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hiPathDB's Running Environment
Database Content Information
Data Representation
Search hiPathDB
Search reformatted pathway
Search unified super-pathway
Manual for pathway visualization
Main window
Exploring Network
Legend for pathway element


Manual for pathway visualization

The integrated pathway in hiPathDB is visualized by the embedded module of Modular Network Generation and Visualization Platform with Knowledge Integration Environment(MONGKIE) which is an integrated network visualization platform to explore and analyze interconnected biological data with integrated environment. MONGKIE is optimized for exploring protein interaction network or biological pathways and also applicable to any bio-medical data with network structure, such as gene-disease association network. The visualization and user interface are implemented by the Prefuse visualization toolkit(http://prefuse.org) and Gephi (http://gephi.org). It is being developed and released as open source software with the support of Korean Bioinformation Center(KOBIC) and available at http://www.monkie.org.


Main window   TOP

This is the main window for pathway visualization.


Exploring Network   TOP

To support explorative study of pathway network, We provides rich methods to explore the network such as selecting, dragging, zooming, highlighting, searching and panning the display. We also provides the overview of the whole network and you can also expand and delete the network dynamically depending on the context of the network.


Legend for pathway element   TOP

Pathway network automatically generated by the visualization environment of hiPathDB. The role of each relation participant is denoted by the edge style and arrow shape.

Reformatted pathway network is shown as below:

Unified super-pathway network is shown as below:

Various elements of the pathway network are as follows:

Pathway visualization displayed in hiPathDB contain several types of nodes and edges. Both nodes and edges differ in their shape and color. Circular nodes represent entities (genes, proteins, compounds, etc.) and rectangular nodes represent enzymes and biological processes. The color of physical entity nodes shows the type of the physical entity, and the same is true for interaction nodes. The Name of each entity in the graph is displayed inside the representing node by default. The features (states, family, dimer) associated with each entity are represented by feature variables, which are labeled in the small circular icon adorning the shape of the corresponding node. Edges linking a relation participant with the according interaction node also differ in their style, arrow shape, and color. The edge style and arrow shape indicate the role of the according entity in the relation. The origin of relations is indicated by the edge color: multiple edges with the same style and arrow shape but with different colors may exist between a physical entity and a relation.

A detailed graph legend is available in the visualization environment and is shown by clicking on the graph legend link from the menu panel of the visualization environment.