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

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1844, Issue 1 PART A, 2014, Pages 98-107

  Mayer, Gerhard ^a   Jones, Andrew R ^b   Binz, Pierre Alain ^c   Deutsch, Eric W ^d   Orchard, Sandra ^e   Montecchi Palazzi, Luisa ^e   Vizcaíno, Juan Antonio ^e   Hermjakob, Henning ^e   Oveillero, David ^e   Julian, Randall ^f   Stephan, Christian ^a,g   Meyer, Helmut E ^a   Eisenacher, Martin ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

^b UNIVERSITY OF LIVERPOOL   (United Kingdom)

^c SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^d INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^e WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^f Indigo BioSystems Inc   (United States)

^g KAIROS GMBH   (Germany)

Author keywords

Controlled vocabularies; Ontologies in proteomics; Ontology editors and software; Ontology formats; Ontology maintenance; Proteomics data standards

Indexed keywords

COMPUTER PROGRAM; CONTROLLED STUDY; CONTROLLED VOCABULARY; INFORMATION PROCESSING; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEOMICS; PROTEOMICS STANDARD INITIATIVE; REVIEW;

AMERICAN SOCIETY FOR TESTING AND MATERIALS; AMERICAN STANDARD CODE FOR INFORMATION INTERCHANGE; ANALYTICAL DATA INTERCHANGE FORMAT FOR MASS SPECTROMETRY; ANALYTICAL INFORMATION MARKUP LANGUAGE; ANDI-MS; ANIML; API; APPLICATION PROGRAMMING INTERFACE; ASCII; ASTM; BRENDA (BRAUNSCHWEIG ENZYME DATABASE) TISSUE ONTOLOGY; BTO; CHEBI; CHEMICAL ENTITIES OF BIOLOGICAL INTEREST; CONTROLLED VOCABULARIES; CONTROLLED VOCABULARY; CV; DESCRIPTION LOGIC; DL; EBI; EUROPEAN BIOINFORMATICS INSTITUTE; EXTENSIBLE STYLESHEET LANGUAGE TRANSFORMATION; HDF5; HIERARCHICAL DATA FORMAT, VERSION 5; HUMAN PROTEOME ORGANISATION-PROTEOMICS STANDARDS INITIATIVE; HUPO-PSI; ICD; INTERNATIONAL CLASSIFICATION OF DISEASES; INTERNATIONAL UNION FOR PURE AND APPLIED CHEMISTRY; IUPAC; JCAMP-DX; JOINT COMMITTEE ON ATOMIC AND MOLECULAR PHYSICAL DATA-DATA EXCHANGE FORMAT; MALDI; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION; MEDICAL SUBJECT HEADINGS; MESH; MI; MIAPE; MIBBI; MINIMAL INFORMATION FOR BIOLOGICAL AND BIOMEDICAL INVESTIGATIONS; MINIMUM INFORMATION ABOUT A PROTEOMICS EXPERIMENT; MITAB; MOLECULAR INTERACTION; MOLECULAR INTERACTIONS TABULAR FORMAT; MS; NATIONAL CENTER FOR BIOMEDICAL ONTOLOGY; NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION; NCBI; NCBO; NETCDF; NETWORK COMMON DATA FORMAT; OBI; OBO; OLS; ONTOLOGIES IN PROTEOMICS; ONTOLOGY EDITORS AND SOFTWARE; ONTOLOGY FOR BIOMEDICAL INVESTIGATIONS; ONTOLOGY FORMATS; ONTOLOGY LOOKUP SERVICE; ONTOLOGY MAINTENANCE; OPEN BIOLOGICAL AND BIOMEDICAL ONTOLOGIES; OWL; PAR; PATO; PHENOTYPE ATTRIBUTE TRAIT ONTOLOGY; PRIDE; PROTEIN AFFINITY REAGENTS; PROTEOMICS DATA STANDARDS; PROTEOMICS IDENTIFICATIONS DATABASE; RDF(S); RESOURCE DESCRIPTION FRAMEWORK (SCHEMA); SELECTED REACTION MONITORING; SRM; TPP; TRANS-PROTEOMIC PIPELINE; UNIFORM RESOURCE IDENTIFIER; URI; WEB ONTOLOGY LANGUAGE; XSLT; YAFMS; YET ANOTHER FORMAT FOR MASS SPECTROMETRY;

PROGRAMMING LANGUAGES; PROTEOMICS; SOFTWARE; VOCABULARY, CONTROLLED;

EID: 84890429234     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2013.02.017     Document Type: Article

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