, Uberon, VAO, ZFA), phenotype (PATO), and biomedical resource ontologies (OBI, ERO). Her interest is in using ontologies for translational research to link human diseases to model organism data, and to infer experimental details relating to the use of organismally derived research resources.

=== James A. Overton ===

:[http://knocean.com Knocean.com], Toronto, Canada
:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He is also the release manager for the Ontology for Biomedical Investigations (OBI) and contributor to several other OBO ontologies. James has built ontology testing and release tools for OBI and contributed to OWLTools development. His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications.

=== Bjoern Peters ===

:La Jolla Institute for Allergy and Immunology
:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is Principal Investigator or Co-Investigator on multiple projects ranging from leading the bioinformatics component of the Immune Epitope Database to designing and analyzing clinical and basic studies of immune responses in the context of allergy, Dengue fever, Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO foundry, and is actively contributing to several other ontologies. He has led several workshops for users of the IEDB.

=== Alan Ruttenberg ===

:University at Buffalo School of Dental Medicine
:alanruttenberg@gmail.com
Alan Ruttenberg's research interest is in structuring and using biological and clinical knowledge to enable computational interpretation of clinical and experimental data, and the scope of his current work spans technical, medical, and organizational aspects of improving access to essential knowledge. In that context, he has been an active member in a number of open biomedical ontology efforts, including: the Ontology for Biomedical Investigations (OBI), the Basic Formal Ontology (BFO) that forms the upper level ontology for the OBO Foundry, of which he is a coordinating editor, the Infectious Disease Ontology (IDO), the Program on Ontologies of Neural Structures (PONS), and the Information Artifact Ontology (IAO). He has been an active participant in W3C Semantic Web activities, and was chair of the OWL working group, developing the Neurocommons project as a prototype of how to deploy biomedical knowledge using Semantic Web technologies.

=== Barry Smith ===

:University at Buffalo Department of Philosophy
:phismith@buffalo.edu
Barry Smith is Professor of Philosophy, Biomedical Informatics, Neurology and Computer Science and Director of the National Center for Ontological Research at the University at Buffalo. He is also one of the principal scientists of the National Center for Biomedical Ontology (NCBO), an NIH Roadmap National Center for Biomedical Computing, a member of the Scientific Advisory Board of the Gene Ontology Consortium, a PI of the Protein Ontology and Infectious Disease Ontology projects, and head of the ontology team for the NIAID Bioinformatics Integrating Support Contract (BISC). He is a Coordinating Editor of the OBO Foundry initiative, and plays a guiding role in Basic Formal Ontology, the Ontology for General Medical Science, the Environment Ontology, and the Plant Ontology initiatives.

=== Jie Zheng ===

:Department of Genetics, Perelman School of Medicine, University of Pennsylvania
:jiezheng@upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical metadata analysis and biomedical data integration including ontology development and data modeling. She has contributed to the development of several ontologies such as the Ontology for Biomedical Investigations (OBI), the Ontology of Biological and Clinical Statistics (OBCS) and application ontologies based on OBI (Beta Cell Genomics Ontology (BCGO) and biobank ontology). She has taken responsibility for making releases of several ontologies, such as OBI, OBCS, and BCGO. She has been involved in the development of ontology subset extraction and Basic Formal Ontology version conversion tools. She is currently working on biosample metadata standardization and biomedical data integration from different resources with various representations and annotations based on OBI semantic framework.

Ontology and Imaging Informatics

2014-06-25T12:43:52Z

James Overton: Update link and affiliation for Heiner at his request.

'''Third Clinical and Translational Science Ontology Workshop'''

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

*Venue: [http://www.ramadahotelamherst.com/ Ramada Hotel & Conference Center, Amherst, NY 14068]. For logistics details please contact [mailto:sgsmith2@buffalo.edu Sandra Smith].
:'''PLEASE NOTE:''' The Ramada Hotel & Conference Center is now sold out for the evening of Tuesday, June 24. If you require lodging and have not yet booked your room, please contact [mailto:sgsmith2@buffalo.edu Sandra Smith] for a listing of other area hotels.

