MIMTool: A Tool for Drawing Molecular Interaction Maps

TL;DR

MIMTool is a specialized software for creating and editing molecular interaction maps in Kohn's MIM notation, featuring full interactivity, export options, and a semi-automatic drawing algorithm to enhance visualization and sharing of protein interaction networks.

Contribution

It introduces the first comprehensive tool for drawing MIM notation with advanced features like semi-automatic line construction and orthogonal edge drawing.

Findings

Supports full interactivity and object manipulation.

Enables export in MIMML, SBML, and line formats.

Facilitates faster and more accurate map creation.

Abstract

Background: To understand protein function, it is important to study protein- protein interaction networks. These networks can be represented in network diagrams called protein interaction maps that can lead to better understanding by visualization. We address the problem of drawing of protein interactions in Kohn's Molecular Interaction Map (MIM) notation. Even though there are some existing tools for graphical visualization of protein interactions in general, there is no tool that can draw protein interactions with MIM notation with full support. Results: MIMTool was developed for drawing protein interaction maps in Kohn's MIM notation. MIMTool was developed using the Qt toolkit libraries and introduces several unique features such as full interactivity, object dragging, ability to export files in MIMML, SBML and line drawing with automatic bending and crossover minimization, which are not available in other diagram editors. MIMTool also has a unique orthogonal edge drawing method that is both easy and more flexible than other orthogonal drawing methods present in other interaction drawing tools. Conclusions: MIMTool facilitates faster drawing, updating and exchanging of MIMs. Among its several features, it also includes a semi-automatic drawing algorithm that makes use of shortest path algorithm for constructing lines with small number of bends and crossings. MIMTool contributes a much needed software tool that was missing and will facilitate wider adoption of Kohn's MIM notation.