AEON development workflow - how I managed to never open the command line and yet have automated workflows

May 17, 2021VIVO 2021 Conference SubmissionReaders: Everyone
  • Keywords: ontology engineering, automated workflows, CI/CD
  • Abstract: The the Academic Event Ontology (AEON) development toolbox is comprised of Protégé, a GitHub repository (interfaced via GitHub Desktop) and a plain text editor. Although user friendly, this ontology development setup and associated workflow does not provide quality checks. Common human errors can easily pass unnoticed onto the ontology. In order to mitigate such errors, as well as minimize the human labor that goes onto building an ontology, The OBO Foundry has developed an array of tools, such as ROBOT and the Ontology Development Kit (ODK). Although powerful, such tools are more suited to the workflow of software developers, than those of ontology and knowledge engineers, or require a technical setup that may not be present. But what if we could combine the best of both worlds? Integrating OBO Foundry command-line tooling with the automated workflows interfaces, provided by continuous integration platforms such as Github Actions, Gitlab CI, or Jenkins? What if the ontology engineer could test an ontology with Robot Report at the click of a button? Or extract only a module (SLIME) from a given ontology by entering a few values and clicking 2 buttons? Very much possible. And in this talk we will present, how we integrated key features of the OBO tool ROBOT and GitHub actions into the development of AEON, without ever opening the command line.
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