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


ready Molecular Interaction eXtensible Markup Language

Abbreviation: PSI-MI XML


Recommended
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

Taxonomic range



In the following recommendations:



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: Jun 19 2021 5:10 a.m.


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

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

Show edit history




Support

General

Additional Information


Tools

    No tools defined


Schemas
Download

Access / Retrieve Data


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

View Paper (PubMed) View Publication

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

View Paper (PubMed) View Publication

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

View Paper (PubMed) View Publication


Related Databases (15)
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. 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 uses the information in CATH to predict the locations of structural domains on millions of protein sequences available in public databases. Sequence data from UniProtKB and Ensembl for domains with no experimentally determined structures are scanned against CATH HMMs to predict domain sequence boundaries and make homologous superfamily assignments.

Termini-Oriented Protein Function INferred Database
The Termini-Oriented Protein Function INferred Database (TopFIND) is an integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing state of proteins and functional implications thereof derived from research literature, contributions by the scientific community and biological databases.

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.

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
The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans. BioGRID currently holds over 1,740,000 interactions curated from both high-throughput datasets and individual focused studies, as derived from over 70,000+ publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. All data are freely provided via our search index and available for download in many 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.

Database of Interacting Proteins
The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both manually by expert curators and automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the core DIP data.

Interologous Interaction Database
The I2D (Interologous Interaction Database) is a database of known and predicted mammalian and eukaryotic protein-protein interactions (PPIs). It has been built by mapping high-throughput (HTP) data between species.

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. virus mentha offers direct access to viral families such as: Orthomyxoviridae, Orthoretrovirinae and Herpesviridae plus, it offers the unique possibility of searching by host organism.

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.

Scroll for more...



Credit

Record Maintainer

Maintains