Automating the Ontology Lifecycle: Version 1.5 of the ODK

The Ontology Development Kit (ODK) is a system for managing workflows in and around the ontology lifecycle, including release management, import management and quality control. It comes with a toolbox which bundles all tools necessary for successful ontology lifecycle management, including ROBOT for ontology transformation, various SSSOM-powered tools for ontology mapping, the Ontology Access Kit (OAK) for using ontologies in data science workflows, and LinkML for building data models. With over 100 successful deployments and growing, the ODK is not just a toolkit; it’s a community-driven effort that shapes the way we publish and manage ontologies. The project is led by members of the Monarch Initiative, but powered by Open Science and ontology enthusiasts around the world.

The latest ODK 1.5 release was a year in the making and comes with a number of improvements, including:

• Introduction of the “International Release” and a complete workflow system for ontology internationalisation. We have devised a system which allows us to manage ontology translations simply outside the ontology, using a standard format with provenance metadata called Babelon. Its has been tested for more than a year in widely used ontologies such as the Human Phenotype Ontology (HPO) and the Mammalian Phenotype Ontology (MP), and has now been further enhanced for the latest ODK release, including features such as automated LLM-mediated translations and configurable language profile pre-processing.
• Redefinition of “Base Release”: Base files are a fundamental piece of our vision for decentralised ontology development. They are the “essence” of a domain ontology, excluding any content imported from other ontologies. This allows ODK users to combine ontologies that were developed in a decentralised manner while minimising versioning clashes.
• Built-in support for ROBOT plugins: We now directly support the inclusion of custom ROBOT plugins into your ODK workflows. This allows the integration of your OWL API-based ontology pipelines right into regular ROBOT pipelines!

This update is a reflection of our commitment to making ontology development more standardised, faster, and more inclusive. For a detailed overview of all the updates, visit our Release page.

Your feedback is our driving force. We thank you for being a part of this journey towards a more connected and efficient world of ontology management.

— Anita Caron, Damien Goutte-Gattat and Nico Matentzoglu (Lead Developers, on behalf of the ODK Core Team)

More information:

• ODK 1.5 Release
• Tutorials
• GitHub repository and issue tracker
• Publication (Matentzoglu et al., Database 2022)