Molecular Interaction Tabular
How to cite this record FAIRsharing.org: MITAB; Molecular Interaction Tabular; DOI: https://doi.org/10.25504/FAIRsharing.ve0710; Last edited: Jan. 8, 2019, 1:27 p.m.; Last accessed: May 20 2019 2:08 a.m.
Record updated: July 30, 2018, 2:16 p.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.ve0710' by 'The FAIRsharing Team' at 14:16, 30 Jul 2018 (approved): 'description' has been modified: Before: The MITAB27 format is an extention of the PSI-MI 2.5 (1) and 2.6 standard. It has been derived from the tabular format provided by BioGrid.. MITAB27 only describes binary interactions, one pair of interactors per row. Columns are separated by tabulations. After: The MITAB27 format is an extension of the PSI-MI 2.5 (1) and 2.6 standard. It has been derived from the tabular format provided by BioGrid. MITAB27 only describes binary interactions, qith one pair of interactors per row.
Edits to 'https://fairsharing.org/FAIRsharing.ve0710' by 'The FAIRsharing Team' at 07:31, 16 Jul 2018 (approved): 'homepage' has been modified: Before: http://www.psidev.info/index.php?q=node/31 After: http://psicquic.github.io/MITAB27Format.html
Edits to 'https://fairsharing.org/FAIRsharing.ve0710' by 'The FAIRsharing Team' at 13:06, 19 Sep 2016 (approved): 'contactName' has been modified: Before: HUPO PSI After: Samuel Kerrien Added: Removed:
No XSD schemas defined
Conditions of Use
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
Models and Formats
No identifier schema standards defined
No metrics standards defined
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.
Protein Interaction Network Analysis
The Protein Interaction Network Analysis (PINA)- is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms.
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.
Reactome - a curated knowledgebase of biological pathways
The cornerstone of Reactome is a freely available, open source relational database of signaling and metabolic molecules and their relations organized into biological pathways and processes. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer therapeutics and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways. Examples of biological pathways in Reactome include classical intermediary metabolism, signaling, transcriptional regulation, apoptosis and disease. Inferred orthologous reactions are available for 17 non-human species including mouse, rat, chicken, puffer fish, worm, fly, yeast, rice, and Arabidopsis.
STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations.
MatrixDB: Extracellular Matrix interactions database
MatrixDB is a database reporting mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. Full-length molecules, fragments and multimers present in the extracellular matrix are all included in the database.
VirHostNet 2.0 integrates an extensive and original literature-curated dataset of virus/virus and virus/host protein-protein interactions complemented with publicly available data.
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.
Microbial Protein Interaction Database
The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.
Biological General Repository for Interaction Datasets
BioGRID is an interaction repository with data compiled through comprehensive curation efforts. BioGRID currently holds over 980,000 interactions curated from both high-throughput datasets and individual focused studies, as derived from over 55,000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding year (S. cerevisiae), fission yeast (S. pome), and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. All data are freely provided via the search index and available for download in standardized formats.
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
Interologous Interaction Database
Experimentally-determined interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection
Host Pathogen Interaction Database
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.
Human Protein-Protein Interaction rEference
HIPPIE integrates human protein-protein interactions from several manually curated source databases. It provides a web tool to query the interaction data, generate highly reliable, context-specific interaction networks and to make sense out of them.
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U.S. Department of Energy (Government body)
ELIXIR Italy (Government body)
European Commission (Government body)
HUPO-PSI initiative; MI administrators (Consortium)
021902 (RII3) (European Commission)
1 R01 GM071909 (ELIXIR Italy)
DE-FC03-02ER63421 (U.S. Department of Energy)
GM070064 (ELIXIR Italy)