Configuring Interactions

You can change the interaction effect, and add or edit annotations. An interaction's title indicates the entities involved, you cannot edit this. Configuring interactions fine tunes the model to behave as expected in a specific context, for example for a given disease or a specific tissue. Annotations provide evidence supported by scientific details.

This task shows you how to:

See Also
Introductory Concepts
Configuring Entities

Add Annotations

You can add annotations to interactions. You can include one or more pieces of evidence for each annotation.

  1. Open the Model Overview panel for a map model.
  2. For the interaction of interest, click .
    The annotations for the interaction expand. If there are any annotations already, their sections expand.
  3. For the category of annotation to add, click .
    This adds a new empty annotation, with your trigram and the current date.
  4. Enter a reason for the annotation.

    For a number of standard biological data resources, you can enter the URL for the evidence in the annotation. The URL converts automatically to a readable annotation. For more information on the supported resources, see Pathways.

    Note: When you add cross reference annotations to Intact or Mint data resources, the corresponding Interaction Information panel's Reference ID Card tab automatically displays their information. For more information, see Review Interactions.

  5. Optional: For the annotation, click .
  6. Optional: In the new field, enter the web address for the Evidence.

This automatically updates the pathway model with your annotations.

Edit an Interaction

You can make changes to existing interactions, changing their contributions and effects.

  1. Do one of the following:
    • Select an interaction in the pathway model and click . Click to enter edit mode for the tab.
    • In the Model Overview panel, click for a component in the Interactions tab.
  2. For the interaction of interest, click the connector in the Contributor cell. Select the contributor type you need.
  3. For the interaction of interest, click the connector in the Interaction Effect cell. Select the interaction effect type you need.
  4. Optional: For edits in the Interaction Information panel, click again to exit edit mode.

The interaction updates with your choices. The pathway model in the map area displays the selected interaction types. For more information on interaction types, see Model Overview Panel.