_______________________________________________________________________________________________________________

'''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 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''' (Ramada Hotel's University D/E Room)==

:10:00 Registration

: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

:12:30 Lunch Buffet

: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

:15:00 Refreshment Break

: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

== '''Workshop - Day 1: Tuesday, June 24''' (Ramada Hotel's Ellicott Room)==

 Morning 

:8:30 Registration and Continental Breakfast

:9:00 Participant Introductions

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

:10:15 Refreshment Break

: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]: [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 Buffet Lunch

 Afternoon 

: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]: [http://ncor.buffalo.edu/images/Bernard-Gibaud.ppt Ontology of Imaging Datasets as a Prerequisite for Ontologies of Imaging Biomarkers]'''

:14:20 '''[http://www.informatik.uni-augsburg.de/en/chairs/swt/ds/staff/oberkampf/ Heiner Oberkampf] and [http://knocean.com James A. Overton]: Expressing Medical Image Measurements using the Ontology for Biomedical Investigations'''

:15:00 Refreshment Break

: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'''

:16:40 '''[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'''

: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)

== '''Workshop - Day 2: Wednesday, June 25''' (Ramada Hotel's Ellicott Room)==

 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:

:'''[https://www.linkedin.com/in/alanruttenberg 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 [mailto:alanruttenberg@gmail.com].

:'''[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'''

: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 and Mathias Brochhausen]: 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'''

:12:00 Lunch Buffet

 Afternoon 

:13:00 Hackathon: Building an Ontology for Digital Pathology'''
:Facilitators: James Overton and Barry Smith

: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.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.

: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

:2. [http://www.openmicroscopy.org/site/support/ome-model/developers/model-overview.html OME Data Model]

:3. TBD

== Sponsors ==

*[http://wings.buffalo.edu/smbs/biomedicalinformatics/ Department of Biomedical Informatics], 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

*[[Clinical and Translational Science Ontology Group]].

*[http://bioontologies.org National Center for Biomedical Ontology (NCBO)]
:This meeting forms part of a series of [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki ontology workshops] sponsored by the NCBO. A [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images precursor event] in this series, devoted to the ontology of images, was held in 2006.

== Background ==

*[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/pubmed/23589184 Qualitative Imaging Biomarker Ontology]
*[http://www.openmicroscopy.org/ The Open Microscopy Environment] (OME)
*[[Gamuts | The Radiology Gamuts Ontology]]
*[http://www.aperio.com/healthcare/eslide Aperio ePathology]
*[http://obi-ontology.org/page/Main_Page Ontology for Biomedical Investigations] (OBI)

== 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 ([http://www.ltsi.univ-rennes1.fr/?q=en/node/269 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 ([http://Knocean.com 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)

Ontology and Imaging Informatics

2014-06-24T14:27:37Z

James Overton: Minor change to spelling of my name.

'''Third Clinical and Translational Science Ontology Workshop'''

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

*Venue: [http://www.ramadahotelamherst.com/ Ramada Hotel & Conference Center, Amherst, NY 14068]. For logistics details please contact [mailto:sgsmith2@buffalo.edu Sandra Smith].
:'''PLEASE NOTE:''' The Ramada Hotel & Conference Center is now sold out for the evening of Tuesday, June 24. If you require lodging and have not yet booked your room, please contact [mailto:sgsmith2@buffalo.edu Sandra Smith] for a listing of other area hotels.

_______________________________________________________________________________________________________________

'''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 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''' (Ramada Hotel's University D/E Room)==

:10:00 Registration

: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

:12:30 Lunch Buffet

: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

:15:00 Refreshment Break

: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

== '''Workshop - Day 1: Tuesday, June 24''' (Ramada Hotel's Ellicott Room)==

 Morning 

:8:30 Registration and Continental Breakfast

:9:00 Participant Introductions

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

:10:15 Refreshment Break

: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''' (On Gamuts see [http://ncorwiki.buffalo.edu/index.php/Gamuts here].)

:12:00 Buffet Lunch

 Afternoon 

: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'''
::[[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'''

:14:20 '''[http://www.researchgate.net/profile/Heiner_Oberkampf Heiner Oberkampf] and [http://knocean.com James A. Overton]: Expressing Medical Image Measurements using the Ontology for Biomedical Investigations'''

: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'''

:16:00 '''[http://www.hcklab.org/ Paolo Ciccarese]: 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'''

: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 (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)

== '''Workshop - Day 2: Wednesday, June 25''' (Ramada Hotel's Ellicott Room)==

 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:

:'''[https://www.linkedin.com/in/alanruttenberg 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 [mailto:alanruttenberg@gmail.com].

