Cytoscape WikiThe LinkOut plugin provides a mechanism to link nodes to external web resources within Cytoscape. Right-clicking on a node item in Cytoscape view opens a popup menu with a list of web links.
The external links are specified in the linkout.props file, which includes a number of default links such as Entrez, SGD, iHOP, Google, as well as a number of species-specific links. In addition to the default links, users can customize the LinkOut menu by adding (or removing) links without the need to restart Cytoscape or reload the network.
External links are listed as ‘key’-‘value’ pairs in the linkout.props file where key specifies the name of the link and value is the search URL. The LinkOut menus are organized in a hierarchical structure that is specified in the key. All key terms start with the keyword linkouturl.
For example, the following entry: linkouturl.yeast.SGD=http://db.yeastgenome.org/cgi-bin/locus.pl?locus\=%ID%
places the SGD link under the yeast submenu. This link will appear in Cytoscape as:
attachment:Figure1_linkout.png
In a similar fashion one can added new submenus.
The %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 YIM protein is: http://db.yeastgenome.org/cgi-bin/locus.pl?locus\=YIM1
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 label will produce a link to Entrez using ensembl ID, which results in an incorrect link. It is the users responsibility to ensure that the node label that is used as the search term in the URL link will result in a meaningful link.
Adding or Removing links The default links are defined in a linkout.props file contained in the linkout.jar. These links are normal java properties and can be editited while running in the Edit → Preferences menu. New links can be defined this way as well. New links can be defined at startup in a separate file and loaded from the command line, either by specifying a file containing the links cytoscape.sh -P new_linout.props or as individual properties cytoscape.sh -P linkouturl.yeast.SGD=http://db.yeastgenome.org/cgi-bin/locus.pl?locus\=%ID%. Any links defined on the command line will supersede the default links.
To remove a link from the menu simply delete the property from the Edit → Preferences menu.