Import the Gene Ontology

Before we proceed with setup of our example genomics site we will want to load the Gene Ontology. This is because we will be loading a whole genome, genes and transcripts with annotations. These annotations include Gene Ontology terms. To load the Gene Ontolgoy, navigate to Tripal → Data Loaders → OBO Vocabulary Loader. You will see the following page:

../../_images/controlled_vocabs.1.png

The Ontology loader allows you to select a pre-defined vocabulary for loading or allow you to provide your own. If you provide your own, you give the remote URL of the OBO file or provide the full path on the local web server where the OBO file is located. In the case of a remote URL, Tripal first downloads and then parses the OBO file for loading. If you do provide your own OBO file it will appear in the saved drop down list for loading of future updates to the ontology.

To import for example, the Sequence Ontology, select it from the drop-down and click the Import Vocabulary button. You will notice a job is added to the jobs system. Now manually launch the jobs

drush trp-run-jobs --username=administrator --root=/var/www/html

If Tripal is running from a docker container named $cntr_name,

docker exec -it $cntr_name drush trp-run-jobs --username=drupaladmin --root=/var/www/drupal/web

Note

Loading an Ontology may take several hours.