Ontology Pipeline

• Minimal infrastructure for automatically testing and building released versions of ontologies
• Made with ROBOT and automated with GNU Make
• Continuously tested, built, and deployed using Github Actions
• Inspired by ongoing efforts to use simple and sustainable techniques for ontology engineering

Usage

• Set the ontology details and metadata in the Makefile
• Add an ontology file and SPARQL query files to the locations specified
  • By default, the sample ontology included in this repo is a copy of http://purl.obolibrary.org/obo/bfo/2.0/bfo.owl
• Currently, commits on any branch will trigger the test automations
  • The results of tests are visible in each executed Github Action and also downloadable as "artifacts". See examples here and here.
• Commits to the master branch trigger the test and release automations
  • The release automation will draft a Github Release here with the release build of the ontology attached, which contains annotations of the version metadata.

Setup

• There are 3 different ways this repo can be used:
  • Option 1: Fork this repo and replace the sample ontology and Makefile settings with your own. Updates to this repo can be automatically synced to yours.
  • Option 2: Copy the Makefile, Github Action files, and license into your own repo. Updates to this repo would need to be manually copied to yours.
  • Upcoming Option 3: This repo could be published as a Github Action that you may reference in your repo, without needing a Makefile. However, this would make your project more dependent on Github. (The Makefile is intended to be completely usable without Github.)

Architecture

• This basic pipeline & other upcoming advanced versions are documented here
• Downloaded dependencies like ROBOT are cached for re-use in the Github Actions. The cache is currently cleared after 7 days of no use.
• The Makefile can be used independently of a Github Action by running it locally with Make

Related Tools

• For more advanced ontology engineering automation, see ODK and OAK