The Ontology for Biomedical Investigations

被引：185

作者：

Bandrowski, Anita ^{[1
]}

Brinkman, Ryan ^{[2
]}

Brochhausen, Mathias ^{[3
]}

Brush, Matthew H. ^{[4
]}

Bug, Bill ^{[5
]}

Chibucos, Marcus C. ^{[6
]}

Clancy, Kevin ^{[7
]}

Courtot, Melanie ^{[8
]}

Derom, Dirk ^{[9
]}

Dumontier, Michel ^{[10
]}

Fan, Liju ^{[11
]}

Fostel, Jennifer ^{[12
]}

Fragoso, Gilberto ^{[13
]}

Gibson, Frank ^{[14
]}

Gonzalez-Beltran, Alejandra ^{[15
]}

Haendel, Melissa A. ^{[4
]}

He, Yongqun ^{[16
]}

Heiskanen, Mervi ^{[17
]}

Hernandez-Boussard, Tina ^{[10
]}

Jensen, Mark ^{[18
]}

Lin, Yu ^{[16
]}

Lister, Allyson L. ^{[15
]}

Lord, Phillip ^{[19
]}

Malone, James ^{[20
]}

Manduchi, Elisabetta ^{[21
]}

McGee, Monnie ^{[22
]}

Morrison, Norman ^{[23
]}

Overton, James A. ^{[24
]}

Parkinson, Helen ^{[20
]}

Peters, Bjoern ^{[24
]}

Rocca-Serra, Philippe ^{[15
]}

Ruttenberg, Alan ^{[18
]}

Sansone, Susanna-Assunta ^{[15
]}

Scheuermann, Richard H. ^{[25
]}

Schober, Daniel ^{[26
]}

Smith, Barry ^{[18
]}

Soldatova, Larisa N. ^{[27
]}

Stoeckert, Christian J., Jr. ^{[21
]}

Taylor, Chris F. ^{[20
]}

Torniai, Carlo ^{[4
]}

Turner, Jessica A. ^{[28
]}

Vita, Randi ^{[24
]}

Whetzel, Patricia L. ^{[1
]}

Zheng, Jie ^{[21
]}

机构：

[1] Univ Calif San Diego, La Jolla, CA 92093 USA

[2] British Columbia Canc Res Ctr, Vancouver, BC V5Z 1L3, Canada

[3] Univ Arkansas Med Sci, Little Rock, AR 72205 USA

[4] Oregon Hlth & Sci Univ, Portland, OR 97201 USA

[5] Drexel Univ, Coll Med, Philadelphia, PA 19104 USA

[6] Univ Maryland, Sch Med, Baltimore, MD 21201 USA

[7] Thermo Fisher Sci, Carlsbad, CA USA

[8] Simon Fraser Univ, Burnaby, BC V5A 1S6, Canada

[9] Vrije Univ Brussel, Brussels, Belgium

[10] Stanford Univ, Stanford, CA 94305 USA

[11] Ontol Workshop LLC, Columbia, MD USA

[12] NIEHS, Natl Toxicol Program, NIH, POB 12233, Res Triangle Pk, NC 27709 USA

[13] NIH, Ctr Biomed Informat & Informat Technol, Rockville, MD USA

[14] Royal Soc Chem, Cambridge, England

[15] Univ Oxford, Oxford, England

[16] Univ Michigan, Sch Med, Ann Arbor, MI USA

[17] NCI, Rockville, MD USA

[18] Univ Buffalo, Buffalo, NY USA

[19] Newcastle Univ, Newcastle Upon Tyne NE1 7RU, Tyne & Wear, England

[20] European Bioinformat Inst, European Mol Biol Lab, Hinxton, Cambs, England

[21] Univ Penn, Philadelphia, PA 19104 USA

[22] So Methodist Univ, Dallas, TX 75275 USA

[23] Univ Manchester, Manchester, England

[24] La Jolla Inst Allergy & Immunol, La Jolla, CA USA

[25] J Craig Venter Inst, La Jolla, CA USA

[26] Leibniz Inst Plant Biochem, Halle, Saxony Anhalt, Germany

[27] Brunel Univ London, Uxbridge, Middx, England

[28] Georgia State Univ, Atlanta, GA 30303 USA

来源：

PLOS ONE | 2016年 / 11卷 / 04期

基金：

英国生物技术与生命科学研究理事会; 美国国家科学基金会; 欧盟地平线“2020”; 美国国家卫生研究院; 英国工程与自然科学研究理事会;

关键词：

FUNCTIONAL GENOMICS; MINIMUM INFORMATION; MICROARRAY DATA; OBO FOUNDRY; STANDARDS; DATABASE; FORMAT; TAB; SPECIFICATION; FRAMEWORK;

D O I：

10.1371/journal.pone.0154556

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

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