{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T19:05:17Z","timestamp":1776711917192,"version":"3.51.2"},"reference-count":15,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2021,10,26]],"date-time":"2021-10-26T00:00:00Z","timestamp":1635206400000},"content-version":"vor","delay-in-days":25,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R24HG010032"],"award-info":[{"award-number":["R24HG010032"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Director Office of Basic Energy Sciences Office of Science U.S. Department of Energy","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,10,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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\u2019s 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).<\/jats:p>\n                  <jats:p>Database URL http:\/\/obofoundry.org\/<\/jats:p>","DOI":"10.1093\/database\/baab069","type":"journal-article","created":{"date-parts":[[2021,10,13]],"date-time":"2021-10-13T15:56:16Z","timestamp":1634140576000},"source":"Crossref","is-referenced-by-count":173,"title":["OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies"],"prefix":"10.1093","volume":"2021","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4871-5569","authenticated-orcid":false,"given":"Rebecca","family":"Jackson","sequence":"first","affiliation":[{"name":"Bend Informatics LLC, 20770 Double Peaks Drive, Bend, OR 97701, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7356-1779","authenticated-orcid":false,"given":"Nicolas","family":"Matentzoglu","sequence":"additional","affiliation":[{"name":"Semanticly, 71-75 Shelton Street, London WC2H 9JQ, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5139-5557","authenticated-orcid":false,"given":"James A","family":"Overton","sequence":"additional","affiliation":[{"name":"Knocean Inc., 2-107 Quebec Ave., Toronto, ON M6P 2T3, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8957-7612","authenticated-orcid":false,"given":"Randi","family":"Vita","sequence":"additional","affiliation":[{"name":"La Jolla Institute for Immunology, 9420 Athena Cir, La Jolla, CA 92037, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8688-6599","authenticated-orcid":false,"given":"James P","family":"Balhoff","sequence":"additional","affiliation":[{"name":"Renaissance Computing Institute, University of North Carolina, 100 Europa Drive, Suite 540, Chapel Hill, NC 27517, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4366-3088","authenticated-orcid":false,"given":"Pier Luigi","family":"Buttigieg","sequence":"additional","affiliation":[{"name":"Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, Bremerhaven 27570, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8244-1536","authenticated-orcid":false,"given":"Seth","family":"Carbon","sequence":"additional","affiliation":[{"name":"Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9551-6370","authenticated-orcid":false,"given":"Melanie","family":"Courtot","sequence":"additional","affiliation":[{"name":"European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9990-8331","authenticated-orcid":false,"given":"Alexander D","family":"Diehl","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, University at Buffalo, 77 Goodell St, Buffalo, NY 14203, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8844-9165","authenticated-orcid":false,"given":"Damion M","family":"Dooley","sequence":"additional","affiliation":[{"name":"Centre for Infectious Disease Genomics and One Health, Simon Fraser University, 8888 University Dr, Burnaby, BC V5A 1S6, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9625-1899","authenticated-orcid":false,"given":"William D","family":"Duncan","sequence":"additional","affiliation":[{"name":"Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6315-3707","authenticated-orcid":false,"given":"Nomi L","family":"Harris","sequence":"additional","affiliation":[{"name":"Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9114-8737","authenticated-orcid":false,"given":"Melissa A","family":"Haendel","sequence":"additional","affiliation":[{"name":"Biochemistry and Molecular Genetics Department, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8343-612X","authenticated-orcid":false,"given":"Suzanna E","family":"Lewis","sequence":"additional","affiliation":[{"name":"Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5809-9523","authenticated-orcid":false,"given":"Darren A","family":"Natale","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, 2115 Wisconsin Avenue NW, Washington, DC 20007, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7073-9172","authenticated-orcid":false,"given":"David","family":"Osumi-Sutherland","sequence":"additional","affiliation":[{"name":"European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1604-3078","authenticated-orcid":false,"given":"Alan","family":"Ruttenberg","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, University at Buffalo, 77 Goodell St, Buffalo, NY 14203, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8910-9851","authenticated-orcid":false,"given":"Lynn M","family":"Schriml","sequence":"additional","affiliation":[{"name":"School of Medicine, University of Maryland, 655 W Baltimore St S, Baltimore, MD 21201, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1384-116X","authenticated-orcid":false,"given":"Barry","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, University at Buffalo, 77 Goodell St, Buffalo, NY 14203, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5714-991X","authenticated-orcid":false,"given":"Christian J","family":"Stoeckert Jr.","sequence":"additional","affiliation":[{"name":"Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5208-3432","authenticated-orcid":false,"given":"Nicole A","family":"Vasilevsky","sequence":"additional","affiliation":[{"name":"Biochemistry and Molecular Genetics Department, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8815-0078","authenticated-orcid":false,"given":"Ramona L","family":"Walls","sequence":"additional","affiliation":[{"name":"Critical Path Institute, 1730 E River Rd #200, Tucson, AZ 85718, 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