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

Autor: Pierre-Alain Binz, David Oveillero, Martin Eisenacher, Randall K. Julian, Sandra Orchard, Henning Hermjakob, Andrew R. Jones, Christian Stephan, Eric W. Deutsch, Luisa Montecchi-Palazzi, Helmut E. Meyer, Juan Antonio Vizcaíno, Gerhard Mayer
Rok vydání: 2014
Předmět:
Proteomics
MIBBI
Minimal Information for Biological and Biomedical Investigations
Ontology formats
MI
Molecular Interaction
Computer science
NCBI
National Center for Biotechnology Information
ASTM
American Society for Testing and Materials
MeSH
Medical Subject Headings
MIAPE
Minimum Information About a Proteomics Experiment
Review
Ontology (information science)
Bioinformatics
Biochemistry
Analytical Chemistry
Description logic
Ontology maintenance
Ontologies in proteomics
YAFMS
Yet Another Format for Mass Spectrometry
computer.programming_language
CV
Controlled Vocabulary
OWL
Web Ontology Language
Proteomics Standards Initiative
Application programming interface
TPP
Trans-Proteomic Pipeline
ANDI-MS
Analytical Data Interchange format for Mass Spectrometry
BTO
BRENDA (BRaunschweig ENzyme DAtabase) Tissue Ontology
HUPO-PSI
Human Proteome Organisation-Proteomics Standards Initiative
Web Ontology Language
NCBO
National Center for Biomedical Ontology
IUPAC
International Union for Pure and Applied Chemistry
MALDI
Matrix Assisted Laser Desorption Ionization
Vocabulary
Controlled
PAR
Protein Affinity Reagents
Controlled vocabularies
JCAMP-DX
Joint Committee on Atomic and Molecular Physical data-Data eXchange format
URI
Uniform Resource Identifier
GeneralLiterature_INTRODUCTORYANDSURVEY
RDF Schema
Biophysics
AniML
Analytical Information Markup Language
OBI
Ontology for Biomedical Investigations
EBI
European Bioinformatics Institute
Proteomics data standards
DL
Description Logic
Controlled vocabulary
netCDF
Network Common Data Format
OBO
Open Biological and Biomedical Ontologies
XSLT
eXtensible Stylesheet Language Transformation
Molecular Biology
SRM
Selected Reaction Monitoring
ASCII
American Standard Code for Information Interchange
Ontology for Biomedical Investigations
MS
Mass Spectrometry
PRIDE
PRoteomics IDEntifications database
RDF(S)
Resource Description Framework (Schema)
OLS
Ontology Lookup Service
HDF5
Hierarchical Data Format
version 5
Data science
ICD
International Classification of Diseases
API
Application Programming Interface
Programming Languages
ChEBI
Chemical Entities of Biological Interest
MITAB
Molecular Interactions TABular format
computer
Software
Ontology editors and software
PATO
Phenotype Attribute Trait Ontology
Zdroj: Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics; Vol 1844
Biochimica et Biophysica Acta
ISSN: 1570-9639
DOI: 10.1016/j.bbapap.2013.02.017
Popis: 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.
Highlights ► 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.
Databáze: OpenAIRE
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