1. Integrating Phenotypic Data With Genomic, Genetic and Genotypic Data Using Chado Sook Jung, Taein Lee, Stephen Ficklin, Jing Yu, Dorrie Main

2. Outline  Introduction of GDR and CottonGen  Chado the generic schema  Storing Stock Data  Storing Phenotypic Data (trait, dataset, etc)  Storing Genotypic Data  Integration with genetic and genomic Data  Conclusion

3. Database projects of Main lab  Major databases with genomic, genetic, phenotypic and genotypic data 1.GDR: Genome Database for Rosaceae Genomic. Gemetoc and Breeding data (Private data and data from RosBreed project) Fruit and Nut, Sat, 12 PM Computer Demo, Mon, 1:35 PM P0946, RosBreed BIM System, Mon, 10-11:30 AM 2.CottonGen: Replaced CottonDB and Cotton Marker Database Cotton Genome Initiative, Sun, 3:50 PM Computer Demo, Mon, 1:50 PM  Other databases:  Citrus Genome Database, Cool season food legume database, Genome database for Vacciniium  Built using Chado schema and Tripal (Drupal front end for Chado)  Tripal presentation, GMOD workshop, Wed 11:50 AM

4. Chado: Modular, Generic and Ontology-driven schema natural diversity general cv pub organism map genetic mage companalysis sequence stock phenotype

5. Publication

6. Chado: Modular, Generic and Ontology-driven schema Feature Feature_id Name Uniquename Type_id Organism_id residues Feature_relationship Feature_relationship_id 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

7. 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_size Subject_id object_id stockcollection stockcollction_id Name uniquename Type_id Contact_id Gala Maternal_parent_of Sonya pedigree stock center

8. 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_phenotype project_relationship Nd_geolocation Nd_geolocation_id Description Latitude Longitude Geodetic_datum NE_project

9. Storing phenotype data (enabling comparison among datasets) stock Feature_id Name Uniquename Type_id Organism_id residues phenotype phenotype_id Uniquename value attr_id cvterm cvterm_id Name definition cv_id Dbxref_id Nd_experiment cv phenotype_id Uniquename value attr_id cvtermprop cvtermprop_id cvterm_id Type_id Value rank attr_id: SkinCol_0 value: 2 RB(cv), SkinCol_0(cvterm) valuerank Orange1 Orange-red2 Pink-red3 Red4 Dark red5 If skin_color_harvest is 1-10 In Standard(cv), we can store the value in standard descriptor again attr_id: Skin_color_harvest value: 4

10. 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 sequences around marker in GBrowse

11. Relationship between genotype and phenotype (haplotype and haplotype effect) 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: MA_H3|H4b description: H3|H4b Uniquename:Ma Type:MTL map phenotype phenotype_id Uniquename value attr_id NE_phenotype phenstatement phenstatement_id Type_id Genotype_id phenotype_id Environment pub attr_id: crisp value: 2.2 Germplasm with H3|H4b alleles of MA locus has value of 2.2 for crisp

12.  Flexibility and generic characteristic of Chado enables us to store and integrate complex biological data from widely different projects and species  The ontology-driven characteristic makes adding new data types relatively easy.  Performance issue mostly resolved by the use of materialized views Conclusion

13.  Natural diversity module working group Naama Menda, Seth Redmond, Robert M. Buels, Maren Friesen, Yuri Bendana, Lacey- Anne Sanderson, Hilmar Lapp, Taein Lee, Bob MacCallum, Kirstin E. Bett, Scott Cain, Dave Clements, Lukas A. Mueller and Dorrie Main  Main Lab team  All Project CoPIs (tfGDR, RosBreed and CottonGen)  Funding Sources USDA NIFA SCRI, NSF Plant Genome Program, USDA-ARS, Washington Tree Fruit Research Commission, Cotton Incorporated, Washington State University, Clemson University, University of Florida, Boyce Thompson Institute, North Carolina State University Acknowledgement Taein Lee Stephen Ficklin Chun-Huai Cheng Ping Zheng Anna Blenda Sushan Ru Dorrie Main Jing Yu