This repository provides a Dockerised setup for Ontop with preloaded R2RML mappings and an instance of DuckDB containing a MomCARE sample dataset. It is intended to demonstrate virtual knowledge graph querying using SPARQL over relational data in DuckDB.
The mappings used in this framework are based on an ontologised conceptual model, largely oriented to NCIT terms. An advantage of this approach is that the model can be extended to include other ontologies, which is also reflected in the SPARQL endpoint.
The figure below is a simplified illustration of the conceptual model used in this framework:
- Docker must be installed on your machine. If you don't have it yet, follow the official installation guide here:
https://docs.docker.com/get-docker/
git clone https://github.com/PharmAccess/momcare_sql_to_rdf.git
cd momcare_sql_to_rdfdocker compose up
This will:
- Start an Ontop SPARQL endpoint
- Mount the DuckDB database and mapping files
- Serve the endpoint at
http://localhost:8080/
Once the container is running, you access the SPARQL GUI at http://localhost:8080/ via your browser.
Examples of queries:
- List mothers who received a C-section and their age
- List patients that were diagnosed with hypertension during their pregnancy
Mappings: The DataModel.obda file contains the mappings used by Ontop. You can open and edit the related OWL file using Protégé for a graphical interface.
Ontop allows you to query relational databases as virtual RDF graphs using mappings based on R2RML or OBDA. This approach avoids materialising large RDF datasets and supports efficient, on-the-fly SPARQL querying.
DuckDB is an in-process analytical database management system, ideal for OLAP workloads. This project demonstrates that Ontop can also work with DuckDB as a backend for virtual knowledge graph querying.
This project is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) License.
You are free to share and adapt the material, provided appropriate credit is given.
See the full license text at: https://creativecommons.org/licenses/by/4.0/
Feel free to open an issue or submit a pull request. Contributions are welcome!