August 2012

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KAM Navigator

KAM Navigator Overview

• KAM Navigator is a Cytoscape plugin which enables the exploration of large BEL Knowledge Assembly Models (KAMs) and creation of sub-networks

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Contents

• Installation and Requirements• Configuration• Adding nodes to a network– By node function– From a list of identifiers– By finding neighbors of existing nodes

• Investigating KAM Node and Edge Properties

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Installation and Requirements

• See wiki for more details:– https://github.com/OpenBEL/Cytoscape-Plugins/wiki

• Current version 0.9• Requirements– BEL Framework 2.0.0 or later– BEL Framework Server must be running– Cytoscape 2.8– At least one KAM available in the KAM store

• Installation– Can use the plugin manager

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Installation

• In Cytoscape, select Plugins -> Manage Plugins – The plugin manager window will be displayed

• Click the Settings tab at the top of the Window

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Installation

• Click the Add button to add a new Plugins download site

• Add a name and URL, then click OK – https://raw.github.com/OpenBEL/Cytoscape-Plugins/mast

er/plugins.xml

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Installation

• Select the BEL Portal bookmark you just created and the available plugins will be shown

• Navigate through the Theme folder and select the desired version of KAM Navigator– Click Install– Click Close

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Contents

• Installation and Requirements• Configuration• Adding nodes to a network– By node function– From a list of identifiers– By finding neighbors of existing nodes

• Investigating KAM Node and Edge Properties

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Configuration

• The default WSDL URL (for locally installed BEL Framework) is:– http://localhost:8080/openbel-ws/belframework.wsdl– Make sure to start your server!

• OpenBEL demo server WSDL (use provided KAMs)– http://demo.openbel.org/openbel-ws/belframework.wsdl

• You may want to increase the timeout for working with larger KAMs

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Contents

• Installation and Requirements• Configuration• Adding nodes to a network– By node function– From a list of identifiers– By finding neighbors of existing nodes

• Investigating KAM Node and Edge Properties

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Adding Nodes to a Network – Getting Started• First, open a new empty network

– File -> New -> Network -> Empty Network

• Change Visual Style to "KAM Visualization" (optional)– From VizMapper tab in the Control Panel– The KAM Navigator comes with two specific Visual Styles

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Adding Nodes to a Network - By Node Function• Go to Plugins -> KAM Navigator -> Add KAM Nodes

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Adding Nodes to a Network - By Node Function• Select a KAM

– Here "Large Corpus" is selected– If you have already added nodes to

your network from one KAM, you will be limited to that KAM

• Select a Function Type– Here "PHOSPHATASE_ACTIVITY" is

selected

• Click Search– All nodes in the selected KAM with

the selected function will be returned

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Adding Nodes to a Network - By Node Function• To limit your results, type a text

string in the Filter window– Here the PHOSPHATASE_ACTIVITY

results have been filtered with the text string "RGD"

– This returns all of the phosphatase activity nodes in the KAM that have labels using the RGD namespace for Rat Gene Symbols

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Adding Nodes to a Network - By Node Function• Select one or more KAM nodes

– Here phos(p(RGD:Pten)) is selected

• Select from Expand Edge Options– None – adds only the selected

node(s)– All Edges - adds all associated edges– Downstream Edges – adds all edges

directed out– Upstream Edges – adds all edges

directed in– Interconnect Nodes – adds any

edges connecting the selected nodes

• Click Add

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© 2012, Open BEL Community 16

Adding Nodes to a Network - By Node Function• Your nodes and edges will

be added to the network• Tip – Apply a layout to

arrange your network– Here, the Apply force-

directed layout button was used

• Note that the node you added by your search is selected (yellow) and its neighbors (other colors) are not

© 2012, Open BEL Community 17

Adding Nodes to a Network – From List

• You will need a text file containing a list of values from any namespace supported by your BEL Framework installation– E.g., Entrez Gene IDs, Affymetrix probe set IDs, human gene symbols

• Go to Plugins -> KAM Navigator -> Add KAM Nodes From List

© 2012, Open BEL Community 18

Adding Nodes to a Network – From List

• Select a KAM• Select a Function Type• Select the Namespace that

contains the identifiers from your list

• Click Browse to load the file with your list

• Select Expand Edges option• Click Search, then Add

– All nodes found will be added

© 2012, Open BEL Community 19

Adding Nodes to a Network – From List

• In this example, a file with a list of Affymetrix Mouse Genome 430 2.0 probe set identifiers was selected– Selected RNA_ABUNDANCE as

function type– 37 identifiers in the file map to 24

unique RNA abundance nodes in the selected KAM

© 2012, Open BEL Community 20

Adding Nodes to a Network – From List

• This network resulted from adding the selected RNA abundance nodes (yellow) and expanding to upstream edges

© 2012, Open BEL Community 21

Adding Nodes to a Network - By Finding Neighbors of Existing Nodes• Once you have selected a KAM

and added node(s) to your network you can select and add neighboring nodes and edges– First select one or more nodes– Move the cursor over any node

and right-click– From KAM Node, select option

for expanding the network– Options are similar to those for

the Add KAM Nodes menus– Knowledge Neighborhood

provides the most user control

© 2012, Open BEL Community 22

Adding Nodes to a Network - By Finding Neighbors of Existing Nodes• Knowledge

Neighborhood allow selection of– Direction of expansion– Source term function

and/or label– Relationship– Target term function

and/or label

• Select desired edges and click Add

Contents

• Installation and Requirements• Configuration• Adding nodes to a network– By node function– From a list of identifiers– By finding neighbors of existing nodes

• Investigating KAM Node and Edge Properties

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© 2012, Open BEL Community 24

Investigating KAM Node and Edge Properties• Go to View -> Show Results Panel• Select a KAM Node

– The terms for the selected node will appear in the KAM Node Info tab– Here, r(HGNC:DDIT3) represents the equivalent terms r(HGNC:DDIT3)

and r(EG:1649)

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Investigating KAM Node and Edge Properties• Select a KAM Edge

– The statements for the selected edge will appear in the KAM Edge Info Tab

• Select a supporting BEL statement to see citation and other Annotation information