Paula Mabee, University of South Dakota Eva Huala, Carnegie Institution for Science Andy Deans, North Carolina State University Suzanna Lewis, Lawrence.

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Presentation transcript:

Paula Mabee, University of South Dakota Eva Huala, Carnegie Institution for Science Andy Deans, North Carolina State University Suzanna Lewis, Lawrence Berkeley National Lab

Research Coordination Networks  ‘To encourage and foster interactions among scientists to create new research directions or advance a field.’ NSF solicitation:

Phenotype RCN goal:  To establish a network of scientists who are interested in comparing phenotypes across species and in developing the tools and methods [ontologies] needed in making this possible.

Motivations for RCN: 1. Opportunity 2. Research potential 3. Community interest

Text 1. Opportunity: Genomics -> Phenomics… (12 Feb 2011 Science)

Text 1. Opportunity: Genomics -> Phenomics… ‘…NIH plans to create a National Center for Advancing Translational Sciences’ Francis S. Collins ‘Among the any improvements that are needed in human genome research, the most important is the collection of human phenotypes (according to agreed-upon parameters and standards…’ J. Craig Venter ‘If I could move the clock back to 2001 and change course, I would invest significantly more in developing large clinical resources with detailed clinical histories, deep phenotyping, ….’ Tom Hudson Comments on 10 yr anniversary of human genome sequence (4 Feb 2011 Science) Comments on 10 yr anniversary of human genome sequence (4 Feb 2011 Science)

Images: Web Tree of Life ( Regier et al (2010 Text Phenotype is the next/now big challenge

2. Research potential Phenoscape (kb.phenoscape.org)Washington et al. (2009) Zebrafish genes Zebrafish genes Teleost fish species Zebrafish genes Human genes Human genes Drosophila genes Drosophila genes Used shared phenotype ontologies to identify candidate genes for evolutionary novelties and human disease & aggregate data across studies

3. Community interest Genetics Developmental biology Comparative morphology & evolution Medicine Population genetics Behavior Functional morphology  Enthusiastic working groups  Community involvement with annotation  May 2009 workshop report

Specific RCN goals: 1. Develop community network 2. Make phenotype data interoperable:  Develop high-level anatomy ontologies for three key taxonomic clades  Align and synchronize anatomical ontologies using homology and various types of similarity relations  Define standards and best practices, publish manual

Develop a community…  Annual summit meetings  Working group meetings  Collaborative exchanges  Presentations at meetings

Make phenotype data interoperable: 1. Develop high-level anatomy ontologies for three key taxonomic clades 2. Align and synchronize anatomical ontologies using homology and various types of similarity relations 3. Define standards and best practices, publish manual Informatics (Lewis) Vertebrates (Mabee) Plants (Huala) Arthropods (Deans)

Bilateria Ever more inclusive… Plants Protostomes Deuterostomes Fungi Arthropods Vertebrates

Ontology coordinator:  Erik Segerdell  Will help groups develop and integrate high-level ontologies CARO VAO TAO

Outreach to ancillary phenotype groups Vertebrates (Mabee) Plants (Huala) Arthropods (Deans) Taxonomy (year 2) Taxonomy (year 2) Behavior (year 3) New taxa (year 5) Function (year 4)

Objectives for this meeting:  Begin to create network  Who are we? Who are we missing? Lightning talks Friday am  Vision? Talks Friday pm  What resources do we have? Saturday am (sign up)  Initiate anatomy ontology integration  How many anatomy ontologies? Saturday talks and panel discussions  Which anatomy ontologies? Saturday pm breakouts  Where to begin? Sunday am reports

Concrete outcomes from this meeting:  List of participants for future workshops  List of resources (on website)  Working document for anatomy ontology integration  For each working group  First steps; final outcome  Feedback: other ideas for RCN activities

Genetics, development Evolution, function, behavior Vertebrate phenotype ontology data & resources Chicken (Burgess) Human (Robinson) Mouse (Smith) Mouse (Smith) Xenbase Birds (Cracraft) Fishes (Westneat; Mabee; Dahdul) Fishes (Westneat; Mabee; Dahdul) Mammals (Weksler ) Amphibs (Wake) Zebrafish ( Westerfield ) Zebrafish ( Westerfield )