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

Once ontologies have been loaded and enabled in your folder, you can use Concept Annotations to link fields in your data with their concepts in the ontology vocabulary. A "concept picker" interface makes it easy for users to find desired annotations.

Browse Concepts

Reach the grid of ontologies available by selecting (Admin) > Go To Module > More Modules > Ontology.
  • Click Browse Concepts below the grid to see the concepts, codes, and synonyms loaded for any ontology.
  • On the next page, select the ontology to browse.
    • Note that you can shortcut this step by viewing ontologies in the "Shared" project, then clicking Browse for a specific row in the grid.
  • Type into the search bar to immediately locate terms. See details below.
  • Scroll to find terms of interest, click to expand them.
  • Details about the selected item on the left are shown to the right.
    • The Code is in a shaded box, including the ontology prefix.
    • Any Synonyms will be listed below.
  • Click Show Path or the Path Information tab to see the hierarchy of concepts that lead to the selection. See details below

Search Concepts

Instead of manually scrolling and expanding the ontology hierarchy, you can type into the search box to immediately locate and jump to concepts containing that term. The search is specific to the current ontology; you will not see results from other ontologies.

As soon as you have typed a term of at least three characters, the search results will populate in a clickable dropdown. Only full word matches are included. You'll see both concepts and their codes. Click to see the details for any search result. Note that search results will disappear if you move the cursor (focus) outside the search box, but will return when you focus there again.

Search terms will not autocomplete any suggestions as you type or detect any 'stem' words, i.e. searching for "foot" will not find "feet".

Path Information

When you click Show Path you will see the hierarchy that leads to your current selection.

Click the Path Information for a more complete picture of the same concept, including any Alternate Paths that may exist to the selection.

Add Concept Annotation

  • Open the field editor where you want to use concept annotations. This might mean editing the design of a list or the definition of a dataset.
  • Expand the field of interest.
  • Under Name and Linking Options, click Select Concept.
  • In the popup, select the ontology to use. If only one is loaded, you will skip this step.
  • In the popup, browse the ontology to find the concept to use.
  • Click Apply.
  • You'll see the concept annotation setting in the field details.
  • Save your changes.

View Concept Annotations

In the data grid, hovering over a column header will now show the Concept Annotation set for this field.

Edit Concept Annotation

To change the concept annotation for a field, reopen the field in the field editor, click Concept Annotation, make a different selection, and click Apply.

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