The CottonGen homepage is divided into a few key areas to help facilitate navigation. The Major Species Quick Start (Fig. 1A) has icons for the major production species. Clicking on the species icon takes you to the Species Overview page (see Species Overview tutorial) which allows for quick access to all the data associated with that species. The full list of species represented in CottonGen can be found in the Species pull-down menu (Fig. 1D). To the right of the Species Quick Start is the Tools Quick Start (Fig. 1B). This area has links to common tools and data search interfaces. The center region of the homepage contains a News and Events section (Fig. 1C) which has news about CottonGen as well as from the community. The homepage also has the traditional pull-down menu bar in the header (Fig. 1D) which provides access to the species overview pages, data, search pages, tools, and general information.
Figure 1. CottonGen Homepage
The items under the Search and Tools menus are discussed in other tutorials, but we want to highlight the Data and General menus in this section of the tutorial. Under the Data menu (Fig. 2A), you can view a list of people who have contributed data to CottonGen, see an overview of the current data, download data, learn how to submit new data, view a list of community projects and a list of standardized trait ontology terms, and find links to outside resources. A summary overview of all data on CottonGen which can be broken down by various categories is found on the Overview page. Under Data Submission, there are details about submitting data to CottonGen, which accepts published data. We highly recommend contacting us before starting to fill in the data templates. There are two links to the contact form on this page.
The Data Download page contains links to the various data types in CottonGen. These links take you to either a search page, list, or table with information about the data and links to download files. For phenotyping data, the link takes you to the search page for that data. Here, choose your parameters and click submit to retrieve data. The resulting table can then be downloaded.
The Cotton Trait Ontology page contains the QTL traits that are in CottonGen and the abbreviations that are used for the internal CottonGen database generated QTL ID. We have tried to keep our abbreviations consistent with those used in the trait and crop ontologies.
Links to USDA-ARS cotton variety test data and NCBI SRA datasets are also available via the Data menu.
Figure 2. Data and General menu items.
The General menu (Fig. 2B) contains links to a variety of different items. If you would like to subscribe to the CottonGen mailing list, please click on Mailing Lists and complete the web form. The General menu also has links to past presentations about CottonGen, work that is in progress and completed, and how to reference CottonGen. The Help menu (Fig. 2C) has a link to this CottonGen User Manual. There is also a Contact Us link that opens a fillable web form. We appreciate feedback as well as reports of website bugs and data errors.