Features

The BELNav (BEL Navigator) App provides an interface to Knowledge Networks managed by the BEL Framework.

This lesson covers:

1. BELNav VizMapper Styles

2. Search Nodes

3. Link to Knowledge Network

4. Expand Nodes

5. Knowledge Neighborhood

6. Table Panel - Node, Edge, BEL Evidence

7. Results Panel - Evidence view

Styles

KamNav includes two Styles specifically designed for BEL Knowledge Networks:

1. KAM Visualization

   • KAM Visualization provides distinct colors and shapes for different BEL node types (by outer BEL function).

2. KAM Visualization Minimal

   • KAM Visualization Minimal uses the same node shapes and edges, but omits the color.

Search Nodes

You can use the Search Nodes function to add nodes from a BEL Knowledge Network to any open Cytoscape Network window. If you do not have an open network, a new network "Network" will be launched. To launch the Search Nodes dialog window, go to Apps → BEL Navigator → Search Nodes (Ctrl + Alt + N)

1. Select a Knowledge Network from dropdown.

2. Select a BEL Function (or All).

3. Select a Namespace.

4. Enter text to match value(s) from the selected namepace in the Entities box. You can use a wild card (*) for the end of the value.

5. Click Search.

6. Select one or more search results to add to your network view. Ctrl + A will select the entire table.

7. Select Connect to Network to add edges between selected nodes and the network view when the nodes are added.

8. Click Add to add the selected Nodes. The node(s) will be added to the active (selected) network view.

TIPS

• You can sort the search results by column: BEL Function, Label, or whether an entry is already Present in the network view.

• Some results may have node labels outside of the selected namespace. These should be equivalent to values matching the selected namespace and entity text.

Search Nodes Using Entities From File

You can also search nodes using a list of entities (namespace values) from a tab or comma delimited file. Select the appropriate Knowledge Network, Function, and Namespace. Then, instead of entering text in the Search Nodes window Entities box, click Load entities from file, navigate to a locally-saved file, click Open, then click Search.

Link to Knowledge Network

If you import a BEL network, you will need to link it to a Knowledge Network, in order to Expand nodes or view Evidence. From the menu bar, or right-click menu, go to Apps → BEL Navigator → Link to Knowledge Network (Ctrl + Alt + L).

TIP

You can also use this function to switch the Knowledge Network associated with your network.

Expand Node

To expand your network to include all of the adjacent nodes and edges from the linked Knowledge Network, select one or more nodes and right-click on any selected node. From the right-click menu, go to Apps → BEL Navigator → Expand Node.

All of the nodes and edges immediately adjacent to the selected node(s) will be added to the network view.

TIP

After adding nodes, you will likely want to apply a layout. Go to the Layout menu to select your favorite ( y-files organic or hierarchic are generally reasonable).

Knowledge Neighborhood

The Knowledge Neighborhood allows you to filter, select, and add adjacent nodes and edges. Select one or more nodes and right-click on any selected node. From the right-click menu, go to Apps → BEL Navigator → Show Neighborhood. The Knowledge Neighborhood window will launch.

Knowledge Neighborhood Window

The Knowledge Neighborhood window consists of facets for filtering (left) and a results table (right) containing a row for each statement associated with an adjacent edge.

Key facets

• Direction - Filter for edges Upstream/Downstream of selected node(s).

• Entities - Namespace Values in the edge Source or Target terms.

• Functions - BEL Functions for the edge Source or Target terms.

• Relationship - The BEL relationship connecting source and target.

Additional facets are included for Citation, Species, and other annotations. Click the arrow icon in the upper right hand corner of a facet to expand.

Here, within the Direction facet, the Downstream edges are selected for inclusion.

Here, within the Functions facet, rnaAbundance is selected for inclusion.

Here, within the Relationship facet, the direct relationships directlyIncreases and directlyDecreases are selected for inclusion.

After applying the above filters (Direction, Functions, Relationship), 9 of 235 statements remain. Select one or more edges and click Add Selected Edges.

TIPS

• Use Ctrl + A to select all edges in the table.

• You will need to apply a Layout after adding edges.

Node tscript(p(HGNC:NFAT5)) with selected edges from Knowledge Neighborhood, and organic layout applied.

Table Panel

The Table Panel contains a set of tables with information about the Nodes, Edges, and Network. For the Node and Edge tables, click the icon in the upper left hand corner to toggle between showing all or showing only information about selected nodes/edges.

Table Panel - BEL.Evidence Table

The BEL.Evidence table appears in the Unassigned Tables tab in the Table Panel if your network view includes edges. A row with each Evidence (statement plus citation and annotation information) associated with the edges in your network is provided. These are indexed by edge ID (SUID in the Edge Table).

TIP

The BEL.Evidence table (or any other Table Panel Table) can be exported via menu File → Export → Table.

View Evidence

A view of the Evidence (statements together with Citation and any other annotations) associated with each edge is available through the Results Panel.

1. Select an edge (if multiple edges are selected, the last one selected will be used). Selected edges are red by default.

2. Right click on the edge and go to Apps → BEL Navigator → Show Evidence. The results panel will launch if it not already open.

3. All statements associated with the selected edge will display in the Statements window. Select a statement to view the associated citation and annotations; the first statement is selected by default.

4. Citation information and Annotations.

5. To associate a specific evidence with the edge, check the Add to Edge Table box. Evidence added to the edge table can be saved or exported along with your network.

TIP

You can also access the Evidence view directly through the Results Panel (open via View → Show Results Panel). If you have selected an edge, the Evidence tab will display the information for that edge.

Open Knowledge Network

Instead of adding specific nodes and edges, you can open an entire BEL Knowledge Network at once; go to File → New → Network → From Knowledge Network. This is a useful feature if you have smaller networks compiled in your BEL Framework and would like to load the entire network.

This is NOT recommended for large networks. For example, a network compiled from the OpenBEL Small Corpus, contains more than 7,500 nodes and may not load completely before timing out.