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How to Add New Edges

One feature of the Network Viewer environment is the ability to add new edges to a selected network that expand the biological pathway related to a protein(s) of interest.
New edges added will appear in the list for other users to review.
This tutorial outlines the steps necessary for adding new edges within the Network Viewer environment.

"Nodes" Drop-Down Menu Provides Quick Access to Proteins of Interest

Select "Nodes" button to display a list of all nodes found in the network.

Select Any Node From List to Highlight Existing Edge Connections

Click on any node to reveal additional information specific to the entity. The search tool may also be employed to quickly locate a node of interest.

Network Viewer Environment Updates To Display Information Pertinent to User-Selected Node

  1. Network view updates to focus on selected node and its neighbors. Click on labels to show/hide labels.
  2. Data panel displays all edges involving selected node.

"Selected-Node" Data Panel Provides Node Details and Available Actions

  1. "New Edge" button provides option to create a new edge from selected node.
  2. Text list of all existing edges connected to the selected node.
  3. Panel indicates list of additional networks in which the selected node may be found.

Select the "New Edge" Button to Access Form to Create New Relationship

"New Edge" Form Will Load to Allow Input of New Relationship Parameters

  1. Specify edge relationship. Note that the previously seledcted node may be used as subject or object of the relationship.
  2. (Optional) Access BEL Helper to obtain more information on constructing BEL (Biological Expression Language) Statements.
  3. (Optional) There is possiblility to retrieve BEL statements thanks to a beta text mining tool. Click on "Concert Text to BEL (beta)" to explore.

Actively-Selected Node May Be Selected As "Subject" or "Object" in New Edge Relationship

Selection of active node as 'Subject' will automatically populate the proper form entry. Selecting 'Object' will instead place the node into the Object field.

Select Type of Edge Relationship

Select edge relationship type from the drop-down menu to enter within the form.

Specify Remaining Node of New Edge Relationship

Enter the remaining edge node in BEL language format to define complete relationship. Notice the incremental searches of the BEL Helper content to support your edge creation.

Enter Details of Supporting Scientific Literature

  1. Enter PubMed ID of scientific study.
  2. Designate species in which study was conducted.
  3. Designate tissue context in which study was conducted (if available).
  4. Designate disease context in which study was conducted (if applicable).
  5. Designate cell line in which study was conducted (if available).
  6. Enter quotation(s) from manuscript supporting the new edge relationship.
  7. Click Next to have a chance to review your edge and evidence and finally save it.