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| The !LinkOut plugin provides a mechanism to link nodes to external web resources within the Cytoscape viewer. Right-clicking on a node item in a Cytoscape view opens a popup menu with a list of web links. Selecting a link initiates a search at the specified website using the node label as the query term. | The !LinkOut plugin provides a mechanism to link nodes to external web resources within the Cytoscape viewer. Right-clicking on a node opens a popup menu with a list of web links. Selecting a link initiates a search at the specified website using the node label as the query term. |
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| The external links are specified in the linkout.props file (included in the Cytoscape release?), which includes a number of default links such as NCBI !PubMed, 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 even at runtime without the need to restart Cytoscape. | LinkOut includes a number of predefined links to commonly used web resources such as NCBI, UniProt as well as species-specific databases. In addition to the default links, users can customize the !LinkOut menu by adding (or removing) links even at runtime without the need to restart Cytoscape. |
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| External links are listed as ''‘key’-‘value’'' pairs 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 `url`. | Similar to other properties external links are listed as ''‘key’-‘value’'' pairs where ''key'' specifies the name of the link and ''value'' is the URL link. The !LinkOut menus are organized in a hierarchical structure that is specified in the key. All key terms start with the keyword `linkouturl`. |
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| `url.yeast.SGD=http://db.yeastgenome.org/cgi-bin/locus.pl?locus\=%ID%` | `linkouturl.yeast.SGD=http://db.yeastgenome.org/cgi-bin/locus.pl?locus\=%ID%` |
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| In a similar fashion one can added new submenus. | In a similar fashion one can add new links under existing submenu or place them in a new submenu. |
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| 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. | 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 that will return an empty page. 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. |
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=== Current linkout.props === These are the current links included in `linkout.props`. Additional suggestions are welcome. `url.Pubmed=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=PubMed&term\=%ID%` `url.yeast.BioGRID=http://www.thebiogrid.org/search.php?keywords=%ID%&searchbutton=GO&organismid=4932` `url.yeast.iHOP=http\://www.ihop-net.org/UniPub/iHOP/?search\=%ID%&field\=all&ncbi_tax_id\=0` `url.mouse.Entrez=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=Protein&term\=%ID%&doptcmdl\=GenPept` `url.human.iHOP=http\://www.ihop-net.org/UniPub/iHOP/?search\=%ID%&field\=all&ncbi_tax_id\=0` `url.yeast.SGD=http\://db.yeastgenome.org/cgi-bin/locus.pl?locus\=%ID%` `url.human.Entrez=http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd\=Search&db\=Protein&term\=%ID%&doptcmdl\=GenPept` `url.mouse.MGI=http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=searchTool&query=%ID%&selectedQuery=Genes+and+Markers` `url.BioGRID=http://www.thebiogrid.org/search.php?keywords=%ID%&searchbutton=GO&organismid=0` `url.google=http://www.google.com/search?hl=en&q=%ID%&btnG=Google+Search` |
LinkOut PlugIn
The LinkOut plugin provides a mechanism to link nodes to external web resources within the Cytoscape viewer. Right-clicking on a node opens a popup menu with a list of web links. Selecting a link initiates a search at the specified website using the node label as the query term.
LinkOut includes a number of predefined links to commonly used web resources such as NCBI, UniProt as well as species-specific databases. In addition to the default links, users can customize the LinkOut menu by adding (or removing) links even at runtime without the need to restart Cytoscape.
If you don't have the LinkOut plugin with your version of Cytoscape, you can download is from here: <TODO: attach jar>. LinkOut currently only works with Cytoscape version 2.3.
LinkOut properties format
Similar to other properties external links are listed as ‘key’-‘value’ pairs where key specifies the name of the link and value is the URL link. 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 add new links under existing submenu or place them in a new submenu.
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: url.yeast.SGD=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 that will return an empty page. 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 new links
To add additional links open the linkout.props file in a text editor and add the new key=url links. The external links do not need to be listed in the order they appear in the LinkOut menu. The key string has to follow the format specified above including the URL prefix. To specify the URL launch an example query to a website and then copy the URL address of the result page.