🔧 Neo4j Desktop Setup & n10s Installation

🧠 What is Neosemantics (n10s)?

Neosemantics is an extension that allows Neo4j to store and query data in RDF format. It is the engine that processed our medical ontologies, transforming complex OWL logic into a navigable graph of Diseases and Symptoms.

Before you can run any Cypher queries for ontologies, you must prepare your Neo4j instance.

0. Prerequisites: Install Neo4j Desktop

If you don’t have Neo4j installed on your machine, you need to download it first:

  • Download Neo4j Desktop from the official Neo4j website.
  • Install the application (available for Windows, macOS, and Linux) and create a free account if prompted.
  • Open Neo4j Desktop to begin the setup.

1. Create a New Database Instance

  • Open Neo4j Desktop.

  • Click Create instance.

  • Instance Details: Give it a name (e.g., NeSy-Graph).

  • Create database user: Set your password (ensure it matches the NEO4J_PASSWORD in your .env file).

  • Load from .dump: Browse for the neo4j.dump file (found in the /data folder of this repo) .

  • Click Create.

2. Install n10s

Even though the data is loaded, you must still enable the required logic engines.

Note: Neosemantics (n10s) is not available directly in the Desktop UI it must be downloaded manually.

Install Neosemantics (n10s):

  • Download the compiled .jar file from the official n10s GitHub Releases. Make sure to download the version that matches your Neo4j database version (e.g., 5.x).

  • In Neo4j Desktop, click the … (three dots) next to your instance.
  • Select Open -> Instance Folder.
  • Open the plugins folder and paste the downloaded .jar file inside.
  • Go back to Neo4j Desktop, click … -> Open -> neo4j.conf.

  • Scroll to the bottom of the configuration file and add this exact line:

    server.unmanaged_extension_classes=n10s.endpoint=/rdf
dbms.security.procedures.allowlist=apoc.*,n10s.*
dbms.security.procedures.unrestricted=apoc.*,n10s.*

Restart the Database

After modifying the neo4j.conf file, you must restart the database for the plugin configuration to take effect.

  • Go back to Neo4j Desktop.
  • Click Stop on your database.
  • Wait a few seconds.
  • Click Start to run the database again.

Once the database restarts, the n10s plugin will be loaded and ready to use.

Next Steps

Now that your ontologies are loaded and labeled, you need to calculate weights and embeddings. ➡️ Go to Data Enrichment Instructions