Molecular Interaction Tabular
How to cite this record FAIRsharing.org: MITAB; Molecular Interaction Tabular; DOI: https://doi.org/10.25504/FAIRsharing.ve0710; Last edited: July 2, 2019, 1:30 p.m.; Last accessed: Jun 24 2021 1:41 a.m.
Record updated: July 2, 2019, 1:29 p.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.ve0710' by 'The FAIRsharing Team' at 13:29, 02 Jul 2019 (approved): 'description' has been modified: Before: 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. 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, with one pair of interactors per row.
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. 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 platform
Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization, and management. It integrates protein-protein interaction (PPI) data from public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. In particular, it provides a variety of built-in tools to filter and analyze the networks for gaining biological and functional insights into the network.
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.
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 15 non-human species including mouse, rat, chicken, zebrafish, worm, fly, and yeast.
STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations.
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.
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
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 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.
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.
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.
Alliance of Genome Resources
The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease.
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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)