Reviewing Models, Entities, and Interactions

You can review the overall pathway model, its entities, their states, behavior, and formulas, and the interactions in the Model Overview panel.

This task shows you how to:

See Also
Model Overview Panel
Introductory Concepts

Review Models

You can review the biological components of a pathway model on the Entities tab of the Model Overview panel.

  1. For an open pathway model, click in the toolbar.
    This opens the Model Overview panel with the Entities tab active.
  2. To filter the list of entities, enter some text in the Find field.
    This reduces the list to show only entities whose name or formula matches the text.
  3. To sort the entities, click a column heading for:
    • Preferred Name: choose ascending or descending alphabetical order or phenotype.
    • Initial State
    • Behavior Type

    Note: You cannot sort by formula.

  4. Click to expand the entity and any categories of annotation with at least one entry..
  5. Select an entity in either the map area or the Entities tab.
    This highlights the selected entity with a blue border in both the Map Area and the entities list.

You can review all the features of the entities in the pathway model. You can edit entity interactions and formulas. For more information see Configuring Entities and Configuring Formulas.

Review Entities

You can review the details of each entity in a model.

  1. Do one of the following:
    • Select an entity in the pathway model and click .
    • In the Model Overview panel, click for a component in the Entities tab.
    This opens the entity's Information panel. For more information, see Entity Information Panel.
  2. On the Contextual Information tab, review the basic information and annotations for the entity.
  3. On the Reference ID Card tab, review the details of reference database entries for the entity.
    The tab updates with the latest information in the Uniprot and HGNC databases for this entity. You can click the HGNC ID or Uniprot ID links to open the corresponding database entries.
  4. Optional: For entities with multiple cross references in the Uniprot and HGNC databases, select the reference for which you want to review the database entries.
  5. To make changes to the entity, click to open the Model Overview with this entity selected.

    For more information, see Configuring Entities.

Review Interactions

You can review the relationships between biological components of a pathway model.

  1. Do one of the following:
    • Select an interaction in the pathway model and click .
    • In the Model Overview panel, click for a component in the Interactions tab.
    This opens the interaction's Information panel. See Interaction Information Panel.
  2. On the Contextual Information tab, review the basic information and annotations for the interaction.
  3. On the Reference ID Card tab, review the details of reference database entries if this is a protein -protein interaction.
    The tab updates with the latest information in the Intact or Mint databases for this interaction. You can click the Intact ID or Mint ID links to open the corresponding database entries.
  4. Optional: For interactions with multiple cross references in the Intact or Mint databases, select the reference for which you want to review the database entries.
  5. To make changes to the interaction, click to open the Model Overview with this interaction selected.

    For more information, see Configuring Interactions.

You can review all the features of the interactions in the pathway model and you can add annotations. For more information, see Configuring Interactions.