Development of data representation standards by the human proteome organization proteomics standards initiative.
OBJECTIVE
To describe the goals of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization, the methods that the PSI has employed to create data standards, the resulting output of the PSI, lessons learned from the PSI's evolution, and future directions and synergies for the group.


METHODS
The PSI has 5 categories of deliverables that have guided the group. These are minimum information guidelines, data formats, controlled vocabularies, resources and software tools, and dissemination activities. These deliverables are produced via the leadership and working group organization of the initiative, driven by frequent workshops and ongoing communication within the working groups. Official standards are subjected to a rigorous document process that includes several levels of peer review prior to release.


RESULTS
We have produced and published minimum information guidelines describing what information should be provided when making data public, either via public repositories or other means. The PSI has produced a series of standard formats covering mass spectrometer input, mass spectrometer output, results of informatics analysis (both qualitative and quantitative analyses), reports of molecular interaction data, and gel electrophoresis analyses. We have produced controlled vocabularies that ensure that concepts are uniformly annotated in the formats and engaged in extensive software development and dissemination efforts so that the standards can efficiently be used by the community.Conclusion In its first dozen years of operation, the PSI has produced many standards that have accelerated the field of proteomics by facilitating data exchange and deposition to data repositories. We look to the future to continue developing standards for new proteomics technologies and workflows and mechanisms for integration with other omics data types. Our products facilitate the translation of genomics and proteomics findings to clinical and biological phenotypes. The PSI website can be accessed at http://www.psidev.info.
Institute for Systems Biology, Seattle, USA eric.deutsch@systemsbiology.org.
Eric W
EW
Deutsch
Died July 18, 2014 Proteomics Facility, Centro Nacional de Biotecnología - CSIC, Madrid, Spain ProteoRed Consortium, Spanish National Institute of Proteomics, Madrid, Spain.
Juan Pablo
JP
Albar
CHUV Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
Pierre-Alain
PA
Binz
Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, Bochum, Germany.
Martin
M
Eisenacher
Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
Andrew R
AR
Jones
Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, Bochum, Germany.
Gerhard
G
Mayer
Institute for Systems Biology, Seattle, USA Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, USA.
Gilbert S
GS
Omenn
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Sandra
S
Orchard
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Juan Antonio
JA
Vizcaíno
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Henning
H
Hermjakob
D019992:Databases as Topic / Q000592:standards*; D017408:Guidelines as Topic; D006801:Humans; D013058:Mass Spectrometry / Q000592:standards; D020543:Proteome; D040901:Proteomics / Q000592:standards*; D012955:Societies, Medical; D018875:Vocabulary, Controlled
D020543:Proteome
HUPO; data formats; data standards; guidelines; proteomics; proteomics standards initiative; standards; standards organization