This file format is designed to allow user to add various database IDs, as well as alias and functional descriptions, to the corresponding proteins/genes of a network in a batch mode. Aliases and functional descriptions, will be shown in the tooltip when mouse-over the node; aliases and IDs are searchable in VisANT. In addition, it also allows each database IDs to be mapped to an URL so that corresponding web links can be directly loaded into browser from VisANT, under Available Links menu of the Nodes menu.
As usual, VisANT recognize the format of the file by its internal context. There are two section of the file:
All lines starts with the # are named as file header, as shown in the following example. The header must have the first line and last lines shown below, all others are optional.
#!ID Mapping AddNewNode=false
#following URL is for swiss-prot database linkout
The file must start with the #!ID Mapping line so that VisANT can load correct parser. There is one parameter AddNewNode for this line. If this parameter is true, then those nodes that do not match any nodes in the network using the the first column of the data section will be added to the network; otherwise, they will be ignored. This parameter is optional, the default value is false.
The 2nd line in the above example is comment line, you can have as many comment lines as you want.
The 3rd line tells VisANT to have an link-out menu for those nodes that has the swiss-prot IDs. It must follow the format:
ID-Name:Menu Name=web URL
Where ID-Name is the database id listed in the ID-List line, once matched, a menu will be created under Nodes/Available Links, using the name specified by Menu Name, as shown in the following figure:
As shown in the above figure, the actual URL will be the web URL+ID-Name. For an example, the corresponding URL for node YIL047C is
The last line of the file header in the above example list the total columns of the IDs. The first column must be #VisANT_ID, which represents the name or ids that can be uniquely identified by VisANT in the current network. This line must be Tab-delimited. Although the name of the IDs can be determined by the user, there are two key names that are reserved by VisANT: alias and description. See example below for more detail.
Note: The default names of the node used in VisANT can be be exported.
The data section is relatively simple. Each line must be Tab-delimited. The first column is the ID/Name of the node. Use space as the value of the column if the certain IDs are not available for some nodes.
alias: If multiple alias exist, use "," as the delimiter.
description: No Tab allowed in the description.
A more detailed example of ID-Mapping file is shown below, and can be downloaded here.
Note: Copy & Paste following text may not work, please download file directly from above link.
#!ID Mapping AddNewNode=true
#PDB_id:Protein Data Bank=http://www.rcsb.org/pdb/explore.do?structureId=
#VisANT_ID swiss-prot description PDB_id alias Gene3D
YIL047C P40528 Membrane; multi-pass membrane protein SYG1
YCL032W P25344 Involved in growth arrest during conjugation. May interact with the G protein alpha subunit 1Z1V STE50 G3DSA:126.96.36.199
YLR286C P29028 Soluble cell wall protein 2 CTS1
YDR264C P39010 Ankyrin repeat-containing protein AKR1,AKRR G3DSA:188.8.131.52
YLR362W P23561 Serine/threonine-protein kinase 1X9X STE11 G3DSA:184.108.40.206
Load ID-Mapping file
The file can be directly loaded loaded into VisANT using File menu. As usually, the context of the file can also directly copy paste to Add textbox and load it by clicking Add button, as shown below:
To add nodes to an existing metanode, simply select the nodes and drag then over the metanode, as shown in the following figure.
A confirmation window will be popped out, select "Y" will add selected nodes to the metanode, as shown above.
Note: if one of the selected nodes belongs to a metanode which is not selected, VisANT will ignore this functionality.
Note: to add a node already belongs to a metanode to another metanode, duplicate the node first, and then drag the duplicated instance to the target metanode.