NCBO Phenotype Workshop

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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

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 ( Please visit this Wiki to obtain current information on the projects and activities related to these efforts.


(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


Maryann Martone (BIRN)

Nigam Shah (Stanford)

Some Relevant Links

Neuroimaging Informatics Technology Initiative