title: The Ontology for Biomedical Investigations.
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.affiliation: University of California San Diego, La Jolla, California, United States of America.
authors.forename: Anita
authors.initials: A
authors.lastname: Bandrowski
authors.affiliation: British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
authors.forename: Ryan
authors.initials: R
authors.lastname: Brinkman
authors.affiliation: University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America.
authors.forename: Mathias
authors.initials: M
authors.lastname: Brochhausen
authors.affiliation: Oregon Health and Science University, Portland, Oregon, United States of America.
authors.forename: Matthew H
authors.initials: MH
authors.lastname: Brush
authors.affiliation: Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America.
authors.forename: Bill
authors.initials: B
authors.lastname: Bug
authors.affiliation: University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Marcus C
authors.initials: MC
authors.lastname: Chibucos
authors.affiliation: Thermo Fisher Scientific, Carlsbad, California, United States of America.
authors.forename: Kevin
authors.initials: K
authors.lastname: Clancy
authors.affiliation: Simon Fraser University, Burnaby, British Columbia, Canada.
authors.forename: Mélanie
authors.initials: M
authors.lastname: Courtot
authors.affiliation: The Vrije Universiteit Brussel, Ixelles, Brussels, Belgium.
authors.forename: Dirk
authors.initials: D
authors.lastname: Derom
authors.affiliation: Stanford University, Stanford, California, United States of America.
authors.forename: Michel
authors.initials: M
authors.lastname: Dumontier
authors.affiliation: Ontology Workshop, LLC, Columbia, Maryland, United States of America.
authors.forename: Liju
authors.initials: L
authors.lastname: Fan
authors.affiliation: National Toxicology Program, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, United States of America.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Fostel
authors.affiliation: Center for Biomedical Informatics and Information Technology, National Institutes of Health, Rockville, Maryland, United States of America.
authors.forename: Gilberto
authors.initials: G
authors.lastname: Fragoso
authors.affiliation: Royal Society of Chemistry, Cambridge, Cambridgeshire, United Kingdom.
authors.forename: Frank
authors.initials: F
authors.lastname: Gibson
authors.affiliation: University of Oxford, Oxford, Oxfordshire, United Kingdom.
authors.forename: Alejandra
authors.initials: A
authors.lastname: Gonzalez-Beltran
authors.affiliation: Oregon Health and Science University, Portland, Oregon, United States of America.
authors.forename: Melissa A
authors.initials: MA
authors.lastname: Haendel
authors.affiliation: University of Michigan Medical School, Ann Arbor, Michigan, United States of America.
authors.forename: Yongqun
authors.initials: Y
authors.lastname: He
authors.affiliation: National Cancer Institute, Rockville, Maryland, United States of America.
authors.forename: Mervi
authors.initials: M
authors.lastname: Heiskanen
authors.affiliation: Stanford University, Stanford, California, United States of America.
authors.forename: Tina
authors.initials: T
authors.lastname: Hernandez-Boussard
authors.affiliation: University at Buffalo, Buffalo, New York, United States of America.
authors.forename: Mark
authors.initials: M
authors.lastname: Jensen
authors.affiliation: University of Michigan Medical School, Ann Arbor, Michigan, United States of America.
authors.forename: Yu
authors.initials: Y
authors.lastname: Lin
authors.affiliation: University of Oxford, Oxford, Oxfordshire, United Kingdom.
authors.forename: Allyson L
authors.initials: AL
authors.lastname: Lister
authors.affiliation: Newcastle University, Newcastle-upon-Tyne, Tyne and Wear, United Kingdom.
authors.forename: Phillip
authors.initials: P
authors.lastname: Lord
authors.affiliation: European Molecular Biology Laboratory- European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom.
authors.forename: James
authors.initials: J
authors.lastname: Malone
authors.affiliation: University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Manduchi
authors.affiliation: Southern Methodist University, Dallas, Texas, United States of America.
authors.forename: Monnie
authors.initials: M
authors.lastname: McGee
authors.affiliation: The University of Manchester, Manchester, Greater Manchester, United Kingdom.
authors.forename: Norman
authors.initials: N
authors.lastname: Morrison
authors.affiliation: La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.
authors.forename: James A
authors.initials: JA
authors.lastname: Overton
authors.affiliation: European Molecular Biology Laboratory- European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom.
authors.forename: Helen
authors.initials: H
authors.lastname: Parkinson
authors.affiliation: La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.
authors.forename: Bjoern
authors.initials: B
authors.lastname: Peters
authors.affiliation: University of Oxford, Oxford, Oxfordshire, United Kingdom.
authors.forename: Philippe
authors.initials: P
authors.lastname: Rocca-Serra
authors.affiliation: University at Buffalo, Buffalo, New York, United States of America.
authors.forename: Alan
authors.initials: A
authors.lastname: Ruttenberg
authors.affiliation: University of Oxford, Oxford, Oxfordshire, United Kingdom.
authors.forename: Susanna-Assunta
authors.initials: SA
authors.lastname: Sansone
authors.affiliation: J. Craig Venter Institute, La Jolla, California, United States of America.
authors.forename: Richard H
authors.initials: RH
authors.lastname: Scheuermann
authors.affiliation: Leibniz Institute of Plant Biochemistry, Halle, Saxony-Anhalt, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Schober
authors.affiliation: University at Buffalo, Buffalo, New York, United States of America.
authors.forename: Barry
authors.initials: B
authors.lastname: Smith
authors.affiliation: Brunel University London, Uxbridge, Middlesex, United Kingdom.
authors.forename: Larisa N
authors.initials: LN
authors.lastname: Soldatova
authors.affiliation: University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Stoeckert
authors.affiliation: European Molecular Biology Laboratory- European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom.
authors.forename: Chris F
authors.initials: CF
authors.lastname: Taylor
authors.affiliation: Oregon Health and Science University, Portland, Oregon, United States of America.
authors.forename: Carlo
authors.initials: C
authors.lastname: Torniai
authors.affiliation: Georgia State University, Atlanta, Georgia, United States of America.
authors.forename: Jessica A
authors.initials: JA
authors.lastname: Turner
authors.affiliation: La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.
authors.forename: Randi
authors.initials: R
authors.lastname: Vita
authors.affiliation: University of California San Diego, La Jolla, California, United States of America.
authors.forename: Patricia L
authors.initials: PL
authors.lastname: Whetzel
authors.affiliation: University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
authors.forename: Jie
authors.initials: J
authors.lastname: Zheng
mesh_terms: D000818:Animals; D064229:Biological Ontologies / Q000458:organization & administration / Q000706:statistics & numerical data / Q000639:trends; D019295:Computational Biology; D016208:Databases, Factual; D006801:Humans; D020407:Internet; D000071253:Metadata; D012660:Semantics; D012984:Software