iRefScape plugin menu

From irefindex
Revision as of 16:57, 4 July 2011 by PaulBoddie (talk | contribs) (Put the user variables section into the "Search tools" menu. Moved the batch file searching section. Various formatting and stylistic edits, plus link fixes.)

Search tools

Retrieve interactions for the selected nodes

To load all protein-protein interactions and complexes involving one or more selected nodes. This action is the same as performing a iteration=1 search using iRefScape for the selected nodes.

Expand one level

To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes.

Load interactions between neighbours

To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape, the network returned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is the same as performing an iteration=0 search using iRefScape for all the nodes. This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.

Clear load history (Reload everything next time)

This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keeps track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice,the network will not be re-loaded unless the user has requested that results be shown in a new view or they have selected this menu option. If the user wishes to reload the network then this option has to be used. When using other methods of expanding the network like “Expand one level” iRefScape handles the cache clearing automatically.

Reset node degree

This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters).

Load user variables


This section is being updated.

User variables can be attached to nodes and be browsed using the attribute browser. This file can not be used as a searchable index (can not be used as a search type). Please see section iRefScape user searchable index for details on searchable indices.

There are three ways to load own variables for the user.

  1. Use the Cytoscape attribute loading feature (Cytoscape manual)
  2. Use a use attribute file with iRefScape (described in this section)
  3. Include the attribute with the batch search file. (Described in the section Attribute batch file.)

The iRefScape user attribute loader is provided as a complementing feature to the Cytoscape node attribute loading (Cytoscape manual). For most of the attribute loading operations the Cytoscape node attribute loader is sufficient and easier to use. However, when the iRefScape node attribute file is used, this can be used by using the menu entry iRefScape-> Search tools > Load user variables. In addition the file will be available for subsequent operations.

iRefScape user variable file format

The first line of the file provides instructions and this line is compulsory.

#i.rog	New_attribute

The first line always starts with a hash ("#") and immediately followed by the iReFscape variable name. This iRefScape variable name is used to locate the nodes via the new attribute will be attached. Then a tab is used as a column separator, followed by the name of the user attribute name.This user attribute name should be unique( not already used). In the above example the user attribute to use is the i.rog and the user attribute name is "New_attribute".

From the second line onwards, the attributes with the mapping attribute are provided.

4399398	TENC1|UniProtKB:Q63HR2|

The first column provides the iRefScape attribute to use and the second column provides the user attribute. Multiple attributes should be separated with a pipe ("|"). The example line shown would locate the node with i.rog=4399398 and attach the "TENC1|UniProtKB:Q63HR2|" value to it with the attribute name "New_attribute"

  • Each column is separated by a TAB.
  • Each line ends with a new line character ("\n")
  • The file should be constructed using a plain text editor (e.g. Kate, notepad) and word processing software like Microsoft word should not be used to construct this file.
  • The file extension is ".txt"
  • Sample file "ONE__EXT__ROG_#Name_5_.iruv" can be found in the iRefScape installation directory (iRefIndex directory)
  • The file name should have the format _rog_USER_VARIABLE_NAME.iruv (The text in bold is supplied by the user. e.g., _rog_myAttribute.iruv ).
Sample file
#i.rog	New_name
4399398	TENC1|UniProtKB:Q63HR2|
452957	GFI1B|UniProtKB:Q5VTD9|
561552	TENC1|UniProtKB:Q63HR2-4|
534065	GFI1B_MOUSE|UniProtKB:O70237|

View tools

Toggle selected multi-edges

iRefScape creates multiple edges between nodes to represent multiple evidences. If an interaction between two proteins has evidence from both MINT and IntAct, there will be 2 edges; one for MINT and one for IntAct. Although this provides more information for the user, sometime the user may prefer to collapse these edges to a single edge to facilitate viewing. When this action is performed on a network, all but a randomly selected edge between each node is hidden. The edges which are hidden has the i.flag=1 and the one remaining has i.flag=0. Therefore, while this process is random by default, the user can control which edges to keep and which to hide by editing the i.flag edge attribute before using the toggle multi-edge option.

Zoom to selected

This action brings the selected node(s) to the centre of the screen and makes the nodes as large as possible given that all selected nodes are visible. This action can also be performed manually using Cytoscape's zoom tool.

Select last iRefScape selection

This action shows the last selection performed by an iRefScape operation. This features does not record user selections or selections made by using Cytoscape tools (e.g filters).

