QLever SPARQL Endpoints: ORDO, HOOM, WikiPathways

This repository sets up three QLever SPARQL endpoints:

• ORDO – Orphanet Rare Disease Ontology
• HOOM – The HPO-ORDO ontological module
• WikiPathways – RDF export of biological pathways

Each endpoint is configured using a Qleverfile and includes a get-data.sh script for downloading or preparing its data.

Prerequisites

• Python 3.10+ with venv
• Docker (including Compose plugin)
• Recommended: Add your user to the Docker group

sudo usermod -aG docker $USER
sudo reboot

Installation

1. Clone this repository and enter it:

   git clone https://github.com/ERDERA/qlever-sparql-deployment.git
   cd qlever-sparql-deployment

2. Create and activate a Python virtual environment:

   python3 -m venv qlever-venv
   source qlever-venv/bin/activate
   pip install --upgrade pip
   pip install qlever

Run Each Endpoint

For each endpoint folder (ordo/, hoom/, wikipathways/), run the following commands:

cd <folder>
./get-data.sh       # Downloads or prepares the RDF data
qlever index        # Indexes the data using the Qleverfile
qlever start        # Starts the SPARQL endpoint

Example:

cd ordo
./get-data.sh
qlever index
qlever start
qlever ui

Repeat the same steps for hoom/ and wikipathways/.

Accessing the SPARQL Endpoints

Then visit http://localhost: in your browser.

Folder Structure

.
├── ordo/
│   ├── Qleverfile
│   └── get-data.sh
├── hoom/
│   ├── Qleverfile
│   └── get-data.sh
├── wikipathways/
│   ├── Qleverfile
│   └── get-data.sh
└── qlever-ui-multi-config.json

Disclaimer

This is a first draft release of a set of configuration scripts and documentation for setting up QLever SPARQL endpoints for ERDERA. The scripts are not yet fully tested and may require adjustments for specific use cases. The documentation is a work in progress and may not cover all aspects of the setup process. Please use this repository at your own risk and feel free to contribute improvements or report issues.