R3VM0R last accessed: 2022-11-04

t3db
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:34.231588

Other names: T3DB, Toxic Exposome Database, t3db

Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.

Webpage:

http://www.t3db.org/

Licence:

Name: T3DB Attribution required
URL: http://www.t3db.ca/about

Publications:

Publications
More detailed information about this field from each metasource.

T3DB: the toxic exposome database
PMID: 25378312
metasource: Fairsharing.org
version: FAIRsharing.org: T3DB; Toxin and Toxin Target Database; DOI: https://doi.org/10.25504/FAIRsharing.psn0h2; Last edited: April 26, 2021, 3:30 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

T3DB: a comprehensively annotated database of common toxins and their targets
PMID: 19897546
metasource: Fairsharing.org
version: FAIRsharing.org: T3DB; Toxin and Toxin Target Database; DOI: https://doi.org/10.25504/FAIRsharing.psn0h2; Last edited: April 26, 2021, 3:30 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:34.231588

http://dx.doi.org/10.1093/nar/gku1004
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

T3DB: the toxic exposome database PubMed citations: 81.

81 articles citing: T3DB: the toxic exposome database

A Narrative Literature Review of Natural Language Processing Applied to the Occupational Exposome. PMID:35886395
DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases. PMID:35877764
Precision environmental health monitoring by longitudinal exposome and multi-omics profiling. PMID:35667843
A Role for Gene-Environment Interactions in Autism Spectrum Disorder Is Supported by Variants in Genes Regulating the Effects of Exposure to Xenobiotics. PMID:35663546
Omics-based ecosurveillance for the assessment of ecosystem function, health, and resilience. PMID:35403668
Integrative interactomics applied to bovine fescue toxicosis. PMID:35318361
Regulatory Testing for Endocrine Disruptors; Need for Validated Methods and Integrated Approaches. PMID:35295107
Integrated bioinformatics analysis identifies established and novel TGFβ1-regulated genes modulated by anti-fibrotic drugs. PMID:35197532
Peptide-Based Vaccines for Tuberculosis. PMID:35173740
DDPD 1.0: a manually curated and standardized database of digital properties of approved drugs for drug-likeness evaluation and drug development. PMID:35139189
Phage Annotation Guide: Guidelines for Assembly and High-Quality Annotation. PMID:35083439
Computer-Aided Drug Design (CADD) to De-Orphanize Marine Molecules: Finding Potential Therapeutic Agents for Neurodegenerative and Cardiovascular Diseases. PMID:35049908
Not Drug-like, but Like Drugs: Cnidaria Natural Products. PMID:35049897
Emerging technologies and their impact on regulatory science. PMID:34783606
Natural products for infectious microbes and diseases: an overview of sources, compounds, and chemical diversities. PMID:34705221
Defining the Scope of Exposome Studies and Research Needs from a Multidisciplinary Perspective. PMID:34660833
DTI-HeNE: a novel method for drug-target interaction prediction based on heterogeneous network embedding. PMID:34479477
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Utilizing a Biology-Driven Approach to Map the Exposome in Health and Disease: An Essential Investment to Drive the Next Generation of Environmental Discovery. PMID:34435882
Untargeted high-resolution paired mass distance data mining for retrieving general chemical relationships. PMID:34337162
REPRODUCTIVE TOXICOLOGY: Endocrine disruption and reproductive disorders: impacts on sexually dimorphic neuroendocrine pathways. PMID:33929341
Integration of data across toxicity endpoints for improved safety assessment of chemicals: the example of carcinogenicity assessment. PMID:33830278
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data. PMID:33597026
Metabolome-wide association study of flavorant vanillin exposure in bronchial epithelial cells reveals disease-related perturbations in metabolism. PMID:33360165
The Chemical Exposome of Human Aging. PMID:33329714
INTEDE: interactome of drug-metabolizing enzymes. PMID:33045737
Named Entity Recognition and Relation Detection for Biomedical Information Extraction. PMID:32984300
Phexpo: a package for bidirectional enrichment analysis of phenotypes and chemicals. PMID:32734156
Interplay between Cellular Metabolism and the DNA Damage Response in Cancer. PMID:32722390
Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling. PMID:32663517
Towards the routine use of in silico screenings for drug discovery using metabolic modelling. PMID:32369553
DRUGPATH: The Drug Gene Pathway Meta-Database. PMID:32365960
DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases. PMID:32308806
High-throughput screening tools facilitate calculation of a combined exposure-bioactivity index for chemicals with endocrine activity. PMID:32050122
Integrating Exposure Knowledge and Serum Suspect Screening as a New Approach to Biomonitoring: An Application in Firefighters and Office Workers. PMID:31971370
The Promises and Challenges of Toxico-Epigenomics: Environmental Chemicals and Their Impacts on the Epigenome. PMID:31950866
Metabolome-Wide Association Study of Deployment to Balad, Iraq or Bagram, Afghanistan. PMID:31800448
The metaRbolomics Toolbox in Bioconductor and beyond. PMID:31548506
A precision medicine approach to defining the impact of doxorubicin on the bioenergetic-metabolite interactome in human platelets. PMID:31546171
Towards Mass Spectrometry-Based Chemical Exposome: Current Approaches, Challenges, and Future Directions. PMID:31426576
Statistical Workflow for Feature Selection in Human Metabolomics Data. PMID:31336989
Use of big data in drug development for precision medicine: an update. PMID:31286058
Literature-Based Enrichment Insights into Redox Control of Vascular Biology. PMID:31223421
Tackling the Complexity of the Exposome: Considerations from the Gunma University Initiative for Advanced Research (GIAR) Exposome Symposium. PMID:31174297
Navigating in vitro bioactivity data by investigating available resources using model compounds. PMID:31036807
CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification. PMID:31013937
Multi LC-MS/MS and LC-HRMS Methods for Determination of 24 Mycotoxins including Major Phase I and II Biomarker Metabolites in Biological Matrices from Pigs and Broiler Chickens. PMID:30893895
BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification. PMID:30612223
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. PMID:30567491
Chemical Composition and Antifungal In Vitro and In Silico, Antioxidant, and Anticholinesterase Activities of Extracts and Constituents of Ouratea fieldingiana (DC.) Baill. PMID:30524481
Therapeutic Potential of a New Jumbo Phage That Infects Vibrio coralliilyticus, a Widespread Coral Pathogen. PMID:30405564
DES-Mutation: System for Exploring Links of Mutations and Diseases. PMID:30190574
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. PMID:30084866
Changing Trends in Computational Drug Repositioning. PMID:29874824
In silico design of novel proton-pump inhibitors with reduced adverse effects. PMID:29845582
The role of the Human Metabolome Database in inborn errors of metabolism. PMID:29663269
Assessing health risks from multiple environmental stressors: Moving from G×E to I×E. PMID:29555026
In Silico Prediction of Chemical Toxicity for Drug Design Using Machine Learning Methods and Structural Alerts. PMID:29515993
Induction of Amyloid-β42 Production by Fipronil and Other Pyrazole Insecticides. PMID:29504531
Beyond genomics: understanding exposotypes through metabolomics. PMID:29373992
Integrating tools for non-targeted analysis research and chemical safety evaluations at the US EPA. PMID:29288256
DDR: efficient computational method to predict drug-target interactions using graph mining and machine learning approaches. PMID:29186331
PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database. PMID:29106626
DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species. PMID:28729549
The Exposome Paradigm in Human Health: Lessons from the Emory Exposome Summer Course. PMID:28669935
From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. PMID:28520864
An Overview of Literature Topics Related to Current Concepts, Methods, Tools, and Applications for Cumulative Risk Assessment (2007-2016). PMID:28387705
DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. PMID:28387604
Assessing the Exposome with External Measures: Commentary on the State of the Science and Research Recommendations. PMID:28384083
Predicting drug-target interactions by dual-network integrated logistic matrix factorization. PMID:28079135
Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health. PMID:28068484
The BioGRID interaction database: 2017 update. PMID:27980099
xMSannotator: An R Package for Network-Based Annotation of High-Resolution Metabolomics Data. PMID:27977166
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. PMID:27867422
Deployment-Associated Exposure Surveillance With High-Resolution Metabolomics. PMID:27501099
Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database. PMID:27170236
A mechanism-based 3D-QSAR approach for classification and prediction of acetylcholinesterase inhibitory potency of organophosphate and carbamate analogs. PMID:27055524
Cancer Metabolomics and the Human Metabolome Database. PMID:26950159
Analytical Complexity in Detection of Gene Variant-by-Environment Exposure Interactions in High-Throughput Genomic and Exposomic Research. PMID:26809563
ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. PMID:26481353
PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more. PMID:25925572
T3DB: a comprehensively annotated database of common toxins and their targets PubMed citations: 45.

45 articles citing: T3DB: a comprehensively annotated database of common toxins and their targets

A Role for Gene-Environment Interactions in Autism Spectrum Disorder Is Supported by Variants in Genes Regulating the Effects of Exposure to Xenobiotics. PMID:35663546
Exploring Toxins for Hunting SARS-CoV-2 Main Protease Inhibitors: Molecular Docking, Molecular Dynamics, Pharmacokinetic Properties, and Reactome Study. PMID:35215266
Knowledge-Driven Approaches to Create the MTox700+ Metabolite Panel for Predicting Toxicity. PMID:35094093
Not Drug-like, but Like Drugs: Cnidaria Natural Products. PMID:35049897
MitoTox: a comprehensive mitochondrial toxicity database. PMID:34266386
NFnetFu: A novel workflow for microbiome data fusion. PMID:34216888
Integration of data across toxicity endpoints for improved safety assessment of chemicals: the example of carcinogenicity assessment. PMID:33830278
DTiGEMS+: drug-target interaction prediction using graph embedding, graph mining, and similarity-based techniques. PMID:33431036
Review on natural products databases: where to find data in 2020. PMID:33431011
Recent Progress and Development of G-Quadruplex-Based Luminescent Assays for Ochratoxin A Detection. PMID:33088800
Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling. PMID:32663517
DRUGPATH: The Drug Gene Pathway Meta-Database. PMID:32365960
The metaRbolomics Toolbox in Bioconductor and beyond. PMID:31548506
HyperFoods: Machine intelligent mapping of cancer-beating molecules in foods. PMID:31270435
eToxPred: a machine learning-based approach to estimate the toxicity of drug candidates. PMID:30621790
Therapeutic Potential of a New Jumbo Phage That Infects Vibrio coralliilyticus, a Widespread Coral Pathogen. PMID:30405564
In silico design of novel proton-pump inhibitors with reduced adverse effects. PMID:29845582
Candidate-gene based GWAS identifies reproducible DNA markers for metabolic pyrethroid resistance from standing genetic variation in East African Anopheles gambiae. PMID:29440767
Beyond genomics: understanding exposotypes through metabolomics. PMID:29373992
ToxiM: A Toxicity Prediction Tool for Small Molecules Developed Using Machine Learning and Chemoinformatics Approaches. PMID:29249969
Assessing human metal accumulations in an urban superfund site. PMID:28704752
Network mirroring for drug repositioning. PMID:28539121
Comprehensive strategy for the design of precision drugs and identification of genetic signature behind proneness of the disease-a pharmacogenomic approach. PMID:28470340
Drug-target interaction prediction via class imbalance-aware ensemble learning. PMID:28155697
xMSannotator: An R Package for Network-Based Annotation of High-Resolution Metabolomics Data. PMID:27977166
Comparative analysis of housekeeping and tissue-selective genes in human based on network topologies and biological properties. PMID:26897376
PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine. PMID:26555441
pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures. PMID:25860834
On the role of physics and evolution in dictating protein structure and function. PMID:25484448
Proteomics for systems toxicology. PMID:25379146
T3DB: the toxic exposome database. PMID:25378312
In vitro platforms for evaluating liver toxicity. PMID:24764241
Pathways of Toxicity. PMID:24127042
DGIdb: mining the druggable genome. PMID:24122041
Interplay of physics and evolution in the likely origin of protein biochemical function. PMID:23690621
GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis. PMID:23650583
Chapter 3: Small molecules and disease. PMID:23300405
Scorpion toxins specific for potassium (K+) channels: a historical overview of peptide bioengineering. PMID:23202307
ECMDB: the E. coli Metabolome Database. PMID:23109553
In-silico studies in Chinese herbal medicines' research: evaluation of in-silico methodologies and phytochemical data sources, and a review of research to date. PMID:22326356
DNAtraffic--a new database for systems biology of DNA dynamics during the cell life. PMID:22110027
YMDB: the Yeast Metabolome Database. PMID:22064855
HIT: linking herbal active ingredients to targets. PMID:21097881
The Comparative Toxicogenomics Database: update 2011. PMID:20864448
Xenobiotic metabolism: a view through the metabolometer. PMID:20232918
http://dx.doi.org/10.1093/nar/gku1004

Tags:

Tags
More detailed information about this field from each metasource.

molecular entity
metasource: Fairsharing.org
version: FAIRsharing.org: T3DB; Toxin and Toxin Target Database; DOI: https://doi.org/10.25504/FAIRsharing.psn0h2; Last edited: April 26, 2021, 3:30 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

protein
metasource: Fairsharing.org
version: FAIRsharing.org: T3DB; Toxin and Toxin Target Database; DOI: https://doi.org/10.25504/FAIRsharing.psn0h2; Last edited: April 26, 2021, 3:30 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

other molecular biology databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

drugs and drug design
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

biochemistry
metasource: re3data.org
version: re3data.org: T3DB; editing status 2022-03-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VM0R last accessed: 2022-11-04

bioinformatics
metasource: re3data.org
version: re3data.org: T3DB; editing status 2022-03-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VM0R last accessed: 2022-11-04

cellular interactions
metasource: re3data.org
version: re3data.org: T3DB; editing status 2022-03-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VM0R last accessed: 2022-11-04

chemical structure
metasource: re3data.org
version: re3data.org: T3DB; editing status 2022-03-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VM0R last accessed: 2022-11-04

drugs
metasource: re3data.org
version: re3data.org: T3DB; editing status 2022-03-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VM0R last accessed: 2022-11-04

food toxins
metasource: re3data.org
version: re3data.org: T3DB; editing status 2022-03-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VM0R last accessed: 2022-11-04

medicine
metasource: re3data.org
version: re3data.org: T3DB; editing status 2022-03-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VM0R last accessed: 2022-11-04

molecular interactions
metasource: re3data.org
version: re3data.org: T3DB; editing status 2022-03-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VM0R last accessed: 2022-11-04

pesticides
metasource: re3data.org
version: re3data.org: T3DB; editing status 2022-03-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VM0R last accessed: 2022-11-04

pollutants
metasource: re3data.org
version: re3data.org: T3DB; editing status 2022-03-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VM0R last accessed: 2022-11-04

toxic exposome
metasource: re3data.org
version: re3data.org: T3DB; editing status 2022-03-28; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VM0R last accessed: 2022-11-04

small molecules
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:34.231588

toxicology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:34.231588

metabolomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:34.231588

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:34.231588

molecular entity protein molecular biology drug biochemistry bioinformatics cellular interactions chemical structure drugs food toxins medicine molecular interactions pesticides pollutants toxic exposome small molecule toxicology metabolomics molecular interactions, pathways and networks

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