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YMDB specifications

Information


Unique identifier OMICS_04807
Name YMDB
Alternative name Yeast Metabolome Database
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Version 2.0
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Yeast_Metabolome_Database

Taxon


  • Plants and Fungi
    • Saccharomyces cerevisiae

Documentation


Publications for Yeast Metabolome Database

YMDB citations

 (6)
library_books

Enhanced Isotopic Ratio Outlier Analysis (IROA) Peak Detection and Identification with Ultra High Resolution GC Orbitrap/MS: Potential Application for Investigation of Model Organism Metabolomes

2018
PMCID: 5875999
PMID: 29346327
DOI: 10.3390/metabo8010009

[…] EI characteristic ion, which is m/z 131. As shown in , only 2,3-dihydroxyisovalerate and 2,3-dihydroxyvlerate has a 131 m/z EI fragment and an equivalent ranking. Only 2,3-dihydroxyisovalerate was in YMDB database and obtainable for purchase (obtained from Sigma-Aldrich). The spectrum of the authentic standard showed the characteristic ions of m/z 131.0879 and 292.1358 (, middle in green color), w […]

library_books

Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy

2017
J Cheminform
PMCID: 5445034
DOI: 10.1186/s13321-017-0219-x

[…] S-FINDER. This local compound database covers structures from the 13 most important metabolomic databases, including BMDB, CheBI, DrugBank, ECMDB, FoodDB, HMDB, KNApSack, PlantCyc, SMPDB, T3DB, UNPD, YMDB and STOFF-IDENT [], containing 220,213 entries sorted according to InChIKey, PubChem, exact mass, formula and SMILES.(2) Using database presence emphasis factors Many compounds in the CASMI train […]

library_books

MBROLE 2.0—functional enrichment of chemical compounds

2016
Nucleic Acids Res
PMCID: 4987872
PMID: 27084944
DOI: 10.1093/nar/gkw253

[…] public databases. In addition to the databases available in the first release (KEGG, HMDB, ChEBI and PubChem), we have included data from 10 new resources comprising metabolome databases such as the Yeast Metabolome Database (YMDB) () and the E.coli Metabolome Database (ECMDB) (), pathway and metabolic reaction databases such as the BioCyc Database Collection (), Rhea () and UniPathway (), and re […]

library_books

Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB

2015
Proteins
PMCID: 4329070
PMID: 25546632
DOI: 10.1002/prot.24751

[…] To gain initial insight on the putative interacting surfaces of RNase III and YmdB we performed a blind docking calculation that involved no prior assumptions or information on the interacting surfaces. We used the crystal structure of Ec-YmdB (PDB entry 1SPV) and a structural […]

library_books

Chemometric evaluation of Saccharomyces cerevisiae metabolic profiles using LC–MS

2014
Metabolomics
PMCID: 4289532
PMID: 25598766
DOI: 10.1007/s11306-014-0689-z

[…] re mass spectra, Sj,T, were used to match a metabolic feature to a single or small number of molecular formula in combination with chemical and biological knowledge. Accurate mz data were searched in Yeast Metabolome Database (YMDB) (Jewison et al. ). The candidates were checked in full scan MS chromatogram from LTQ-Orbitrap direct data acquisition having full MS accuracy. MZmine 2 framework (Plus […]

library_books

Methodological approaches to help unravel the intracellular metabolome of Bacillus subtilis

2013
Microb Cell Fact
PMCID: 3722095
PMID: 23844891
DOI: 10.1186/1475-2859-12-69

[…] es have exactly the same mass (e.g. glucose-6-phosphate and fructose-6-phosphate or succinyl-CoA and methyl-malonyl-CoA). Although large online databases such as the human metabolome database [], the yeast metabolome database [] and METLIN [] exist, mostly the measurement of pure standard compounds is necessary for targeted metabolomics. In this context, the main problem is the limited commercial […]

Citations

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YMDB institution(s)
Departments of Computing Science, University of Alberta, Edmonton, AB, Canada; Biological Sciences, University of Alberta, Edmonton, AB, Canada; National Institute for Nanotechnology, Edmonton, AB, Canada
YMDB funding source(s)
Genome Alberta (a division of Genome Canada), Canadian Institutes of Health Research (CIHR), Alberta Innovates

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