Welcome Screen

When you start Cytoscape, you can access basic functions from the Welcome Screen:

The Welcome Screen is designed to access commonly used features of Cytoscape including:

• Create new network
• Import network
  • From file
  • From public database
• Import interactome for model organisms
• Open recently used session file

Also, a news panel always display latest information for users. For information on user privacy, see the Cytoscape Privacy Policy.

Basic Features

When a network is loaded, Cytoscape will look similar to the image below:

Most functionalities are self-explanatory, but we'll go through a concise explanation for clarity. The main window here has several components:

• The Menu Bar at the top (see below for more information about each menu).
• The Tool Bar, which contains icons for commonly used functions. These functions are also available via the menus. Hover the mouse pointer over an icon and wait momentarily for a description to appear as a tooltip.
• The Network Panel (Network tab of the Control Panel, top left). This contains an optional network overview pane (shown at the bottom left).
• The main Network View Window, which displays the network.
• The Table Panel (bottom right panel), which displays columns of selected nodes and edges and enables you to modify the values of column data.

The Network Panel and Table Panel are dockable tabbed Panels. You can undock any of these panels by clicking on the Float Window control in the upper-right corner of the CytoPanel. This is useful when you want assign the network panel as much screen space as possible. To dock the window again, click the Dock Window icon . Clicking the Hide Panel icon will hide the panel; this can be shown again by choosing View → Show and selecting the relevant panel.

If you click this control, for example on the Table Panel, you will now have two Cytoscape windows, the main window, and a new window labeled Table Panel, similar to the one shown below. A popup will be displayed when you put the mouse pointer on a cell.

Note that Table Panel now has a Dock Window control. If you click this control, the window will dock onto the main window. For more information on the panels in Cytoscape, see the Panels section.

Network Editing

Cytoscape also has an edit functionality that enables you to build and modify networks interactively within the network canvas. To edit a network, just right-click on the open space of network window, select the menu item Add → Node, a new node will be added to the canvas. To add an edge, right click on a node, choose the menu item Edit → Add Edge. Then select the target node, a new edge will be added between the two nodes. In a similar way annotation objects can be added; pictures, shapes or textboxes; much like in MS PowerPoint or similar software. Detailed information on network editing can be found in the Editing Networks section.

The Menus

File

The File menu contains most basic file functionality: File → Open for opening a Cytoscape session file; File → New for creating a new network, either blank for editing, or from an existing network; File → Save for saving a session file; File → Import for importing data such as networks and data; and File → Export for exporting data and images. File → Export → Network View as Graphics lets you export the network in either JPEG, PDF, PNG, Post Script or SVG format.

File → Recent Session will list recently opened session files for quick access. File → Run allows you to specify a Cytoscape script file to run, and File → Print Current Network... allows printing.

Edit

The Edit menu contains Cut, Copy and Paste functions, as well as Undo and Redo functions which undo and redo edits made in the Table Panel, the Network Editor and to layout.

There are also options for creating and destroying views (graphical representations of a network) and networks (the raw network data – not yet visualized), as well as an option for deleting selected nodes and edges from the current network. All deleted nodes and edges can be restored to the network via Edit → Undo.

There are also other editing options; Remove Duplicated Edges will delete edges that are complete duplicates, keeping one edge, Remove Self-Loops removes edges that have the same source and target node, and Delete Selected Nodes and Edges... deletes a selected subset of the network. Rename Network... allows you to rename the currently selected network.

Editing preferences for properties and apps is found under Edit → Preferences → Properties.... More details on how to edit preferences can be found here.

View

The View menu allows you to display or hide the Control Panel, Table Panel, Tool Panel and the Result Panel. It also provides the control of other view-related functionality.

Select

The Select menu contains different options for selecting nodes and edges.

Layout

The Layout menu has an array of features for visually organizing the network. The features in the top portion of the network (Bundle Edges, Clear Edge Bends, Rotate, Scale, Align and Distribute) are tools for manipulating the network visualization. The bottom section of the menu lists a variety of layout algorithms which automatically lay a network out.

Apps

The Apps menu gives you access to the App Manager (Apps → App Manager) for managing (install/update/delete) your apps and may have options added by apps that have been installed. Depending on which apps are loaded, the apps that you see may be different than what appear here. The below picture shows a Cytoscape installation without installed apps.

In previous versions of Cytoscape, apps were called plugins and served a similar function.

Tools

The Tools menu contains advanced features like the Command Line Dialog, Network Analyzer, Network Merge and Workflow.

Help

The Help menu allows you to launch the online help viewer and browse the table of contents for this manual (Contents).

The Citations option displays the main literature citation for Cytoscape, as well as a list of literature citations for installed apps. The list will be different depending on the set of apps you have installed.

The Help menu also allows you to connect directly to Cytoscape Help Desk and the Bug Report interface.

Network Management

Cytoscape allows multiple networks to be loaded at a time, either with or without a view. A network stores all the nodes and edges that are loaded by the user and a view displays them.

