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License: CC0-1.0 Universal Python 3.1 PyPI - Downloads

O2WB: A tool for ontology reuse in Wikibase

O2WB is a Python command line tool that enables ontology reuse in Wikibase, a popular data publishing platform. The tool aligns the Wikibase data model with RDF and facilitates the import and export of RDF Schema and OWL ontologies within Wikibase. This will help to tighten the connection between existing linked data resources and Wikibase instances.

Features

  • Import ontologies from a local file or URL
  • Follow owl:imports to recursively import ontologies
  • Represent IRIs, Blank Nodes, and Literals in the Wikibase data model
  • Instantiate Statements that correspond to the Triples
  • Correctly include Datatypes and Qualifiers
  • Enable editing of imported ontologies through the Wikibase GUI
  • Export ontologies in a variety of formats

Requirements

  • Python 3.x
  • rdflib 6.2.0+
  • wikibase-integrator 0.12.2+
  • antlr4-python3-runtime 4.9.3+
  • argparse 1.4.0+

Installation

O2WB can be installed using pip:

  python3 -m pip install o2wb

Alternatively, you can clone this repository to your machine and install the required packages from requirements.txt.

Make sure the following requirements are fulfilled:

The next two sections guide through the process of fulfilling these requirements:

Setting up a Wikibase Suite instance

The full Wikibase Suite required for O2WB to work consists of the MediaWiki base platform with Wikibase extensions, the MySQL (MariaDB) database and the Elasticsearch, QuickStatements and Wikidata query services (a Blazegraph SPARQL endpoint).

There are two main approaches to setting up a Wikibase Suite instance, a Docker-based setup (extended install) and a full manual setup. Follow the corresponding links for the respective installation manuals. In the Docker-based setup, the components of the Wikibase Suite are automatically set up in Docker containers, making the installation and configuration process much easier. In the full manual setup, each component must be installed separately. We recommend using the Docker-based setup.

Creating a bot account in Wikibase

In order to use O2WB, you need to set up a Wikibase bot with the necessary permissions. Follow these steps:

Create a new Wikibase bot with the following permissions related to page editing:

  • High-volume editing
  • Edit existing pages
  • Create, edit, and move pages

Now that you have set up the Wikibase bot account, you are ready to start using O2WB to import and export ontologies.

Importing an ontology

The process of importing an ontology into Wikibase is straightforward with the help of the o2wb-imp command or the manual import.py script.

To import an ontology, you need to have the following details:

  • The location of the ontology to import, either as a file or a URL
  • The name of the ontology

You can choose to import the ontology either non-recursively or recursively (by adding the --recursive flag). If you choose to import recursively, then all the dependencies of the ontology (owl:imports statements) will be imported along with the main ontology. You can also define the depth of the recursive imports (--recursive ).

Additionally, you can create a csv mapping file that documents the mapping of the ontology IRIs to Wikibase Properties and Items (--mapping ).

To run the import process, open a terminal or command prompt and run the following command:

  o2wb-imp {--url <URL of your ontology> | --file <path to ontology file>} --name <ontology name> [--recursive <Depth of recursive imports>] [--mapping <path to export the mapping scheme>]

If you have cloned the repository, you can run the following command:

  python import.py {--url <URL of your ontology> | --file <path to ontology file>} --name <ontology name> [--recursive <Depth of recursive imports>] [--mapping <path to export the mapping scheme>]

Replace the values in the brackets with your own values and run the command. The import process will start, and you will see the progress of the import in the terminal.

Note that the import process can take a while, depending on the size of the ontology and the number of dependencies. You can monitor the progress of the import and then browse all newly created Properties and Items on the Recent Changes Special Page of the Wikibase UI.

Editing an ontology

After having imported the ontology, we now can edit it using the Wikibase UI. There are three types of edits that we look at:

  • adding new Statements
  • editing existing Statements
  • deleting Statements

To add a new Statement, first consider the Entities that make it up as well as their respective Datatypes in Wikibase.

:warning: If such an Entity does not exist yet or there is no Property that has the appropriate Datatype to be used in the Statement, you should create it through either the Create a new Item or Create a new Property Special Page. When creating a new Entity, use the o2wb:representsIRI Property to indicate the IRI that will be exported later or the o2wb:typeOf Property with the value of o2wb:BNodeRepresentation to indicate that the Entity is a Blank Node.

After making sure that all the necessary Entities exist, navigate to the page of the Entity that is supposed to be the subject of the new Statement. On this page you can add a new Statement selecting the already existing Entities.

:warning: To include the recently created Statement in an ontology, add a Reference with the Property o2wb:fromOntology and an Item that stands for the respective ontology.

In a similar manner, you can edit Statements by editing or replacing their constituent Entities or chaning their non-Entity Values.

When replacing an Entity, make sure that it is created beforehand and has an appropriate Datatype. Finally, you can exclude Statements from a given ontology by deleting them or removing their o2wb:fromOntology References.

Exporting an ontology

The o2wb-exp command exports an ontology stored in your Wikibase instance to a file in RDF format. The --file option specifies the output file name in any of the common RDF serialization formats (supported serializations) and the --name option specifies the name of the ontology you want to export.

Analogously to the o2wb-imp command, you can also use the --mapping option to create a mapping file that maps the IRIs in the exported RDF file to Iteams and Properties in Wikibase. Please note that the exported RDF file will contain only the data related to the specified ontology.

To run the import process, open a terminal or command prompt and run the following command:

  o2wb-exp --file <path to ontology file> --name <ontology name> [--mapping <path to export the mapping scheme>]

If you have cloned the repository, you can run the following command:

  python export.py --file <path to ontology file> --name <ontology name> [--mapping <path to export the mapping scheme>]

Note that the export process can take a while depending on the size of the ontology. You can monitor the progress of the export with a progress bar. Exported RDF files might have a different presentation from the initial imported file: order of triples and defined prefixes might differ despite the exported files being identical with regards to their content.

Examples

To import the DCAT ontology from a URL, run:

  o2wb-imp --url "https://www.w3.org/TR/vocab-dcat-2/" --name "DCAT Ontology"

To also recursively import one level of owl:imports ontologies, run:

  o2wb-imp --url "https://www.w3.org/TR/vocab-dcat-2/" --name "DCAT Ontology" --recursive 1

To import the FOAF ontology from a file and create a mapping file, run:

  o2wb-imp --file "pathTo/foaf.owl" --name "FOAF Ontology"  --mapping "pathTo/mapping.csv"

To export the FOAF ontology in Turtle format, run:

  o2wb-exp --file "pathTo/foafExported.ttl" --name "FOAF Ontology"

To also generate a mapping, run:

  o2wb-exp --file "pathTo/foafExported.ttl" --name "FOAF Ontology"  --mapping "pathTo/mapping.csv"

Contributing

Contributions are welcome. Please open an issue or submit a pull request if you would like to contribute.

License

O2WB is licensed under the CC0 1.0 Universal license.

Authors

  • Daniil Dobriy - (Institute for Data, Process and Knowledge Management - WU Vienna)
  • Axel Polleres - (Institute for Data, Process and Knowledge Management - WU Vienna)

Institute for Data, Process and Knowledge Management, Vienna University of Economics and Busioness.

Acknowledgements