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.
ANDI-MS, Analytical Data Interchange format for Mass Spectrometry; AniML, Analytical Information Markup Language; API, Application Programming Interface; ASCII, American Standard Code for Information Interchange; ASTM, American Society for Testing and Materials; BTO, BRENDA (BRaunschweig ENzyme DAtabase) Tissue Ontology; ChEBI, Chemical Entities of Biological Interest; CV, Controlled Vocabulary; DL, Description Logic; EBI, European Bioinformatics Institute; HDF5, Hierarchical Data Format, version 5; HUPO-PSI, Human Proteome Organisation-Proteomics Standards Initiative; ICD, International Classification of Diseases; IUPAC, International Union for Pure and Applied Chemistry; JCAMP-DX, Joint Committee on Atomic and Molecular Physical data-Data eXchange format; MALDI, Matrix Assisted Laser Desorption Ionization; MeSH, Medical Subject Headings; MI, Molecular Interaction; MIBBI, Minimal Information for Biological and Biomedical Investigations; MITAB, Molecular Interactions TABular format; MIAPE, Minimum Information About a Proteomics Experiment; MS, Mass Spectrometry; NCBI, National Center for Biotechnology Information; NCBO, National Center for Biomedical Ontology; netCDF, Network Common Data Format; OBI, Ontology for Biomedical Investigations; OBO, Open Biological and Biomedical Ontologies; OLS, Ontology Lookup Service; OWL, Web Ontology Language; PAR, Protein Affinity Reagents; PATO, Phenotype Attribute Trait Ontology; PRIDE, PRoteomics IDEntifications database; RDF(S), Resource Description Framework (Schema); SRM, Selected Reaction Monitoring; TPP, Trans-Proteomic Pipeline; URI, Uniform Resource Identifier; XSLT, eXtensible Stylesheet Language Transformation; YAFMS, Yet Another Format for Mass Spectrometry; Proteomics data standards; Controlled vocabularies; Ontologies in proteomics; Ontology formats; Ontology editors and software; Ontology maintenance