:'''[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'''

: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 and Mathias Brochhausen]: 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'''

:12:00 Lunch Buffet

 Afternoon 

:13:00 Hackathon: Building an Ontology for Digital Pathology'''
:Facilitators: James Overton and Barry Smith

: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.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.

: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

:2. [http://www.openmicroscopy.org/site/support/ome-model/developers/model-overview.html OME Data Model]

:3. TBD

== Sponsors ==

*[http://wings.buffalo.edu/smbs/biomedicalinformatics/ Department of Biomedical Informatics], 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

*[[Clinical and Translational Science Ontology Group]].

*[http://bioontologies.org National Center for Biomedical Ontology (NCBO)]
:This meeting forms part of a series of [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki ontology workshops] sponsored by the NCBO. A [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images precursor event] in this series, devoted to the ontology of images, was held in 2006.

== Background ==

*[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/pubmed/23589184 Qualitative Imaging Biomarker Ontology]
*[http://www.openmicroscopy.org/ The Open Microscopy Environment] (OME)
*[[Gamuts | The Radiology Gamuts Ontology]]
*[http://www.aperio.com/healthcare/eslide Aperio ePathology]
*[http://obi-ontology.org/page/Main_Page Ontology for Biomedical Investigations] (OBI)

== 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 ([http://www.ltsi.univ-rennes1.fr/?q=en/node/269 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)

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

Ontology and Imaging Informatics

2014-06-24T14:26:35Z

James Overton: Change the link to Heiner's research, at his request.

'''Third Clinical and Translational Science Ontology Workshop'''

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

*Venue: [http://www.ramadahotelamherst.com/ Ramada Hotel & Conference Center, Amherst, NY 14068]. For logistics details please contact [mailto:sgsmith2@buffalo.edu Sandra Smith].
:'''PLEASE NOTE:''' The Ramada Hotel & Conference Center is now sold out for the evening of Tuesday, June 24. If you require lodging and have not yet booked your room, please contact [mailto:sgsmith2@buffalo.edu Sandra Smith] for a listing of other area hotels.

_______________________________________________________________________________________________________________

'''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 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''' (Ramada Hotel's University D/E Room)==

:10:00 Registration

: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

:12:30 Lunch Buffet

: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

:15:00 Refreshment Break

: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

== '''Workshop - Day 1: Tuesday, June 24''' (Ramada Hotel's Ellicott Room)==

 Morning 

:8:30 Registration and Continental Breakfast

:9:00 Participant Introductions

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

:10:15 Refreshment Break

: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''' (On Gamuts see [http://ncorwiki.buffalo.edu/index.php/Gamuts here].)

:12:00 Buffet Lunch

 Afternoon 

: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'''
::[[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'''

:14:20 '''[http://www.researchgate.net/profile/Heiner_Oberkampf Heiner Oberkampf] and [http://knocean.com James Overton]: Expressing Medical Image Measurements using the Ontology for Biomedical Investigations'''

: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'''

:16:00 '''[http://www.hcklab.org/ Paolo Ciccarese]: 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'''

: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 (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)

== '''Workshop - Day 2: Wednesday, June 25''' (Ramada Hotel's Ellicott Room)==

 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:

:'''[https://www.linkedin.com/in/alanruttenberg 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 [mailto:alanruttenberg@gmail.com].

:'''[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'''

: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 and Mathias Brochhausen]: 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'''

:12:00 Lunch Buffet

 Afternoon 

:13:00 Hackathon: Building an Ontology for Digital Pathology'''
:Facilitators: James Overton and Barry Smith

: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.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.

: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

:2. [http://www.openmicroscopy.org/site/support/ome-model/developers/model-overview.html OME Data Model]

:3. TBD

== Sponsors ==

*[http://wings.buffalo.edu/smbs/biomedicalinformatics/ Department of Biomedical Informatics], 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

*[[Clinical and Translational Science Ontology Group]].

*[http://bioontologies.org National Center for Biomedical Ontology (NCBO)]
:This meeting forms part of a series of [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki ontology workshops] sponsored by the NCBO. A [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images precursor event] in this series, devoted to the ontology of images, was held in 2006.

