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Elsevier, BBA - Proteins and Proteomics, 1(1844), p. 98-107, 2014

DOI: 10.1016/j.bbapap.2013.02.017

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

Journal article published in 2014 by Gerhard Mayer, Andrew R. Jones, Pierre-Alain Binz ORCID, Eric W. Deutsch ORCID, Sandra Orchard, Luisa Montecchi-Palazzi, Juan Antonio Vizcaíno ORCID, Henning Hermjakob, David Oveillero, Randall Julian, Christian Stephan, Helmut E. Meyer, Martin Eisenacher
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Abstract

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.