KAM Navigator

Report
KAM Navigator
August 2012
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1
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
2
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
3
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
4
Installation
• In Cytoscape, select Plugins -> Manage Plugins
– The plugin manager window will be displayed
• Click the Settings tab at the top of the Window
5
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/CytoscapePlugins/master/plugins.xml
6
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
7
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
8
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
9
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
10
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
11
Adding Nodes to a Network - By Node Function
• Go to Plugins -> KAM Navigator -> Add KAM Nodes
12
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
13
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
14
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
15
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 forcedirected 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
16
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
17
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
18
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
19
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
20
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
21
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
© 2012, Open BEL Community
22
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
23
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
24
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
© 2012, Open BEL Community
25

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