== Background ==

*[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/pubmed/23589184 Qualitative Imaging Biomarker Ontology]
*[http://www.openmicroscopy.org/ The Open Microscopy Environment] (OME)
*[[Gamuts | The Radiology Gamuts Ontology]]
*[http://www.aperio.com/healthcare/eslide Aperio ePathology]
*[http://obi-ontology.org/page/Main_Page Ontology for Biomedical Investigations] (OBI)

== 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 ([http://www.ltsi.univ-rennes1.fr/?q=en/node/269 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)

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

2014 ICBO OBO Tutorial

2014-06-23T14:15:58Z

James Overton: Update description of first topic

A tutorial at the [http://icbo14.com 5th International Conference on Biomedial Ontologies] in Houston, October 6-9 2014.

== Getting Things Done with Open Biological and Biomedical Ontologies ==

In this hands-on tutorial participants will learn about the tools, techniques, and best practices available for developing and working with OBO projects. We will cover three main topics: the use and reuse of ontologies; processing data with ontologies; and development workflows, including updates, testing, and managing releases. Participants will work with us through a range of real-world examples using OBO Foundry and Library ontologies.

== Summary ==

The Open Biological and Biomedical Ontologies (OBO) provide a suite of interoperable ontologies for biology and medicine. Close collaboration between diverse projects brings many benefits to ontology users, but it also requires commitment to standards and disciplined development practices. In this hands-on half-day tutorial we will cover a wide range of best practices for using and contributing to OBO projects. Participants will be asked to bring their laptops and work with us through a series of real-world examples of ontology development focused on OBO Foundry and Library ontologies, covering these topics:

* A brief introduction to the OBO Library and to the OBO Foundry
* Using and Reusing Ontologies
** assessing ontologies for reuse
** importing single terms with MIREOT
** importing sets of terms using OntoFox
** importing lists of terms with Quick Term Templates
** importing full ontologies in Protégé
** extracting and importing ontology modules
* Processing Data with Ontologies
** converting relational data to RDF
** using SPARQL with OWL ontologies
** converting instance data to OWL
** querying instance data with DL Query and SPARQL
** best practises for reasoning over large data sets
* Updating, Testing, and Releasing Ontologies
** tracking changes with ontology diff tools
** filing effective term requests and bug reports with issue trackers and TermGenie
** best practices for committing changes to an ontology
** quality checking for ontologies
** unit testing for ontologies
** continuous integration with Jenkins
** release workflows with OWLTools
** publishing ontologies
** managing PURLs

== Organizers ==

=== Mélanie Courtot ===

:BC Cancer Agency
:mcourtot@gmail.com
Mélanie Courtot is a PhD Candidate whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. She has actively contributed to several biomedical ontologies, including the Ontology for Biomedical Investigations (OBI), the Information Artifact Ontology (IAO), the Vaccine Ontology (VO) and the Influenza Ontology. She co-developed the Minimum Information to Reference an External Ontology Term (MIREOT), increasing their interoperability. She co-founded and organized the Semantic Web Meetup group in Vancouver, which currently counts more than 140 members. She is an elected steering committee member of the OWL Experiences and Directions (OWLED) workshop series since 2008, and chaired the OWLED 2011 workshop. She chaired the workshop session at ICBO 2012 and co-organized the OBO tutorial at ICBO 2013.

=== Melissa Haendel ===

:Department of Medical Informatics and Epidemiology, Oregon Health and Science University
:haendel@ohsu.edu
Melissa Haendel has led several previous ontology workshops and has participated in development of a number of other Open Bio-Ontology (OBO) standards for anatomy (CARO, Uberon, VAO, ZFA), phenotype (PATO), and biomedical resource ontologies (OBI, ERO). Her interest is in using ontologies for translational research to link human diseases to model organism data, and to infer experimental details relating to the use of organismally derived research resources.

=== James A. Overton ===

:[http://knocean.com Knocean.com], Toronto, Canada
:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He is also the release manager for the Ontology for Biomedical Investigations (OBI) and contributor to several other OBO ontologies. James has built ontology testing and release tools for OBI and contributed to OWLTools development. His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications.

=== Bjoern Peters ===

:La Jolla Institute for Allergy and Immunology
:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is Principal Investigator or Co-Investigator on multiple projects ranging from leading the bioinformatics component of the Immune Epitope Database to designing and analyzing clinical and basic studies of immune responses in the context of allergy, Dengue fever, Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO foundry, and is actively contributing to several other ontologies. He has led several workshops for users of the IEDB.

