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

BioaRxiv (2021)
  Copy   BIBTEX

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 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 FAIR. Competing Interest StatementThe authors have declared no competing interest.

Similar books and articles

The Industrial Ontologies Foundry (IOF) Perspectives.Mohamed Karray, Neil Otte, Rahul Rai, Farhad Ameri, Boonserm Kulvatunyou, Barry Smith, Dimitris Kiritsis, Chris Will, Rebecca Arista & Others - 2021 - Proceedings: Industrial Ontology Foundry (IOF) Achieving Data Interoperability Workshop, International Conference on Interoperability for Enterprise Systems and Applications, Tarbes, France, March 17-24, 2020.
A Unified Framework for Biomedical Terminologies and Ontologies.Werner Ceusters & Barry Smith - 2010 - Studies in Health Technology and Informatics 160:1050-1054.
Ontologies of Cellular Networks.Arp Robert & Barry Smith - 2008 - Science Signalling 1 (50):1--3.
Putting Biomedical Ontologies to Work.Barry Smith & Mathias Brochhausen - 2010 - Methods of Information in Medicine 49 (2):135-40.
Dealing with Elements of Medical Encounters: An Approach Based on Ontological Realism.Farinelli Fernanda, Almeida Mauricio, Elkin Peter & Barry Smith - 2016 - Proceedings of the Joint International Conference on Biological Ontology and Biocreative 1747.

Analytics

Added to PP
2021-08-17

Downloads
105 (#116,620)

6 months
34 (#32,188)

Historical graph of downloads
How can I increase my downloads?

Author Profiles

William Duncan Sharkey
University of Southampton
Barry Smith
State University of New York, Buffalo
Alan Ruttenberg
University at Buffalo

Citations of this work

The Industrial Ontologies Foundry (IOF) Core Ontology.Milos Drobnjakovic, Boonserm Kulvatunyou, Farhad Ameri, Chris Will, Barry Smith & Albert Jones - 2022 - FOMI 2022: 12th International Workshop on Formal Ontologies Meet Industry, September 12-15, 2022, Tarbes, France.

Add more citations

References found in this work

No references found.

Add more references