ChiBE accepts data in BioPAX Level 2 format. Section 1
of Supplementary Material
summarizes how BioPAX models are interpreted by ChiBE. We call the entire set of biological information loaded from a BioPAX file a pathway model
. As defined by BioPAX, a pathway
is a set or series of interactions, often forming a network, which biologists have assembled for organizational, historic, biophysical or other reasons. We use pathways to determine the boundaries of a coherent view. Each loaded pathway is displayed in a separate canvas, organized with tabs (). A pathway model may be expanded by merging it with another BioPAX file or PC query.
ChiBE views are organized in canvasses, each displaying one or more BioPAX pathways.
A pathway view is composed of pathway objects and their interactions. Compound nodes are exclusively used to represent molecular complexes
and cellular compartments
(). Our notation is similar to that of PATIKA (Demir et al.
). ChiBE has context-sensitive pop-up menus associated with pathway objects, providing fast access to popular operations for the associated pathway object. All kinds of nodes and edges in a pathway view have distinct properties and UIs (User Interfaces). These properties can be changed by using inspectors
for each pathway object.
Viewing and editing pathways: the user has various mechanisms for navigating and editing the topology as well as the geometry of pathway views. These mechanisms range from standard zoom/scroll and highlight operations to modifying the UI associated with each pathway object and to automatic layout of the pathway view.
Pathway operations: any subset of available pathways in a model may be displayed as a separate view, and may be saved as an image or printed. Each subset may then be modified as desired. Also, new pathway views may be created by duplicating, cropping or capturing a neighborhood of a view.
Querying PC: PC is a convenient point of access to biological pathway information collected from public pathway databases, which one can browse or search. ChiBE provides a graphical user interface to search this knowledge base to find pathways that contain a specified molecule (using its UniProt or Entrez Gene ID), and present the results in a visual form. The resulting view may contain either the whole pathway or only the immediate neighborhood of the specified molecule in all the pathways in which it appears.
: SIF (simple interaction format) is a format introduced by Cytoscape (Yeung et al.
) for describing interactions in a biological network. ChiBE can reduce BioPAX pathways to SIF using a customizable set of rules to obtain a simpler view. Pathways can also be saved in SIF.
Visualizing high-throughput data
: multiple types of high-throughput data, such as gene expression or proteomics profiles, copy number variation and mutation data, can be loaded into ChiBE, and overlaid onto pathway views using color coding or displayed in tables that can be searched and filtered (Section 2
of Supplementary Material