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Published, Version of Record (VoR)CC0 V1.0, Open
Journal article
The Ontology for Biomedical Investigations
PloS one, v 11(4), pp e0154556-e0154556
2016
PMID: 27128319
Featured in Collection : UN Sustainable Development Goals @ Drexel
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.
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Details
- Title
- The Ontology for Biomedical Investigations
- Creators
- Anita Bandrowski - University of California, San DiegoRyan Brinkman - BC Cancer Research CentreMathias Brochhausen - University of Arkansas for Medical SciencesMatthew H Brush - Oregon Health & Science UniversityBill Bug - Drexel UniversityMarcus C Chibucos - University of Maryland, BaltimoreKevin Clancy - Thermo Fisher ScientificMélanie Courtot - Simon Fraser UniversityDirk Derom - Vrije Universiteit BrusselMichel Dumontier - Stanford UniversityLiju Fan - Ontology Workshop, LLC, Columbia, Maryland, United States of America.Jennifer Fostel - National Institute of Environmental Health SciencesGilberto Fragoso - Center for Biomedical Informatics and Information Technology, National Institutes of Health, Rockville, Maryland, United States of AmericaFrank Gibson - Royal Society of ChemistryAlejandra Gonzalez-Beltran - University of OxfordMelissa A Haendel - Oregon Health & Science UniversityYongqun He - University of Michigan–Ann ArborMervi Heiskanen - National Cancer InstituteTina Hernandez-Boussard - Stanford UniversityMark Jensen - University at Buffalo, State University of New YorkYu Lin - University of Michigan–Ann ArborAllyson L Lister - University of OxfordPhillip Lord - Newcastle UniversityJames Malone - European Bioinformatics InstituteElisabetta Manduchi - Annenberg Public Policy CenterMonnie McGee - Southern Methodist UniversityNorman Morrison - University of ManchesterJames A Overton - La Jolla Institute For Allergy & ImmunologyHelen Parkinson - European Bioinformatics InstituteBjoern Peters - La Jolla Institute For Allergy & ImmunologyPhilippe Rocca-Serra - University of OxfordAlan Ruttenberg - University at Buffalo, State University of New YorkSusanna-Assunta Sansone - University of OxfordRichard H Scheuermann - J. Craig Venter InstituteDaniel Schober - Leibniz Institute of Plant BiochemistryBarry Smith - University at Buffalo, State University of New YorkLarisa N Soldatova - Brunel University LondonChristian J Stoeckert, Jr - University of Pennsylvania, Philadelphia, Pennsylvania, United States of AmericaChris F Taylor - European Bioinformatics InstituteCarlo Torniai - Oregon Health & Science UniversityJessica A Turner - Georgia State University, Atlanta, Georgia, United States of AmericaRandi Vita - La Jolla Institute For Allergy & ImmunologyPatricia L Whetzel - University of California, San DiegoJie Zheng - Annenberg Public Policy CenterYing Lin - Information Science (Informatics)
- Publication Details
- PloS one, v 11(4), pp e0154556-e0154556
- Publisher
- Public LIbrary of Science (PLOS)
- Grant note
- R01 GM080646 / NIGMS NIH HHS HHSN272201400028C / NIAID NIH HHS U19 AI118626 / NIAID NIH HHS BB/G000638/1 / Biotechnology and Biological Sciences Research Council U24 DA039832 / NIDA NIH HHS R01 AI081062 / NIAID NIH HHS HHSN272201200010C / NIAID NIH HHS R24 OD011883 / NIH HHS UL1 TR001412 / NCATS NIH HHS BB/C008200/1 / Biotechnology and Biological Sciences Research Council R01 GM093132 / NIGMS NIH HHS BB/I000771/1 / Biotechnology and Biological Sciences Research Council HHSN272201400030C / NIAID NIH HHS P41 HG003619 / NHGRI NIH HHS BB/E025080/1 / Biotechnology and Biological Sciences Research Council U01 DK072473 / NIDDK NIH HHS
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Information Science
- Web of Science ID
- WOS:000375212600038
- Scopus ID
- 2-s2.0-84967317201
- Other Identifier
- 991019173522004721
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- Collaboration types
- Industry collaboration
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biotechnology & Applied Microbiology