TY - JOUR
T1 - Controlled vocabularies and ontologies in proteomics
T2 - Overview, principles and practice
AU - Mayer, Gerhard
AU - Jones, Andrew R.
AU - Binz, Pierre Alain
AU - Deutsch, Eric W.
AU - Orchard, Sandra
AU - Montecchi-Palazzi, Luisa
AU - Vizcaíno, Juan Antonio
AU - Hermjakob, Henning
AU - Oveillero, David
AU - Julian, Randall
AU - Stephan, Christian
AU - Meyer, Helmut E.
AU - Eisenacher, Martin
N1 - Funding Information:
GM, JAV and PAB are funded by the European Union project ‘ProteomeXchange’ ( http://www.proteomexchange.org , EU FP7 grant number 260558 ). JAV is also supported by the Wellcome Trust [grant number WT085949MA ]. PAB is funded also by the Swiss Federal Government through the Federal Office of Education and Science . ME is funded by P.U.R.E. ( http://www.pure.rub.de , Protein Unit for Research in Europe), a project of Nordrhein-Westfalen, a federal state of Germany. ARJ gratefully acknowledges funding from the UK BBSRC [ BB/I000909/1 and BB/H024654/1 ]. EWD is funded in part by NIGMS grants R01 GM087221, P50 GM076547/Center for Systems Biology, and from the Luxembourg Centre for Systems Biomedicine and the University of Luxembourg.
PY - 2014/1/1
Y1 - 2014/1/1
N2 - 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.
AB - 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.
KW - Controlled vocabularies
KW - Ontologies in proteomics
KW - Ontology editors and software
KW - Ontology formats
KW - Ontology maintenance
KW - Proteomics data standards
UR - http://www.scopus.com/inward/record.url?scp=84890429234&partnerID=8YFLogxK
U2 - 10.1016/j.bbapap.2013.02.017
DO - 10.1016/j.bbapap.2013.02.017
M3 - Article
C2 - 23429179
AN - SCOPUS:84890429234
SN - 1570-9639
VL - 1844
SP - 98
EP - 107
JO - Biochimica et Biophysica Acta - Proteins and Proteomics
JF - Biochimica et Biophysica Acta - Proteins and Proteomics
IS - 1 PART A
ER -