Controlled vocabularies and ontologies in proteomics: Overview, principles and practice

被引：30

作者：

Mayer, Gerhard ^{[1
]}

Jones, Andrew R. ^{[2
]}

Binz, Pierre-Alain ^{[3
]}

Deutsch, Eric W. ^{[4
]}

Orchard, Sandra ^{[5
]}

Montecchi-Palazzi, Luisa ^{[5
]}

Vizcaino, Juan Antonio ^{[5
]}

Hermjakob, Henning ^{[5
]}

Oveillero, David ^{[5
]}

Julian, Randall ^{[6
]}

Stephan, Christian ^{[1
,7
]}

Meyer, Helmut E. ^{[1
]}

Eisenacher, Martin ^{[1
]}

机构：

[1] Ruhr Univ Bochum, MPC, D-44801 Bochum, Germany

[2] Univ Liverpool, Inst Integrat Biol, Liverpool L69 7ZB, Merseyside, England

[3] SIB, Swiss Prot Grp, CH-1211 Geneva 4, Switzerland

[4] Inst Syst Biol, Seattle, WA 98109 USA

[5] EMBL EBI, Cambridge CB10 1SD, England

[6] Indigo BioSyst, Indianapolis, IN 46240 USA

[7] Kairos GmbH, D-44799 Bochum, Germany

来源：

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS | 2014年 / 1844卷 / 01期

基金：

英国生物技术与生命科学研究理事会; 英国惠康基金;

关键词：

Proteomics data standards; Controlled vocabularies; Ontologies in proteomics; Ontology formats; Ontology editors and software; Ontology maintenance; SOURCE [!text type='JAVA']JAVA[!/text] API; PROTEIN IDENTIFICATION; DATA FORMAT; COMMUNITY STANDARD; MARKUP LANGUAGE; LOOKUP SERVICE; PSI STANDARD; COMMON DATA; MASS; GUIDELINES;

D O I：

10.1016/j.bbapap.2013.02.017

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the "mapping files" used to ensure correct controlled vocabulary terms that are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. (C) 2013 Elsevier B.V. All rights reserved.

引用

页码：98 / 107

页数：10

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