Import Network into VisANT

Interaction/Pathway/Network data with various formats can be directly imported into VisANT, either copy/paste (CTRL-C/CTRL-V) the data into Your Data Text Area in the ToolBox Panel in VisANT, or directly load them from a local file (for local application and web start only). Different formats are recognized by VisANT automatically, here is the list of supported format:

• Edge List: Default text format for non-XML-based data

• VisML :Default XML format, containing all the network information. Network stored as VisML format can be safely replayed as it was stored.

• Expression : Expression matrix file, the first line must start with #!Expression. Optional parameter addNewNode to determine whether to abandon the nodes that are not in the current network, e.g. addNewNode=false.

• Macro/Batch :The file format to store a list of commands for VisANT to carry out. The first line must start with #!batch commands

• ID-Mapping :This file format is designed to allow user to add various database IDs, as well as alias and functional descriptions, to the nodes in a network, must start with #!ID Mapping

• KGML: The KEGG Markup Language (KGML) is an exchange format of the KEGG graph objects, especially the KEGG pathway maps that are manually drawn and updated.

• GML : Graph Markup Language, a common graph file format supported by several network software

• PSI-MI : XML standard format for molecular interactions supported by molecular interaction databases

• BioPAX: Biological PAthway eXchange, standard format for pathway information supported by multiple pathway databases

To ensure the performance, except for VisML, the Fine Arts option under Option Menu will be turned off when the total size of nodes and edges > 12000. You can, of course, turn this option back on if necessary.

KGML

  KGML Homepage    

One nice feature of KGML is that it keeps the visual properties. However, the name of the nodes will need to be resolved using the MetaGraph-->Resolve All Nodes Name menu (NOT  the Nodes-->Resolve Selected Nodes Name menu because there are many nodes hidden in collapsed metanode) when data integration is required, such as the case where expression data need to be mapped to the nodes. Here is a macro file illustrates the steps to use KEGG pathway for expression enrichment analysis. Click here to try out.

hsa04310 [ xml | graphics ] Wnt signaling pathway. Click the graphics will load the KGML of the pathway at http://www.genome.jp/kegg/xml/hsa/hsa04310.xml

Please contact VisANT@zlab.bu.edu if you find bugs.

Tip: a KEGG pathway can be easily loaded into VisANT if the searched term starts with the "map", such "map04110" where 04110 is the pathway id (cell cycle pathway), the pathway for the current species will be loaded into VisANT. VisANT supports many different ways to load KEGG pathway, which are detailed in our publication VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.

GML

 GML Homepage    

VisANT has primary support of GML. Here is a GML example file, it can be loaded into VisANT directly, here is the network looks like:

Here is a macro file that will loop through 5 GML files for animation purpose,  Click here to try out.

Note: per user request, VisANT renders the shape circle in GML with VBALL shape, as shown above.

Please contact VisANT@zlab.bu.edu if you find bugs, or you have suggestions/comments.

PSI-MI

 PSI-MI 1.0 Homepage   PSI-MI 2.5 Homepage 

The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. The PSI-MI format is a data exchange format for protein-protein interactions.

VisANT supports importing of PSI-MI data file. Here are two sample files in the format PSI-MI 1.0:

psi_sample.xml   Load this file in VisANT    |   Ito_expand.xml    Load this file in VisANT

Here is a sample file of PSI-MI 2.5:

BIOGRID-GENE-113010-2.0.32.psi25.xml   Load this file in VisANT

Please contact VisANT@zlab.bu.edu if you find bugs.

Note: if the interaction involves two interactors that belong to the different organisms, it will be ignored in the current implementation.

BioPAX

BioPAX Homepage

BioPAX is a collaborative effort to create a data exchange format for biological pathway data. VisANT supports importing data file of BioPAX format, both Level 1 and Level 2.

Level 1:BioPAX Level 1 represents metabolic pathway information. Here are two sample files (so far our parser only supports BioPAX file with only one pathway, we are working on to enhance it) :

We apply the graphic annotation similar to KEGG pathway. For a given bio-chemical reaction A ---> B, if a catalysis C is presented, then the reaction will look similar to A ---> C ---> B. Same rule has been applied to modulation.

The pathway's layout is based on their pathways steps using a top-down manner. If there are more than one reactors/products in one Biochemical reaction, they are grouped; if one of the reactors is also one of the products in the previous pathway step, it is duplicated and grouped separately. For example, for two given reactions: R1+R2 ---> P1+P2, and P1+R3 ---> P3, then R1 will be grouped with R2, and P1 will be grouped with P2, P1 is then duplicated and grouped with R3. Each modulation and catalysis is counted separately.

Level 2:BioPAX Level 2 expands BioPAX to cover molecular interactions which are compatible with PSI-MI format supported by VisANT. In addition, the featured invention of Meta-Network in VisANT makes it nature for us to support unique features of BioPAX Level 2, including Pathway Hierarchy and Black-Box pathway. In fact, VisANT is so far the only network software that is capable to support visualization of network hierarchy. However, because Level 2 has not been finalized yet, sample files are not available. We are contacting BioPAX group in an effort to get earlier release of sample files.

Please contact VisANT@zlab.bu.edu if you find bugs.

Edge List

See User Manual for more information

The simplest format for network in VisANT, can also be used to create new nodes (one node per line, such as ste4 below) and edges. Users can simply enter or copy/paste text in the Add textbox in VisANT's toolbox and click the Add button to add a list of edges/nodes. This simple format also supports creation of Meta-Node, and a sample is listed below:
YAL054C YLR153C 0 M0020
YAL054C YLR153C 0 M0031
YAL054C YLR049C 0 M0034
YAL054C YHL043W 0 M0046
YAL054C YNL189W 0 M0034
YAL054C YMR280C -1 M004
YAL054C YBR117C 0 M0046
YAL054C YDR216W -1 M004
YAL054C YBR046C 0 M0036
YAL054C YBR049C -1 M004
YAL054C YER061C 0 M0036
YAL054C YDR207C -1 M004
YAL054C YHR041C 0 M0034
YAL054C YKL112W -1 M004

ste4
#complex M4453
YAL054C YLR153C YLR049C YHL043W
#group xx2323
YAL054C YLR049C YHL043W
#group
YBR049C
YER061C
YHR041C
#group myGroup
YER061C
YDR207C
YHR041C

Copy/paste above sample data to the Add textbox and click the Add button, then do a circle layout with the Layout-->Circle* menu and then click the Fit to Page button, a metanetwork will be shown similar to the one shown below:

VisANT supports the weighted edge, and a complete line of a weighted edge includes 5 columns:

Node_1 Node_2 direction Method_id Weight

Here is an example:

YAL054C YDR207C 0 M0037 0.263304413189123

Above line represents a weighted binary interaction between node 1 (first column) and node 2 (second column). The integer in the third column represents the direction of the interaction, i.e., 0 signifies an undirected link, 1 indicates that the link has a direction from node 1 to node 2 (we support KEGG notation for edge type, try out number 0-9 to see different type of edge), and negative sign "-" indicates the direction is from node 2 to node 1. The forth column represents the method id as can be viewed from method table in VisANT. The user can also add their own method in VisANT. The last column indicates the weight of this edge.

If you forgot the format, simply export a network in the format of edge-list using the File-->Export as Tab-Delimited File-->All menu.