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 Pilgrim; Ray Stefancsik; Sofia M.C. Robb; Sabrina Toro; Nicole A. Vasilevsky; Ramona Walls; Christopher J. Mungall; David Osumi-Sutherland

doi:10.1093/database/baac087

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 journal › Article › peer-review

16 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 language	English (US)
Article number	baac087
Journal	Database
Volume	2022
DOIs	https://doi.org/10.1093/database/baac087
State	Published - 2022
Externally published	Yes

ASJC Scopus subject areas

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

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10.1093/database/baac087

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Matentzoglu, N., Goutte-Gattat, D., Tan, S. Z. K., Balhoff, J. P., Carbon, S., Caron, A. R., Duncan, W. D., Flack, J. E., Haendel, M., Harris, N. L., Hogan, W. R., Hoyt, C. T., Jackson, R. C., Kim, H., Kir, H., Larralde, M., McMurry, J. A., Overton, J. A., Peters, B., ... Osumi-Sutherland, D. (2022). Ontology Development Kit: A toolkit for building, maintaining and standardizing biomedical ontologies. Database, 2022, Article baac087. https://doi.org/10.1093/database/baac087

Matentzoglu, N, Goutte-Gattat, D, Tan, SZK, Balhoff, JP, Carbon, S, Caron, AR, Duncan, WD, Flack, JE, Haendel, M, Harris, NL, Hogan, WR, Hoyt, CT, Jackson, RC, Kim, H, Kir, H, Larralde, M, McMurry, JA, Overton, JA, Peters, B, Pilgrim, C, Stefancsik, R, Robb, SMC, Toro, S, Vasilevsky, NA, Walls, R, Mungall, CJ & Osumi-Sutherland, D 2022, 'Ontology Development Kit: A toolkit for building, maintaining and standardizing biomedical ontologies', Database, vol. 2022, baac087. https://doi.org/10.1093/database/baac087

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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",

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

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AU - Caron, Anita R.

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AU - Overton, James A.

AU - Peters, Bjoern

AU - Pilgrim, Clare

AU - Stefancsik, Ray

AU - Robb, Sofia M.C.

AU - Toro, Sabrina

AU - Vasilevsky, Nicole A.

AU - Walls, Ramona

AU - Mungall, Christopher J.

AU - Osumi-Sutherland, David

PY - 2022

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

Abstract

ASJC Scopus subject areas

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