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HUPO-PSI specifications


Unique identifier OMICS_31094
Alternative name Human Proteome Organization Proteomics Standards Initiative
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Version 3.0
Maintained Yes


  • person_outline Sandra Orchard

Additional information

Publications for Human Proteome Organization Proteomics Standards Initiative

HUPO-PSI citations


New perspectives: systems medicine in cardiovascular disease

BMC Syst Biol
PMCID: 5921396
PMID: 29699591
DOI: 10.1186/s12918-018-0579-5
call_split See protocol

[…] tabase knowledge include the BioPAX-ontology [], Systems Biology Markup Language (SBML) [], the Human Proteome Organization (HUPO) Proteomics Standards Initiative standard for Molecular Interactions (HUPO PSI-MI) [] and NDEx []. In combination with mapping services, for example BioMart [], these packages enable the integration and merging of prior knowledge for further analyses. Table  includes a […]


Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

J Proteome Res
PMCID: 5715286
PMID: 28849660
DOI: 10.1021/acs.jproteome.7b00370

[…] distribution of the data. A prototype service will be built at EMBL-EBI for testing by other service providers before a final decision is made.All formats and CVs are available at and accompanying tools at The work of the PSI-MI is described at […]


Flexible Data Analysis Pipeline for High Confidence Proteogenomics

J Proteome Res
PMCID: 5703597
PMID: 27786492
DOI: 10.1021/acs.jproteome.6b00765

[…] tExporter tool to convert the idXML files into tabular text files (.csv) for further analysis in external tools. It is also possible to convert the idXML files from any stage of the pipeline into the HUPO PSI standard formats mzIdentML and mzTab using the TOPP tools IDFileConverter and MzTabExporter, respectively. […]


APP Is a Context Sensitive Regulator of the Hippocampal Presynaptic Active Zone

PLoS Comput Biol
PMCID: 4836664
PMID: 27092780
DOI: 10.1371/journal.pcbi.1004832

[…] ition considers indirect relationships and was recently merged into IntAct []. Data were returned and stored in the Human Proteome Organization Proteomics Standards Initiative—Molecular Interactions (HUPO PSI-MI) Tab 2.5 format. In this text format one binary interaction is stored per line. Supplementary data for each interaction is stored in 15 columns and contains, for example, information regar […]


Exploring the potential of public proteomics data

PMCID: 4738454
PMID: 26449181
DOI: 10.1002/pmic.201500295

[…] l. .The next milestone was the development of data‐sharing standards and associated software libraries, allowing ready access to otherwise proprietary data formats . This ongoing endeavor, led by the HUPO‐PSI (Human Proteome Organization−Proteomics Standards Initiative−, has resulted in key data standards for the field, including mzML (for MS data), mzIdentML (for peptide/pr […]


Data standards can boost metabolomics research, and if there is a will, there is a way

PMCID: 4648992
PMID: 26612985
DOI: 10.1007/s11306-015-0879-3

[…] nsone et al. ) within the Metabolomics Standards Initiative (MSI) and work at the Wishart lab and earlier reporting requirements (Rubtsov et al. ). The format has also heavily borrowed ideas from the HUPO-PSI mzML standard (Martens et al. ), including an XML schema that defines the structure of an nmrML file and a supporting controlled vocabulary (nmrCV), which allows the reuse of nmrCV terms in o […]


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HUPO-PSI institution(s)
European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, UK; Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), Salamanca, Spain; [etc.]
HUPO-PSI funding source(s)
Supported by BBSRC MIDAS grant (BB/L024179/1), by European Commission (FP7-HEALTH-2009- 242129 SyBoSS), by ELIXIR-IIB, the Italian Node of the European ELIXIR infrastructure, by Ontario Research Fund (GL2–01-030, #34876) and Canada Research Chair Program (#225404), by EMBL Australia and FP7-HEALTH2011-278568, by Fondation pour la Recherche Médicale (grant n° DBI20141231336) and by the French Institute of Bioinformatics (2015 call), NHC and RCL by British Heart Foundation (RG/13/5/30112), by the European Research Council (Grant Agreement 32274), by the Wellcome Trust (grant numbers 103139, 063412, 203149) and by National Institutes of Health (R01GM071909).

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