An example where a number of networks have been loaded is shown below:

The network manager (in Control Panel) shows the networks that are loaded. Clicking on a network here will make that view active in the main window, if the view exists. Each network has a name and size (number of nodes and edges), which are shown in the network manager. If a network is loaded from a file, the network name is the name of the file.

Some networks are very large (thousands of nodes and edges) and can take a long time to display. For this reason, a network in Cytoscape may not contain a "view". Networks that have a view are in normal black font and networks that don’t have a view are highlighted in red. You can create or destroy a view for a network by right-clicking the network name in the network manager or by choosing the appropriate option in the Edit menu. You can also destroy previously loaded networks this way.

Certain operations in Cytoscape will create new networks. If a new network is created from an old network, for example by selecting a set of nodes in one network and copying these nodes to a new network (via the File → New → Network option), it will be shown immediately follows the network that it was derived from.

The available network views are also arranged as multiple overlapping windows in the network view window. You can maximize, minimize, and destroy network views by using the normal window controls for your operating system.

Arrange Network Windows

When you work on multiple networks, you can arrange the network view windows under View → Arrange Network Windows.

Vertical

Grid

The Network Overview Window

The network overview window shows an overview (or "bird’s eye view") of the network. It can be used to navigate around a large network view. The blue rectangle indicates the portion of the network currently displayed in the network view window, and it can be dragged with the mouse to view other portions of the network. Zooming in will cause the rectangle to appear smaller and vice versa.

usage: cytoscape.{sh|bat} [OPTIONS]
 -h,--help             Print this message.
 -v,--version          Print the version number.
 -s,--session <file>   Load a cytoscape session (.cys) file.
 -N,--network <file>   Load a network file (any format).
 -P,--props <file>     Load cytoscape properties file (Java properties
                       format) or individual property: -P name=value.
 -V,--vizmap <file>    Load vizmap properties file (Cytoscape VizMap
                       format).
 -S,--script <file>    Execute commands from script file.
 -R,--rest <port>      Start a rest service.

Any file specified for an option may be specified as either a path or as a URL. For example you can specify a network as a file (assuming that myNet.sif exists in the current working directory): cytoscape.sh -N myNet.sif.

Note: if there are spaces in the file path, be sure to put quotes around it: cytoscape.bat -N "C:\Program Files\Cytoscape\sampleData\galFiltered.sif".

Or you can specify a network as a URL: cytoscape.sh -N http://example.com/myNet.sif.

All options described above (except for starting a REST service) can be accessed from the menu once Cytoscape is running.

Managing Properties

The Cytoscape properties editor, accessed via Edit → Preferences → Properties…, is used to specify default properties. Any changes made to these properties will be saved in .props files under the CytoscapeConfiguration subdirectory of the user's home directory.

Cytoscape properties are configurable using the Add, Modify and Delete buttons as seen below.

App properties may also be edited in the same way as editing Cytoscape properties. For example, to edit the properties of Linkout, select 'linkout' from the combobox of the Preferences Editor. Some apps may store properties inside session files in addition to (or instead of) storing them in the CytoscapeConfiguration directory.

Managing Bookmarks

Cytoscape contains a pre-defined list of bookmarks, which point to sample network files located on the Cytoscape web server. Users may add, modify, and delete bookmarks through the Bookmark manager, accessed by going to Edit → Preferences → Bookmarks….

There are currently several types of bookmarks (based on data categories), including network and table. Network bookmarks are URLs pointing to Cytoscape network files. These are normal networks that can be loaded into Cytoscape. Table bookmarks are URLs pointing to data table files.

Managing Proxy Servers

You can define and configure a proxy server for Cytoscape by going to Edit → Preferences → Proxy Settings….

After the proxy server is set, all network traffic related to loading a network from URL will pass through the proxy server. Cytoscape apps use this capability as well. The proxy settings are saved in cytoscape3.props. Each time you click the OK button after making a change to the proxy settings, an attempt is made to connect to a well known site on the Internet (e.g., google.com) using your settings. For both success and failure you are notified and for failure you are given an opportunity to change your proxy settings.

If you no longer need to use a proxy to connect to the Internet, simply set the Proxy type to "direct" and click the OK button.

Managing Group View

The configuration of Cytoscape group view may also be edited through Edit → Preferences → Group Preferences….

1. Importing pre-existing, fixed-format network files.
2. Importing pre-existing, unformatted text or Excel files.
3. Importing data from from public databases.
4. Creating an empty network and manually adding nodes and edges.

Import Fixed-Format Network Files

Network files can be specified in any of the formats described in the Supported Network Formats section. Networks are imported into Cytoscape through the File → Import → Network menu. The network file can either be located directly on the local computer, or found on a remote computer (in which case it will be referenced with a URL).

Load Networks from Local Computer

In order to load a network from a local file you can select File → Import → Network → File... or click on on the tool bar. Choose the correct file in the file chooser dialog and press Open. Some sample network files of different types have been included in the sampleData folder in Cytoscape.

