OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies

Jackson, R. C.; Matentzoglu, N.; Overton, J. A.; Vita, R.; Balhoff, J. P.; Buttigieg, P. L.; Carbon, S.; Courtot, M.; Diehl, A. D.; Dooley, D.; Duncan, W.; Harris, N. L.; Haendel, M. A.; Lewis, S. E.; Natale, D. A.; Osumi-Sutherland, D.; Ruttenberg, A.; Schriml, L. M.; Smith, B.; Stoeckert, C. J.; Vasilevsky, N. A.; Walls, R. L.; Zheng, J.; Mungall, C. J.; Peters, B.

doi:10.1101/2021.06.01.446587

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bioRxiv · 10.1101/2021.06.01.446587

OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies

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Abstract

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 ontologys 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 FAIR.

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Jackson, R. C., Matentzoglu, N., Overton, J. A., Vita, R., Balhoff, J. P., Buttigieg, P. L., Carbon, S., Courtot, M., Diehl, A. D., Dooley, D., Duncan, W., Harris, N. L., Haendel, M. A., Lewis, S. E., Natale, D. A., Osumi-Sutherland, D., Ruttenberg, A., Schriml, L. M., Smith, B., Stoeckert, C. J., Vasilevsky, N. A., Walls, R. L., Zheng, J., Mungall, C. J., Peters, B.. 2021-06-02. OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies. https://doi.org/10.1101/2021.06.01.446587

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