=== Alan Ruttenberg ===

:University at Buffalo School of Dental Medicine
:alanruttenberg@gmail.com
Alan Ruttenberg's research interest is in structuring and using biological and clinical knowledge to enable computational interpretation of clinical and experimental data, and the scope of his current work spans technical, medical, and organizational aspects of improving access to essential knowledge. In that context, he has been an active member in a number of open biomedical ontology efforts, including: the Ontology for Biomedical Investigations (OBI), the Basic Formal Ontology (BFO) that forms the upper level ontology for the OBO Foundry, of which he is a coordinating editor, the Infectious Disease Ontology (IDO), the Program on Ontologies of Neural Structures (PONS), and the Information Artifact Ontology (IAO). He has been an active participant in W3C Semantic Web activities, and was chair of the OWL working group, developing the Neurocommons project as a prototype of how to deploy biomedical knowledge using Semantic Web technologies.

=== Barry Smith ===

:University at Buffalo Department of Philosophy
:phismith@buffalo.edu
Barry Smith is Professor of Philosophy, Biomedical Informatics, Neurology and Computer Science and Director of the National Center for Ontological Research at the University at Buffalo. He is also one of the principal scientists of the National Center for Biomedical Ontology (NCBO), an NIH Roadmap National Center for Biomedical Computing, a member of the Scientific Advisory Board of the Gene Ontology Consortium, a PI of the Protein Ontology and Infectious Disease Ontology projects, and head of the ontology team for the NIAID Bioinformatics Integrating Support Contract (BISC). He is a Coordinating Editor of the OBO Foundry initiative, and plays a guiding role in Basic Formal Ontology, the Ontology for General Medical Science, the Environment Ontology, and the Plant Ontology initiatives.

=== Jie Zheng ===

:Department of Genetics, Perelman School of Medicine, University of Pennsylvania
:jiezheng@upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical metadata analysis and biomedical data integration including ontology development and data modeling. She has contributed to the development of several ontologies such as the Ontology for Biomedical Investigations (OBI), the Ontology of Biological and Clinical Statistics (OBCS) and application ontologies based on OBI (Beta Cell Genomics Ontology (BCGO) and biobank ontology). She has taken responsibility for making releases of several ontologies, such as OBI, OBCS, and BCGO. She has been involved in the development of ontology subset extraction and Basic Formal Ontology version conversion tools. She is currently working on biosample metadata standardization and biomedical data integration from different resources with various representations and annotations based on OBI semantic framework.

2014 ICBO OBO Workshop

2014-06-19T18:17:17Z

James Overton: New page for OBO Workshop at ICBO 2014

A workshop at the [http://icbo14.com 5th International Conference on Biomedial Ontologies] in Houston, October 6-9 2014.

== Hands-On with Open Biological and Biomedical Ontologies ==

OBO developers use online development workflows every day, but there is no substitute for face-to-face communication. This participant-driven workshop is open to developers and users of any OBO project. We will focus on technical problems we are facing, aiming for concrete solutions that we can begin to implement during the session. The primary topic will be improving OBO development workflows, but participants will be invited to suggest their own topics and benefit from the collective experience of the workshop attendees.

== Summary ==

The Open Biological and Biomedical Ontologies (OBO) embrace open source development practices and the online tools that support them, including public mailing lists, issue trackers, wikis, teleconferences, etc. Despite all these tools, there is no substitute for face-to-face meetings and the rich communication they allow. The OBO Technical Workshop is an opportunity for developers and users of any OBO project to meet face-to-face, discuss technical problems, and start solving them. By sharing experience, advice, code, and best practices with a group of like-minded developers, we aim to generate small breakthroughs that push projects forward, and to build foundations for future collaboration.

The agenda for this workshop will be driven by the participants. While we hope to have both experts and beginners present, we expect all attendees to be active participants in the workshop. Proposed topics will be shared in advance and goals will be set at the beginning of the workshop. The focus will be on problems (1) with a technical element, and (2) for which we can make concrete progress during the session. By the end of the session we will have deliverables such as requirement documents, new code, new or enhanced ontologies, tracker items, etc.

