The quick and dirty reproducible local setup II

Georgi Iliev · January 21, 2025

Encounter

2. Semantic repository

Virtuoso Open-Source Edition

Referring back to our container diagram, the solution requires a semantic repository to maintain both reference bird data and encounter data. We are going to use a local Virtuoso Open-Source Edition instance for that.

We continue on the path of least resistance to set up a local development environment, hence Virtuoso is going to be served out of a Docker container. Following the instructions unchanged (creating a local directory my_virtdb and initializing an empty repository in it) I was able to spin up the Virtuoso instance (take note of the DBA_PASSWORD setting, we will need this later).

$ docker run \
--name my_virtdb \
--interactive \
--tty \
--env DBA_PASSWORD=mysecret \
--publish 1111:1111 \
--publish  8890:8890 \
--volume `pwd`:/database \
openlink/virtuoso-opensource-7:latest
Unable to find image 'openlink/virtuoso-opensource-7:latest' locally
latest: Pulling from openlink/virtuoso-opensource-7
[...]
06:59:27 HTTP/WebDAV server online at 8890
06:59:27 Server online at 1111 (pid 1)

Point your browser to http://localhost:8890 and you should be able to load the Virtuoso GUI.

Loading reference data

The reference data we will need in our photo annotation app to generate suggestions to partial user input and to build the linked data according to the minimal Encounter model can be downloaded in RDF format from the official site of the Finnish Ontology Library Service ONKI. This is a single RDF/XML file that can be saved locally and imported into your Virtuoso instance by:

1. Logging into Virtuoso CONDUCTOR (user: dba, password: the password you provided to the docker run command above)
2. Selecting the tabs Linked Data -> Quad Store Upload. You can then either browse your local system for the downloaded avio.rdf file or enter the above link in the Resource URL field.

3. It’s good practice to save the data in a named graph, set it in the Named Graph IRI field as http://www.yso.fi/onto/avio (feel free to use any other IRI you find suitable – this is the namespace used to manage and query the reference data separate from the encounter data).

   

4. We can now check if the data has loaded correctly by executing a simple SPARQL query. Selectng the tabs Linked Data -> SPARQL loads the SPARQL shell. Assuming you have loaded the ontology into the suggested named graph, try

    PREFIX avio: <http://www.yso.fi/onto/avio/>
   
    SELECT * WHERE {
    ?species a avio:species .
    ?species skos:prefLabel ?prefLabel .
    ?prefLabel bif:contains "crow" .
    OPTIONAL {
            ?species avio:linkToEnglishWikipedia ?wikipediaLink .
            }
    }
    LIMIT 5
   

   

5. To finish the local setup of the semantic repository we need to allow the SPARQL client to write to the database, as this permission is not granted by default. Select the tabs System Admin -> User Accounts, then choose the SPARQL account. Go to edit and give the user the SPARQL_UPDATE role as shown.

   

   Depending on the version of Virtuoso you may also have to follow the instructions from this post in case you still can’t insert new data via the SPARQL endpoint.

Coming up next

• The quick and dirty: reproducible local setup (part III)