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

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 tool...

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Published in:	Biochimica et biophysica acta Vol. 1844; no. 1; pp. 98 - 107
Main Authors:	Mayer, Gerhard, Jones, Andrew R., Binz, Pierre-Alain, Deutsch, Eric W., Orchard, Sandra, Montecchi-Palazzi, Luisa, Vizcaíno, Juan Antonio, Hermjakob, Henning, Oveillero, David, Julian, Randall, Stephan, Christian, Meyer, Helmut E., Eisenacher, Martin
Format:	Journal Article
Language:	English
Published:	Netherlands Elsevier B.V 01.01.2014
Subjects:	computer analysis computer software Controlled vocabularies data analysis Ontologies in proteomics Ontology editors and software Ontology formats Ontology maintenance Programming Languages proteins Proteomics Proteomics data standards Software Vocabulary, Controlled PAR Ontology maintenance MIAPE PRIDE MITAB RDF(S) ChEBI DL PATO HDF5 ASCII EBI URI ANDI-MS SRM Proteomics data standards TPP Ontologies in proteomics OBI OLS NCBI AniML MI HUPO-PSI OBO YAFMS Controlled vocabularies OWL MALDI MS NCBO MeSH IUPAC XSLT ICD MIBBI netCDF CV JCAMP-DX Ontology editors and software Ontology formats ASTM API BTO PRoteomics IDEntifications database Controlled Vocabulary Analytical Data Interchange format for Mass Spectrometry Resource Description Framework (Schema) Molecular Interaction eXtensible Stylesheet Language Transformation Chemical Entities of Biological Interest Joint Committee on Atomic and Molecular Physical data-Data eXchange format Molecular Interactions TABular format Yet Another Format for Mass Spectrometry International Classification of Diseases Web Ontology Language Hierarchical Data Format, version 5 National Center for Biomedical Ontology BRENDA (BRaunschweig ENzyme DAtabase) Tissue Ontology European Bioinformatics Institute Selected Reaction Monitoring Minimum Information About a Proteomics Experiment International Union for Pure and Applied Chemistry Minimal Information for Biological and Biomedical Investigations Trans-Proteomic Pipeline Application Programming Interface National Center for Biotechnology Information Ontology for Biomedical Investigations Description Logic Phenotype Attribute Trait Ontology Mass Spectrometry Analytical Information Markup Language Medical Subject Headings Open Biological and Biomedical Ontologies Matrix Assisted Laser Desorption Ionization Ontology Lookup Service Network Common Data Format Protein Affinity Reagents American Society for Testing and Materials American Standard Code for Information Interchange Human Proteome Organisation-Proteomics Standards Initiative Uniform Resource Identifier
ISSN:	1570-9639, 0006-3002, 1878-1454
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Summary:	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. ► The semantic annotation using ontologies is a prerequisite for the semantic web. ► The HUPO-PSI defined a set of XML-based standard formats for proteomics. ► These standard formats allow the referencing of CV terms defined in obo files. ► The CV terms can be used to enforce MIAPE compliance of the data files. ► The mass spectrometry CV is constantly maintained in a community process.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 ObjectType-Review-3 content type line 23
ISSN:	1570-9639 0006-3002 1878-1454
DOI:	10.1016/j.bbapap.2013.02.017