Format

Send to

Choose Destination
PLoS One. 2016 Apr 29;11(4):e0154556. doi: 10.1371/journal.pone.0154556. eCollection 2016.

The Ontology for Biomedical Investigations.

Author information

1
University of California San Diego, La Jolla, California, United States of America.
2
British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
3
University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America.
4
Oregon Health and Science University, Portland, Oregon, United States of America.
5
Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America.
6
University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
7
Thermo Fisher Scientific, Carlsbad, California, United States of America.
8
Simon Fraser University, Burnaby, British Columbia, Canada.
9
The Vrije Universiteit Brussel, Ixelles, Brussels, Belgium.
10
Stanford University, Stanford, California, United States of America.
11
Ontology Workshop, LLC, Columbia, Maryland, United States of America.
12
National Toxicology Program, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, United States of America.
13
Center for Biomedical Informatics and Information Technology, National Institutes of Health, Rockville, Maryland, United States of America.
14
Royal Society of Chemistry, Cambridge, Cambridgeshire, United Kingdom.
15
University of Oxford, Oxford, Oxfordshire, United Kingdom.
16
University of Michigan Medical School, Ann Arbor, Michigan, United States of America.
17
National Cancer Institute, Rockville, Maryland, United States of America.
18
University at Buffalo, Buffalo, New York, United States of America.
19
Newcastle University, Newcastle-upon-Tyne, Tyne and Wear, United Kingdom.
20
European Molecular Biology Laboratory- European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom.
21
University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
22
Southern Methodist University, Dallas, Texas, United States of America.
23
The University of Manchester, Manchester, Greater Manchester, United Kingdom.
24
La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.
25
J. Craig Venter Institute, La Jolla, California, United States of America.
26
Leibniz Institute of Plant Biochemistry, Halle, Saxony-Anhalt, Germany.
27
Brunel University London, Uxbridge, Middlesex, United Kingdom.
28
Georgia State University, Atlanta, Georgia, United States of America.

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.

PMID:
27128319
PMCID:
PMC4851331
DOI:
10.1371/journal.pone.0154556
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Public Library of Science Icon for PubMed Central
Loading ...
Support Center