TY - JOUR
T1 - OBO Foundry in 2021
T2 - operationalizing open data principles to evaluate ontologies
AU - Jackson, Rebecca
AU - Matentzoglu, Nicolas
AU - Overton, James A.
AU - Vita, Randi
AU - Balhoff, James P.
AU - Buttigieg, Pier Luigi
AU - Carbon, Seth
AU - Courtot, Melanie
AU - Diehl, Alexander D.
AU - Dooley, Damion M.
AU - Duncan, William D.
AU - Harris, Nomi L.
AU - Haendel, Melissa A.
AU - Lewis, Suzanna E.
AU - Natale, Darren A.
AU - Osumi-Sutherland, David
AU - Ruttenberg, Alan
AU - Schriml, Lynn M.
AU - Smith, Barry
AU - Stoeckert, Christian J.
AU - Vasilevsky, Nicole A.
AU - Walls, Ramona L.
AU - Zheng, Jie
AU - Mungall, Christopher J.
AU - Peters, Bjoern
N1 - Publisher Copyright:
© 2021 The Author(s).
PY - 2021
Y1 - 2021
N2 - Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies (OBO) Foundry was created to address this by facilitating the development, harmonization, application and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here, we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology's compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable, federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data Findable, Accessible, Interoperable, and Reusable (FAIR).
AB - Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies (OBO) Foundry was created to address this by facilitating the development, harmonization, application and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here, we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology's compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable, federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data Findable, Accessible, Interoperable, and Reusable (FAIR).
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U2 - 10.1093/database/baab069
DO - 10.1093/database/baab069
M3 - Article
C2 - 34697637
AN - SCOPUS:85123900962
SN - 1758-0463
VL - 2021
JO - Database
JF - Database
M1 - baab069
ER -