Select nodes with different taxid than query node

Some interactions may involve proteins from multiple species. An interaction may truly occur between proteins from two species (e.g. an interaction between a Human protein and a virus protein). In other cases, this may be an artefact of how data was entered by the source database.

Select between nodes

This option highlights (selects) nodes interacting with at least two nodes that have been pre-selected by the user. The node attribute i.alive_degree will be recalculated to reflect the degree of each node with respect to this pre-selection.

Show spoke-represented complexes

Some complexes are represented as a set of binary interactions by some sources. This action attempts to highlight such complexes as a single unit by attaching them all to a single pseudonode.


Hide selected nodes

This action hides the selected nodes. This operation is performed in a independent thread and more efficient than hiding using Cytoscape's 'hide node' utility for large networks.

Hide nodes (except pseudonodes)

This action hides all select nodes which represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.

Hide nodes not selected

Hides all nodes which are not currently selected

Hide nodes not selected (except pseudonodes)

Hides all nodes which are not currently selected and that represent proteins. This will not hide pseudonodes representing a complex, a collapsed area or a collapsed hub.

Un-hide all

Un-hides all nodes which are hidden by the user.

Safe mode

This option is only available when using Java 1.5 and will not appear for Java 1.6 or newer. Selecting this will un-dock the iRefScape window and handles errors and exceptions thrown due to bugs in Java 1.5. When this mode is activated not all graphic features will be available.

iRefScape search with batch file

When there are many search queries, it is convenient to construct a batch file and load this to iRefScape. There are 3 type of batch files;

  1. Simple batch file (recommended for users just wanting to search for a list of things)
  2. Attribute batch file (Attach additional attributes)
  3. User index batch file (Explained in section iRefScape user searchable index.)

Simple batch file

Example file content:
  • The first line starts with a hash ("#") and this line is compulsory.
  • Immediately after the hash (no space in between) the iRefScape attribute name should be provided. Please see below for accepted list of identifier with the corresponding label.
Label to use in the batch file Description
rog iROGID, the integer reference redundant object group identifier (details of mapper files to locate the iROGID can be found in the Protein identifier mapping document
geneID NCBI Gene ID, this is always an integer
UniProt_Ac UniProt/KB accession
RefSeq_Ac RefSeq Accession
UniProt_ID UniProt identifier
geneSymbol NCBI Gene symbol
PMID PubMed identifier
src_intxn_id Interaction identifiers used by source databases
omim OMIM identifier (OMIM home page)
digid diseases group identifier (DiG home page)

Attribute batch file

Users can attach additional attributes when performing batch queries (instead of loading the attributes after the search).

The example shown below attaches an additional index "NOONAN_SYNDROME_TYPE" to the matching nodes.

Example indexable batch file
  1. The first line is compulsory and contains controlling information. the fist value after the hash ('#') is the iRefindex attribute type to be used. (Please see Simple batch file for attribute types.) The second value is the NCBI taxonomy identifier (NCBI taxonomy browser). The third value is the name of the user attribute. All three values are seperated by a colon ":". It is possible to include multiple attributes in the same file. To do this first the attribute name should be defined in the first line and additional columns should be used to include the values. (Please not that if the batch file is also used as the template to construct user searchable index, only one user attribute is allowed in the file)

iRefScape user searchable index

Users can construct their own indices to be used as search type. The easiest way to include a index is to use the advanced batch file mode. This process will;

  1. Find the iROGID for the user variable
  2. Construct searchable index.

The example shown below constructs an index, where the user can perfume search using the Noonan syndrom type.

Example indexable batch file
  1. The first line is compulsory and contains controlling information. The first value after the hash ('#') is the iRefIndex attribute type to be used. (Please see Simple batch file for attribute types.) The second value is the NCBI taxonomy identifier (NCBI taxonomy browser). The third value is the name of the user attribute. All three values are seperated by a colon ":".

The data rows should always be two columns, where the columns are separated by a tab. The first value in a data row is the search string (what should be used to search iRefIndex). The values in the first column will appear in the search box at the end of the operation. The second column contains the user attribute.

  • the file name of the batch file should contain the prefix "INDEX_THIS_" to be considered for the indexing.
Example file name
  • The attribute does not appear as a separate attribute, but should instead look in the i.query field.

All iRefIndex Pages

Follow this link for a listing of all iRefIndex related pages (archived and current).