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Loading Trait Ontology

Trait dictionary ontology can be obtained from http://www.cropontology.org/ontology/. Each crop has a Crop Ontology identifier which, when added to the path, gives access to the associated trait dictionary as a downloadable file.

For the DivSeek Canada pilot project crops - sunflower, lentil and flax -, the following three dictionaries will be available by adding the following suffixes to the base URL http://www.cropontology.org/ontology/:

  1. CO_359/Sunflower (currently offline for iterative refinement, as of October 2018)

  2. CO_339/Lentil (based on ICARDA compilation)

  3. CO_362/Flax (under development)

Once on the Crop Ontology page for the target crop, click "DOWNLOAD" button and select the OBO formatted file for downloading (see screen capture below).

CropOntology Trait Dictionary Download

Save this file inside the data subdirectory of your target crop-specific DivSeek Canada Portal ("Portal") deployment project directory. After the trait dictionary is loaded into the Portal data subdirectory, the following steps will load it into your crop-specific portal.

Loading via the Tripal Dashboard

Trait data loading is not yet fully automated by the Portal Docker Compose build but currently requires user interaction with the Tripal web site. Thus, it is assumed that the crop-specific DivSeek Canada Portal Docker containers are running so that the web site is accessible, for the following sequence of "administrative" user initiated operations.

  1. Ensure that the obtained .OBO file file permissions are set to the user account running the loading script.
  2. Log into an "administrative" account of the site, to see the admin panel at the top.
  3. Click "Tripal" tab at the top admin panel and find and click on "Data Loaders".
  4. In "Data loaders", find and click on "Chado Vocabularies", then "OBO Vocabulary Loader".
  5. In "OBO Vocabulary Loader", click on "ADD A NEW ONTOLOGY OBO REFERENCE".
  6. Enter the name for the trait ontology in "New Vocabulary Name" field and put the path to the data folder containing the .OBO file, in the "Local File" field.
  7. Double-check that the path to the OBO file is correct, then click "Import OBO file" - this should enqueue a Tripal job into the job list.
  8. Navigate to "Tripal" tabs from the top admin panel again, and click "Jobs".
  9. In the "Jobs" list, find the Job named "Import OBO File" and click Execute on the right.
  10. The Trait Ontology should be loaded into Chado after the job is successfully executed.