gelML spec document - HUPO-PSI Working Groups and …：gelml规格文档hupo-psi工作组….doc

GelML: Gel Markup Language (Version 1.1) Specification Status of This Memo This memo provides information to the Proteomics community about the modelling of the experimental procedures of gel electrophoresis in a proteomics pipeline, prior to protein identification, for example by mass spectrometry. It includes the acquisition of an image of a gel but does not contain any information derived from image analysis. This document is a recommendation for a standard released by the Proteomics Standards Initiative. Distribution is unlimited. Version: Version 1.1 draft document, June 2010. Abstract The Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparison, exchange and verification. The Protein Separation (PSI-PS) Working Group is developing standards for describing the processing and separations of proteins in samples using gel electrophoresis, within a proteomics experiment. This document defines models that can be used to describe the process of gel electrophoresis, which can be used to separate, and in some instances to quantify, proteins within a proteomics workflow. This is important, as the quality and interpretation of protein identifications are affected by the experimental processes to which a sample is subjected. Contents Abstract 1 1. Introduction 5 2. Concepts and Terminology 6 3. Relationship to Other Specifications 6 3.1 Important concepts from FuGE 6 3.2 Changes from GelML version 1.0 7 3.3 The PSI Sample Processing and Separations Controlled Vocabulary (sepCV) 7 3.4 Validation of controlled vocabulary terms 8 4. Model Overview 8 4.1 Schema overview 9 4.2 Model of a gel 9 4.3 One-dimensional gel electrophoresis 13 4.4 Two dimensional gel electrophoresis 15 4.5 Other Gel Electrophoresis 17 4.6 Sample loading 18 4.7 Electrophoresis 19 4.8 Detection 21 4.9 Image acquisition 21 4.10 The excision of locations on gels 25 4.11 SubstanceMixtureProtoco