The Ontology for Biomedical Investigations.

Journal: PloS one
Published Date: Apr 29, 2016

Abstract

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.

Authors

  • Anita Bandrowski
    FDI Lab Dept of Neuroscience, UCSD, 9500 Gilman Drive M/C 0608, La Jolla, CA, 92093-0608, USA.
  • Ryan Brinkman
    British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
  • Mathias Brochhausen
    Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
  • Matthew H Brush
    Oregon Health and Science University, Portland, Oregon, United States of America.
  • Bill Bug
    Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America.
  • Marcus C Chibucos
    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.
  • Kevin Clancy
    Thermo Fisher Scientific, Carlsbad, California, United States of America.
  • 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.
  • Dirk Derom
    The Vrije Universiteit Brussel, Ixelles, Brussels, Belgium.
  • Michel Dumontier
    Stanford University, Stanford, CA USA.
  • Liju Fan
    Ontology Workshop, LLC, Columbia, Maryland, United States of America.
  • Jennifer Fostel
    National Toxicology Program, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, United States of America.
  • Gilberto Fragoso
    Center for Biomedical Informatics and Information Technology, National Institutes of Health, Rockville, Maryland, United States of America.
  • Frank Gibson
    Royal Society of Chemistry, Cambridge, Cambridgeshire, United Kingdom.
  • Alejandra Gonzalez-Beltran
    University of Oxford, Oxford, Oxfordshire, United Kingdom.
  • Melissa A Haendel
    Library, Oregon Health & Science University, Portland, OR 97239, USA.
  • Yongqun He
    University of Michigan Medical School, Ann Arbor, MI 48109 USA ; Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, and Comprehensive Cancer Center, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Dr., Ann Arbor, MI 48109 USA.
  • Mervi Heiskanen
    National Cancer Institute, Rockville, Maryland, United States of America.
  • Tina Hernandez-Boussard
    Stanford Center for Biomedical Informatics Research, Stanford, California 94305, USA.
  • Mark Jensen
    University at Buffalo, Buffalo, New York, United States of America.
  • Yu Lin
    Research School of Computer Science, Australian National University, Canberra, 2601, ACT, Australia.
  • Allyson L Lister
    University of Oxford, Oxford, Oxfordshire, United Kingdom.
  • Phillip Lord
    Newcastle University, Newcastle-upon-Tyne, Tyne and Wear, United Kingdom.
  • James Malone
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Elisabetta Manduchi
    University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
  • Monnie McGee
    Southern Methodist University, Dallas, Texas, United States of America.
  • Norman Morrison
    The University of Manchester, Manchester, Greater Manchester, United Kingdom.
  • James A Overton
    La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.
  • Helen Parkinson
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Bjoern Peters
    La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.
  • Philippe Rocca-Serra
    The University of Oxford, Oxford e-Research Centre, Oxford, UK.
  • Alan Ruttenberg
    School of Dental Medicine, State University of New York at Buffalo, Buffalo, New York, United States of America.
  • Susanna-Assunta Sansone
    University of Oxford, Oxford, Oxfordshire, United Kingdom.
  • Richard H Scheuermann
    J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA. RScheuermann@jcvi.org.
  • Daniel Schober
    Leibniz Institute of Plant Biochemistry, Halle, Saxony-Anhalt, Germany.
  • Barry Smith
    Department of Philosophy, University at Buffalo, NY, USA.
  • Larisa N Soldatova
    Brunel University, London, UK.
  • 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.
  • Chris F Taylor
    European Molecular Biology Laboratory- European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom.
  • Carlo Torniai
    Oregon Health and Science University, Portland, Oregon, United States of America.
  • Jessica A Turner
    Psychology Department & Neuroscience Institute, Georgia State University, Atlanta GA, USA.
  • Randi Vita
    La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.
  • Patricia L Whetzel
    University of California San Diego, La Jolla, California, United States of America.
  • Jie Zheng
    State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan, China.

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