There are 4 different ways of creating networks in Cytoscape:

  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 chapter. 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 fils you can select File → Import → Network → File... or click on Cy3_icon_net_file_import.png 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.

choose_network_collection.png

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... or click on Cy3_icon_net_url_import.png on the tool bar. 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.

Cy3_network_import_url_dialog.png

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 Server... . This is further described in the Preferences chapter.

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.

Cy3_network_table_import.png

Supported Files

The "Import Network from Table" function supports delimited text files and single-sheet Microsoft Excel Workbooks. The following is a sample table file:

source  target  interaction  boolean attribute  string attribute        floating point attribute
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 attributes. This means that a network file is considered a combination of network data and edge attributes. A table may contain columns that aren't meant to be edge attributes. 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):

sampleTableData1.png

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

The network import function cannot import node attributes - only edge attributes. To import node attributes from this table, please see the Attributes 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://www.cytoscape.org/cgi-bin/moin.cgi/Data_Sets/

Basic Operations

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

  1. Select File → Import → Network → File... or click on Cy3_icon_net_file_import.png 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. Setting the Interaction Type as Default Interaction will result in all interactions being given the value pp; this value can be modified in Advanced Options (below).
  4. (Optional) Define edge attribute columns, if applicable. Network table files can have edge attribute columns in addition to network data.
    • Enable/Disable Attribute Column - By left-clicking on a column header in the preview table, you can enable/disable edge attributes. If the header is checked and entries are blue, the column will be imported as an edge attribute. For example, the table below shows that columns 1 through 3 will be used as network data, column 4 will not be imported, and columns 5 and 6 will be imported as edge attributes.

      • Cy3_network_table_sample.png

    • Change Attribute Name and Data Types - If you right-click on a column header in the preview table, you can modify the attribute name and data type. For more detail, see "Modify Attribute Name/Type" below.

  5. Click the Import 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

Cy3_network_import_advanced.png

You can select several options by checking the Show Text File Import Options checkbox.

Modify Attribute Name/Type

Cy3_network_table_attr_dialog1.png

Attribute names and data types can be modified here.

Cytoscape has a basic data type detection function that automatically suggests the attribute data type of a column 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...

Web Service Client Manager

Cytoscape has a feature called Web Service Client Manager. This is a framework to manage various kinds of web service clients in Cytoscape. By using web service clients, users can access remote data sources easily.

What is a Web Service?

A web service is a standardized, platform-independent mechanism for machines to interact over the network. These days, many major biological databases publish their data with web service API:

This enables developers to write a program to access these services. Cytoscape core developer team have developed several web service clients using this framework. Cytoscape supports many web services including:

In the following sections, users learn how to import network from external databases.

Getting Started

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

file_import.png

Example #1: Retrieving Protein-Protein Interaction Networks from IntAct

intact_import.png

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

node_context2.png

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.

Example #2: Retrieving Pathways and Networks from Pathway Commons

Then, follow the three-step process outlined below:

3_steps.png

Downloading Pathways and Interaction Networks

In Step 3, you can simply double-click on a pathway of interest, or click on the Interaction Networks tab. The Interaction Networks tab enables you to filter interactions by data source and/or interaction type. For example, you can choose to restrict your network to direct physical interactions from intAct and MINT only:

intxn_filter.png

Pathway Commons Options

You can configure access options from the Options tab. There are two retrieval options:

By default, the simplified binary model is selected.

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.

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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