The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data

By H. Hermjakob, L. Montecchi-Palazzi, Gary D. Bader, J. Wojcik, Lukasz Salwínski, Arnaud Céol, S. Moore, S. Orchard, Ugis Sarkans, C. von Mering and 29 more. Nature Biotechnology, 2004

687 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b70756663de2278449501ff29a6cbf19f8da8da2

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Citations in the corpus

The MIPS mammalian protein?Cprotein interaction database (2005, methodology): “For detailed analysis, the entire dataset is available for download in the recently defined PSI-MI standard format (Hermjakob et al., 2004).”
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored (2010, methodology): “Consequently, considerable information is needed to describe the various aspects of a given protein–protein association and a number of standards have been developed for this purpose with distinct levels of expressivity and specialization (9–13).”
CORUM: the comprehensive resource of mammalian protein complexes (2007, background): “In order to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification the PSI-MI standard was introduced (13).”
GC–MS libraries for the rapid identification of metabolites in complex biological samples (2005, background): “The goal of HPI is to deliver this information in high quality to facilitate further investigations of the genomic and proteomic data [4].”
MPact: the MIPS protein interaction resource on yeast (2005, result): “html), in accordance with the PSI-MI standard for exchange of protein interaction data ( 18 ).”
ConsensusPathDB—a database for integrating human functional interaction networks (2008, methodology): “Apart from the possibility to export interaction networks from the visualization environment, the user can upload an interaction network ﬁle in any of three diﬀerent formats: BioPAX (level 2), PSI-MI (level 2.5) and SBML (level 2) (27).”
NetPath: a public resource of curated signal transduction pathways (2010, methodology): “PSI-MI data representation facilitates data comparison, exchange and verification [8].”
The Database of Interacting Proteins: 2004 update (2004, methodology): “The METHOD table provides a list of controlled vocabulary terms, together with references to the corresponding PSI ontology entries (7), which are used to annotate the experiments.”
Online Predicted Human Interaction Database (2005, positive): “The entire dataset can be downloaded as a tab-delimited text file, or in the PSI-compliant XML format (Hermjakob et al., 2004).”
Integration of biological networks and gene expression data using Cytoscape (2007, background): “The cPath site will grow to include a larger number of databases that share data in the BioPAX or PSI-M”
Using graph theory to analyze biological networks (2011, methodology): “Other file formats that can represent biological networks are the Proteomics Standards Initiative Interaction (PSI-MI) [51], Chemical Markup Language ( CML ) [52,53] for chemicals or BioPAX [54] for pathways.”
IntAct—open source resource for molecular interaction data (2006, positive): “The data are made publicly available using the PSI-MI XML Standard (2), providing end users with the highest level of details without compromising the integrity and simplicity of access to the data, thanks to the use of well established standards.”
Large-scale mapping of human protein–protein interactions by mass spectrometry (2007, methodology): “The complete data set is provided as a table of bait–prey pairs with associated confidence values (Supplementary Table II) and in PSI-MI (Hermjakob et al, 2004) format from the Intact database (www.ebi.ac.uk/intact), accession EBI-1059370.”