Difference between revisions of "NCBO Phenotype Workshop"
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== Background == | == Background == | ||
| − | The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the | + | 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 | + | 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. |
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| + | 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: | 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 [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) | + | - the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 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 http://nihroadmap.nih.gov/bioinformatics]. | |
| − | + | Additional support is being provided by | |
| − | == | + | == Working Groups and Mailing List == |
| − | At the conclusion of the workshop, | + | 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 | + | 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 == | == Agenda == | ||
| − | ( | + | '''8:45 Introduction (Mark Musen) |
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| + | -- Welcome and workshop goals | ||
| − | + | -- Participant self-introductions | |
| − | 9:00am | + | '''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 Session I (Part 3)''' | |
| − | + | -- Phenotypes in cognitive science (NDAR; Amar) | |
| − | + | -- Phenotypes in pharmacogenomics (Russ/Teri) | |
| − | ''' | + | '''12:30pm Lunch''' |
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| − | 1:30pm | + | '''1:30pm Discussion: commonalities in phenotype descriptions''' |
| − | 2: | + | '''2:30pm Session II: Methods for Representing Phenotypes''' XXX (Moderator) |
| − | -- | + | -- PaTO and PhenoXML (Chris M) |
| − | -- | + | -- SWRL (Samson) |
| − | -- | + | -- Discussion |
3:30pm Coffee | 3:30pm Coffee | ||
| − | + | '''3:00pm Commonalities/differences in requirements for representing phenotypes''' | |
| − | + | 4:30pm Summary and Next Steps | |
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== Participants == | == Participants == | ||
| − | + | Mark Musen (NCBO) | |
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| − | + | Daniel Rubin (NCBO) | |
| − | + | Suzi Lewis (NCBO) | |
| − | + | Chris Mungall (NCBO) | |
| − | + | Nigam Shah (NCBO) | |
| − | + | Amar Das (Stanford) | |
| − | + | Samson Tu (Stanford) | |
| − | + | Mor Peleg (University of Haifa) | |
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Maryann Martone (BIRN) | Maryann Martone (BIRN) | ||
| − | + | Russ Altman (PharmGKB) | |
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| − | + | Teri Klein (PharmGKB) | |
| − | + | Barry Coller (Rockefeller CTSA) | |
| − | + | Jon Blumenfeld (Rockefeller CTSA) | |
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== Some Relevant Links == | == Some Relevant Links == | ||
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[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative] | [http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative] | ||
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| + | [[Venue]] | ||
---- | ---- | ||
| − | + | Availability: | |
| − | + | MA: NOT July 14-23 or Aug 13-15 | |
| − | + | IS: NOT July 21-Aug 8 | |
| + | JB: NOT last week in August before Labor Day | ||
Latest revision as of 23:30, 22 April 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
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 Session I (Part 3)
-- Phenotypes in cognitive science (NDAR; Amar)
-- Phenotypes in pharmacogenomics (Russ/Teri)
12:30pm Lunch
1:30pm Discussion: commonalities in phenotype descriptions
2:30pm 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
Mark Musen (NCBO)
Daniel Rubin (NCBO)
Suzi Lewis (NCBO)
Chris Mungall (NCBO)
Nigam Shah (NCBO)
Amar Das (Stanford)
Samson Tu (Stanford)
Mor Peleg (University of Haifa)
Maryann Martone (BIRN)
Russ Altman (PharmGKB)
Teri Klein (PharmGKB)
Barry Coller (Rockefeller CTSA)
Jon Blumenfeld (Rockefeller CTSA)
Some Relevant Links
Neuroimaging Informatics Technology Initiative
Availability: MA: NOT July 14-23 or Aug 13-15 IS: NOT July 21-Aug 8 JB: NOT last week in August before Labor Day