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 Duncan^{5

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

Affiliations

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.

PMID: 36208225
PMCID: PMC9547537
DOI: 10.1093/database/baac087

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

Nicolas Matentzoglu et al. Database (Oxford). 2022.

. 2022 Oct 8:2022:baac087.

doi: 10.1093/database/baac087.

Authors

Affiliations

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.

PMID: 36208225
PMCID: PMC9547537
DOI: 10.1093/database/baac087

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.

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References

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

Affiliations

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

Authors

Affiliations

Abstract

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources