The HUPO proteomics standards initiative - easing communication and minimizing data loss in a changing world

@article{Orchard2008TheHP,
  title={The HUPO proteomics standards initiative - easing communication and minimizing data loss in a changing world},
  author={Sandra E. Orchard and Henning Hermjakob},
  journal={Briefings in bioinformatics},
  year={2008},
  volume={9 2},
  pages={
          166-73
        }
}
The amount of data currently being generated by proteomics laboratories around the world is increasing exponentially, making it ever more critical that scientists are able to exchange, compare and retrieve datasets when re-evaluation of their original conclusions becomes important. Only a fraction of this data is published in the literature and important information is being lost every day as data formats become obsolete. The Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI… 
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References

SHOWING 1-10 OF 30 REFERENCES
Advances in the development of common interchange standards for proteomic data
TLDR
Work by the Proteomics Standards Initiative of the Human Proteome Organisation has laid the foundation for the development of standards by which experimental design can be described and data exchange facilitated.
The minimum information about a proteomics experiment (MIAPE)
TLDR
The processes and principles underpinning the development of guidance modules for reporting the use of techniques such as gel electrophoresis and mass spectrometry are described and the ramifications for various interest groups such as experimentalists, funders, publishers and the private sector are discussed.
The Proteomics Standards Initiative
TLDR
The Protein‐Protein Interactions group expects to publish the Level 1 PSI data exchange format for protein‐protein interactions soon and discussions as to the content of Level 2 have been initiated.
Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
TLDR
The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes.
The PeptideAtlas project
TLDR
A summary of the process and details about the Human, Drosophila and Yeast PeptideAtlas builds are presented and a uniform statistical validation ensures a consistent and high-quality set of peptide and protein identifications.
Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories
TLDR
The relative merits and caveats associated with centralized storage and dissemination of raw data and/or peak lists are detailed, building on the extensive experience gained during the PPP pilot phase.
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
TLDR
The effort to merge the existing mass spectrometry XML interchange formats, mzData and mzXML, into one single standard mzML yielded significant progress and the preliminary design of AnalysisXML was extended to include several new use cases and better support for quantification information.
The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data
TLDR
This work proposes a community standard data model for the representation and exchange of protein interaction data, jointly developed by members of the Proteomics Standards Initiative (PSI) and the Human Proteome Organization (HUPO).
Submit Your Interaction Data the IMEx Way
TLDR
The potential submitter is walked through the various routes by which data may be deposited with the databases and the tools which have been developed to assist in this process are described.
Representing, storing and accessing molecular interaction data: a review of models and tools
TLDR
This article compares the recent updates to the three standard representations for exchange of data SBML, PSI MI and BioPAX and gives an overview of available tools for these three standards and a discussion on how these developments support possibilities for data exchange and integration.
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