Molecular Interaction eXtensible Markup Language
Names
More detailed information about this field from each metasource.
Molecular Interaction eXtensible Markup Language
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
PSI-MI XML
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
Names
More detailed information about this field from each metasource.
Molecular Interaction eXtensible Markup Language
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
PSI-MI XML
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
Names
More detailed information about this field from each metasource.
Molecular Interaction eXtensible Markup Language
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
PSI-MI XML
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
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.
Description
More detailed information about this field from each metasource.
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.
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
Webpage:
http://www.psidev.info/groups/molecular-interactionsWebpage
More detailed information about this field from each metasource.
http://www.psidev.info/groups/molecular-interactions
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data
PMID: 14755292
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions
PMID: 17925023
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions
PMID: 29642841
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
Publications
More detailed information about this field from each metasource.
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data
PMID: 14755292
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions
PMID: 17925023
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions
PMID: 29642841
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
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The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data
PubMed citations: 223.
223 articles citing: The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data
Challenges and Limitations of Biological Network Analysis. PMID:35892929
IMEx Databases: Displaying Molecular Interactions into a Single, Standards-Compliant Dataset. PMID:35507258
A novel screening strategy to identify histone methyltransferase inhibitors reveals a crosstalk between DOT1L and CARM1. PMID:35441144
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction. PMID:34789143
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
DOME: recommendations for supervised machine learning validation in biology. PMID:34316068
Towards reproducible computational drug discovery. PMID:33430992
OscoNet: inferring oscillatory gene networks. PMID:32838730
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). PMID:32637990
MIPPIE: the mouse integrated protein-protein interaction reference. PMID:32496562
A Guide to Conquer the Biological Network Era Using Graph Theory. PMID:32083072
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update. PMID:31665520
Cross-linking Proteomics Indicates Effects of Simvastatin on the TLR2 Interactome and Reveals ACTR1A as a Novel Regulator of the TLR2 Signal Cascade. PMID:31221720
Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PMID:31199794
A quantitative analysis of heterogeneities and hallmarks in acute myelogenous leukaemia. PMID:30988472
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. PMID:30793173
Variation in Membrane Trafficking Linked to SNARE AtSYP51 Interaction With Aquaporin NIP1;1. PMID:30687352
KDEL Receptors Are Differentially Regulated to Maintain the ER Proteome under Calcium Deficiency. PMID:30428351
Strategies for Pathway Analysis Using GWAS and WGS Data. PMID:30387919
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. PMID:30357405
Genomic data integration systematically biases interactome mapping. PMID:30332399
Comprehensive network map of interferon gamma signaling. PMID:30191398
A network map of netrin receptor UNC5B-mediated signaling. PMID:30084000
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
Recurrent Patterns of Protein Expression Signatures in Pediatric Acute Lymphoblastic Leukemia: Recognition and Therapeutic Guidance. PMID:29669823
Recognition of Recurrent Protein Expression Patterns in Pediatric Acute Myeloid Leukemia Identified New Therapeutic Targets. PMID:29669821
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
SPV: a JavaScript Signaling Pathway Visualizer. PMID:29590303
Interactome INSIDER: a structural interactome browser for genomic studies. PMID:29355848
Predictive and Experimental Approaches for Elucidating Protein-Protein Interactions and Quaternary Structures. PMID:29206185
ComplexViewer: visualization of curated macromolecular complexes. PMID:29036573
Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis. PMID:28804499
The yeast noncoding RNA interaction network. PMID:28701522
KIAA1377 is associated with lymph node metastasis in esophageal squamous cell carcinoma. PMID:28144289
Automatic query generation using word embeddings for retrieving passages describing experimental methods. PMID:28077568
Glycosaminoglycanomics: where we are. PMID:27900575
HINT: a database of annotated protein-protein interactions and their homologs. PMID:27857549
Ten Simple Rules for Developing Public Biological Databases. PMID:27832061
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. PMID:27794551
VEGF-A/VEGFR2 signaling network in endothelial cells relevant to angiogenesis. PMID:27619687
Signaling network map of the aryl hydrocarbon receptor. PMID:27465749
Where next for the reproducibility agenda in computational biology? PMID:27422148
An integrated signal transduction network of macrophage migration inhibitory factor. PMID:27139435
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data. PMID:26966684
Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain. PMID:26894958
LEAFDATA: a literature-curated database for Arabidopsis leaf development. PMID:26884807
The Electron Microscopy eXchange (EMX) initiative. PMID:26873784
BioGRID: A Resource for Studying Biological Interactions in Yeast. PMID:26729913
Differential ligand-signaling network of CCL19/CCL21-CCR7 system. PMID:26504105
Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor. PMID:26384938
Detecting modules in biological networks by edge weight clustering and entropy significance. PMID:26379697
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases. PMID:26249223
Detection and categorization of bacteria habitats using shallow linguistic analysis. PMID:26201262
GFVO: the Genomic Feature and Variation Ontology. PMID:26019997
KaBOB: ontology-based semantic integration of biomedical databases. PMID:25903923
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. PMID:25759811
Development of data representation standards by the human proteome organization proteomics standards initiative. PMID:25726569
Characterization of protein complexes and subcomplexes in protein-protein interaction databases. PMID:25722891
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. PMID:25652942
xiNET: cross-link network maps with residue resolution. PMID:25648531
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. PMID:25648416
Using VisANT to Analyze Networks. PMID:25422679
Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. PMID:25254076
Construction and analysis of the protein-protein interaction networks based on gene expression profiles of Parkinson's disease. PMID:25170921
A dedicated database system for handling multi-level data in systems biology. PMID:25053973
R-based software for the integration of pathway data into bioinformatic algorithms. PMID:24833336
In silico prediction of protein-protein interactions in human macrophages. PMID:24636261
A network map of the gastrin signaling pathway. PMID:24584707
Guidelines for managing data and processes in bone and cartilage tissue engineering. PMID:24564199
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PMID:24550716
Differential expression of serum/plasma proteins in various infectious diseases: specific or nonspecific signatures. PMID:24293340
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis. PMID:24270792
Biomarkers in autism spectrum disorder: the old and the new. PMID:24096533
Capturing cooperative interactions with the PSI-MI format. PMID:24067240
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. PMID:23981286
Extracting reaction networks from databases-opening Pandora's box. PMID:23946492
mentha: a resource for browsing integrated protein-interaction networks. PMID:23900247
MIMO: an efficient tool for molecular interaction maps overlap. PMID:23672344
A new reference implementation of the PSICQUIC web service. PMID:23671334
A network map of BDNF/TRKB and BDNF/p75NTR signaling system. PMID:23606317
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. PMID:23599424
The SH2 domain interaction landscape. PMID:23545499
An integrated map of corticotropin-releasing hormone signaling pathway. PMID:23504413
Precise generation of systems biology models from KEGG pathways. PMID:23433509
Proteome-wide prediction of self-interacting proteins based on multiple properties. PMID:23422585
Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework. PMID:23383610
A multicellular signal transduction network of AGE/RAGE signaling. PMID:23161412
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
The ConsensusPathDB interaction database: 2013 update. PMID:23143270
A travel guide to Cytoscape plugins. PMID:23132118
Gene Fusion Markup Language: a prototype for exchanging gene fusion data. PMID:23072312
A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient-Derived Dermal Fibroblasts and iPS Cells. PMID:22969728
File formats commonly used in mass spectrometry proteomics. PMID:22956731
HINT: High-quality protein interactomes and their applications in understanding human disease. PMID:22846459
Genes2FANs: connecting genes through functional association networks. PMID:22748121
A pathway map of prolactin signaling. PMID:22684822
Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. PMID:22611043
Stringent response of Escherichia coli: revisiting the bibliome using literature mining. PMID:22587779
Systems biology of fungal infection. PMID:22485108
The autoimmune tautology: an in silico approach. PMID:22474574
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. PMID:22453911
HIPPIE: Integrating protein interaction networks with experiment based quality scores. PMID:22348130
Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). PMID:22180826
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. PMID:22151929
Detection of interaction articles and experimental methods in biomedical literature. PMID:22151872
Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions. PMID:22151701
ELM--the database of eukaryotic linear motifs. PMID:22110040
Chronic morphine alters the presynaptic protein profile: identification of novel molecular targets using proteomics and network analysis. PMID:22043286
