Controlled vocabularies and ontologies in proteomics: Overview, principles and practice
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- 作者：Gerhard Mayer ; Andrew R. Jones ; Pierre-Alain Binz ; Eric W. Deutsch ; S ; ra Orchard ; Luisa Montecchi-Palazzi ; Juan Antonio Vizca铆no ; Henning Hermjakob ; David Oveillero ; R ; all Julian ; Christian Stephan ; Helmut E. Meyer ; Martin Eisenacher
- 关键词：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 ; versio
- 刊名：Biochimica et Biophysica Acta - Proteins and Proteomics
- 出版年：January, 2014
- 年：2014
- 卷：1844
- 期：1_part_PA
- 页码：98-107
- 全文大小：881 K
文摘
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 鈥渕apping files鈥?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.