The primary topic for the workshop is improving development workflows for OBO projects. The outcome will be a list of requirements and a plan for improvements. We will also discuss and create tracker items for current tools. Other topics may include:

* getting started with a new application ontology
* improving reasoner or query performance for an ontology project
* improving domain modelling using OBO ontologies
* improving OBO tools, such as OWLTools
* improving OBO infrastructure
* debugging software installation and configuration problems
* tackling tricky tracker items

== Organizers ==

=== Mélanie Courtot ===

:BC Cancer Agency
:mcourtot@gmail.com
Mélanie Courtot is a PhD Candidate whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. She has actively contributed to several biomedical ontologies, including the Ontology for Biomedical Investigations (OBI), the Information Artifact Ontology (IAO), the Vaccine Ontology (VO) and the Influenza Ontology. She co-developed the Minimum Information to Reference an External Ontology Term (MIREOT), increasing their interoperability. She co-founded and organized the Semantic Web Meetup group in Vancouver, which currently counts more than 140 members. She is an elected steering committee member of the OWL Experiences and Directions (OWLED) workshop series since 2008, and chaired the OWLED 2011 workshop. She chaired the workshop session at ICBO 2012 and co-organized the OBO tutorial at ICBO 2013.

=== Melissa Haendel ===

:Department of Medical Informatics and Epidemiology, Oregon Health and Science University
:haendel@ohsu.edu
Melissa Haendel has led several previous ontology workshops and has participated in development of a number of other Open Bio-Ontology (OBO) standards for anatomy (CARO, Uberon, VAO, ZFA), phenotype (PATO), and biomedical resource ontologies (OBI, ERO). Her interest is in using ontologies for translational research to link human diseases to model organism data, and to infer experimental details relating to the use of organismally derived research resources.

=== James A. Overton ===

:[http://knocean.com Knocean.com], Toronto, Canada
:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He is also the release manager for the Ontology for Biomedical Investigations (OBI) and contributor to several other OBO ontologies. James has built ontology testing and release tools for OBI and contributed to OWLTools development. His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications.

=== Bjoern Peters ===

:La Jolla Institute for Allergy and Immunology
:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is Principal Investigator or Co-Investigator on multiple projects ranging from leading the bioinformatics component of the Immune Epitope Database to designing and analyzing clinical and basic studies of immune responses in the context of allergy, Dengue fever, Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO foundry, and is actively contributing to several other ontologies. He has led several workshops for users of the IEDB.

=== Alan Ruttenberg ===

:University at Buffalo School of Dental Medicine
:alanruttenberg@gmail.com
Alan Ruttenberg's research interest is in structuring and using biological and clinical knowledge to enable computational interpretation of clinical and experimental data, and the scope of his current work spans technical, medical, and organizational aspects of improving access to essential knowledge. In that context, he has been an active member in a number of open biomedical ontology efforts, including: the Ontology for Biomedical Investigations (OBI), the Basic Formal Ontology (BFO) that forms the upper level ontology for the OBO Foundry, of which he is a coordinating editor, the Infectious Disease Ontology (IDO), the Program on Ontologies of Neural Structures (PONS), and the Information Artifact Ontology (IAO). He has been an active participant in W3C Semantic Web activities, and was chair of the OWL working group, developing the Neurocommons project as a prototype of how to deploy biomedical knowledge using Semantic Web technologies.

=== Jie Zheng ===

:Department of Genetics, Perelman School of Medicine, University of Pennsylvania
:jiezheng@upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical metadata analysis and biomedical data integration including ontology development and data modeling. She has contributed to the development of several ontologies such as the Ontology for Biomedical Investigations (OBI), the Ontology of Biological and Clinical Statistics (OBCS) and application ontologies based on OBI (Beta Cell Genomics Ontology (BCGO) and biobank ontology). She has taken responsibility for making releases of several ontologies, such as OBI, OBCS, and BCGO. She has been involved in the development of ontology subset extraction and Basic Formal Ontology version conversion tools. She is currently working on biosample metadata standardization and biomedical data integration from different resources with various representations and annotations based on OBI semantic framework.

2014 ICBO OBO Tutorial

2014-06-19T18:16:23Z

James Overton: New page for OBO Tutorial at ICBO 2014

A tutorial at the [http://icbo14.com 5th International Conference on Biomedial Ontologies] in Houston, October 6-9 2014.

== Getting Things Done with Open Biological and Biomedical Ontologies ==

In this hands-on tutorial participants will learn about the tools, techniques, and best practices available for developing and working with OBO projects. We will cover three main topics: the use and reuse of ontologies; processing data with ontologies; and development workflows, including updates, testing, and managing releases. Participants will work with us through a range of real-world examples using OBO Foundry and Library ontologies.

