Diff for "Cytoscape_3/UserManual/Attributes"

In Cytoscape 3.0 data columns with primitive data types (string, boolean, floating point, and integer) can be selected as the key column using the dropdown list provided. Complex data attributes such as lists are not supported as keys.

Text file import options

When the text file import options box is checked, several additional parameters can be selected to tune the way the data file will be imported. The first line can be used to specify column header names. Another data delimiter (default is tab) can be chosen, and the comment prefix (signifying lines to be ignored) can be defined.

Import from Public Databases

You can import various kinds of ID sets from the BioMart (http://www.biomart.org/index.html) public database. The BioMart web service client is integrated into Cytoscape.

When importing a network from a table, columns other than the node identifier can be imported as data also. For more detail on these options, please see the "Import Free-Format Table Files" section of the user manual in the Creating Networks chapter.

Table Panel

When Cytoscape is started, the Table Panel appears in the bottom CytoPanel. This panel can be hidden and restored using the View → Show/Hide Table Panel menu option. Like other CytoPanels, the panel can be undocked by pressing the little icon in the panel’s top right corner.

To swap between displaying node, edge, and network tables use the tabs on the bottom of the panel labeled "Node Table", "Edge Table", and "Network Table".

In Cytoscape 3.0 there are two display modes for the table: show selected nodes/edges only and show all rows. This configuration can be set using button (the left most) in the figure. The Table Panel displays data belonging to the currently selected network.

Using the three buttons (left 2nd to 4th) in the figure, it is possible to make some or all columns visible and hide others or all of them. Also, a new column can be created by pressing button the (left 5th) or mutable columns can be deleted by button (left 6th). Button f(x) is for writing equations to manipulate the data which is further explained in the section attribute functions and equations.

Most data values can be edited by double-clicking on their table cell (only the SUID cannot be edited). Newline characters can be inserted into String attributes either by pressing Enter or by typing "\n". Once finished editing, click outside of the editing cell in the Table Panel or press Shift-Enter to save your edits. Pressing Esc while editing will undo any changes.

The standard file formats used in Cytoscape Ontology Server are OBO and Gene Association. The GO website details these file formats:

• Ontologies and Definitions: http://www.geneontology.org/GO.downloads.shtml#ont

• Current Associtations: http://www.geneontology.org/GO.current.annotations.shtml

OBO File

An OBO file is the ontology DAG itself. This file defines the relationships between ontology terms. Cytoscape can load all ontology files written in OBO format. The full listing of ontology files are available from the Open Biomedical Ontologies (OBO) website:

• OBO Ontology Browser: http://obo.sourceforge.net/browse.html

Sample OBO File - gene_ontology.obo: http://www.geneontology.org/ontology/gene_ontology_edit.obo

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

Default List of Ontologies

Cytoscape provides a list of ontologies available in OBO format. If an Internet connection is available, Cytoscape will import ontology and associatation files directly from the remote source. The table below lists the included ontologies.

Although Cytoscape can import all kinds of ontologies in OBO format, association files are associated with specific ontologies. Therefore, you need to provide the correct ontology-specific association file to annotate nodes/edges/networks in Cytoscape. For example, while you can annotate human network data using the GO Full ontology with human Gene Association files, you cannot use a combination of the human Disease Ontology file and human Gene Association files, because the Gene Association file is only compatible with GO.

Visualize and Browse Ontology DAG (for Advanced Users)

Relationships between ontology terms are usually represented as Directed Acyclic Graphs (DAGs). This is a special case of a network (or graph), where nodes are ontology terms and edges are relationships between terms. Ontology data is stored in the same data structure as normal networks. This enables users and App writers to visualize, browse and manipulate ontology DAGs just like other networks. The following is an example of visualization of an ontology DAG (Generic GO Slim):

Every ontology term and relationship can have attributes. In the OBO files, ontology terms have optional fields such as definition, synonyms, comments, or cross-references. These fields will be imported as node attributes. To browse those attributes, please use the attribute browser (see the example below):

• Note 1: Some ontologies have a lot of terms. For example, the full Gene Ontology contains more than 20,000 terms. If you need to save memory, you can remove this ontology DAG from Network Panel (right-click on the ontology name at the left-hand side of the screen and select Destroy Network).
• Note 2: All ontology DAGs will be saved in the session file. To minimize the session file size, you can delete the Ontology DAG before saving session.

Gene Association File

If you have a network file and an association file, they should have a common key to map attributes onto network data. If those two do not have a common key, you need to do an extra step to add a shared key by mapping the current key to a common key as described above (Node Name Mapping).

Import Gene Ontology and Gene Association Files

For convenience, Cytoscape has a list of URLs for commonly used ontology data and a complete set of Gene Association files. To import Gene Ontology and Gene Association files for the loaded networks, please follow these steps:

• 

  Select File → Import → Ontology and Annotation... to open the "Import Ontology and Annotation" window. From the Annotation dropdown list, select a gene association file for your network. For example, if you want to annotate the yeast network, select "Gene Association file for Saccharomyces cerevisiae".

Step 2. Select an Ontology File

• Select an Ontology data (OBO file) from the Ontology dropdown list. If the file is not loaded yet, it will be shown in red. The first three files are Gene Ontology files. You can load other ontologies, but you need your own annotation file to annotate networks.

Step 3. Import the files

• Once you click the Import button, Cytoscape will start loading OBO and Gene Association files from the remote sources. If you choose GO Full it may take a while since it is a large data file.