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Query and visualize Ricgraph

To query and visualize Ricgraph nodes and edges, there are several possibilities:

Return to main README.md file.

Start Neo4j Desktop

  1. Click on the downloaded AppImage. It will be called something like neo4j-desktop-X.Y.Z-x86_64.AppImage, where X.Y.Z is a version number.
  2. At the top right there is a text "No active DBMS".
  3. Move your mouse to the text "Graph DBMS". When you hoover it, a button will appear with the text "Start". Click it.
  4. Wait until the Neo4j graph database engine has started. It may ask for a password that has been changed. Enter the password you have used while creating your database. Click "Save".
  5. Now, next to the text "Graph DBMS" a green icon appears with the text "ACTIVE". Your graph database engine is active and ready for use.

How to use Bloom

Bloom is Neo4j Desktop's graph visualization tool. It is included with Neo4j Desktop. According to Neo4j it is: "A beautiful and expressive data visualization tool to quickly explore and freely interact with Neo4j’s graph data platform with no coding required". Neo4j has extensive documentation how to use Bloom and a Bloom overview. Below are some examples for a quick start.

Install the Bloom configuration file

If you have not installed the Bloom configuration file yet, read Install Bloom configuration.

Open Bloom

  1. Start Neo4j Desktop.
  2. Click on the icon on the left side of Neo4j Desktop.
  3. Click on "Neo4j Bloom". A new window appears.

Execute queries

The Ricgraph Bloom configuration file contains four different shortcuts for Cypher queries:

  • "Node name [value of node to find]": finds a node where property name of a node has value [value of node to find].
  • "Node category [value of node to find]": similar to "Node name ..." for property category.
  • "Node value [value of node to find]": similar to "Node name ..." for property value.
  • "Node comment [value of node to find]": similar to "Node name ..." for property comment.

These queries can be entered in the Bloom text box "Search graph", by typing e.g. "Node name ORCID" or "Node category data set". For more information see Bloom search bar and Boom pattern search.

Nodes found can be examined or expanded as described in the section Actions while clicking on a node. The result will be visualized as described in section Visualization of nodes.

Actions while clicking on a node

The following are some examples of actions while clicking on a node:

  • Double left-click on a node: the properties of a node are shown in a window.
  • Right-click right on a node, choose "Expand", choose "All": The node will be expanded with all nodes connected to it.
  • Multiple nodes can be selected by selecting one node, holding the Control key and selecting other nodes.
  • Right-click on a node, choose "Dismiss": This node will be removed from the visualization.
  • Right-click on a node, choose "Dismiss other nodes": All other nodes will be removed from the visualization.
  • For other actions, see Bloom actions.

Visualization of nodes

Nodes can be visualized in different ways, by changing e.g. their size or color. This can be changed as follows:

  1. On the right side of the Bloom window, there is an icon . Click it (Neo4j has extensive documentation how to use it).
  2. A new window appears. It shows the default settings for the display of nodes. You can change the color, size, the property to show on the node, and the icon.
  3. In the tab "Rule-based" you can add your own rules.

The Ricgraph Bloom configuration file contains a few rules based on the value of properties. Rules which determine the color of a node:

  • if property category = "person": color = blue.
  • if property category = "data set": color = green.
  • if property category = "journal article": color = yellow.
  • if property category = "software": color = red.
  • all other nodes: color = grey.

Rules which determine the size of a node:

  • if property url_main contains "uu01": size of the node = small. This indicates which nodes have been harvested from the data repository Yoda.
  • if property url_other contains "research-software-directory": size of the node = large. This indicates which nodes have been harvested from the Research Software Directory.
  • all other nodes: size = medium.

Return to main README.md file

Return to main README.md file.