How to Effectively Search and Download Data in CottonGen Chun-Huai Cheng, Jing Yu, Sook Jung, Ping Zheng, Jodi Humann, Taein Lee, Morgan Frank, Deah McGaughey, Amita Mohan, Heidi Hough, Josh Udall, Don Jones and Dorrie Main Hi, my name is Chun-Huai. I’m one of the developers of the CottonGen website. Today, I’d like to introduce you with the search functionalities on CottonGen and hopefully, my presentation will help you find the data you are interested in quickly and effectively. 2018 International Cotton Genomics Initiative Conference May 28 – June 1, 2018 Edinburgh, Scotland

CottonGen Search Interface and Searchable Content CottonGen is a curated and integrated web-based relational database. It hosts a collection of genomic, genetic and breeding data such as whole genome sequences, reference transcriptomes, gene sequences from NCBI, pathways, genetic maps, trait, germplasm, marker, breeding, publication and community member data. Because of the vast amount of information, finding just the right data you need can be challenging. On the website, all search interfaces can be accessed through the menu toolbar. Some of the searches are more complicated which may offer sub-menus or grouped tabs that return different results. The figure on the right shows the searchable content types on CottonGen. Not sure I would say the following text Chun-Huai but if you can do the whole talk in 4 mins then keep it in. For example, you can search germplasm by its name, by collection, by pedigree, by country of origin, or even by the description of its image. The Genotype Search allows you to search through genotype data for either SNP or SSR markers. The Trait Evaluation Search allows you to search up to three traits and return the germplasm that match the trait description. Other searchable contents include Colleague, Publication, Map, QTL, etc. The results can be downloaded as a table in the CSV format. For the sequence type of search such as Gene and Transcript Search, Sequence Search, and Marker Search, a FASTA file can also be downloaded in addition to the result table.

Initiate Search and Retrieve/Download Results The search process usually involves four steps. 1. Select the desired search from the menu toolbar based on the content type. Here we show an example of the Gene and Transcript Search. 2. Apply the filters on the search form. For the Gene and Transcript Search, you can restrict the results by specifying an organism or choose to return genes only from a specific genome assembly. You can also provide a list of gene names and retrieve the sequences for them. Or use the Keyword field to return genes of a certain function. 3. Click on the search button. 4. The results will be returned in the tabular format. From there, you can either sort the results by clicking on the header, follow the link to get detail information of a result, or download the result table and/or a FASTA file.

Example: Search Germplasm/Search Traits In this example we show the Germplasm Searches. All search interfaces are grouped in the tabs at the top of the form so that you can search by Name, Collection, Pedigree, Country, or Image. Here if you type in a description of the image, for example, boll open, it will return a list of germplasm with that image description. From the result table, you can either click on the germplasm name to get its detail information or click on the image get a hi-resolution image. On the right is another example. Trait Evaluation Search allows you to find germplasm by specifying three traits at most. You can use the ‘AND’ or ‘OR’ operator to return the intersection or union results of the matching germplasm.

Example: Search Polymorphic SNP Markers Download only polymorphic results Lastly, I’d like to show you a new search that was recently implemented. It is the SNP Genotype Search that allows you to search polymorphic SNP markers. You can filter the genotype data by Dataset, Species, Germplasm name or Marker name, etc. The results will be presented as a table that lists the genotypes of a marker in different germplasm. Here, you can download the result as usually or you’ll have an option to download only the polymorphic results. Clicking on the marker name will take you to all that marker details page.

Acknowledged with thanks Finally, I’d like to thank the organizations listed here for providing funding to support CottonGen. If you have any questions or suggestions, please don’t hesitate to use the contact form on the website to contact us or catch us in person during the conference Any Questions? Contact us: https://www.cottongen.org/contact Cite us: Yu et al., 2014