august 2012 this work is licensed under the creative commons attribution 3.0 unported license. to...

August 2012

This work is licensed under the Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.

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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)

© 2012, Open BEL Community 25

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