After you choose a network file, another dialog will pop up. Here, you can choose either to create a new network collection for the new network, or load the new network into an existing network collection. When you choose the latter, make sure to choose the right mapping column to map the new network to the existing network collection.

Network files in SIF, GML, and XGMML formats may also be loaded directly from the command line using the –N option.

Load Networks from a Remote Computer (URL import)

To load a network from a remote file, you can select File → Import → Network → URL.... In the import network dialog, insert the appropriate URL, either manually or using URL bookmarks. Bookmarked URLs can be accessed by clicking on the arrow to the right of the text field (see the Bookmark Manager in Preferences for more details on bookmarks). Also, you can drag and drop links from a web browser to the URL text box. Once a URL has been specified, click on the OK button to load the network.

Another issue for network import is the presence of firewalls, which can affect which files are accessible to a computer. To work around this problem, Cytoscape supports the use of proxy servers. To configure a proxy server, go to Edit → Preferences→ Proxy Settings.... This is further described in the Preferences section.

Import Networks from Unformatted Table Files

Cytoscape supports the import of networks from delimited text files and Excel workbooks using File → Import → Network → File.... An interactive GUI allows users to specify parsing options for specified files. The screen provides a preview that shows how the file will be parsed given the current configuration. As the configuration changes, the preview updates automatically. In addition to specifying how the file will be parsed, the user must also choose the columns that represent the source and target nodes as well as an optional edge interaction type.

Supported Files

The Import Network from Table function supports delimited text files and Microsoft Excel Workbooks. For Excel Workbooks with multiple sheets, one sheet can be selected for import at a time. The following is a sample table file:

source  target  interaction  boolean data       string data     floating point data
YJR022W YNR053C pp      TRUE    abcd12371       1.2344543
YER116C YDL013W pp      TRUE    abcd12372       1.2344543
YNL307C YAL038W pp      FALSE   abcd12373       1.2344543
YNL216W YCR012W pd      TRUE    abcd12374       1.2344543
YNL216W YGR254W pd      TRUE    abcd12375       1.2344543

The network table files should contain at least two columns for creating network with edges. If the file has only one column, the created network will not contain any edges. The interaction type is optional in this format. Therefore, a minimal network table looks like the following:

YJR022W YNR053C
YER116C YDL013W
YNL307C YAL038W
YNL216W YCR012W
YNL216W YGR254W

One row in a network table file represents an edge and its edge data columns. This means that a network file is considered a combination of network data and edge column data. A table may contain columns that aren't meant to be edge data. In this case, you can choose not to import those columns by clicking on the column header in the preview window. This function is useful when importing a data table like the following (1):

This data file is a tab-delimited text file and contains network data (interactions), edge data, and node data. To import network and edge data from this table, choose Unique ID A as source, Unique ID B as target, and Interactor types as interaction type. Next, turn off columns used for node data (Alternative ID A, species B, etc.). Other columns can be imported as edge data.

The network import function cannot import node table columns - only edge table columns. To import node table columns from this table, please see the Node and Edge Column Data section of this manual.

Note (1): This data is taken from the A merged human interactome datasets by Andrew Garrow, Yeyejide Adeleye and Guy Warner (Unilever, Safety and Environmental Assurance Center, 12 October 2006). Actual data files are available at http://wiki.cytoscape.org/Data_Sets/

Basic Operations

To import network from text/Excel tables, please follow these steps:

1. Select File → Import → Network → File... or click on on the tool bar.

2. Select a table file in the file chooser dialog.
3. Define the interaction parameters by specifying which columns of data contain the Source Interaction, Target Interaction, and Interaction Type. Clicking on any column header will bring up the interface for selecting source, interaction and target:

   • 

4. (Optional) Define edge table columns, if applicable. Network table files can have edge table columns in addition to network data.

   • Enable/Disable Table Columns: You can enable/disable column data by selecting the symbol in the column editor.

     • 

   • Change Column Name and Data Types: You can also modify the column name and data type in the column editor. For more detail, see Modify Column Name/Type below.

5. Click the OK button.

Import List of Nodes Without Edges

The table import feature supports lists of nodes without edges. If you select only a source column, it creates a network without interactions. This feature is useful with the node expansion function available from some web service clients. Please read the section Importing Networks from External Database for more detail.

Advanced Options

You can select several options by clicking the Advanced Options button in the main import interface.

• Delimiter: You can select multiple delimiters for text tables. By default, Tab and Space are selected as delimiters.
• Default Interaction
• Transfer first line as column names: Selecting this option will cause all edge columns to be named according to the first data entry in that column.
• Start Import Row: Set which row of the table to begin importing data from. For example, if you want to skip the first 3 rows in the file, set 4 for this option.
• Ignore lines starting with: Rows starting with this character will not be imported. This option can be used to skip comment lines in text files.

Modify Column Name/Type

In the Import Network from Table interface, you can change the name and data type of column by clicking on any column header:

Column names and data types can be modified here.

