Aber-OWL 2: Distributed Ontology Query System

Aber-OWL 2 is a refactored version of Aber-OWL. This version provided a distributed architecture, where each ontology is encapsulated in a separate docker container. The system enables different types of queries:

• DL Queries,
• SPARQL queries,
• Natural language queries

Dependencies

• Linux
• Groovy
• Anaconda/Miniconda
• Docker and Docker Compose

Installation

Requirements

To use Aber-OWL 2, take the following steps:

• Clone the repository
• Set up OpenRouter API key variable (optional to use natural language queries)
• Start the docker

---

1. Cloning the repository

   git clone https://github.com/bio-ontology-research-group/aberowl2.git
   cd aberowl2
   conda env create -f environment.yml
   

2. To use the LLM service, you need to set the OPENROUTER_API_KEY environment variable with your OpenRouter API key

   export OPENROUTER_API_KEY=your_api_key_here

3. Start the docker

   To use your own ontology file you first need to place it in the data directory. Copy your ontology to the data directory first:

   cp /path/to/your_ontology.owl ./data/

   Then choose a port (i.e., 89) and run the command:

   ./start_docker.sh data/your_ontology.owl 89
   

   You can shutdown the docker as follows:

   ./shutdown_docker.sh 89
   

Developing mode

Dockers are available at DockerHub. If you wish to rebuild the docker: change the following lines in start_docker.sh

# docker compose -p "$PROJECT_NAME" up --build -d
docker compose -f dockerhub-compose.yml -p "$PROJECT_NAME" up -d

to

docker compose -p "$PROJECT_NAME" up --build -d
# docker compose -f dockerhub-compose.yml -p "$PROJECT_NAME" up -d

Notes:

LLM Query Parser Service

The project includes an LLM-powered query parser service that can interpret natural language queries about ontologies. This service:

• Uses the CAMEL framework with the free version of DeepSeek (via OpenRouter) to parse natural language queries
• Extracts the entity and query type (superclass, subclass, equivalent) from natural language
• Provides a REST API endpoint for integration with other services