A comprehensive curated resource for follicle stimulating hormone signaling. PMID:21996254
Medusa: A tool for exploring and clustering biological networks. PMID:21978489
NetSlim: high-confidence curated signaling maps. PMID:21959865
A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway. PMID:21742767
PSICQUIC and PSISCORE: accessing and scoring molecular interactions. PMID:21716279
Interaction databases on the same page. PMID:21552234
Using graph theory to analyze biological networks. PMID:21527005
Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. PMID:21418653
Assessing the biological significance of gene expression signatures and co-expression modules by studying their network properties. PMID:21408226
The Biomolecular Interaction Network Database in PSI-MI 2.5. PMID:21233089
Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components. PMID:21124865
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. PMID:21045058
ProHits: integrated software for mass spectrometry-based interaction proteomics. PMID:20944583
Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. PMID:20927658
The BioPAX community standard for pathway data sharing. PMID:20829833
BioXSD: the common data-exchange format for everyday bioinformatics web services. PMID:20823319
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. PMID:20727200
Curating the innate immunity interactome. PMID:20727158
Encoding the states of interacting proteins to facilitate biological pathways reconstruction. PMID:20707925
The function of communities in protein interaction networks at multiple scales. PMID:20649971
Annotation of SBML models through rule-based semantic integration. PMID:20626923
PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. PMID:20428315
Visualization of omics data for systems biology. PMID:20195258
Lists2Networks: integrated analysis of gene/protein lists. PMID:20152038
Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging. PMID:20128910
An ontology-based search engine for protein-protein interactions. PMID:20122195
Biana: a software framework for compiling biological interactions and analyzing networks. PMID:20105306
NetPath: a public resource of curated signal transduction pathways. PMID:20067622
Snazer: the simulations and networks analyzer. PMID:20056001
The Negatome database: a reference set of non-interacting protein pairs. PMID:19920129
ELM: the status of the 2010 eukaryotic linear motif resource. PMID:19920119
DRYGIN: a database of quantitative genetic interaction networks in yeast. PMID:19880385
NAViGaTOR: Network Analysis, Visualization and Graphing Toronto. PMID:19837718
A community standard format for the representation of protein affinity reagents. PMID:19674966
PathBuilder--open source software for annotating and developing pathway resources. PMID:19628504
Challenges in the analysis of mass-throughput data: a technical commentary from the statistical machine learning perspective. PMID:19458765
Public databases and software for the pathway analysis of cancer genomes. PMID:19455256
SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. PMID:19454602
Database resources in metabolomics: an overview. PMID:19418229
Protein-protein interaction as a predictor of subcellular location. PMID:19243629
Assembling proteomics data as a prerequisite for the analysis of large scale experiments. PMID:19166578
Literature-curated protein interaction datasets. PMID:19116613
Integrated network analysis platform for protein-protein interactions. PMID:19079255
Identifying and classifying biomedical perturbations in text. PMID:19074486
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
A survey of visualization tools for biological network analysis. PMID:19040716
Arena3D: visualization of biological networks in 3D. PMID:19040715
EcID. A database for the inference of functional interactions in E. coli. PMID:19004873
Human Proteinpedia: a unified discovery resource for proteomics research. PMID:18948298
ConsensusPathDB--a database for integrating human functional interaction networks. PMID:18940869
OntoGene in BioCreative II. PMID:18834491
InnateDB: facilitating systems-level analyses of the mammalian innate immune response. PMID:18766178
Standardization Initiatives in the (eco)toxicogenomics domain: a review. PMID:18629184
Human Proteinpedia as a resource for clinical proteomics. PMID:18573810
VisANT: an integrative framework for networks in systems biology. PMID:18463131
PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains. PMID:18160410
Generating confidence intervals on biological networks. PMID:18053130
Framework for a protein ontology. PMID:18047702
CORUM: the comprehensive resource of mammalian protein complexes. PMID:17965090
Integration of biological networks and gene expression data using Cytoscape. PMID:17947979
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. PMID:17925023
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. PMID:17916244
PepBank--a database of peptides based on sequence text mining and public peptide data sources. PMID:17678535
Reuse of structural domain-domain interactions in protein networks. PMID:17640363
putzig is required for cell proliferation and regulates notch activity in Drosophila. PMID:17634285
FlyMine: an integrated database for Drosophila and Anopheles genomics. PMID:17615057
GenMAPP 2: new features and resources for pathway analysis. PMID:17588266
bZIPDB: a database of regulatory information for human bZIP transcription factors. PMID:17535445
