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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
Published on: April 11, 2019
Controlled vocabularies and ontologies in proteomics: overview, principles and practice
Gerhard Mayer1, Andrew R Jones, Pierre-Alain Binz
1Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany.
Biochimica Et Biophysica Acta
|February 23, 2013
Abstract
None:
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.
Keywords:
ANDI-MSAPIASCIIASTMAmerican Society for Testing and MaterialsAmerican Standard Code for Information InterchangeAnalytical Data Interchange format for Mass SpectrometryAnalytical Information Markup LanguageAniMLApplication Programming InterfaceBRENDA (BRaunschweig ENzyme DAtabase) Tissue OntologyBTOCVChEBIChemical Entities of Biological InterestControlled VocabularyControlled vocabulariesDLDescription LogicEBIEuropean Bioinformatics InstituteHDF5HUPO-PSIHierarchical Data Format, version 5Human Proteome Organisation-Proteomics Standards InitiativeICDIUPACInternational Classification of DiseasesInternational Union for Pure and Applied ChemistryJCAMP-DXJoint Committee on Atomic and Molecular Physical data-Data eXchange formatMALDIMIMIAPEMIBBIMITABMSMass SpectrometryMatrix Assisted Laser Desorption IonizationMeSHMedical Subject HeadingsMinimal Information for Biological and Biomedical InvestigationsMinimum Information About a Proteomics ExperimentMolecular InteractionMolecular Interactions TABular formatNCBINCBONational Center for Biomedical OntologyNational Center for Biotechnology InformationNetwork Common Data FormatOBIOBOOLSOWLOntologies in proteomicsOntology Lookup ServiceOntology editors and softwareOntology for Biomedical InvestigationsOntology formatsOntology maintenanceOpen Biological and Biomedical OntologiesPARPATOPRIDEPRoteomics IDEntifications databasePhenotype Attribute Trait OntologyProtein Affinity ReagentsProteomics data standardsRDF(S)Resource Description Framework (Schema)SRMSelected Reaction MonitoringTPPTrans-Proteomic PipelineURIUniform Resource IdentifierWeb Ontology LanguageXSLTYAFMSYet Another Format for Mass SpectrometryeXtensible Stylesheet Language TransformationnetCDFMore Related Videos
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