== Summary ==

The Open Biological and Biomedical Ontologies (OBO) provide a suite of interoperable ontologies for biology and medicine. Close collaboration between diverse projects brings many benefits to ontology users, but it also requires commitment to standards and disciplined development practices. In this hands-on half-day tutorial we will cover a wide range of best practices for using and contributing to OBO projects. Participants will be asked to bring their laptops and work with us through a series of real-world examples of ontology development focused on OBO Foundry and Library ontologies, covering these topics:

* A brief introduction to the OBO Consortium.
* Using and Reusing Ontologies
** assessing ontologies for reuse
** importing single terms with MIREOT
** importing sets of terms using OntoFox
** importing lists of terms with Quick Term Templates
** importing full ontologies in Protégé
** extracting and importing ontology modules
* Processing Data with Ontologies
** converting relational data to RDF
** using SPARQL with OWL ontologies
** converting instance data to OWL
** querying instance data with DL Query and SPARQL
** best practises for reasoning over large data sets
* Updating, Testing, and Releasing Ontologies
** tracking changes with ontology diff tools
** filing effective term requests and bug reports with issue trackers and TermGenie
** best practices for committing changes to an ontology
** quality checking for ontologies
** unit testing for ontologies
** continuous integration with Jenkins
** release workflows with OWLTools
** publishing ontologies
** managing PURLs

== Organizers ==

=== Mélanie Courtot ===

:BC Cancer Agency
:mcourtot@gmail.com
Mélanie Courtot is a PhD Candidate whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. She has actively contributed to several biomedical ontologies, including the Ontology for Biomedical Investigations (OBI), the Information Artifact Ontology (IAO), the Vaccine Ontology (VO) and the Influenza Ontology. She co-developed the Minimum Information to Reference an External Ontology Term (MIREOT), increasing their interoperability. She co-founded and organized the Semantic Web Meetup group in Vancouver, which currently counts more than 140 members. She is an elected steering committee member of the OWL Experiences and Directions (OWLED) workshop series since 2008, and chaired the OWLED 2011 workshop. She chaired the workshop session at ICBO 2012 and co-organized the OBO tutorial at ICBO 2013.

=== Melissa Haendel ===

:Department of Medical Informatics and Epidemiology, Oregon Health and Science University
:haendel@ohsu.edu
Melissa Haendel has led several previous ontology workshops and has participated in development of a number of other Open Bio-Ontology (OBO) standards for anatomy (CARO, Uberon, VAO, ZFA), phenotype (PATO), and biomedical resource ontologies (OBI, ERO). Her interest is in using ontologies for translational research to link human diseases to model organism data, and to infer experimental details relating to the use of organismally derived research resources.

=== James A. Overton ===

:[http://knocean.com Knocean.com], Toronto, Canada
:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He is also the release manager for the Ontology for Biomedical Investigations (OBI) and contributor to several other OBO ontologies. James has built ontology testing and release tools for OBI and contributed to OWLTools development. His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications.

=== Bjoern Peters ===

:La Jolla Institute for Allergy and Immunology
:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is Principal Investigator or Co-Investigator on multiple projects ranging from leading the bioinformatics component of the Immune Epitope Database to designing and analyzing clinical and basic studies of immune responses in the context of allergy, Dengue fever, Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO foundry, and is actively contributing to several other ontologies. He has led several workshops for users of the IEDB.

=== Alan Ruttenberg ===

:University at Buffalo School of Dental Medicine
:alanruttenberg@gmail.com
Alan Ruttenberg's research interest is in structuring and using biological and clinical knowledge to enable computational interpretation of clinical and experimental data, and the scope of his current work spans technical, medical, and organizational aspects of improving access to essential knowledge. In that context, he has been an active member in a number of open biomedical ontology efforts, including: the Ontology for Biomedical Investigations (OBI), the Basic Formal Ontology (BFO) that forms the upper level ontology for the OBO Foundry, of which he is a coordinating editor, the Infectious Disease Ontology (IDO), the Program on Ontologies of Neural Structures (PONS), and the Information Artifact Ontology (IAO). He has been an active participant in W3C Semantic Web activities, and was chair of the OWL working group, developing the Neurocommons project as a prototype of how to deploy biomedical knowledge using Semantic Web technologies.

