Owl2Anything Converter

The SUTURO Owl2Anything Converter is a Java-based tool that can be used to convert OWL ontology files into other formats like CSV and JSON.

It can be used to extract information from an ontology and export it into a tabular or annotation format, which can be easily imported into other tools or used for analysis. One of the main features of the converter is the ability to export relevant information from the ontology into a CSV file, which can be used to easily display the ontology in a searchable table format.

Examples of the exported formats can be found in the Downloads section of the Objects page of the SUTURO Knowledge website.

Requirements

• Java 17 or higher

Usage

To use the Owl2Anything Converter, you need to run the Jar file with the following options:

java -jar owl2anything.jar -i [input_file] -r [root_class_iri] [-m [iri_mapping_file]] [-n [iri_namespaces_file]]

The options are described below:

• -i, --input: Path to the input ontology file in OWL format (required).
• -r, --root: IRI of the root class. Every sublass of this IRI will be exported. (required).
• -m, --mapping: Path to the IRI mapping file (optional). If not specified, the default SUTURO IRI mapping will be used.
• -n, --namespaces: Path to the IRI namespaces file (optional). If not specified, the default SUTURO IRI namespaces will be used.

The IRI mapping file is a CSV file that maps (invalid) ontology IRIs to replacements. The file should have the following format:

original;replacement
"package://knowrob/owl/URDF.owl";"http://knowrob.org/owl/URDF.owl"

The IRI namespaces file is a CSV file that maps ontology IRIs to a short form namespace. The file should have the following format:

iri;namespace
http://www.ease-crc.org/ont/SUTURO.owl#;suturo
http://www.ease-crc.org/ont/SOMA.owl#;soma

Contributing

Recommend Code Editor

We recommend using IntelliJ IDEA as code editor for this project with the following plugins:

• Lombok

Getting Started

1. Open the project in IntelliJ IDEA
2. Place the suturo.owl file in the projects root folder
3. Execute the Run-Configuration Run Owl2Anything or start the application via the main method in Owl2Anything.java with the required arguments.
4. The generated files will be placed in the owl2anything/output folder

Create a Release

To publish a new release, you need to create a new tag with the version number and push it to the repository. The release is then published automatically by the GitHub Actions release.yml workflow.

Example:

git tag -a 1.3.0 -m "v1.3.0" -m "- Fix bug in CSV export"
git push origin 1.3.0

• The tag name should be a valid SemVer version number.
• The tag message head should start with a v prefix and then the tag name (e.g. v1.3.0).
• The tag message body should contain a short description of the changes since the last release.

To use the new release, change the OWL2ANYTHING_VERSION in the owl2anything.yml workflow of the Knowledge Project.

License

The SUTURO Owl2Anything Converter is licensed under the Apache License, Version 2.0. See the LICENSE file for details.