1. CottonGen: Enabling Cotton Research through Big-Data Analysis and Integration
Jing Yu, Sook Jung, Chun-Huai Cheng, Taein Lee, Katheryn Buble, Ping Zheng, Jodi L. Humann, Deah McGaughey, James Crabb, Heidi Hough, B. Todd Campbell, Don C. Jones and Dorrie Main
PAG XXVII – ICGI Workshop, Jan 13, 2019, San Diego, CA

2. Introduction
CottonGen is an online genomics, genetics and breeding (GGB) database, developed in Tripal to help facilitate basic, translational and applied research in cotton
It integrates curated publicly available GGB data into a single portal with a suite of querying and analysis tools

3. Transcripts/RefTrans
CottonGen Data
Genomes
9 (A2, D5, AD1, AD2)
Genes/mRNAs
399,958/729,129
Transcripts/RefTrans
5.8 billion/214,180
Genetic Maps/QTLs
109/4,923
Markers
573,548
Genotypes
25,491,746
Phenotypes
540,643
Germplasm/Images
17,629/12,471
Publications
16,961
CottonGen has the standard types of data you get in a GGB database. In the last year we added RefTrans which combines peer-reviewed published RNA-Seq and EST data sets to create a Reference Transcriptome (RefTrans) for individual Gossypium species and provides putative gene function identified by homology to known proteins.

4. CottonGen Tools BLAST+ Map Viewer Genome Browser CottonCyc
Proteins, Genes, Markers, Transcriptoms, Genomes,
Map Viewer
All Maps
Genome Browser
All Genome Assemblies
CottonCyc
D5 & AD1
Synteny Browser
All sequenced Genomes
Sequence Retrieval
All Genome Assemblies and RefTrans
Cotton Trait Ontology
A central location with controlled vocabulary for cotton phenotypic traits
CottonGen BIMS
For breeders to store, manage, archive and analyze their private breeding data

6. Species Dropdown - Links to Species Data and Tools

7. Data Dropdown - Cotton Trait Ontology

9. Search - Genes and Transcripts

12. Search – QTL

13. Search - Germplasm

14. Tools: Synteny Viewer

15. Tools: Synteny Viewer (cont.)

16. Tools - MapViewer
Similar to CMap, but uses the Chado data already in database
Access MapViewer from “Tools” menu or any genetic map details page
MapViewer is a web based genetic map visualization tool that uses the D3 Javascript technology. It allows viewing of genetic maps and will show comparison of genetic maps that share the same markers, across the same or different species.
It is similar in functionality to the existing CMap but offers the benefit of using map data directly stored in Chado, a generic database schema.

17. Tools - MapViewer

18. Tools - Breeding Information Management System
To provide individual breeders with a secure and comprehensive online breeding management system which will allow them to:
Store, manage, archive and analyze their private breeding program data
Fully integrate their data with publicly available genomic, genetic and breeding data in the community database
Manage data from the Field Book App, an android app for collecting phenotype data in the field
Utilize their integrated phenotype and genotype data in performing genomic analysis and making breeding decisions.
Keep incorporating open-source new analysis tool and breeding decision tools with seamless access to HPC – powerful!

19. BIMS Home
These next two slides just gives you an idea of what BIMS looks like

20. BIMS interfaces
You can view multiple locations via google map, get basic information of traits, to search data in bims, and to compare data among different trails and locations

21. Acknowledged with thanks
Contact us:
Join our mailing lists:
Cite us:

22. CottonGen at PAG XXVII
CottonGen Poster - #P0605
AgBioData Outreach Booth #618