Molecular Interaction Tabular
Names
More detailed information about this field from each metasource.
Molecular Interaction Tabular
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:13 p.m.
MITAB
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:13 p.m.
Names
More detailed information about this field from each metasource.
Molecular Interaction Tabular
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:13 p.m.
MITAB
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:13 p.m.
Names
More detailed information about this field from each metasource.
Molecular Interaction Tabular
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:13 p.m.
MITAB
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:13 p.m.
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.
Description
More detailed information about this field from each metasource.
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.
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:13 p.m.
Webpage:
http://psicquic.github.io/MITAB27Format.htmlWebpage
More detailed information about this field from each metasource.
http://psicquic.github.io/MITAB27Format.html
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:13 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions
PMID: 17925023
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:13 p.m.
Publications
More detailed information about this field from each metasource.
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions
PMID: 17925023
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:13 p.m.
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Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions
PubMed citations: 139.
139 articles citing: Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions
The Landscape of Virus-Host Protein-Protein Interaction Databases. PMID:35910656
The Intricacy of the Viral-Human Protein Interaction Networks: Resources, Data, and Analyses. PMID:35531299
Harmonizing model organism data in the Alliance of Genome Resources. PMID:35380658
Interactomes: Experimental and In Silico Approaches. PMID:35113398
ECO: the Evidence and Conclusion Ontology, an update for 2022. PMID:34986598
The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction. PMID:34789143
The IntAct database: efficient access to fine-grained molecular interaction data. PMID:34761267
Databases for Protein-Protein Interactions. PMID:34236665
CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator. PMID:33547799
Towards a unified open access dataset of molecular interactions. PMID:33262342
How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource. PMID:32696353
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
Conserved Central Intraviral Protein Interactome of the Herpesviridae Family. PMID:31575665
The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs). PMID:31347048
Membrane protein-regulated networks across human cancers. PMID:31311925
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. PMID:30793173
The BioGRID interaction database: 2019 update. PMID:30476227
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. PMID:30357405
Leveraging Experimental Details for an Improved Understanding of Host-Pathogen Interactome. PMID:30040202
A network map of thrombopoietin signaling. PMID:30039510
JAMI: a Java library for molecular interactions and data interoperability. PMID:29642846
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. PMID:29642841
The eukaryotic linear motif resource - 2018 update. PMID:29136216
DiffSLC: A graph centrality method to detect essential proteins of a protein-protein interaction network. PMID:29121073
ComplexViewer: visualization of curated macromolecular complexes. PMID:29036573
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. PMID:28849660
The amyloid interactome: Exploring protein aggregation. PMID:28249044
The use of gene interaction networks to improve the identification of cancer driver genes. PMID:28149674
Automatic query generation using word embeddings for retrieving passages describing experimental methods. PMID:28077568
The BioGRID interaction database: 2017 update. PMID:27980099
Glycosaminoglycanomics: where we are. PMID:27900575
Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. PMID:27881428
DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems. PMID:27650316
Automated detection of discourse segment and experimental types from the text of cancer pathway results sections. PMID:27580922
HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. PMID:27384951
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
Using biological networks to integrate, visualize and analyze genomics data. PMID:27036106
BioGRID: A Resource for Studying Biological Interactions in Yeast. PMID:26729913
Fundamentals of protein interaction network mapping. PMID:26681426
ELM 2016--data update and new functionality of the eukaryotic linear motif resource. PMID:26615199
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. PMID:26581338
Tools for visualization and analysis of molecular networks, pathways, and -omics data. PMID:26082651
Development of data representation standards by the human proteome organization proteomics standards initiative. PMID:25726569
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. PMID:25652942
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. PMID:25648416
Virus-host interactomics: new insights and opportunities for antiviral drug discovery. PMID:25593595
Finding gene regulatory network candidates using the gene expression knowledge base. PMID:25490885
The BioGRID interaction database: 2015 update. PMID:25428363
VirHostNet 2.0: surfing on the web of virus/host molecular interactions data. PMID:25392406
The role of the interactome in the maintenance of deleterious variability in human populations. PMID:25261458
PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers. PMID:25075287
The human plasma membrane peripherome: visualization and analysis of interactions. PMID:25057483
DBSecSys: a database of Burkholderia mallei secretion systems. PMID:25030112
The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. PMID:24980485
R-based software for the integration of pathway data into bioinformatic algorithms. PMID:24833336
Guidelines for managing data and processes in bone and cartilage tissue engineering. PMID:24564199
Variation ontology: annotator guide. PMID:24533660
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. PMID:24234451
Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis. PMID:24214996
The eukaryotic linear motif resource ELM: 10 years and counting. PMID:24214962
