Difference between revisions of "NCBO Phenotype Workshop"

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== Agenda ==
 
== Agenda ==
  
'''9:00 Welcome and workshop goals (Mark Musen)
+
'''8:45 Introduction (Mark Musen)
 +
 
 +
-- Welcome and workshop goals
  
 
-- Participant self-introductions
 
-- Participant self-introductions
  
'''9:30am Session I: The spectrum of phenotypes''' XXX (Moderator)  
+
'''9:00am Session I (Part 1): The spectrum of phenotypes: a review of use cases''' XXX (Moderator)  
  
-- Phenotypes in model organisms  
+
-- Phenotypes in model organisms (Suzi, Chris M)
  
-- The OBO Foundry Project
+
-- Phenotypes in neurobiology (Maryann)
  
-- The OBO Relation Ontology
+
'''10:30am Coffee'''
  
11:00am Coffee
+
'''11:00am Session I (Part 2)'''
  
11:00am Discussion
+
-- Phenotypes in clinical research (Ida)
  
12:30pm Lunch
+
-- Phenotypes in clinical medicine (Barry C)
  
'''Session II: Methods for Representing Phenotypes''' XXX (Moderator)
+
'''11:30am ession I (Part 3)'''
  
1:30pm 
+
-- Phenotypes in cognitive science (NDAR; Amar)
  
2:00pm Ontologies and Terminologies in Radiology and Biological Imaging
+
'''12:00pm Lunch'''
  
-- Curt Langlotz: RadLex
+
'''1:00pm Discussion: commonalities in phenotype descriptions'''
  
-- Maryann Martone: BIRNLex
+
'''2:00pm Session II: Methods for Representing Phenotypes'''  XXX (Moderator)
  
-- Anand Kumar: DICOM
+
-- PaTO and PhenoXML (Chris M)
  
3:30pm Coffee
+
-- SWRL (Samson)
  
4:00pm Relations and Reasoning in Image Ontologies
+
-- Discussion
  
-- Dirk Marwede: Relations in Image Ontologies and Anatomy Ontologies
+
3:30pm Coffee
 
 
-- Mariana Casella dos Santos: Bootstrapping an Image Ontology
 
  
-- Helen Chen: Building Real-World Applications and Reasoning in Radiology
+
'''3:00pm Commonalities/differences in requirements for representing phenotypes'''
 
 
'''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
+
4:30pm Summary and Next Steps
  
 
== Participants ==
 
== Participants ==

Revision as of 08:55, 26 February 2008

Some Relevant Links

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

Working Groups 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.bioontology.org/wiki/index.php/NCBO_Phenotype_Workshop). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.

Agenda

8:45 Introduction (Mark Musen)

-- Welcome and workshop goals

-- Participant self-introductions

9:00am Session I (Part 1): The spectrum of phenotypes: a review of use cases XXX (Moderator)

-- Phenotypes in model organisms (Suzi, Chris M)

-- Phenotypes in neurobiology (Maryann)

10:30am Coffee

11:00am Session I (Part 2)

-- Phenotypes in clinical research (Ida)

-- Phenotypes in clinical medicine (Barry C)

11:30am ession I (Part 3)

-- Phenotypes in cognitive science (NDAR; Amar)

12:00pm Lunch

1:00pm Discussion: commonalities in phenotype descriptions

2:00pm Session II: Methods for Representing Phenotypes XXX (Moderator)

-- PaTO and PhenoXML (Chris M)

-- SWRL (Samson)

-- Discussion

3:30pm Coffee

3:00pm Commonalities/differences in requirements for representing phenotypes

4:30pm Summary and Next Steps

Participants

Maryann Martone (BIRN)

Nigam Shah (Stanford)


Some Relevant Links

Neuroimaging Informatics Technology Initiative


Hotel

Venue