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The Ontology for Biomedical Investigations

Lookup NU author(s): Dr Phillip Lord



This is the final published version of an article that has been published in its final definitive form by Public Library of Science, 2016.

For re-use rights please refer to the publisher's terms and conditions.


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 owl.

Publication metadata

Author(s): Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan LJ, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He YQ, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, Mcgee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J

Publication type: Article

Publication status: Published

Journal: PLoS ONE

Year: 2016

Volume: 11

Issue: 4

Online publication date: 29/04/2016

Acceptance date: 17/04/2016

Date deposited: 26/07/2016

ISSN (electronic): 1932-6203

Publisher: Public Library of Science


DOI: 10.1371/journal.pone.0154556


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Funder referenceFunder name
1U19AI118626National Institutes of Health
1458400National Science Foundation Division of Biological Infrastructure
BB/E025080/1Biotechnology and Biological Sciences Research Council
503630European Network of Excellence (NoE)
BB/I000917/1Biotechnology and Biological Sciences Research Council
BB/L024101/1Biotechnology and Biological Sciences Research Council
BB/C008200/1Biotechnology and Biological Sciences Research Council
BB/G000638/1Biotechnology and Biological Sciences Research Council
EP/K030582/1Engineering and Physical Sciences Research Council UK
EP/M015661/1Engineering and Physical Sciences Research Council UK
H2020-EU. 654241European Commission
H2020-EU.3.1634107European Commission
HHSN272201400030CNational Institutes of Health
GC1R-06673-BCalifornia Institute for Regenerative Medicine
HHSN272201200010CNational Institutes of Health
HHSN272201400028CNational Institutes of Health
P41 HG003619National Institutes of Health
R01AI081062National Institute of Allergy and Infectious Diseases
R01GM093132National Institutes of Health
U01 DK 072473National Institutes of Health