Data Download, Web Services, and BrAPI

CarrotOmics has data download links associated with any content type which includes data files. You can search for downloadable files at the File Search page. A summary of some of the more "popular" downloads is available on the Data Download page.

In the following example we will search for a gene prediction analysis. Go to the home page, and on the Search menu select Project, Analysis, or Assay Search
In the Name box, enter DCAR V1.0 Gene Prediction and click on the Search button

The search results should provide a link to DCAR V1.0 Gene Prediction. If we click on this, we see that this analysis has links for downloading various files.
Select the first one [A] "DCARv2 V1.0 Gene Prediction JBrowse GFF3" by clicking on the link in the File column
Data Download Figure 1

This leads to the page for that file. Simply click on the link [B] in the Download File Name column to download the file. File size and an MD5 checksum are provided for most files stored at CarrotOmics.
Data Download Figure 2

Web Services

In addition to the main web interface, CarrotOmics provides a way to programmatically access all available data using RESTful web services. These web services are designed to support the following:

  1. Allow end-users to access data programmatically using any language of their choice.
  2. Allow Tripal sites to share data among themselves.

Web services for Tripal are meant to be:

  1. Fully discoverable
  2. Searchable
  3. Provide access to the same data as that which appears on the visible content pages.
  4. Adjustable via Drupal’s content management interface (i.e. no programming required for existing content)
  5. Provide a programmers API for easy addition of new content.
  6. Share data the way scientists expect to see it.
  7. Use controlled vocabularies to ensure maximal interoperability.

You can access the CarrotOmics web services at https://www.carrotomics.org/web-services/
This initial resource “home page” of the web services returns results in JSON format. When using the JSONView extension within Firefox you can explore web services by clicking the links that are present in the browser.

For more detailed information consult the Tripal Web Services documentation at https://tripal.readthedocs.io/en/latest/user_guide/web_services.html

Breeding API (BrAPI)

The Breeding API (BrAPI) project is an effort to enable interoperability among plant breeding databases. BrAPI is a standardized RESTful web service API specification for communicating plant breeding data. The BrAPI home page https://brapi.org/ describes BrAPI in more detail.

CarrotOmics supports BrAPI through the Tripal BrAPI module https://github.com/tripal/brapi and currently supports version 1.2 of the BrAPI standard. Unfortunately, not all BrAPI calls are currently supported. Contact us with requests for additional supported calls.

Relevant BrAPI pages on CarrotOmics: