Sparql Service

The (Fuseki) Sparql service allows the integration of ontological hierarchies in RDF or OWL format into UCE's searches. It does so through a SPARQL graph database which stores RDF triplets.

Out-of-the-box Ontologies

Please refer to our list of plug-and-play Ontologies to see what ontologies have already been made accessible in UCE without you having to develop anything. We are continuously expanding plug-and-play compatibility with other ontologies, and if you want to incorporate your own compatibility into UCE, feel free to make a pull request or get in touch!

User Setup

For this, the following parameters in the .env file need to be set correctly:

TDB2_DATA=./../tdb2-database
TDB2_ENDPOINT=tdb2-database-name

where TDB2_DATA is the local path to your TDB2 database and TDB2_ENDPOINT is the name under which this database will be queryable. This endpoint must match the first part of the sparql.endpoint parameter in the common.conf file (tdb2-database-name/sparql).

Afterwards, simply start the uce-fuseki-sparql container:

docker-compose up --build uce-fuseki-sparql

Developer Setup

You can easily set up the SPARQL database as outlined in the User Setup. However, for more efficient testing and to take advantage of the web interface provided by Apache Jena, it may be advisable to install a local Fuseki SPARQL instance as well. For that:

Download the latest Apache Jena Binary Distribution.
Unzip the archive, navigate to the folder, and start the SPARQL server (requires Java to be installed):
```
java -Xmx8G -jar fuseki-server.jar --update
```
--update makes the database persistent.
By default, the SPARQL database and its web interface are accessible at http://localhost:3030.
You can now create a new database through the Web UI. The name of the database will also serve as the endpoint /db_name.

Web UI & Import Option

When installing locally and opening the web UI, you can create a new database and use the Import button to import RDF and OWL files directly. Once the database has been populated, you will find the corresponding TDB2 database as a folder within your program directory (likely under run/databases). You can simply mount this folder as the TDB2_DATA location.

tdb.lock

The database will generate a tdb.lock file to prevent multiple instances from accessing the same TDB2 database simultaneously. Be mindful of this, as it often leads to errors when overlooked.

Disk Space

When importing large volumes of new triplets, the SPARQL database generates log and transaction files, which can quickly consume significant disk space and bloat the database. You can heavily reduce the size and reclaim unnecessary space by using the /compact endpoint once your importing is finished.