Diversity Bioinformatics Terry Casstevens Institute for Genomic Diversity, Cornell University GMOD Meeting at NESCent Durham, NC – June 29-30, 2006.

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Presentation transcript:

Diversity Bioinformatics Terry Casstevens Institute for Genomic Diversity, Cornell University GMOD Meeting at NESCent Durham, NC – June 29-30, 2006

The Genomic Diversity and Phenotype Data Model (GDPDM) Terry M. Casstevens 1, Dallas Kroon 1, Peter Bradbury 2, Edward S. Buckler 1,2, and many other reviewers 1 Institute for Genomic Diversity, Cornell University 2 USDA-ARS

What is GDPDM? Database schema for holding data collected by QTL and Diversity Studies.

Objective of GDPDM schema Hold the basic data behind QTL and diversity studies Focuses on taxa, evaluation environments, trait values, genotyping experiments, and genotypic data Does not focus on genomic location, QTLs, detailed passport data Has no dependencies on QTL schema

GDPDMSchema

Germplasm Basic Passport Details link-out to germplasm banks Curate groups of taxa Supports complex genetic pedigrees Follow seed lots and even plants

Support full range of ploidy Can capture background on methodology Connects to genomic map data Genotype Captures wide range of approaches (SNPs, SSR, sequence alignments, isozyme)

Phenotype (trait) Quantitative or qualitative traits Support ontology integration Range of statistics can be recorded (mean, measure, median, std. deviation, etc.)

Environment Full field design can be recorded (down to the plant if desired) X-Y coordinates Basic planting information, treatments Integrates with locality information Observations can be grouped into experiments

Diversity Schema Web Sites

The Genomic Diversity and Phenotype Connection (GDPC) Supported by National Science Foundation DBI and USDA-ARS. Terry M. Casstevens 1 and Edward S. Buckler 2 1 Institute for Genomic Diversity, Cornell University 2 USDA-ARS, Institute for Genomic Diversity, Cornell University

GDPC Purpose The purpose of GDPC is to simplify access to the large genomic and phenotypic datasets that are becoming available in plant biology.

Database Software Viewer or Analysis Tool User GDPC Data Flow via GDPC

Databases Gramene Diversity (GDPDM schema) Panzea (GDPDM schema) Pea Database (Germinate schema) Aztec (private GDPDM) GRIN (passport data)

GDPC Web Sites

Trait Analysis by aSSociation, Evolution, and Linkage (TASSEL) Edward S. Buckler, Dallas Kroon, Peter Bradbury, Zhiwu Zhang, and Terry Casstevens Institute for Genomic Diversity, Cornell University

TASSEL Web Sites

Pedigree Viewer (beta version) Terry M. Casstevens Institute for Genomic Diversity, Cornell University Supported by National Science Foundation DBI and USDA-ARS.