ReadTheDocs for VIVO ontologies

May 17, 2021VIVO 2021 Conference SubmissionReaders: Everyone
  • Keywords: documentation, ontologies, ReadTheDocs, python
  • TL;DR: A python script has been developed to create ReadTheDocs documentation from ontologies
  • Abstract: ReadTheDocs (RTD) is a system of creating documentation that is common in the python community. RTD uses RestructuredText as a mark-up language and Sphinx as a processor. Each component is open source, readily available, and well-documented. In creating the Organization Ontology, a small python script was created to generate pages for each term in the ontology, as well as tables of terms for inclusion in hand-written pages. Hand-written pages contain overviews, figures, and tables. This hybrid approach has several advantages over the current VIVO documentation method: 1) All documentation text is version-controlled in GitHub; 2) A simple mark-up language (ReStructuredText) makes writing good-looking documentation straightforward; 3) Documentation is searchable and indexed; 4) Documentation always agrees with the ontology; 5) style is completely separated from content. In this talk, we will describe the general setup of an RTD environment, the python script used to create pages, and the resulting documentation for an ontology. The python script is distributed with the Organization Ontology.
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