standards > model/format > DOI:10.25504/FAIRsharing.77e3my


ready Molecular Interaction eXtensible Markup Language

Abbreviation: PSI-MI XML


General Information
The PSI-MI interchange format and accompanying controlled vocabularies was originally designed by a consortium of molecular interaction data providers from both academia and industry, including BIND, DIP, IntAct, MINT, MIPS, GlaxoSmithKline, CellZome, Hybrigenics, Universities of Bielefeld, Bordeaux, Cambridge, and others. It is maintained, and kept fit for purpose by the Molecular Interaction workgroup of the HUPO PSI. It can be used for storing any kind of molecular interaction data including complexes and binary interactions such as protein-protein interactions and nucleic acid interactions.

Homepage http://www.psidev.info/groups/molecular-interactions

Countries that developed this resource European Union , United States

Created in 2003

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How to cite this record FAIRsharing.org: PSI-MI XML; Molecular Interaction eXtensible Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.77e3my; Last edited: April 29, 2019, 11:42 a.m.; Last accessed: Aug 25 2019 9:49 p.m.


This record is maintained by orchard  and HUPO PSI  (HUPOPSI)

Record updated: April 29, 2019, 11:41 a.m. by The FAIRsharing Team.

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Publications

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.

Kerrien S,Orchard S,Montecchi-Palazzi L,Aranda B,Quinn AF,Vinod N,Bader GD,Xenarios I,Wojcik J,Sherman D,Tyers M,Salama JJ,Moore S,Ceol A,Chatr-Aryamontri A,Oesterheld M,Stumpflen V,Salwinski L,Nerothin J,Cerami E,Cusick ME,Vidal M,Gilson M,Armstrong J,Woollard P,Hogue C,Eisenberg D,Cesareni G,Apweiler R,Hermjakob H
BMC Biol 2007

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The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

Hermjakob H,Montecchi-Palazzi L,Bader G,Wojcik J,Salwinski L,Ceol A,Moore S,Orchard S,Sarkans U,von Mering C,Roechert B,Poux S,Jung E,Mersch H,Kersey P,Lappe M,Li Y,Zeng R,Rana D,Nikolski M,Husi H,Brun C,Shanker K,Grant SG,Sander C,Bork P,Zhu W,Pandey A,Brazma A,Jacq B,Vidal M,Sherman D,Legrain P,Cesareni G,Xenarios I,Eisenberg D,Steipe B,Hogue C,Apweiler R
Nat Biotechnol 2004

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Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

Sivade Dumousseau M,Alonso-Lopez D,Ammari M,Bradley G,Campbell NH,Ceol A,Cesareni G,Combe C,De Las Rivas J,Del-Toro N,Heimbach J,Hermjakob H,Jurisica I,Koch M,Licata L,Lovering RC,Lynn DJ,Meldal BHM,Micklem G,Panni S,Porras P,Ricard-Blum S,Roechert B,Salwinski L,Shrivastava A,Sullivan J,Thierry-Mieg N,Yehudi Y,Van Roey K,Orchard S
BMC Bioinformatics 2018

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Implementing Databases (14)
IntAct molecular interaction database
IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.

Molecular INTeraction database
MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. As of September 2013, This resource uses the IntAct database framework to help reduce the effort of scientists and improve on IT development. MINT is an ELIXIR Core Resource.

Gene3D
Gene3D takes CATH domain families (from PDB structures) and assigns them to the millions protein sequences (using Hidden Markov models generated from HMMER) with no PDB structures.

Termini-Oriented Protein Function INferred Database
TopFIND is a protein-centric database for the annotation of protein termini currently in its third version. Non-canonical protein termini can be the result of multiple different biological processes, including pre-translational processes such as alternative splicing and alternative translation initiation or post-translational protein processing by proteases that cleave proteases as part of protein maturation or as a regulatory modification. Accordingly, protein termini evidence in TopFIND is inferred from other databases such as ENSEMBL transcripts, TISdb for alternative translation initiation, MEROPS for protein cleavage by proteases, and UniProt for canonical and protein isoform start sites. Additionally, termini are annotated from user submitted lists of termini and inferred from user submitted lists of cleavage sites. As a protein-centric database, TopFIND presents a website for each protein isoform (organized around UniProt accession codes). These websites contain general protein information, such as organism, chromosome location, and proteins sequence. They then list position information such as specific termini evidences, known cleavage sites, sequence features and domains for each protein. In addition, TopFIND shows each protein in the context of the protease web, a network of proteases and their inhibitors, where a protease can cleave of other proteases and their inhibitors thus influencing their activity. All information in TopFIND can be filtered by a powerful filter engine that relies on rich annotation as to the origin of data in TopFIND. TopFIND can also be programmatically queried using the PSICQUIC or XML API. Recently, software tools were developed to enable quick access to TopFIND data for lists of termini obtained by, for example, proteomic termini screens (terminomics). TopFIND Explorer “TopFINDer” reports position specific protein information for protein termini, such as terminus evidences, prime and non-prime sequences, and protein domains affected by cleavage. TopFINDer further reports summary statistics for protein cleavage by known proteases. PathFINDer is a second tool that reports proteolytic paths from a query protease to identified protein substrates thus enabling the differentiation between direct and indirect protease substrates and yielding mechanistic insights into pathways based on existing information.

Automatic molecular interaction predictions
InteroPorc is an automatic prediction tool to infer protein-protein interaction networks. It is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8.

MatrixDB: Extracellular Matrix Interaction Database
MatrixDB stores experimental data established by full-length proteins, matricryptins, glycosaminoglycans, lipids and cations. MatrixDB reports interactions with individual polypeptide chains or with multimers (e.g. collagens, laminins, thrombospondins) when appropriate. Multimers are treated as permanent complexes, referencing EBI identifiers when possible. Human interactions were inferred from non-human homologous interactions when available.

Human Protein Reference Database
The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.

Biological General Repository for Interaction Datasets
BioGRID is an interaction repository with data compiled through comprehensive curation efforts. Our current index is version 3.5.174 and searches 69,922 publications for 1,706,694 protein and genetic interactions, 28,093 chemical associations and 726,378 post translational modifications from major model organism species. All data are freely provided via our search index and available for download in standardized formats.

InnateDB
InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation.

Interaction Reference Index Web Interface
iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID.

Interologous Interaction Database
I2D (Interologous Interaction Database) is a database of known and predicted mammalian and eukaryotic protein-protein interactions (PPIs).

VirusMentha
VirusMentha is a collection of viral interactions manually curated from protein-protein databases that adhere to the IMEx consortium. This resource offers a series of tools to analyse selected proteins in the context of a network of interactions.

Host Pathogen Interaction Database
HPIDB 3.0 is a resource that helps annotate, predict and display host-pathogen interactions (HPI). HPI that underpin infectious diseases are critical for developing novel intervention strategies. HPIDB is a host-pathogen protein-protein interaction (PPI) database, which serves as a unified resource for host-pathogen interactions. HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource.

mentha
mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. The aggregated data forms an interactome which includes many organisms. mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions.

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