• Modify Column Name - just enter a new column name.
• Modify Column Data Type - The following column data types are supported:
  • String
  • Boolean (True/False)
  • Integer
  • Floating Point
  • List of (one of) String/Boolean/Integer/Floating Point

Cytoscape has a basic data type detection function that automatically suggests the column data type according to its entries. This can be overridden by selecting the appropriate data type from the radio buttons provided. For lists, a global delimiter must be specified (i.e., all cells in the table must use the same delimiter).

Import Networks from Public Databases

Cytoscape has a feature called Import Network from Public Databases. Users can access various kinds of databases through this function, File → Import → Network → Public Databases....

Getting Started

To get started, select File → Import → Network → Public Databases....

Example: Retrieving Protein-Protein Interaction Networks from Multiple Databases

• Select File → Import → Network → Public Databases....

• From the pull-down menu, select the Interaction databases Universal Client.

• Enter one or more search terms, such as BRCA1.

• Click the Search button to start the search.

• Select databases from the hits. This selection will be saved as your default database list.

• Click the Import button to import selected network data.

After confirming the download of interaction data, the network of BRCA1 will be imported and visualized.

Tip: Expanding the Network: Several of the Cytoscape web services provide additional options in the node context menu. To access these options, right-click on a node and select Apps → Extend Network by public interaction database.... For example, in the screenshot, we have loaded the BRCA1 network from IntAct, and have chosen to merge this node's neighbors into the existing network.

PSICQUIC Options

PSICQUIC Web Service Client has three search modes:

• Search by ID
• Search by MIQL
• Search by Species

By default, search mode is set to Search by ID. You can search all databases by ID, such as gene symbol, Uniprot ID, or NCBI gene ID. If the search mode is set to MIQL, you can use MIQL for search. If you want to search interactions by keywords or specific functions, this is the powerful query language to filter the result. The last option is for importing all interactions for the species (i.e., interactome).

Create a New Network Manually

A new, empty network can also be created and nodes and edges manually added. To create an empty network, go to File → New → Network → Empty Network, and then manually add network components by right clicking on the network canvas or on a node.

Adding a Node

To add a new node, right-click on an empty space of the network view panel. Select Add → Node item from the pop-up menu.

Adding an Edge

To add an edge to connect nodes, right-click on the source node. Select Edit → Add Edge from the pop-up menu. Next, click on the target node. The Images below show the two steps for drawing an edge between two nodes. You can abort the drawing of the edge by pressing Esc key. You can also select two or more nodes to connect and in the right-click menu select Add → Edges Connecting Selected Nodes to create edges connecting all selected nodes.

You can delete nodes and edges by selecting a number of nodes and edges, then selecting Edit → Cut. You can also delete selected nodes and edges from the Edit menu, under Edit → Delete Selected Nodes and Edges.... You can recover any nodes and edges deleted from a network by going to Edit → Undo.

Grouping nodes

Any number of nodes can be grouped together and displayed as either one group node or as the individual nodes. To create a group, select two or more nodes and right-click to select Group → Group Selected Nodes. You will be prompted to select a name for the group node. Once a group is created, you can use the right-click menu to collapse or expand the group. You can also quickly collapse/expand a group by double-clicking on the group node or any of its children to toggle back and forth.

Collapsed group

Expanded group

Adding Network Annotations

Annotations in the form of text, images or shapes can be added to the network canvas by right-clicking anywhere on the canvas and selecting one of the Annotation choices in the Add menu. You can add an image of your own, choose from a shapes library or add either plain or bounded text. Shapes and text are customizable and any added annotations can be edited from the right-click context menu.

• Simple interaction file (SIF or .sif format)
• Nested network format (NNF or .nnf format)
• Graph Markup Language (GML or .gml format)
• XGMML (extensible graph markup and modelling language).
• SBML
• BioPAX
• PSI-MI Level 1 and 2.5
• GraphML
• Delimited text
• Excel Workbook (.xls, .xlsx)

• Cytoscape.js JSON

The SIF format specifies nodes and interactions only, while other formats store additional information about network layout and allow network data exchange with a variety of other network programs and data sources. Typically, SIF files are used to import interactions when building a network for the first time, since they are easy to create in a text editor or spreadsheet. Once the interactions have been loaded and network layout has been performed, the network may be saved to GML or XGMML format for interaction with other systems. All file types listed (except Excel) are text files and you can edit and view them in a regular text editor.

SIF Format

The simple interaction format is convenient for building a graph from a list of interactions. It also makes it easy to combine different interaction sets into a larger network, or add new interactions to an existing data set. The main disadvantage is that this format does not include any layout information, forcing Cytoscape to re-compute a new layout of the network each time it is loaded.