Variation Ontology for annotation of variation effects and mechanisms. PMID:24162187
Using biological pathway data with paxtools. PMID:24068901
Capturing cooperative interactions with the PSI-MI format. PMID:24067240
A new reference implementation of the PSICQUIC web service. PMID:23671334
From Peptidome to PRIDE: public proteomics data migration at a large scale. PMID:23533138
Access guide to human proteinpedia. PMID:23504933
Controlled vocabularies and ontologies in proteomics: overview, principles and practice. PMID:23429179
Interactome3D: adding structural details to protein networks. PMID:23399932
Visual data mining of biological networks: one size does not fit all. PMID:23341759
Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana. PMID:23293649
The BioGRID interaction database: 2013 update. PMID:23203989
InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation. PMID:23180781
PhosPhAt goes kinases--searchable protein kinase target information in the plant phosphorylation site database PhosPhAt. PMID:23172287
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. PMID:23071097
PRD: A protein-RNA interaction database. PMID:23055619
Data management strategies for multinational large-scale systems biology projects. PMID:23047157
Minireview: progress and challenges in proteomics data management, sharing, and integration. PMID:22902541
Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. PMID:22844098
A Bioinformatics Resource for TWEAK-Fn14 Signaling Pathway. PMID:22649723
IRView: a database and viewer for protein interacting regions. PMID:22592381
DIPSBC--data integration platform for systems biology collaborations. PMID:22568834
Bayesian integration of networks without gold standards. PMID:22492647
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. PMID:22453911
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. PMID:22438567
The mzIdentML data standard for mass spectrometry-based proteomics results. PMID:22375074
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. PMID:22151178
The IntAct molecular interaction database in 2012. PMID:22121220
INOH: ontology-based highly structured database of signal transduction pathways. PMID:22120663
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. PMID:22115179
Structural and functional protein network analyses predict novel signaling functions for rhodopsin. PMID:22108793
MINT, the molecular interaction database: 2012 update. PMID:22096227
modMine: flexible access to modENCODE data. PMID:22080565
PINA v2.0: mining interactome modules. PMID:22067443
Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal-regulated kinase signaling. PMID:22028469
BioPAX support in CellDesigner. PMID:22021903
ChEMBL: a large-scale bioactivity database for drug discovery. PMID:21948594
Minimum information about a bioactive entity (MIABE). PMID:21878981
ppiTrim: constructing non-redundant and up-to-date interactomes. PMID:21873645
Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. PMID:21767381
PSICQUIC and PSISCORE: accessing and scoring molecular interactions. PMID:21716279
Data standards for Omics data: the basis of data sharing and reuse. PMID:21370078
BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID. PMID:21300700
Literature curation of protein interactions: measuring agreement across major public databases. PMID:21183497
ConsensusPathDB: toward a more complete picture of cell biology. PMID:21071422
The BioGRID Interaction Database: 2011 update. PMID:21071413
Pathway Commons, a web resource for biological pathway data. PMID:21071392
Reactome: a database of reactions, pathways and biological processes. PMID:21067998
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. PMID:21036869
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. PMID:20940177
Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. PMID:20927658
MatrixDB, the extracellular matrix interaction database. PMID:20852260
The BioPAX community standard for pathway data sharing. PMID:20829833
Curating the innate immunity interactome. PMID:20727158
Minimum information about a protein affinity reagent (MIAPAR). PMID:20622827
Ontologies in quantitative biology: a basis for comparison, integration, and discovery. PMID:20520843
MINT, the molecular interaction database: 2009 update. PMID:19897547
The IntAct molecular interaction database in 2010. PMID:19850723
XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services. PMID:19732427
A community standard format for the representation of protein affinity reagents. PMID:19674966
Pathway databases and tools for their exploitation: benefits, current limitations and challenges. PMID:19638971
BioNetBuilder2.0: bringing systems biology to chicken and other model organisms. PMID:19607657
Computational identification of potential molecular interactions in Arabidopsis. PMID:19592425
DASMIweb: online integration, analysis and assessment of distributed protein interaction data. PMID:19502495
DASMI: exchanging, annotating and assessing molecular interaction data. PMID:19420069
Nucleoside diphosphate kinase (NDPK, NM23, AWD): recent regulatory advances in endocytosis, metastasis, psoriasis, insulin release, fetal erythroid lineage and heart failure; translational medicine exemplified. PMID:19415463
Protein-protein interaction databases: keeping up with growing interactomes. PMID:19403463
A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor. PMID:19325550
MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. PMID:19147664
Literature-curated protein interaction datasets. PMID:19116613
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. PMID:18984613
VirusMINT: a viral protein interaction database. PMID:18974184
The Protein Feature Ontology: a tool for the unification of protein feature annotations. PMID:18936051
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. PMID:18834496
iRefIndex: a consolidated protein interaction database with provenance. PMID:18823568
MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions. PMID:18786976
MPIDB: the microbial protein interaction database. PMID:18556668
Tags:
Tags
More detailed information about this field from each metasource.
molecular interaction
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:13 p.m.
protein
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:13 p.m.
Tags
More detailed information about this field from each metasource.
molecular interaction
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:13 p.m.
protein
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:13 p.m.
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