Cytoscape Neo4j Plugin

Categories: database, graph database, Neo4j
# Cytoscape plugin for Neo4j Neo4j Graphs are often too large for Cytoscape: this plugin allows you to write Cypher queries and import the result as a network. Queries can be parameterized and stored for reuse. Citation: [ Mining functional annotations across species; Sven Warris, Steven Dijkxhoorn, Teije van Sloten, T.L.H. van de Vossenberg, bioRxiv, 2018] ## Features Connects to Neo4j with a username/password using the Bolt interface. ### Importing graphs There are three main methods of importing a graph: - Import all nodes and edges from Neo4j into Cytoscape - Import a cypher query into Cystoscape - Import a stored query ([template](doc/ into Cytoscape ### Exporting networks The plugin allows you to export any Cytoscape Network to Neo4j. This can be an updated version of an imported graph or a network from a different source. Nodes / relationships removed from a graph in Cytoscape will also result in these elements being removed from the Neo4j database after the export. ### Expanding nodes The plugin allows you to expand a single node, selected nodes or all nodes in the network at once. This way you can browse through your graph. Main menu: - Expand all (selected) nodes in the network through all edges (bidirectional) - Expand all (selected) nodes, incoming edges only - Expand all (selected) nodes, outgoing edges only Context menu: - Expand single node, bidirectional, incoming or outgoing edges - Expand single node, bidirectional, incoming or outgoing edges, based on the _available edges connected to this node_ - Expand single node, bidirectional, incoming or outgoing edges, based on the _available nodes connected to this node_ ### Other features - Show all edges (relationships) between all nodes in the network or only between selected nodes. - Get the shortest paths from the database between the selected nodes. When more than two nodes are selected, all combinations will be queried: Neo4j does not allow shortest path calculations between more than two nodes (a.k.a. 'via').


Works with Cytoscape 3.9


Works with Cytoscape 3.9

Release Notes

Now supports multiple databases in Neo4j. You can provide the name of the database in the connection dialog.


Works with Cytoscape 3.8


Works with Cytoscape 3.6


Works with Cytoscape 3.5


Works with Cytoscape 3.5


Version 0.5.1

Released 1 Feb 2022

Works with Cytoscape 3.9

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