Lines in the SIF file specify a source node, a relationship type (or edge type), and one or more target nodes:

nodeA <relationship type> nodeB
nodeC <relationship type> nodeA
nodeD <relationship type> nodeE nodeF nodeB
nodeG
...
nodeY <relationship type> nodeZ

A more specific example is:

node1 typeA node2
node2 typeB node3 node4 node5
node0

The first line identifies two nodes, called node1 and node2, and a single relationship between node1 and node2 of type typeA. The second line specifies three new nodes, node3, node4, and node5; here "node2" refers to the same node as in the first line. The second line also specifies three relationships, all of type typeB and with node2 as the source, with node3, node4, and node5 as the targets. This second form is simply shorthand for specifying multiple relationships of the same type with the same source node. The third line indicates how to specify a node that has no relationships with other nodes. This form is not needed for nodes that do have relationships, since the specification of the relationship implicitly identifies the nodes as well.

Duplicate entries are ignored. Multiple edges between the same nodes must have different edge types. For example, the following specifies two edges between the same pair of nodes, one of type xx and one of type yy:

node1 xx node2
node1 xx node2
node1 yy node2

Edges connecting a node to itself (self-edges) are also allowed:

node1 xx node1

Every node and edge in Cytoscape has a name column. For a network defined in SIF format, node names should be unique, as identically named nodes will be treated as identical nodes. The name of each node will be the name in this file by default (unless another string is mapped to display on the node using styles). This is discussed in the section on Styles. The name of each edge will be formed from the name of the source and target nodes plus the interaction type: for example, sourceName (edgeType) targetName.

The tag <edgeType> can be any string. Whole words or concatenated words may be used to define types of relationships, e.g. geneFusion, cogInference, pullsDown, activates, degrades, inactivates, inhibits, phosphorylates, upRegulates, etc.

Some common interaction types used in the Systems Biology community are as follows:

  pp .................. protein – protein interaction
  pd .................. protein -> DNA
  (e.g. transcription factor binding upstream of a regulating gene.)

Some less common interaction types used are:

  pr .................. protein -> reaction
  rc .................. reaction -> compound
  cr .................. compound -> reaction
  gl .................. genetic lethal relationship
  pm .................. protein-metabolite interaction
  mp .................. metabolite-protein interaction

Delimiters

Whitespace (space or tab) is used to delimit the names in the simple interaction file format. However, in some cases spaces are desired in a node name or edge type. The standard is that, if the file contains any tab characters, then tabs are used to delimit the fields and spaces are considered part of the name. If the file contains no tabs, then any spaces are delimiters that separate names (and names cannot contain spaces).

If your network unexpectedly contains no edges and node names that look like edge names, it probably means your file contains a stray tab that's fooling the parser. On the other hand, if your network has nodes whose names are half of a full name, then you probably meant to use tabs to separate node names with spaces.

Networks in simple interactions format are often stored in files with a .sif extension, and Cytoscape recognizes this extension when browsing a directory for files of this type.

NNF

The NNF format is a very simple format that unlike SIF allows the optional assignment of single nested network per node. No other node columns can be specified. There are only 2 possible line formats:

• A node "node" contained in a "network:"

network node

• 2 nodes linked together contained in a network:

network node1 interaction node2

If a network name (first entry on a line) appeared previously as a node name (in columns 2 or 4), the network will be nested in the node with the same name. Also, if a name that has been previously defined as a network (by being listed in the first column), later appears as a node name (in columns 2 or 4), the previously defined network will be nested in the node with the same name. In summary: any time a name is used as both, a network name , and a node name, this implies that the network will be nested in the node of the same name. Additionally comments may be included on all lines. Comments start with a hash mark '#' and continue to the end of a line. Trailing comments (after data lines) and entirely blank lines anywhere are also permissible. Please note that if you load multiple NNF files in Cytoscape they will be treated like a single, long concatenated NNF file! If you need to embed spaces, tabs or backslashes in a name, you must escape it by preceding it with a backslash, so that, e.g. an embedded backslash becomes two backslashes, an embedded space a backslash followed by a space etc.

Examples

Example 1

Example_1      C
Example_1      network1
network1       A        pp        B
network1       B        pp        A
Example_1      C        pp        B

Example 2

Example_2      M1
Example_2      M2
M1             A
M2             B        pp        C
Example_2      A        pp        B
Example_2      M1       im        M2

Example 3

Example_3      M1       im        M2
Example_3      M3       im        M1
Example_3      M2       im        M3
Example_3      C        pp        M3
Example_3      M2       pp        C
M1             A
M2             A        pp        B
M3             B        pp        C

==== Example 4 ==== Example_4 M1*/ /* root M3*/ /* M1 A pp B M1 B pp A Example_4 C pp B M3 M2 M2 D M3 E pp F M3 D pp F M3 D pp E Example_4 D pp C Example_4 A pp M2*/ /* Example_4 B pp M3 Example_4 M2 pp B

Example 5

Example_5      M4
M4             D
M4             M3
M3             M2        pp        C
M2             M1        pp        B
M1             A
M4             C         pp        D

GML Format

In contrast to SIF, GML is a rich graph format language supported by many other network visualization packages. The GML file format specification is available at:

http://www.infosun.fmi.uni-passau.de/Graphlet/GML/

It is generally not necessary to modify the content of a GML file directly. Once a network is built in SIF format and then laid out, the layout is preserved by saving to and loading from GML. Properties specified in a GML file will result in a new style named Filename.style when that GML file is loaded.

