AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations

TLDR

Networks contain tightly connected clusters that reveal shared relationships, and while Cytoscape allows manual shape and label annotations, creating them one at a time is laborious. AutoAnnotate automates cluster identification and visual annotation in Cytoscape. AutoAnnotate automates cluster detection and annotation, offers customizable refinement options, supports collapsing annotated clusters into single nodes, and works with any network type. AutoAnnotate dramatically cuts annotation time and allows experimentation with different cluster identification and labeling strategies.

Abstract

<ns4:p>Networks often contain regions of tightly connected nodes, or clusters, that highlight their shared relationships. An effective way to create a visual summary of a network is to identify clusters and annotate them with an enclosing shape and a summarizing label. Cytoscape provides the ability to annotate a network with shapes and labels, however these annotations must be created manually one at a time, which can be a laborious process. AutoAnnotate is a Cytoscape 3 App that automates the process of identifying clusters and visually annotating them. It greatly reduces the time and effort required to fully annotate clusters in a network, and provides freedom to experiment with different strategies for identifying and labelling clusters. Many customization options are available that enable the user to refine the generated annotations as required. Annotated clusters may be collapsed into single nodes using the Cytoscape groups feature, which helps simplify a network by making its overall structure more visible. AutoAnnotate is applicable to any type of network, including enrichment maps, protein-protein interactions, pathways, or social networks.</ns4:p>