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Standardization of assay representation in the Ontology for Biomedical Investigations.
Vita, Randi; Zheng, Jie; Jackson, Rebecca; Dooley, Damion; Overton, James A; Miller, Mark A; Berrios, Daniel C; Scheuermann, Richard H; He, Yongqun; McGinty, Hande Küçük; Brochhausen, Mathias; Lin, Aisyah Yu; Jain, Sagar B; Chibucos, Marcus C; Judkins, John; Giglio, Michelle G; Feng, Irene Y; Burns, Gully; Brush, Matthew H; Peters, Bjoern; Stoeckert, Christian J.
Affiliation
  • Vita R; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.
  • Zheng J; Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA.
  • Jackson R; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.
  • Dooley D; Knocean Inc, Toronto, 105 Quebec Ave, ON M2P 2T3, Canada.
  • Overton JA; Centre for Infectious Disease Genomics and One Health, Simon Fraser University, 8888 University Dr, Burnaby, BC V5A 1S6, Canada.
  • Miller MA; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.
  • Berrios DC; Knocean Inc, Toronto, 105 Quebec Ave, ON M2P 2T3, Canada.
  • Scheuermann RH; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA.
  • He Y; USRA/NASA Ames Research Center, Building N-260, Moffett Field, CA 94305, USA.
  • McGinty HK; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.
  • Brochhausen M; Department of Informatics, J. Craig Venter Institute, 4120 Capricorn Ln, La Jolla, CA 92037, USA.
  • Lin AY; Department of Pathology, University of California, 9500 Gilman Dr, San Diego, CA 92093, USA.
  • Jain SB; Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, 1500 E Medical Center Dr, Ann Arbor, MI 48109, USA.
  • Chibucos MC; Department of Chemistry and Biochemistry, Ohio University, 1 Ohio University Drive, Athens, OH 45701, USA.
  • Judkins J; Translational Research Institute, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR 72205, USA.
  • Giglio MG; National Center for Ontological Research, University at Buffalo, 126 Park Hall, Buffalo, NY 14260, USA.
  • Feng IY; Department of Informatics, J. Craig Venter Institute, 4120 Capricorn Ln, La Jolla, CA 92037, USA.
  • Burns G; Institute for Genome Sciences, University of Maryland School of Medicine, 655 W Baltimore St, Baltimore, MD 21201, USA.
  • Brush MH; Department of Biology, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA.
  • Peters B; Institute for Genome Sciences, University of Maryland School of Medicine, 655 W Baltimore St, Baltimore, MD 21201, USA.
  • Stoeckert CJ; Department of Psychology, University of Illinois Urbana-Champaign, 506 S. Wright St, Champaign, IL 61820, USA.
Database (Oxford) ; 20212021 07 09.
Article in En | MEDLINE | ID: mdl-34244718
ABSTRACT
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.
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Full text: 1 Database: MEDLINE Main subject: Biological Ontologies / Language Language: En Journal: Database (Oxford) Year: 2021 Type: Article Affiliation country: United States
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Full text: 1 Database: MEDLINE Main subject: Biological Ontologies / Language Language: En Journal: Database (Oxford) Year: 2021 Type: Article Affiliation country: United States