OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.

Journal: Database : the journal of biological databases and curation
Published Date:

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 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). Database URL http://obofoundry.org/.

Authors

  • Rebecca Jackson
    Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.
  • Nicolas Matentzoglu
    School of Computer Science, University of Manchester, Oxford Road, Manchester, UK. nicolas.matentzoglu@manchester.ac.uk.
  • James A Overton
    La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.
  • Randi Vita
    La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.
  • James P Balhoff
    National Evolutionary Synthesis Center, Durham, NC 27705, USA; University of North Carolina, Chapel Hill, NC 27599, USA;
  • Pier Luigi Buttigieg
    Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany.
  • Seth Carbon
    Berkeley Bioinformatics Open-Source Projects, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Rd. MS 977, Berkeley, CA, 94720, USA.
  • Mélanie Courtot
    Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.
  • Alexander D Diehl
    Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.
  • Damion M Dooley
    Centre for Infectious Disease Genomics and One Health, Simon Fraser University, 8888 University Dr, Burnaby, BC V5A 1S6, Canada.
  • William D Duncan
    Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
  • Nomi L Harris
    Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
  • Melissa A Haendel
    Library, Oregon Health & Science University, Portland, OR 97239, USA.
  • Suzanna E Lewis
    Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland, Department of Medicine and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA, School of Information, University of South Florida, Tampa, FL, 33647, USA, Genomics Division, Lawrence Berkeley National Lab, 1 Cyclotron Rd., Berkeley, 94720 CA USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland, ETH Zurich, Department of Computer Science, Universitätstr. 19, 8092 Zürich, Switzerland, SIB Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zürich, Switzerland and University College London, Gower St, London WC1E 6BT, UK.
  • Darren A Natale
    Protein Information Resource, Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, D. C., United States of America.
  • David Osumi-Sutherland
    European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
  • Alan Ruttenberg
    School of Dental Medicine, State University of New York at Buffalo, Buffalo, New York, United States of America.
  • Lynn M Schriml
    Department of Biochemistry and Molecular Medicine, George Washington University, Washington, DC 20037, USA, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Center for Bioinformatics and Information Technology, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892-9760, USA, NASA Jet Propulsion Laboratory, Pasadena, CA, USA, Division of Cancer Prevention, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892-9760, USA, Wellcome Trust Sanger Institute, Cambridge, UK and McCormick Genomic and Proteomic Center, George Washington University, Washington, DC 20037, USA.
  • Barry Smith
    Department of Philosophy, University at Buffalo, NY, USA.
  • Christian J Stoeckert
    Department of Genetics, Institute for Translational Medicine and Therapeutics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
  • Nicole A Vasilevsky
    Ontology Development Group, Library, Oregon Health and Science University, Portland, Oregon, 97239, USA.
  • Ramona L Walls
    CyVerse, University of Arizona, Tucson, AZ 85721 USA.
  • Jie Zheng
    State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan, China.
  • Christopher J Mungall
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Bjoern Peters
    La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.