GDR/CottonGen: Converting legacy sites to Tripal Sook Jung, Jing Yu, Taein Lee, Chun-Huai Cheng, Stephen Ficklin, Dorrie Main

Talk Overview Introduction of GDR Moving to Chado/Tripal o GDR o CottonGen How to store data in Chado Tripal modules developed Future Directions

GDR (2002 ~) Genomics o EST Unigenes o WGS and annotation Genetics o Markers and maps o QTL o Molecular diversity Breeding o Genotypic data o Phenotypic data o Germplasm data Genetics Breeding Germplasm Diversity Genomics Integrated Data & Tools

GDR in Tripal GDR’s Progress GDR in in- house schema (2002 ~) New Custom/Extention Tripal Modules for gene, marker, QTL, genotype, publication (2013) GDR in Drupal (2009) Tripal instance created (Genomic data) (2010) ND schema developed & Breeding data in Chado (2010) Breeders Toolbox developed (Not in Tripal) ( ) Genetic data moved to Chado (2013) CottonDB to CottonGen

CottonGen Released (1 st year) CottonDB to CottonGen CottonDB on WSU servers (Oct 2011) Tripal instance created Develop ICGI website CottonDB data in Chado Add Tools Gene, marker, search pages (Oct 2012) Phenotype, QTL, Publication search pages added (2013)

Chado: Modular, Generic and Ontology-driven schema Feature Feature_id Name Uniquename Type_id Organism_id residues Feature_relationship Feature_relationship_i d Subject_id Object_id Type_id Featureprop Featureprop_id Feature_id Type_id Value rank cvterm cvterm_id Name definition cv_id Dbxref_id gene, mRNA, marker, QTL, etc Abc- mRNA part_of Abc-gene Repeat_motif Product_size Subject_id object_id cv cv_id Name definition Sequence Ontology, Gene Ontology, etc

Storing Stock (from samples to population; pedigree) stock stock_id Name Uniquename Type_id Organism_id residues stock_relationship Feature_relationship_id Subject_id Object_id Type_id stockprop stockprop_id stock_id Type_id value cvterm cvterm_id Name definition cv_id Dbxref_id Population, cultivar, breeding line, clone, sample, etc Gala-001 sample_of Gala Description, population_siz e Subject_id object_id Gala Maternal_parent_of Sonya pedigree

Storing phenotype data (from measurements to projects) stock Feature_id Name Uniquename Type_id Organism_id residues nd_experiment Nd_experiment_id Nd_geolocation_id Type_id phenotype phenotype_id Uniquename value attr_id cvterm cvterm_id Name definition cv_id Dbxref_id Phenotyping Genotyping Cross_experiment project Featureprop_id Feature_id Type_id value NE_stock NE_phenoty pe project_relationshi p NE_project

Genotypic data integrated with genomic/genetic data nd_experiment Nd_experiment_id Nd_geolocation_id Type_id genotype genotype_id name Uniquename description NE_genotype feature_genotype Feature Feature_id Name Uniquename Type_id Organism_id residues project stock uniquename: CPSCT038_190|192 description: 190:192 Uniquename:CPSCT038 Type:microsatellite map Explore sequence s around marker in GBrowse

Tripal Modules Developed (Custom modules) Gene/Sequence Module Genetic Module o Marker Search o QTL Search o Genotype Search

Gene/Sequence Module

Gene Search Results 13

Genetic Module (Marker Search)

Link to the Genotype (Diversity) module

Genetic Module (Diversity Search)

Long Form Wide Form

Genetic Module (QTL/MTL Search)

QTL to map

QTL to Germplasm

QTL to Marker to Diversity data

Future Directions Make the current modules available o With a set of controlled vocabularies o Bulk loader templates Further refinement of the modules o QTL: add graphic interface to view the QTLs in the genome o Further develop diversity module (integrate with phenotypic diversity and germplasm module) o Germplasm (search page, integrate with image module, etc) o Data transformation functionality Introduce flexibility to the modules o Allow adding users’ own CV o Options to display certain data according to the CV

Main Lab team members Taein Lee Stephen Ficklin ChunHuai Cheng Ping Zheng Anna Blenda Sushan Ru Dorrie Main Jing Yu GDR Project coPIs- Dorrie Main (PI), Bert Abbott, Cameron Peace, Kate Evans, Des Layne, Nnadozie Oraguzie, Mercy Olmstead, Fred Gmitter Jr., the RosBREED teams CottonGen – Don Jones, Richard Percy Rosaceae, Cotton and Bioinformatics Community USDA NIFA SCRI, NSF Plant Genome Program, MARS, USDA- ARS, Washington Tree Fruit Research Commission, Cotton Inc, WSU, Clemson University, University of Florida, Boyce Thompson Institute, Texas A&M Acknowledgements