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

Author:

Matentzoglu Nicolas1,Goutte-Gattat Damien2ORCID,Tan Shawn Zheng Kai3ORCID,Balhoff James P4ORCID,Carbon Seth5,Caron Anita R3,Duncan William D56ORCID,Flack Joe E7,Haendel Melissa8ORCID,Harris Nomi L5ORCID,Hogan William R6ORCID,Hoyt Charles Tapley9ORCID,Jackson Rebecca C10ORCID,Kim HyeongSik11,Kir Huseyin3,Larralde Martin12,McMurry Julie A8,Overton James A13ORCID,Peters Bjoern14ORCID,Pilgrim Clare2ORCID,Stefancsik Ray3,Robb Sofia MC15,Toro Sabrina8,Vasilevsky Nicole A8,Walls Ramona16,Mungall Christopher J5ORCID,Osumi-Sutherland David3

Affiliation:

1. Semanticly , Spaces Ermou Ermou 56, Athens 10563 ΓΕΜΗ 160976003000, Greece

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

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

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

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

6. College 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

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

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

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

10. Bend Informatics LLC , 5305 RIVER RD NORTH, STE B, KEIZER, OR 97303, USA

11. Robert Bosch LLC , Sunnyvale, CA 94085, USA

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

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

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

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

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

Abstract

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

Funder

Director, Office of Science, Office of Basic Energy Sciences, of the US Department of Energy

National Institutes of Mental Health

UK Biotechnology and Biological Sciences Research Council / US National Science Foundation Directorate of Biological Sciences

National Human Genome Research Institute “Phenomics First”

Office of the Director, National Institutes of Health

National Heart, Lung, and Blood Institute

Publisher

Oxford University Press (OUP)

Subject

General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,Information Systems

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