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

Journal Article · · Database
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  1. Semanticly, Athens (Greece)
  2. Univ. of Cambridge (United Kingdom)
  3. Wellcome Genome Campus, Hinxton, CB (United Kingdom). Samples Phenotypes and Ontologies Team (SPOT), European Bioinformatics Institute (EMBL-EBI)
  4. Univ. of North Carolina, Chapel Hill, NC (United States). Renaissance Computing Institute (RENCI)
  5. Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Berkeley Bioinformatics Open-source Projects (BBOP)
  6. Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Berkeley Bioinformatics Open-source Projects (BBOP); Univ. of Florida, Gainesville, FL (United States)
  7. Johns Hopkins Univ., Baltimore, MD (United States)
  8. Univ. of Colorado, Aurora, CO (United States). Anschutz Medical Campus
  9. Univ. of Florida, Gainesville, FL (United States)
  10. Harvard Medical School, Boston, MA (United States)
  11. Bend Informatics LLC, Keizer, OR (United States)
  12. Robert Bosch LLC, Sunnyvale, CA (United States)
  13. European Molecular Biology Lab. (EMBL), Heidelberg (Germany)
  14. Knocean Inc., Toronto, ON (Canada)
  15. La Jolla Institute for Immunology, La Jolla, CA (United States)
  16. Stowers Institute for Medical Research, Kansas City, MO (United States)
  17. Critical Path Institute, Tucson, AZ (United States)
+ Show Author Affiliations

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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1994344
Journal Information:
Database, Journal Name: Database Vol. 2022; ISSN 1758-0463
Publisher:
Oxford University Press - International Society for BiocurationCopyright Statement
Country of Publication:
United States
Language:
English

References (21)

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OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies journal October 2021
A Simple Standard for Sharing Ontological Mappings (SSSOM) journal January 2022
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Uberon, an integrative multi-species anatomy ontology journal January 2012
ROBOT: A Tool for Automating Ontology Workflows journal July 2019
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability journal July 2016
Dead simple OWL design patterns journal June 2017
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability journal January 2018
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data journal June 2017
Ten Simple Rules for the Care and Feeding of Scientific Data journal April 2014
Ten quick tips for biocuration journal May 2019

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Related Subjects

96 KNOWLEDGE MANAGEMENT AND PRESERVATION