R3Z51K last accessed: 2022-11-04

Other names: YMDB, The Yeast Metabolome Database

The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases.

Webpage:

http://www.ymdb.ca

Licence:

Name: other
URL: http://www.ymdb.ca/downloads

Publications:

Publications
More detailed information about this field from each metasource.

YMDB: the Yeast Metabolome Database
PMID: 22064855
metasource: Fairsharing.org
version: FAIRsharing.org: YMDB; The Yeast Metabolome DataBase; DOI: https://doi.org/10.25504/FAIRsharing.tawpg2; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

http://dx.doi.org/10.1093/nar/GKR916
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

YMDB: the Yeast Metabolome Database PubMed citations: 65.

65 articles citing: YMDB: the Yeast Metabolome Database

Molecular investigations on Candida glabrata clinical isolates for pharmacological targeting. PMID:35765448
Metabolite discovery through global annotation of untargeted metabolomics data. PMID:34711973
A Review on the Obtaining of Functional Beers by Addition of Non-Cereal Adjuncts Rich in Antioxidant Compounds. PMID:34572969
Large dependency of intracellular NAD and CoA pools on cultivation conditions in Saccharomyces cerevisiae. PMID:34556160
Closing the gap between in vivo and in vitro omics: using QA/QC to strengthen ex vivo NMR metabolomics. PMID:34369014
Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae. PMID:33750414
Phenolic and Volatile Compounds in the Production of Sugarcane Vinegar. PMID:33283107
Candida Species (Volatile) Metabotyping through Advanced Comprehensive Two-Dimensional Gas Chromatography. PMID:33266330
Automated Annotation of Sphingolipids Including Accurate Identification of Hydroxylation Sites Using MSn Data. PMID:33003696
Qualitative Factor-Based Comparison of NMR, Targeted and Untargeted GC-MS and LC-MS on the Metabolomic Profiles of Rioja and Priorat Red Wines. PMID:33003509
Comparative Lipidomics of Different Yeast Species Associated to Drosophila suzukii. PMID:32872268
The Bovine Metabolome. PMID:32517015
Biotechnological Approach Based on Selected Saccharomyces cerevisiae Starters for Reducing the Use of Sulfur Dioxide in Wine. PMID:32429079
Metabolomics as an Emerging Tool for the Study of Plant-Pathogen Interactions. PMID:32013104
Emerging Insights into the Metabolic Alterations in Aging Using Metabolomics. PMID:31847272
Toward a Synthetic Yeast Endosymbiont with a Minimal Genome. PMID:31419116
Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data. PMID:31196115
Nutritional Metabolomics in Cancer Epidemiology: Current Trends, Challenges, and Future Directions. PMID:31129888
Juice Index: an integrated Sauvignon blanc grape and wine metabolomics database shows mainly seasonal differences. PMID:30830411
Peak Annotation and Verification Engine for Untargeted LC-MS Metabolomics. PMID:30586294
Zinc oxide nanoparticles impose metabolic toxicity by de-regulating proteome and metabolome in Saccharomyces cerevisiae. PMID:30581761
Epigenetic Modifiers Induce Bioactive Phenolic Metabolites in the Marine-Derived Fungus Penicillium brevicompactum. PMID:30061488
Isotope Labeling-Assisted Evaluation of Hydrophilic and Hydrophobic Liquid Chromatograph-Mass Spectrometry for Metabolomics Profiling. PMID:29883117
A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry. PMID:29568436
Assessment of chemical and sensory quality of sugarcane alcoholic fermented beverage. PMID:29358797
PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database. PMID:29106626
Deciphering lipid structures based on platform-independent decision rules. PMID:29058722
Sodium Chloride and Its Influence on the Aroma Profile of Yeasted Bread. PMID:28805678
Causal Genetic Variation Underlying Metabolome Differences. PMID:28652377
Livestock metabolomics and the livestock metabolome: A systematic review. PMID:28531195
Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. PMID:28280153
How close are we to complete annotation of metabolomes? PMID:28113135
Molecular Identification of d-Ribulokinase in Budding Yeast and Mammals. PMID:27909055
YMDB 2.0: a significantly expanded version of the yeast metabolome database. PMID:27899612
Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction. PMID:27895706
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. PMID:27867422
NMR based serum metabolomics reveals a distinctive signature in patients with Lupus Nephritis. PMID:27739464
The metabolome 18 years on: a concept comes of age. PMID:27695392
(1)H NMR metabolomic study of auxotrophic starvation in yeast using Multivariate Curve Resolution-Alternating Least Squares for Pathway Analysis. PMID:27485935
Identification of fungal metabolites from inside Gallus gallus domesticus eggshells by non-invasively detecting volatile organic compounds (VOCs). PMID:27457106
Metabolite profiling of Dioscorea (yam) species reveals underutilised biodiversity and renewable sources for high-value compounds. PMID:27385275
The omic approach to parasitic trematode research-a review of techniques and developments within the past 5 years. PMID:27126082
MBROLE 2.0-functional enrichment of chemical compounds. PMID:27084944
Novel structural features of the immunocompetent ceramide phospho-inositol glycan core from Trichomonas vaginalis. PMID:26671321
An overview of bioinformatics methods for modeling biological pathways in yeast. PMID:26476430
ChEBI in 2016: Improved services and an expanding collection of metabolites. PMID:26467479
MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics. PMID:26322134
Metabolic engineering of yeast to produce fatty acid-derived biofuels: bottlenecks and solutions. PMID:26106371
Mass spectrometry tools and workflows for revealing microbial chemistry. PMID:25996313
PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more. PMID:25925572
Dosage Effects of Salt and pH Stresses on Saccharomyces cerevisiae as Monitored via Metabolites by Using Two Dimensional NMR Spectroscopy. PMID:25642011
Chemometric evaluation of Saccharomyces cerevisiae metabolic profiles using LC-MS. PMID:25598766
Identification of metabolites from 2D (1)H-(13)C HSQC NMR using peak correlation plots. PMID:25511422
Multi-capillary column-ion mobility spectrometry of volatile metabolites emitted by Saccharomyces cerevisiae. PMID:25197771
Stable isotope tracer analysis in isolated mitochondria from mammalian systems. PMID:24957021
IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools. PMID:24949626
Metabolomic strategies for the identification of new enzyme functions and metabolic pathways. PMID:24829223
Effects of age, sex, and genotype on high-sensitivity metabolomic profiles in the fruit fly, Drosophila melanogaster. PMID:24636523
Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches. PMID:24432138
Databases and Software for NMR-Based Metabolomics. PMID:24260723
Methodological approaches to help unravel the intracellular metabolome of Bacillus subtilis. PMID:23844891
Bioanalysis of eukaryotic organelles. PMID:23570618
ECMDB: the E. coli Metabolome Database. PMID:23109553
Metab2MeSH: annotating compounds with medical subject headings. PMID:22492643
The metabolism beyond programmed cell death in yeast. PMID:22480867
http://dx.doi.org/10.1093/nar/GKR916

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More detailed information about this field from each metasource.

cellular localization
metasource: Fairsharing.org
version: FAIRsharing.org: YMDB; The Yeast Metabolome DataBase; DOI: https://doi.org/10.25504/FAIRsharing.tawpg2; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

chemical descriptor
metasource: Fairsharing.org
version: FAIRsharing.org: YMDB; The Yeast Metabolome DataBase; DOI: https://doi.org/10.25504/FAIRsharing.tawpg2; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

chemical formula
metasource: Fairsharing.org
version: FAIRsharing.org: YMDB; The Yeast Metabolome DataBase; DOI: https://doi.org/10.25504/FAIRsharing.tawpg2; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

chemical structure
metasource: Fairsharing.org
version: FAIRsharing.org: YMDB; The Yeast Metabolome DataBase; DOI: https://doi.org/10.25504/FAIRsharing.tawpg2; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

concentration
metasource: Fairsharing.org
version: FAIRsharing.org: YMDB; The Yeast Metabolome DataBase; DOI: https://doi.org/10.25504/FAIRsharing.tawpg2; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

dna sequence data
metasource: Fairsharing.org
version: FAIRsharing.org: YMDB; The Yeast Metabolome DataBase; DOI: https://doi.org/10.25504/FAIRsharing.tawpg2; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

gene
metasource: Fairsharing.org
version: FAIRsharing.org: YMDB; The Yeast Metabolome DataBase; DOI: https://doi.org/10.25504/FAIRsharing.tawpg2; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

gene ontology enrichment
metasource: Fairsharing.org
version: FAIRsharing.org: YMDB; The Yeast Metabolome DataBase; DOI: https://doi.org/10.25504/FAIRsharing.tawpg2; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

mass spectrometry spectra
metasource: Fairsharing.org
version: FAIRsharing.org: YMDB; The Yeast Metabolome DataBase; DOI: https://doi.org/10.25504/FAIRsharing.tawpg2; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

metabolite
metasource: Fairsharing.org
version: FAIRsharing.org: YMDB; The Yeast Metabolome DataBase; DOI: https://doi.org/10.25504/FAIRsharing.tawpg2; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

nuclear magnetic resonance (nmr) spectroscopy
metasource: Fairsharing.org
version: FAIRsharing.org: YMDB; The Yeast Metabolome DataBase; DOI: https://doi.org/10.25504/FAIRsharing.tawpg2; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

protein
metasource: Fairsharing.org
version: FAIRsharing.org: YMDB; The Yeast Metabolome DataBase; DOI: https://doi.org/10.25504/FAIRsharing.tawpg2; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

metasource: re3data.org
version: re3data.org: The Yeast Metabolome Database; editing status 2022-06-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3Z51K last accessed: 2022-11-04

polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: YMDB; The Yeast Metabolome DataBase; DOI: https://doi.org/10.25504/FAIRsharing.tawpg2; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metabolic pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

s. cerevisiae
metasource: re3data.org
version: re3data.org: The Yeast Metabolome Database; editing status 2022-06-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3Z51K last accessed: 2022-11-04

saccharomyces cerevisiae
metasource: re3data.org
version: re3data.org: The Yeast Metabolome Database; editing status 2022-06-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3Z51K last accessed: 2022-11-04

baker's yeast
metasource: re3data.org
version: re3data.org: The Yeast Metabolome Database; editing status 2022-06-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3Z51K last accessed: 2022-11-04

brewer's yeast
metasource: re3data.org
version: re3data.org: The Yeast Metabolome Database; editing status 2022-06-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3Z51K last accessed: 2022-11-04

enzyme
metasource: re3data.org
version: re3data.org: The Yeast Metabolome Database; editing status 2022-06-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3Z51K last accessed: 2022-11-04

cellular localization chemical descriptor chemical formula chemical structure concentration dna sequences gene gene ontology enrichment mass spectrometry spectra metabolite nuclear magnetic resonance (nmr) spectroscopy protein polypeptide region metabolic and signaling pathways metabolic and signaling pathways s. cerevisiae saccharomyces cerevisiae baker's yeast brewer's yeast enzyme

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