XGMML Format

XGMML is the XML evolution of GML and is based on the GML definition. In addition to network data, XGMML contains node/edge/network column data. The XGMML file format specification is available at:

http://cgi5.cs.rpi.edu/research/groups/pb/punin/public_html/XGMML/

XGMML is now preferred to GML because it offers the flexibility associated with all XML document types. If you're unsure about which to use, choose XGMML.

There is a java system property "cytoscape.xgmml.repair.bare.ampersands" that can be set to "true" if you have experience trouble reading older files.

This should only be used when an XGMML file or session cannot be read due improperly encoded ampersands, as it slows down the reading process, but this is still preferable to attempting to fix such files using manual editing.

SBML (Systems Biology Markup Language) Format

The Systems Biology Markup Language (SBML) is an XML format to describe biochemical networks. SBML file format specification is available at:

http://sbml.org/documents/

BioPAX (Biological PAthways eXchange) Format

BioPAX is an OWL (Web Ontology Language) document designed to exchange biological pathways data. The complete set of documents for this format is available at:

http://www.biopax.org/

PSI-MI Format

The PSI-MI format is a data exchange format for protein-protein interactions. It is an XML format used to describe PPI and associated data. PSI-MI XML format specification is available at:

http://psidev.sourceforge.net/mi/xml/doc/user/

GraphML

GraphML is a comprehensive and easy-to-use file format for graphs. It is based on XML. The complete set of documents for this format is available at:

http://graphml.graphdrawing.org/

Delimited Text Table and Excel Workbook

Cytoscape has native support for Microsoft Excel files (.xls, .xlsx) and delimited text files. The tables in these files can have network data and edge columns. Users can specify columns containg source nodes, target nodes, interaction types, and edge columns during file import. Some of the other network analysis tools, such as igraph (http://cneurocvs.rmki.kfki.hu/igraph/), has feature to export graph as simple text files. Cytoscape can read these text files and build networks from them. For more detail, please read the Import Free-Format Tables section of the Creating Networks section.

Cytoscape.js JSON

From Cytoscape 3.1.0 on, Cytoscape supports Cytoscape.js JSON files. You can use this feature to export your network visualizations to web browsers. Cytoscape.js has two ways to represent network data, and currently both reader and writer support only the array style graph notation. For example, this network in Cytoscape:

will be exported to this JSON:

{
  "elements" : {
    "nodes" : [ {
      "data" : {
        "id" : "723",
        "selected" : false,
        "annotation_Taxon" : "Saccharomyces cerevisiae",
        "alias" : [ "RPL31A", "RPL34", "S000002233", "ribosomal protein L31A (L34A) (YL28)" ],
        "shared_name" : "YDL075W",
        "SUID" : 723,
        "degree_layout" : 1,
        "name" : "YDL075W"
      },
      "position" : {
        "x" : 693.0518315633137,
        "y" : -49.47506554921466
      },
      "selected" : false
    }, {
      "data" : {
        "id" : "726",
        "selected" : false,
        "annotation_Taxon" : "Saccharomyces cerevisiae",
        "alias" : [ "RP23", "RPL16B", "S000005013", "ribosomal protein L16B (L21B) (rp23) (YL15)" ],
        "shared_name" : "YNL069C",
        "SUID" : 726,
        "degree_layout" : 1,
        "name" : "YNL069C"
      },
      "position" : {
        "x" : 627.3147710164387,
        "y" : -205.99251969655353
      },
      "selected" : false
    }, {
      "data" : {
        "id" : "658",
        "selected" : false,
        "annotation_Taxon" : "Saccharomyces cerevisiae",
        "alias" : [ "RPL11B", "S000003317", "ribosomal protein L11B (L16B) (rp39B) (YL22)" ],
        "shared_name" : "YGR085C",
        "SUID" : 658,
        "degree_layout" : 2,
        "name" : "YGR085C"
      },
      "position" : {
        "x" : 804.3092778523762,
        "y" : -245.6235926946004
      },
      "selected" : false
    }, {
      "data" : {
        "id" : "660",
        "selected" : false,
        "annotation_Taxon" : "Saccharomyces cerevisiae",
        "alias" : [ "KAP108", "S000002803", "SXM1" ],
        "shared_name" : "YDR395W",
        "SUID" : 660,
        "degree_layout" : 8,
        "name" : "YDR395W"
      },
      "position" : {
        "x" : 730.8733342488606,
        "y" : -157.50702317555744
      },
      "selected" : false
    }, {
      "data" : {
        "id" : "579",
        "selected" : false,
        "annotation_Taxon" : "Saccharomyces cerevisiae",
        "alias" : [ "RPL11A", "S000006306", "ribosomal protein L11A (L16A) (rp39A) (YL22)" ],
        "shared_name" : "YPR102C",
        "SUID" : 579,
        "degree_layout" : 2,
        "name" : "YPR102C"
      },
      "position" : {
        "x" : 841.1395696004231,
        "y" : -130.77909119923908
      },
      "selected" : false
    }, {
      "data" : {
        "id" : "578",
        "selected" : false,
        "annotation_Taxon" : "Saccharomyces cerevisiae",
        "alias" : [ "GRC5", "QSR1", "RPL10", "S000004065", "ribosomal protein L10" ],
        "shared_name" : "YLR075W",
        "SUID" : 578,
        "degree_layout" : 2,
        "name" : "YLR075W"
      },
      "position" : {
        "x" : 910.3755162556965,
        "y" : -217.0562556584676
      },
      "selected" : false
    } ],
    "edges" : [ {
      "data" : {
        "id" : "659",
        "source" : "658",
        "target" : "578",
        "selected" : false,
        "interaction" : "pp",
        "shared_interaction" : "pp",
        "shared_name" : "YGR085C (pp) YLR075W",
        "SUID" : 659,
        "name" : "YGR085C (pp) YLR075W"
      },
      "selected" : false
    }, {
      "data" : {
        "id" : "661",
        "source" : "658",
        "target" : "660",
        "selected" : false,
        "interaction" : "pp",
        "shared_interaction" : "pp",
        "shared_name" : "YGR085C (pp) YDR395W",
        "SUID" : 661,
        "name" : "YGR085C (pp) YDR395W"
      },
      "selected" : false
    }, {
      "data" : {
        "id" : "724",
        "source" : "660",
        "target" : "723",
        "selected" : false,
        "interaction" : "pp",
        "shared_interaction" : "pp",
        "shared_name" : "YDR395W (pp) YDL075W",
        "SUID" : 724,
        "name" : "YDR395W (pp) YDL075W"
      },
      "selected" : false
    }, {
      "data" : {
        "id" : "733",
        "source" : "660",
        "target" : "579",
        "selected" : false,
        "interaction" : "pp",
        "shared_interaction" : "pp",
        "shared_name" : "YDR395W (pp) YPR102C",
        "SUID" : 733,
        "name" : "YDR395W (pp) YPR102C"
      },
      "selected" : false
    }, {
      "data" : {
        "id" : "727",
        "source" : "660",
        "target" : "726",
        "selected" : false,
        "interaction" : "pp",
        "shared_interaction" : "pp",
        "shared_name" : "YDR395W (pp) YNL069C",
        "SUID" : 727,
        "name" : "YDR395W (pp) YNL069C"
      },
      "selected" : false
    }, {
      "data" : {
        "id" : "580",
        "source" : "578",
        "target" : "579",
        "selected" : false,
        "interaction" : "pp",
        "shared_interaction" : "pp",
        "shared_name" : "YLR075W (pp) YPR102C",
        "SUID" : 580,
        "name" : "YLR075W (pp) YPR102C"
      },
      "selected" : false
    } ]
  }
}

And this is a sample visualization in Cytoscape.js:

Important Note

Export network and table to Cytoscape.js feature in Cytoscape creates a JSON file WITHOUT style. This means that you need to export the style in a separate JSON file if you apply style to your network. Please read Style section for more details.

Interaction networks are useful as stand-alone models. However, they are most powerful for answering scientific questions when integrated with additional information.

Cytoscape allows the user to add arbitrary node, edge and network data to Cytoscape through a data table. This could include, for example, expression data of a gene or confidence values in a protein-protein interaction. In the data table, information is linked to nodes, edges or networks by mapping the columns to one of their identifiers. Through the Table Panel the values can be further manipulated through the use of column functions and equations

A second type of data that can be associated with networks is ontology data: organized sets of controlled vocabulary terms. Because this type of data is mostly hierarchically organized, this requires a special importing facility, described in the second part of this section.

Data associated with the network elements can be visualized in a user-defined way by setting up a mapping from data in the columns to network properties (colors, shapes, and so on). The section on styles discusses this in greater detail.

Table data

Cytoscape supports several tabular formats. Of course the regular text and table formats: .tsv, .tab, .csv, .txt (comma, tab or any delimiter separated values file), .xls, .xlsx (Microsoft Excel file format). Note that for Excel file formats, only the first sheet of a workbook is currently imported. The legacy native Cytoscape formats: .attrs and .pvals (Cytoscape expression matrix) are also supported (for a more thorough discussion of these formats consult the 2.x manual). For most users the regular data table importing functionality will be sufficient; in case a format is unknown, renaming the file to a .txt extension and experimenting with delimiter and header settings in the import interface will work in most cases.

Importing data

Basic table file

The basic file format consists of a table containing at least one column with identifiers (unique names) for the nodes, edges or networks, and one or (any number) more columns with data you want to associate with these network elements.

Sample Data Table 1

To import such a file:

1. Select File → Import → Table → File...( or URL... if your source data file is accessible through the internet)

2. Select a data file in the file chooser panel (or enter the URL in the displayed box). This file can be in any of the accepted formats mentioned above.

3. In the Import Columns from Table panel, select the Importing Type. Cytoscape can import table columns to node, edge, and network table columns.

4. (Optional) Choose if you would like to import the file for all of the available networks or only selected networks using the check box in the expandable Network Options" panel (this panel is collapsed by default). Select networks from the list.

5. (Optional) If the table is not properly delimited in the preview panel, change the delimiter in the Text File Import Options panel (the default delimiter is Tab).
6. By default, the first column is designated as the primary key. Change the key column if necessary, see below for an example.
7. The data attribute column name can be changed by right clicking on the header. A dialog appears that enables specification of the datatype and column name.
8. Left clicking selects or deselects the column for importing.
9. Click the Import button.

The user interface of the "Import Column from Table" window is similar to that of the "Import Network from Table" window.

If the data only relates to a specific network select the 'Apply to selected networks only' box and select the specific network from the list (click 'Select Networks' to show this list)

Mapping data options

1. Select: File → Import → Table → Public Databases...

2. Select a data source. For ID mapping, select one of the Ensemble Genes data set. You need to choose the correct species for your network.

3. Select Attribute. If you want to import new ID sets matching current node IDs, select shared name.

4. Select Data Type. This should be the type of ID set selected in Attribute list. For example, if you select shared name for Attribute and your network uses Entrez Gene ID for its node ID, you need to select EntrezGene ID(s) for Data Type.

5. Select new ID sets from the list. Because there is a size limitation on the results returned by the!BioMart server, you can select only 3-5 attributes for each import.

6. Press Import.

Data in complete networks

Table rows in the browser can be sorted by a specific column by clicking on a column heading. A new column can be created using the Create New Column button (left 5th), and must be one of four types – integer, string, real number (floating point), or boolean. Attributes can be deleted using the Delete Attributes button (left 6th, trash can icon). NOTE: Deleting attributes removes them from Cytoscape, not just the attribute browser! To remove attributes from the browser without deleting them, simply unselect the attribute using the Select Column button (left 3rd).

The right-click menu on the Table Panel has several functions, such as exporting attribute information to spreadsheet applications. For example, use the right-click menu to select the data and copy for use in a spreadsheet application.

Ontologies

Another type of data that can be associated with network elements are ontologies. An ontology consists of an organized set of controlled vocabulary terms that annotate the objects. Most ontologies in science are organized in a hierarchical way. In biology for example, using the Gene Ontology, the Saccharomyces Cerevisiae CDC55 gene has a biological process described as “protein biosynthesis”, to which GO has assigned the number 6412 (a GO ID).

GO 8150 biological_process
 GO 7582 physiological processes
   GO 8152 metabolism
    GO 44238 primary metabolism
      GO 19538 protein metabolism
        GO 6412 protein biosynthesis

Graphical View of GO Term 6412: protein biosynthesis

Cytoscape can use this ontology DAG (Directed Acyclic Graph) to annotate objects in networks. The Ontology Server is a Cytoscape feature which allows you to load, navigate, and associate ontology terms to nodes and edges in a network. Cytoscape has an GUI for loading ontology and associating it with the network elements, enabling you to load both local and remote files.

Ontology and Association File Format

format-version: 1.2
date: 27:11:2006 17:12
saved-by: midori
auto-generated-by: OBO-Edit 1.002
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_goa "GOA and proteome slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_yeast "Yeast GO slim"
subsetdef: gosubset_prok "Prokaryotic GO subset"
default-namespace: gene_ontology
remark: cvs version: $Revision: 5.49 $

[Term]
id: GO:0000001
name: mitochondrion inheritance
namespace: biological_process
def: "The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton." [GOC:mcc, PMID:10873824, PMID:11389764]
synonym: "mitochondrial inheritance" EXACT []
is_a: GO:0048308 ! organelle inheritance
is_a: GO:0048311 ! mitochondrion distribution

[Term]
id: GO:0000002
name: mitochondrial genome maintenance
namespace: biological_process
def: "The maintenance of the structure and integrity of the mitochondrial genome." [GOC:ai]
is_a: GO:0007005 ! mitochondrion organization and biogenesis

The Gene Association (GA) file provides annotation only for the Gene Ontology. It is a species-specific association file for GO terms. Gene Association files will only work with Gene Ontologies and NOT others!

Sample Gene Association File (gene_association.sgd - association file for yeast):

SGD     S000003916      AAD10           GO:0006081      SGD_REF:S000042151|PMID:10572264        ISS             P       aryl-alcohol dehydrogenase (putative)        YJR155W gene    taxon:4932      20020902        SGD
SGD     S000005275      AAD14           GO:0008372      SGD_REF:S000069584      ND              C       aryl-alcohol dehydrogenase (putative)        YNL331C gene    taxon:4932      20010119        SGD

Important: All data sources in the preset list are remote URLs, meaning a network connection is required!

Step 1. Select an Annotation File