Gremlin Graphs are often too large for Cytoscape: this plugin allows you to write Gremlin queries and import the result as a network. Queries can be parameterized and stored for reuse.
Eventually, the plugin can be downloaded from the Cytoscape App Store - but not yet.
This app is based on the Cytoscape Neo4j Plugin, but ported to Gremlin by Jesper Steen Møller. Citation: Mining functional annotations across species; Sven Warris, Steven Dijkxhoorn, Teije van Sloten, T.L.H. van de Vossenberg, bioRxiv, 2018
Connects to Gremlin with a username/password using the Gremlin Server interface, either as WebSocket or HTTP(s).
There are three main methods of importing a graph:
- Import a Gremlin query into Cytoscape
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 (not yet implemented):
- 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
- Show all edges (relationships) between all nodes in the network or only between selected nodes.
- (Not yet implemented:) Get the shortest paths from the database between the selected nodes. When more than two nodes are selected, all combinations will be queried: Gremlin does not allow shortest path calculations between more than two nodes (a.k.a. 'via').