Load Ontologies

2022-11-26

Premium Feature — Available in the Enterprise Edition of LabKey Server. Learn more or contact LabKey.

This topic covers how to load ontology vocabularies onto your server and enable their use in individual folders. It assumes you have obtained or generated an ontology archive in the expected format. You also must have the ontology module deployed on your server.

Load Ontologies

One or more ontology vocabularies can be loaded onto your server. Ontologies are stored in the "Shared" folder where they are accessible site-wide. You may load ontologies from any location on the server.

  • Select (Admin) > Go To Module > More Modules > Ontology.
  • You will see any ontologies already loaded.
  • Click Add LabKey Archive (.Zip) to add a new one.
  • Enter:
    • Name: (Required)
    • Abbreviation: (Required) This should be a short unique string used to identify this ontology. This value can't be changed later.
    • Description: (Optional)
  • Click Create.
  • On the next page, use Browse or Choose File to locate your archive.
    • Ontology zip archives include the files: concepts.txt, hierarchy.txt, synonyms.txt
  • Click Upload.

You will see the pipeline task status as the ontology is loaded. Depending on the size of the archive, this could take considerable time, and will continue in the background if you navigate away from this page.

Once the upload is complete, return to (Admin) > Go To Module > Ontology (you may need to click "More Modules" to find it).

  • Note that if you access the Ontology module from a folder other than /Shared, you will see "defined in folder /SHARED" instead of the manage links shown below. Click /Shared in that message to go to the manage UI described in the next section.

Manage Ontologies

In the Ontologies module in the /Shared project, you will see all available ontologies on the list.

  • Click Browse to see the concepts loaded for this ontology. See Concept Annotations.
  • Click Re-Import to upload an archive for the ontology in that row.
  • Click Delete to remove this ontology.
  • Click Browse Concepts to see the concepts loaded for any ontology.
  • Click Add LabKey Archive (.Zip) to add another.
Learn about browsing the concepts in your ontologies in this topic: Concept Annotations

Enable Ontologies in Folders

To use the controlled vocabularies in your data, enable the Ontology module in the folders where you want to be able to use them.

  • Navigate to the container where you want to use the ontology.
  • Select (Admin) > Folder > Management and click the Folder Type tab.
  • Check the box to enable the Ontology module.
  • Click Update Folder.

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