Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO‐Proteomics Standards Initiative April 23–25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France

  title={Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO‐Proteomics Standards Initiative April 23–25, 2007 Ecole Nationale Sup{\'e}rieure (ENS), Lyon, France},
  author={Sandra E. Orchard and Luisa Montechi-Palazzi and Eric W. Deutsch and Pierre-Alain Binz and Andrew R. Jones and Norman W. Paton and Angel D. Pizarro and David M. Creasy and J{\'e}r{\^o}me Wojcik and Henning Hermjakob},
Over the last five years, the Human Proteome Organisation Proteomics Standards Initiative (HUPO PSI) has produced and released community‐accepted XML interchange formats in the fields of mass spectrometry, molecular interactions and gel electrophoresis, have led the field in the discussion of the minimum information with which such data should be annotated and are now in the process of publishing much of this information. At this 4th Spring workshop, the emphasis was on consolidating this… 
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The HUPO proteomics standards initiative - easing communication and minimizing data loss in a changing world
The Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) was tasked with the creation of data standards and interchange formats to allow both the exchange and storage of such data irrespective of the hardware and software from which it was generated.
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The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards*
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The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium*
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A guide for integration of proteomic data standards into laboratory workflows
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A Semantic Web Management Model for Integrative Biomedical Informatics
This report identifies a core model for biomedical Knowledge Engineering applications and demonstrates how this new technology can be used to weave a management model where multiple intertwined data structures can be hosted and managed by multiple authorities in a distributed management infrastructure.
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput “omics” Data
This paper introduces a protein-centric approach for systems integration of large and heterogeneous high-throughput “omics” data including microarray, mass spectrometry, protein sequence, protein structure, and protein interaction data, and uses scientific case study to illustrate how one can use varied ‘omics’ data from different laboratories to make useful connections that could lead to new biological knowledge.
MeltDB 2.0–advances of the metabolomics software system
MeltDB 2.0 is a next-generation web application addressing storage, sharing, standardization, integration and analysis of metabolomics experiments and improves both efficiency and effectivity of the entire processing pipeline of chromatographic raw data from pre-processing to the derivation of new biological knowledge.


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The Distributed Annotation System
The Distributed Annotation System (DAS) allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software.
The minimum information required for reporting a molecular interaction experiment (MIMIx)
MIMIx, the minimum information required for reporting a molecular interaction experiment, is proposed, which will support the rapid, systematic capture of molecular interaction data in public databases, thereby improving access to valuable interaction data.
IntAct—open source resource for molecular interaction data
IntAct is an open source database and software suite for modeling, storing and analyzing molecular interaction data that features over 126 000 binary interactions extracted from over 2100 scientific publications and makes extensive use of controlled vocabularies.
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The Universal Protein Resource (UniProt)
During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; the UniProt keyword list got augmented by additional keywords; the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications.