{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T21:27:10Z","timestamp":1773782830210,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2021,7,9]],"date-time":"2021-07-09T00:00:00Z","timestamp":1625788800000},"content-version":"vor","delay-in-days":189,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1169785"],"award-info":[{"award-number":["OPP1169785"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1458400"],"award-info":[{"award-number":["1458400"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HHSN272201400028C, HHSN272201400030C, 75N93019C00001, and R24-HG010032"],"award-info":[{"award-number":["HHSN272201400028C, HHSN272201400030C, 75N93019C00001, and R24-HG010032"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations, logic and hierarchy with a goal to improve and standardize these terms. As a result, inconsistencies in W3C Web Ontology Language (OWL) expressions were identified and corrected, and additionally, standardized design patterns and a formalized template to maintain them were developed. We describe here this informative and productive process to describe the specific benefits and obstacles for OBI and the universal lessons for similar projects.<\/jats:p>","DOI":"10.1093\/database\/baab040","type":"journal-article","created":{"date-parts":[[2021,6,16]],"date-time":"2021-06-16T11:10:30Z","timestamp":1623841830000},"source":"Crossref","is-referenced-by-count":9,"title":["Standardization of assay representation in the Ontology for Biomedical Investigations"],"prefix":"10.1093","volume":"2021","author":[{"given":"Randi","family":"Vita","sequence":"first","affiliation":[{"name":"Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA"}]},{"given":"Jie","family":"Zheng","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\/0000-0003-4871-5569","authenticated-orcid":false,"given":"Rebecca","family":"Jackson","sequence":"additional","affiliation":[{"name":"Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA"},{"name":"Knocean Inc, Toronto, 105 Quebec Ave, ON M2P 2T3, Canada"}]},{"given":"Damion","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"}]},{"given":"James A","family":"Overton","sequence":"additional","affiliation":[{"name":"Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA"},{"name":"Knocean Inc, Toronto, 105 Quebec Ave, ON M2P 2T3, Canada"}]},{"given":"Mark A","family":"Miller","sequence":"additional","affiliation":[{"name":"Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4312-9552","authenticated-orcid":false,"given":"Daniel C","family":"Berrios","sequence":"additional","affiliation":[{"name":"USRA\/NASA Ames Research Center, Building N-260, Moffett Field, CA 94305, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1355-892X","authenticated-orcid":false,"given":"Richard H","family":"Scheuermann","sequence":"additional","affiliation":[{"name":"Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA"},{"name":"Department of Informatics, J. Craig Venter Institute, 4120 Capricorn Ln, La Jolla, CA 92037, USA"},{"name":"Department of Pathology, University of California, 9500 Gilman Dr, San Diego, CA 92093, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9189-9661","authenticated-orcid":false,"given":"Yongqun","family":"He","sequence":"additional","affiliation":[{"name":"Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, 1500 E Medical Center Dr, Ann Arbor, MI 48109, USA"}]},{"given":"Hande K\u00fc\u00e7\u00fck","family":"McGinty","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, Ohio University, 1 Ohio University Drive, Athens, OH 45701, USA"}]},{"given":"Mathias","family":"Brochhausen","sequence":"additional","affiliation":[{"name":"Translational Research Institute, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR 72205, USA"}]},{"given":"Aisyah Yu","family":"Lin","sequence":"additional","affiliation":[{"name":"National Center for Ontological Research, University at Buffalo, 126 Park Hall, Buffalo, NY 14260, USA"}]},{"given":"Sagar B","family":"Jain","sequence":"additional","affiliation":[{"name":"Department of Informatics, J. Craig Venter Institute, 4120 Capricorn Ln, La Jolla, CA 92037, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9586-0780","authenticated-orcid":false,"given":"Marcus C","family":"Chibucos","sequence":"additional","affiliation":[{"name":"Institute for Genome Sciences, University of Maryland School of Medicine, 655 W Baltimore St, Baltimore, MD 21201, USA"}]},{"given":"John","family":"Judkins","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA"}]},{"given":"Michelle G","family":"Giglio","sequence":"additional","affiliation":[{"name":"Institute for Genome Sciences, University of Maryland School of Medicine, 655 W Baltimore St, Baltimore, MD 21201, USA"}]},{"given":"Irene Y","family":"Feng","sequence":"additional","affiliation":[{"name":"Department of Psychology, University of Illinois Urbana-Champaign, 506 S. Wright St, Champaign, IL 61820, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1493-865X","authenticated-orcid":false,"given":"Gully","family":"Burns","sequence":"additional","affiliation":[{"name":"Chan Zuckerberg Initiative, 801 Jefferson Ave, Redwood City, CA 94062, USA"}]},{"given":"Matthew H","family":"Brush","sequence":"additional","affiliation":[{"name":"Oregon Health and Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA"}]},{"given":"Bjoern","family":"Peters","sequence":"additional","affiliation":[{"name":"Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA"},{"name":"Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, 9500 Gilman Drive, La Jolla, CA 92037, USA"}]},{"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"}]}],"member":"286","published-online":{"date-parts":[[2021,7,9]]},"reference":[{"key":"2021071004504585200_R1","doi-asserted-by":"crossref","first-page":"139","DOI":"10.3233\/AO-2010-0079","article-title":"Ontological realism: a methodology for coordinated evolution of scientific ontologies","volume":"5","author":"Smith","year":"2010","journal-title":"Appl. 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