Development of data representation standards by the human proteome organization proteomics standards initiative

Journal of the American Medical Informatics Association : JAMIA
Eric W DeutschHenning Hermjakob

Abstract

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. 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. 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 ana...Continue Reading

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Citations

Nov 5, 2016·Journal of Proteome Research·Eric W DeutschGilbert S Omenn
Nov 5, 2016·Journal of Proteome Research·Jennifer E Van EykGilbert S Omenn
Nov 5, 2016·Journal of Proteome Research·Young-Ki PaikGilbert S Omenn
May 13, 2020·GigaScience·Alejandra N Gonzalez-BeltranLennart Martens
May 12, 2019·Statistical Applications in Genetics and Molecular Biology·Yulan LiangArpad Kelemen
Jan 30, 2015·Proteomics. Clinical Applications·Eric W DeutschRobert L Moritz
Jul 8, 2016·Molecular & Cellular Proteomics : MCP·Paul AshfordMaya Topf
Jul 18, 2017·F1000Research·Juan Antonio VizcaínoOliver Kohlbacher
Sep 14, 2017·Current Protocols in Bioinformatics·Andrew F Jarnuczak, Juan Antonio Vizcaíno
May 19, 2017·Molecular & Cellular Proteomics : MCP·Juan Antonio VizcaínoAndrew R Jones
Nov 7, 2019·Nucleic Acids Research·Eric W DeutschJuan A Vizcaíno
May 26, 2021·Journal of Dental Research·W W LauS Ruhl
Jun 30, 2021·Nature Methods·Eric W DeutschNuno Bandeira
May 14, 2019·Journal of Proteome Research·Pierre-Alain BinzEric W Deutsch
Aug 30, 2017·Journal of Proteome Research·Eric W DeutschAndrew R Jones
Jul 2, 2019·Journal of Proteome Research·Salvador Martínez-BartoloméJohn R Yates
Oct 3, 2018·Journal of Proteome Research·Eric W DeutschHannes Röst
Oct 11, 2019·Journal of Proteome Research·Eric W DeutschGilbert S Omenn
Jul 30, 2016·Journal of the American Society for Mass Spectrometry·Michael R HoopmannRobert L Moritz

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Methods Mentioned

BETA
column chromatography
electrophoresis
nuclear magnetic resonance

Software Mentioned

GI
MOD
mzIdentML
TraML
MI
mzXML
PeptideAtlas
mzData
R
mzML

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