An Ontop tutorial using the Bgee database

Copyrights

• Data (under the data directory): CC0
• Text: CC-BY 4.0
• Code: Apache 2.0

Table of Contents

• 0. Repository structure
• 1. Setting up the PostgreSQL database
• 2. Setting up the VKG using Ontop-Protégé
• 3. Deploy a SPARQL endpoint using Ontop CLI
• 4. Deploy a SPARQL endpoint using Ontop Docker

Repository structure

.
├── data
│   ├── mysql.zip
│   └── postgresql.zip
├── LICENSE
├── obda
│   ├── bgee_v14_genex.obda
│   ├── bgee_v14_genex.owl
│   ├── bgee_v14_genex.properties
│   ├── bgee_v14_genex.q
│   └── bgee_v14_genex.r2rml
└── README.md

• data: MySQL and postgres dumps
• bgee_v14_genex.obda: Mapping file (Ontop syntax)
• bgee_v14_genex.r2rml: Mapping file (R2RML syntax)
• bgee_v14_genex.owl: Ontology file
• bgee_v14_genex.properties: Properties file
• bgee_v14_genex.q: Queries file for Protege

Setting up the PostgreSQL database

1. Create a database called easybgee_v14_2. For example, in pgsql you can use the command:

pgsql> CREATE DATABASE easybgee_v14_2;

2. Unzip the postgres archive to extract the dump file.

3. Use the extracted dump file to create a database easybgee_v14_2. For example, you can use the following bash pgsql invocation:

$> PGPASSWORD=$pwd psql -h $host -p $port --user=$user --dbname=easybgee_v14_2 -f $dump_file

4. Provide the connection parameters to your database in the bgee_v14_genex.properties file. Replace the placeholders <host>,<port>, <user>, and <password> with appropriate values.

jdbc.url=jdbc\:postgresql\://<host>\:<port>/easybgee_v14_2
jdbc.driver=org.postgresql.Driver
jdbc.user=<user>
jdbc.password=<password>

Setting up the VKG using Ontop-Protégé

1. Download the latest version of Ontop+Protégé bundle. For this tutorial, we will use the Ontop 4.1.0 bundle for Linux systems. Choose a bundle suitable to your operating system.

2. Unzip the bundle. Launch Protégé through the dedicated script. In case of linux, the command is

$> ./run.sh

3. Click on the File Menu, then Preferences and then to the JDBC Drivers tab to add the downloaded jdbc driver to Protégé:

4. Click on the File Menu, then Open to open the Bgee ontology (bgee_v14_genex.owl file).

5. Check whether the connection to the database is working property, by clicking the Test Connection button under the Datasource Manager sub-tab of the Ontop Mappings tab.

6. Browse the ontology and mapping in the Ontop Mappings / Mapping Manager tab.

7. Click on the Reasoner Menu, then select Ontop 4.1.0

8. Click again on the Reasoner Menu, and on Start Reasoner to start Ontop

SPARQL Query answering in Ontop-Protégé

1. At this point, you are ready to try Ontop to answer the Bgee queries. To do so, use the Ontop SPARQL tab.

How Ontop Answers your Queries

Ontop operates in virtual mode, that is, the KG extracted from the mappings is not materialized. The SPARQL queries are translated on-the-fly into corresponding SQL queries executable over the original data source, by exploiting the mapping definitions and the ontology axioms. To see what is the SQL translation corresponding to your SPARQL query, you can right-click on the SPARQL query editor field and select the View SQL translation option:

Materialize RDF Triples in Ontop-Protégé

If you do not want to use Ontop for SPARQL query answering, you have the option to materialize the KG and import it into your favorite triple store. To do this, click on the Ontop Menu and then Materialize triples... option.

Deploy a SPARQL endpoint using Ontop CLI

1. Download Ontop CLI. For this tutorial, we will use the Ontop 4.1.0 CLI bundle. Exact the zip file of Ontop CLI to a directory, which is denoted as $ONTOP_CLI_DIR below.

2. Copy the jdbc driver to the $ONTOP_CLI_DIR/jdbc

3. Go to the obda directory and start the Ontop SPARQL Endpoint

$ONTOP_CLI_DIR/ontop endpoint --ontology=bgee_v14_genex.owl --mapping=bgee_v14_genex.obda --properties=bgee_v14_genex.properties --portal=bgee_v14_genex.toml

4. Navigate to http://localhost:8080 to try the Web portal of the SPARQL endpoint

5. A SPARQL endpoint backed by ontop at URL http://localhost:8080/sparql (assuming default port 8880 is used), which may be accessed using any HTTP client, including SPARQL clients and tools using the standard SPARQL HTTP protocol. For instance, using curl:

curl --request POST \
   --url http://localhost:8080/sparql \
   --header 'accept: application/json' \
   --header 'content-type: application/sparql-query' \
   --data 'SELECT * { ?s ?p ?o } LIMIT 5'

Deploy a SPARQL endpoint using Ontop Docker

Requirements

• Docker, version 17.09.0 or higher
• Docker Compose, version 1.17.0 or higher

Steps

1. to start the prototype, downloading / building the required images and containers if needed

docker-compose up

(note: may add option -d to run in background, in which case logs are not be displayed to standard output but are still accessible via docker-compose logs)

Services When running, the prototype exposes the following services:

• a PostgreSQL server with the sample data, with connection information defined in the .env file.

• a Web portal of the SPARQL endpoint backed by ontop at URL http://localhost:8880/

• a SPARQL endpoint backed by ontop at URL http://localhost:8880/sparql (assuming default port 8880 is used).

2. to stop the prototype, if running

docker-compose down

3. to stop the prototype, if running, and also clean any image / container / data associating to it (useful for cleaning up)

docker-compose down --volumes --remove-orphans

(note: the above command does not remove Docker images that may result being unused after stopping and removing this prototype containers; to remove such images, add option --rmi all)

4. to check the status of the containers forming the prototype

docker-compose ps

5. to check the logs of specific container(s) or of all containers (if no container name is supplied)

docker-compose logs <container name 1> ... <contaner name N>