Abstract
PathLinker is a graph-theoretic algorithm originally developed to reconstruct the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network from the receptors to transcription factors (TFs) in a pathway. Since December 2015, PathLinker has been available as an app for Cytoscape. This paper describes how we automated the app to use the CyRest infrastructure and how users can incorporate PathLinker into their software pipelines.
Highlights
PathLinker is an algorithm that automates the reconstruction of any human signaling pathway by connecting the receptors and transcription factors (TFs) in that pathway through a physical and regulatory interaction network[1]
The Swagger annotation allows the PathLinker application programming interface (API) functions to be accessed via the Swagger user interface along with other API functions exposed by CyREST
Summary The subnetwork returned by the PathLinker API is another network in the current Cytoscape session
Summary
PathLinker is an algorithm that automates the reconstruction of any human signaling pathway by connecting the receptors and transcription factors (TFs) in that pathway through a physical and regulatory interaction network[1]. In a comprehensive quantitative evaluation on NetPath pathways, PathLinker achieved higher reconstruction accuracy than several other state-of-the-art algorithms. PathLinker can be used to connect any set of sources to any set of targets in a given network. The PathLinker app for Cytoscape is an implementation of this algorithm. The PathLinker app[2] was first released in the middle of December 2015. While it is possible to use the PathLinker app in conjunction with other Cytoscape apps, it can be cumbersome to create such workflows using the Cytoscape user interface. It is challenging to reproduce the results of these workflows
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