Installation

This tutorial covers multiple use cases with different database backends. The table below shows which components are needed for each:

1. Java 21+¶

Check whether Java is already installed:

java -version

You should see version 21 or higher. If not, install it:

brew install openjdk@21
sudo ln -sfn /opt/homebrew/opt/openjdk@21/libexec/openjdk.jdk \
    /Library/Java/JavaVirtualMachines/openjdk-21.jdk

sudo apt update
sudo apt install openjdk-21-jdk

java -version

2. Ontop CLI¶

Ontop CLI is the core component that powers the SPARQL endpoint.

1. Download the latest 5.x CLI distribution from https://ontop-vkg.org/download/

2. Unzip the archive:

   unzip ontop-cli-5.x.zip

3. Add the bin directory to your PATH:

export PATH=$PATH:/path/to/ontop-cli-5.x/bin

4. Verify the installation:

   ontop --version

   Expected output: Ontop version 5.x

JDBC drivers¶

Place the appropriate JDBC driver .jar files in the Ontop jdbc/ directory:

• PostgreSQL (for solar system and OMERO): Download from https://jdbc.postgresql.org/download/

• DuckDB (for OMOP and GBIF): Download from https://repo1.maven.org/maven2/org/duckdb/duckdb_jdbc/

3. Python 3 with rdflib and pandas (warmup chapter)¶

The warmup exercise uses Python to convert CSV data to RDF:

pip install rdflib pandas

4. Apache Jena — arq (warmup chapter)¶

arq is a command-line SPARQL query tool for testing RDF files locally:

1. Download Apache Jena from https://jena.apache.org/download/

2. Unzip and add the bin/ directory to your PATH

Verify:

arq --version

5. DuckDB (OMOP and GBIF use cases)¶

brew install duckdb

sudo snap install duckdb

Verify:

duckdb --version

6. GraphDB Desktop (optional — Desktop mode only)¶

Download from https://www.ontotext.com/products/graphdb/ and follow the vendor’s installation instructions.

After installation, start GraphDB and open the Workbench at: http://localhost:7200

DuckDB JDBC driver for GraphDB¶

GraphDB’s embedded Ontop needs the DuckDB JDBC driver:

1. Download the driver .jar from: https://repo1.maven.org/maven2/org/duckdb/duckdb_jdbc/

2. Place it in the GraphDB lib/ext directory:

   OS	Path
   macOS	GraphDB.app/Contents/app/lib/ext/
   Linux	graphdb/lib/ext/
   Windows	graphdb\lib\ext\

3. Restart GraphDB after placing the driver.

7. AWS CLI (GBIF extraction only)¶

The GBIF chapter uses the AWS CLI to list S3 bucket contents. No AWS account or credentials are needed — the GBIF bucket is public.

brew install awscli

sudo apt install awscli

Tested versions¶