https://github.com/corwur/cytoscapeneo4j

Cytoscape plugin for neo4j
https://github.com/corwur/cytoscapeneo4j

cypher-query cytoscape java neo4j plugin

Last synced: 5 days ago
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Cytoscape plugin for neo4j

• Host: GitHub
• URL: https://github.com/corwur/cytoscapeneo4j
• Owner: corwur
• License: mit
• Created: 2017-10-21T11:42:26.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2022-05-20T20:51:34.000Z (over 2 years ago)
• Last Synced: 2024-08-01T12:29:45.494Z (3 months ago)
• Topics: cypher-query, cytoscape, java, neo4j, plugin
• Language: Java
• Size: 282 KB
• Stars: 21
• Watchers: 5
• Forks: 7
• Open Issues: 7
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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• awesome-starred - corwur/cytoscapeneo4j - Cytoscape plugin for neo4j (java)

README

        
# 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.  

The plugin can be downloaded from the [Cytoscape App Store](http://apps.cytoscape.org/apps/cytoscapeneo4jplugin)

Citation: [Mining functional annotations across species; Sven Warris, Steven Dijkxhoorn, Teije van Sloten, T.L.H. van de Vossenberg, bioRxiv, 2018](https://www.biorxiv.org/content/early/2018/07/16/369785)

## 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/template.md)) 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').