=== Barry Smith ===

:University at Buffalo Department of Philosophy
:phismith@buffalo.edu
Barry Smith is Professor of Philosophy, Biomedical Informatics, Neurology and Computer Science and Director of the National Center for Ontological Research at the University at Buffalo. He is also one of the principal scientists of the National Center for Biomedical Ontology (NCBO), an NIH Roadmap National Center for Biomedical Computing, a member of the Scientific Advisory Board of the Gene Ontology Consortium, a PI of the Protein Ontology and Infectious Disease Ontology projects, and head of the ontology team for the NIAID Bioinformatics Integrating Support Contract (BISC). He is a Coordinating Editor of the OBO Foundry initiative, and plays a guiding role in Basic Formal Ontology, the Ontology for General Medical Science, the Environment Ontology, and the Plant Ontology initiatives.

=== Jie Zheng ===

:Department of Genetics, Perelman School of Medicine, University of Pennsylvania
:jiezheng@upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical metadata analysis and biomedical data integration including ontology development and data modeling. She has contributed to the development of several ontologies such as the Ontology for Biomedical Investigations (OBI), the Ontology of Biological and Clinical Statistics (OBCS) and application ontologies based on OBI (Beta Cell Genomics Ontology (BCGO) and biobank ontology). She has taken responsibility for making releases of several ontologies, such as OBI, OBCS, and BCGO. She has been involved in the development of ontology subset extraction and Basic Formal Ontology version conversion tools. She is currently working on biosample metadata standardization and biomedical data integration from different resources with various representations and annotations based on OBI semantic framework.

Ontology and Imaging Informatics

2014-06-19T17:32:36Z

James Overton: /* Workshop - Day 1: Tuesday, June 24 */ Change author order for one item, fix spelling.

'''Third Clinical and Translational Science Ontology Workshop'''

*Tutorial: June 23, 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].

_______________________________________________________________________________________________________________

'''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 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 [http://www.ccmb.med.umich.edu/node/192 '''Ulysses Balis]: Introduction to Imaging Informatics: The Problem of Image Data Interoperability'''

:12:30 Lunch Buffet

:13:30 [http://ontology.buffalo.edu/smith '''Barry Smith]: Introduction to Ontology for Imaging Informatics'''

:15:00 Refreshment Break

:15:30 [http://dbmi.uams.edu/faculty/william-r-hogan-m-d/ '''William Hogan]: Ontology in the CTSA Consortium'''

== '''Workshop - Day 1: Tuesday, June 24''' ==

 Morning 

:8:30 Registration and Continental Breakfast

:9:00 Participant Introductions

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

: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'''

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

:12:00 Buffet Lunch

 Afternoon 

: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'''
::[[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'''

:14:20 '''Heiner Oberkampf and [http://knocean.com James Overton]: Expressing Medical Image Measurements using the Ontology for Biomedical Investigations'''

: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'''

:16:00 '''[http://www.hcklab.org/ Paolo Ciccarese]: 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'''

: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] (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:

:'''[https://www.linkedin.com/in/alanruttenberg 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 [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://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'''

: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 and Mathias Brochhausen]: 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'''

:12:00 Lunch Buffet

 Afternoon 

:13:00 Hackathon: Building an Ontology for Digital Pathology'''
:Facilitators: James Overton and Barry Smith

: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.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.

: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

:2. [http://www.openmicroscopy.org/site/support/ome-model/developers/model-overview.html OME Data Model]

:3. TBD

== Sponsors ==

*[http://wings.buffalo.edu/smbs/biomedicalinformatics/ Department of Biomedical Informatics], 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].

*[http://bioontologies.org National Center for Biomedical Ontology (NCBO)]
:This meeting forms part of a series of [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki ontology workshops] sponsored by the NCBO. A [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images precursor event] in this series, devoted to the ontology of images, was held in 2006.

== Background ==

*[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/pubmed/23589184 Qualitative Imaging Biomarker Ontology]
*[http://www.openmicroscopy.org/ The Open Microscopy Environment] (OME)
*[[Gamuts | The Radiology Gamuts Ontology]]
*[http://www.aperio.com/healthcare/eslide Aperio ePathology]
*[http://obi-ontology.org/page/Main_Page Ontology for Biomedical Investigations] (OBI)

== 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)

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)

Bernard Gibaud ([http://www.ltsi.univ-rennes1.fr/?q=en/node/269 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)

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