Difference between revisions of "NCBO Phenotype Workshop"

Revision as of 09:29, 26 February 2008

Background

The National Center for Biomedical Ontology will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the Lane Medical Library in Stanford.

The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes.

The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community.

The following topics will be addressed:

- definition of "phenotype" (and related notions, such as eligibility criteria)

- ontologies needed to represent clinical phenotypes

- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)

- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)

- the use of common relations (along the lines advanced in the OBO Relation Ontology) in grammars

- tool support for creating phenotype descriptions ("annotations") and storing them

The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats.

This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at http://nihroadmap.nih.gov/bioinformatics.

Additional support is being provided by

Workgroups and Mailing List

At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.

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

Agenda

(See Webcast for videos of all sessions.)

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

9:00am Introduction

-- What this Meeting is For

-- Basic Principles of Ontology Design

-- The OBO Foundry Project

-- The OBO Relation Ontology

10:30am Coffee

11:00am Towards an Ontology for the Imaging Domain

-- BIRNLex and RadLex Case Studies

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

12:30pm Lunch

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

1:30pm Participant self-introductions

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

-- Curt Langlotz: RadLex

-- Maryann Martone: BIRNLex

-- Anand Kumar: DICOM

3:30pm Coffee

4:00pm Relations and Reasoning in Image Ontologies

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

-- Mariana Casella dos Santos: Bootstrapping an Image Ontology

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

Session III: Image Ontologies Suzanna Lewis (Moderatrix)

9:00am Examples

-- Matthew Fielding: From RadLex to RadiO

-- C. Forbes Dewey: Experibase

10:30am Coffee

11:00am Reasoning with Image Ontologies

-- W. Lorensen: Engineering Beyond Pixels

-- William Bug: BIRN's Image Ontology Requirements

-- Louis Goldberg: On Reasoning with Images

12:30pm Lunch

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

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

-- David Kennedy: The Internet Analysis Tools Registry

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

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

3:30pm Coffee

-- Strategy Session: How to Build an Image Ontology

Participants

Maryann Martone (BIRN)

Nigam Shah (Stanford)

Some Relevant Links

Neuroimaging Informatics Technology Initiative

Hotel

Venue

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 == Background ==
-The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the ontology of (biomedical) images and imaging. The workshop will take place on March 24-25, 2006 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford.
+The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford.
-The goal of the workshop is to promote interoperability of biomedical image and imaging ontologies through the application of principles of sound ontology construction and through the coordination of current ontology development efforts in the imaging domain. One subsidiary goal is to ensure compatibility of image ontologies with ontologies of those biomedical entities which images represent. The workshop will include hands-on experiments directed towards building a biomedical image ontology on the basis of sample ontologies submitted by participants in advance.
+The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes.
+The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community.
 The following topics will be addressed:
-- coordination and integration of ontologies in the imaging domain
+- definition of "phenotype" (and related notions, such as eligibility criteria)
+- ontologies needed to represent clinical phenotypes
-- ontologies for classification of images, image features, interpretations,
+- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)
-- the role of a reference ontology such as the [http://sig.biostr.washington.edu/projects/fm/AboutFM.html FMA]
+- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)
-- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]), including relations among images, features, interpretations, and the underlying reality
+- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) in grammars
-- use of ontologies in reasoning
+- tool support for creating phenotype descriptions ("annotations") and storing them
-- building an ontology of imaging tools and data, including issues related to the classification of imaging algorithms and to the potential uses of a tools ontology in supporting interoperability of bioinformatics software (in conjunction with the [http://na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group Software and Data Integration Working Group] of the NIH Roadmap National Centers for Biomedical Computing).
+The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats.
-The workshop is designed to be of value to all those involved in biocomputing in the imaging domain, including representatives of those NCBCs who use or develop imaging technologies.
+This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics].
-This workshop was funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. Additional support has been provided by GlaxoSmithKline (GSK), Language & Computing (L&C) and Agfa.
+Additional support is being provided by
 == Workgroups and Mailing List ==
-At the conclusion of the workshop, many participants expressed interest in continuing the discussions and undertaking the work related to imaging ontology. A mailing list for these discussions was set up (https://www.neuroinformatics.org/mailman/listinfo/image-ontology)
+At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.
-In addition, a Wiki to host materials related to a working group in imaging ontology was created (http://www.neuroinformatics.org:8080/xwiki/bin/view/ImageOntology/Main). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.
+In addition, a Wiki to host materials related to the workshop has been created (http://www.neuroinformatics.org:8080/xwiki/bin/view/ImageOntology/Main). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.
 == Agenda ==