Unequal evolutionary conservation of human protein interactions in interologous networks. PMID:17535438
Analysing protein-protein interaction networks of human liver cancer cell lines with diverse metastasis potential. PMID:17458561
Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PMID:17397251
Large-scale mapping of human protein-protein interactions by mass spectrometry. PMID:17353931
From bytes to bedside: data integration and computational biology for translational cancer research. PMID:17319736
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ. PMID:17270041
An evaluation of human protein-protein interaction data in the public domain. PMID:17254303
Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it. PMID:17169146
IntAct--open source resource for molecular interaction data. PMID:17145710
MINT: the Molecular INTeraction database. PMID:17135203
DOMINO: a database of domain-peptide interactions. PMID:17135199
cPath: open source software for collecting, storing, and querying biological pathways. PMID:17101041
XML schemas for common bioinformatic data types and their application in workflow systems. PMID:17087823
Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow. PMID:17018156
Protein-protein interactions more conserved within species than across species. PMID:16854211
BiologicalNetworks: visualization and analysis tool for systems biology. PMID:16845051
APID: Agile Protein Interaction DataAnalyzer. PMID:16845013
The HUPO Brain Proteome Project--no need to hurry? PMID:16835694
The cognitive phenotype of Down syndrome: insights from intracellular network analysis. PMID:16815222
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. PMID:16762047
Standardizing the standards. PMID:16738556
Exploration of biological network centralities with CentiBiN. PMID:16630347
PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns. PMID:16381951
BioGRID: a general repository for interaction datasets. PMID:16381927
Pathguide: a pathway resource list. PMID:16381921
MPact: the MIPS protein interaction resource on yeast. PMID:16381906
Human protein reference database--2006 update. PMID:16381900
Nuclear Receptor Signaling Atlas (www.nursa.org): hyperlinking the nuclear receptor signaling community. PMID:16381851
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. PMID:16351748
An analysis of extensible modelling for functional genomics data. PMID:16188029
MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences. PMID:16043635
VisANT: data-integrating visual framework for biological networks and modules. PMID:15980487
Atlas - a data warehouse for integrative bioinformatics. PMID:15723693
Protein interaction mapping: a Drosophila case study. PMID:15710747
Advances in protein complex analysis using mass spectrometry. PMID:15611014
The European Bioinformatics Institute's data resources: towards systems biology. PMID:15608238
The Biomolecular Interaction Network Database and related tools 2005 update. PMID:15608229
CYGD: the Comprehensive Yeast Genome Database. PMID:15608217
A Drosophila protein-interaction map centered on cell-cycle regulators. PMID:15575970
From ORFeome to biology: a functional genomics pipeline. PMID:15489336
Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. PMID:15212693
BioBuilder as a database development and functional annotation platform for proteins. PMID:15099404
The Database of Interacting Proteins: 2004 update. PMID:14681454 -
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 -
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions
PubMed citations: 19.
19 articles citing: Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions
HumanMine: advanced data searching, analysis and cross-species comparison. PMID:35820040
A Network Biology Approach to Understanding the Tissue-Specific Roles of Non-Coding RNAs in Arthritis. PMID:34803912
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
Complex Portal 2022: new curation frontiers. PMID:34718729
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Analysing the yeast complexome-the Complex Portal rising to the challenge. PMID:33677561
Computational resources for identifying and describing proteins driving liquid-liquid phase separation. PMID:33517364
Towards a unified open access dataset of molecular interactions. PMID:33262342
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). PMID:32637990
An intrinsically disordered proteins community for ELIXIR. PMID:31824649
PhaSePro: the database of proteins driving liquid-liquid phase separation. PMID:31612960
Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration. PMID:31611808
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. PMID:30793173
Integration of macromolecular complex data into the Saccharomyces Genome Database. PMID:30715277
APID database: redefining protein-protein interaction experimental evidences and binary interactomes. PMID:30715274
Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. PMID:30602777
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions. PMID:30371822
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. PMID:30357405
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molecular interaction
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
protein
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
Tags
More detailed information about this field from each metasource.
molecular interaction
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
protein
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
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