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Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies.

Nicolas MatentzogluDamien Goutte-GattatShawn Zheng Kai TanJames P BalhoffSeth CarbonAnita R CaronWilliam D DuncanJoe E FlackMelissa A HaendelNomi L HarrisWilliam R HoganCharles Tapley HoytRebecca C JacksonHyeongSik KimHuseyin KirMartin LarraldeJulie A McMurryJames A OvertonBjoern PetersClare PilgrimRay StefancsikSofia Mc RobbSabrina ToroNicole A VasilevskyRamona WallsChristopher John MungallDavid Osumi-Sutherland
Published in: Database : the journal of biological databases and curation (2022)
Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking and dependency management. To manage these processes, a diverse set of tools is required, from command-line utilities to powerful ontology-engineering environmentsr. Particularly in the biomedical domain, which has developed a set of highly diverse yet inter-dependent ontologies, standardizing release practices and metadata and establishing shared quality standards are crucial to enable interoperability. The Ontology Development Kit (ODK) provides a set of standardized, customizable and automatically executable workflows, and packages all required tooling in a single Docker image. In this paper, we provide an overview of how the ODK works, show how it is used in practice and describe how we envision it driving standardization efforts in our community. Database URL: https://github.com/INCATools/ontology-development-kit.
Keyphrases
  • healthcare
  • quality control
  • primary care
  • life cycle
  • quality improvement
  • mental health
  • emergency department
  • deep learning
  • adverse drug