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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
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