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

Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P. Balhoff, Seth Carbon, Anita R. Caron, William D. Duncan, Joe E. Flack, Melissa Haendel, Nomi L. Harris, William R. Hogan, Charles Tapley Hoyt, Rebecca C. Jackson, Hyeongsik Kim, Huseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare PilgrimRay Stefancsik, Sofia M.C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona Walls, Christopher J. Mungall, David Osumi-Sutherland

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

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

Original languageEnglish (US)
Article numberbaac087
JournalDatabase
Volume2022
DOIs
StatePublished - 2022
Externally publishedYes

ASJC Scopus subject areas

  • Information Systems
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Fingerprint

Dive into the research topics of 'Ontology Development Kit: A toolkit for building, maintaining and standardizing biomedical ontologies'. Together they form a unique fingerprint.

Cite this