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Ontology Development Kit (ODK) Reference

The ODK is essentially two things:

  1. A toolbox. All frequently used tools for managing the ontology life cycle are bundled together into a Docker image: ROBOT, owltools, fastobo-validator, dosdp-tools, riot and many, many more.
  2. A system, you could have say "methodology" for managing the ontology life cycle from continious integration and quality control to imports and release management.

The Toolbox

The ODK bundles a lot of tools together, such as ROBOT, owltools, fastobo-validator and dosdp-tools. To get a better idea, its best to simply read the Dockerfile specifications of the ODK image:

  • ODK Lite Image. This contains the most essentials tools related to ODK development. Most of the day to day activities of ontology developers with ROBOT are well covered by odklite.
  • ODK Full Image. Extends the ODK Lite image with a further round of powerful tools. It contains for example Apache Jena, the OBO Dashboard, the Konclude reasoner and a large array of command line tools.

The system for ontology life cycle management

One of the tools in the toolbox, the "seed my repo" function, allows us to generate a complete GitHub repository with everything needed to manage an OBO ontology according to OBO best practices. The two central components are

  1. A Makefile that encodes the rules by which ontology release files should be derived from the source of truth (the edit file).
  2. A support for CI such as GitHub actions or Travis for running continuous integration checks.