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

Nicolas Matentzoglu1, Damien Goutte-Gattat2, Shawn Zheng Kai Tan3, James P. Balhoff4, Seth Carbon5, Anita R. Caron3, William D. Duncan5,6, Joe E. Flack7, Melissa Haendel8, Nomi L. Harris5, William R. Hogan6, Charles Tapley Hoyt9, Rebecca C. Jackson10, HyeongSik Kim11, Huseyin Kir3, Martin Larralde12, Julie A. McMurry8, James A. Overton13, Bjoern Peters14, Clare Pilgrim2, Ray Stefancsik3, Sofia MC Robb15, Sabrina Toro8, Nicole A. Vasilevsky8, Ramona Walls16, Christopher J. Mungall5, David Osumi-Sutherland3,a

1Semanticly, Spaces Ermou Ermou 56, Athens 10563 ΓEMH 160976003000, Greece

2Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK

3Samples Phenotypes and Ontologies Team (SPOT), European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK

4RENCI, University of North Carolina, Chapel Hill, NC, North Carolina 27517, USA

5Berkeley Bioinformatics Open-source Projects (BBOP), Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Mailstop 977-0257, Berkeley, CA 94720, USA

6College of Dentistry; Health Outcomes and Biomedical Informatics, COllege of Medicine, University of Florida, William D. Duncan: 1395 Center Dr, Gainesville, William R. Hogan: 1600 SW Archer Rd, Gainesville, FL 32610, USA

7School of Medicine, Johns Hopkins University, 733 N Broadway, Baltimore, Baltimore, MD 21205, USA

8University of Colorado Anschutz Medical Campus, 13001 E 17th Pl, Aurora, CO 80045, USA

9Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Avenue Armenise Building Room 109, Boston, MA 02115, USA

10Bend Informatics LLC, 5305 River Rd North, Ste B, Keizer, OR 97303, USA

11Robert Bosch LLC, Sunnyvale, CA 94085, USA

12Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg 69117, Germany

13Knocean Inc, Toronto, Ontario, ON M6P 2T3, Canada

14Institute for Allergy & Immunology, La Jolla Institute for IImmunology, 9420 Athena Circle, La Jolla, CA 92037, USA

15Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA

16Critical Path Institute, 1730 E River Road, Tucson, AZ 85718, USA

aCorresponding author:

This article was published in Database under the terms of the Creative Commons Attribution-NonCommercial License, which permits non-commercial re-use, distribution and reproduction in any medium provided that the original work is properly attributed.

Database, 2022baac087. [full text]


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 environments. 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 the ODK works, show how it is used in practice and describe how we envision it driving standardization efforts in our community.

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