Linkout provides a mechanism to link nodes and edges to external web
resources within Cytoscape. Right-clicking on a node or edge in
Cytoscape opens a popup menu with a list of web links.
By default, Cytoscape includes a number of links such as
Entrez, SGD and Google, as well as a number of species-specific
links. In addition to the default links, users can customize the
External Links menu and add (or remove) links by using the Cytoscape
Preferences Editor (found under Edit → Preferences → Properties…
in the linkout group).
External links are listed as ‘key’-‘value’ pairs in the
editor where Property Name specifies the name of the link and
Value is the search URL. Linkout menus are organized in a
hierarchical structure that is specified as part of the key. Linkout key terms
specific to nodes start with the keyword
nodelinkouturl; for edges
For example, the following entry:
nodelinkouturl.Model Organism DB.SGD (yeast)=http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=%ID%
places the SGD link under the Model Organism DB submenu. This link will
appear in Cytoscape as:
In a similar fashion one can add new submenus.
%ID% string in the URL is a place-holder for the node label.
When the popup menu is generated this marker is substituted with the
node label. In the above example, the generated SGD link for the YNL050C
If you want to query based on a different column, you need to specify a
different node label using Styles.
For edges the mechanism is much the same; however here the placeholders
%ID2% reflect the source and target node label
Currently there is no mechanism to check whether the constructed URL
query is correct and if the node label is meaningful. Similarly, there
is no ID mapping between various identifiers. For example, a link to
NCBI Entrez from a network that uses Ensembl gene identifiers as node
labels will produce a link to Entrez using the Ensembl ID, which results
in an incorrect link. It is the user’s responsibility to ensure that the
node label that is used as the search term in the URL link will result
in a meaningful link.
20.1. Adding and Removing Links
The default links are defined in the
linkout.props file contained in the
CytoscapeConfiguration directory. These links are normal Java properties and can
be edited directly via text editor or by using the Cytoscape Configuration Editor (Edit → Preferences → Properties…) and
selecting linkout (shown below).
In addition, new links can be defined when starting Cytoscape from
command line by specifying individual properties. The formatting of the
cytoscape.sh -P [context_menu_definition]=[link].
context_menu_definition specifies the context menu for showing the
linkout menu item. The structure of this definition is nodelinkouturl or edgelinkouturl followed by
“.” and followed by the “.”-separated menu hierarchy.
For instance this command:
cytoscape.sh -P nodelinkouturl.yeast.SGD=http://db.yeastgenome.org/cgi-bin/locus.pl?locus\=%ID%
will add this menu item:
To remove a link from the menu, simply delete the property using Edit
→ Preferences → Properties… and selecting commandline. Linkouts
added in the command line will be available for the running instance of