Interaction/Pathway/Network data with various
formats can be directly imported into VisANT, either copy/paste
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:
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.
- 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
- 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
- BioPAX: Biological PAthway eXchange, standard format for pathway information
supported by multiple pathway databases
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
Click here to try out.
| graphics ] Wnt signaling pathway. Click the graphics will load the KGML
of the pathway at
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
Please contact VisANT@zlab.bu.edu if
you find bugs.
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:
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.
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) :
The right show the result of VisANT visualization of this short
demo provided by BioPAX group, which involves two pathway steps:
the first step invloves two small molecules for both reactors
and products, which are grouped to indicate this situation. The
biochemical reaction is catalyzed (activation) by protein
glucokinase; while the 2nd step only involves one reactor and
product, and is catalyzed by protein phosphoglucose. All the
participants are grouped into one pathway group.
Load this file in VisANT
The is a real pathway from BioCyc, which enable us to examine
the VisANT visualization schema of BioPAX pathway. The detailed
annotation of the comparison is shown in the right figure, click
on the image to get the full-size one in a
this file in VisANT
original pathway in BioCyc
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.
if you find bugs.
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
textbox in VisANT's toolbox and click the
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
YAL054C YLR153C YLR049C YHL043W
YAL054C YLR049C YHL043W
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:
supports the weighted edge,
and a complete line of a weighted edge includes 5 columns:
Node_1 Node_2 direction Method_id Weight
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.