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Kucera M, Isserlin R, Arkhangorodsky A, et al. AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations. F1000Res. 2016;5:1717doi: 10.12688/f1000research.9090.1.
Kucera, M., Isserlin, R., Arkhangorodsky, A., & Bader, G. D. (2016). AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations. F1000Research, 51717. https://doi.org/10.12688/f1000research.9090.1
Kucera, Mike, et al. "AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations." F1000Research vol. 5 (2016): 1717. doi: https://doi.org/10.12688/f1000research.9090.1
Kucera M, Isserlin R, Arkhangorodsky A, Bader GD. AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations. F1000Res. 2016 Jul 15;5:1717. doi: 10.12688/f1000research.9090.1. eCollection 2016. PMID: 27830058; PMCID: PMC5082607.
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F1000Res. 2016 Jul 15;5:1717. doi: 10.12688/f1000research.9090.1. eCollection 2016.

AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations.

F1000Research

Mike Kucera, Ruth Isserlin, Arkady Arkhangorodsky, Gary D Bader

Affiliations

  1. The Donnelly Centre, University of Toronto, Toronto, Canada.

PMID: 27830058 PMCID: PMC5082607 DOI: 10.12688/f1000research.9090.1

Abstract

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.

Keywords: annotations; complexity reduction; cytoscape; enrichment map; modular networks; network analysis; network clustering; tag cloud

Conflict of interest statement

There are no competing interests.

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