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Protocols

SMPDB specifications

Information


Unique identifier OMICS_02777
Name SMPDB
Alternative name Small Molecule Pathway DataBase
Restrictions to use None
Version 2.0
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Small_Molecule_Pathway_Database

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline David Wishart

Publications for Small Molecule Pathway DataBase

SMPDB citations

 (16)
library_books

Metabolic reprogramming of the urea cycle pathway in experimental pulmonary arterial hypertension rats induced by monocrotaline

2018
PMCID: 5948901
PMID: 29751839
DOI: 10.1186/s12931-018-0800-5

[…] ltiple testing by using one-paired p value, only the urea cycle pathways were enriched with the metabolites of interest (p = 0.02).Fig. 5Figure  shows the related urea cycle pathway from the KEGG and SMPDB. Urea cycle pathway, playing a major role in PAH severity and treatment response [, ], connected five major distinguished metabolites in this study. These metabolites were AMP, 4-hydroxy-proline […]

library_books

Discovery of urinary biomarkers to discriminate between exogenous and semi endogenous thiouracil in cattle: A parallel like randomized design

2018
PLoS One
PMCID: 5896977
PMID: 29649241
DOI: 10.1371/journal.pone.0195351

[…] ID 6001, no direct link with TU could be made. To the best of our knowledge, no studies have reported on these compounds. In addition, pathway analysis software tools such as MetaboAnalyst 3.0 [] and Small Molecule Pathway Database [] did not enclose any information on these compounds as well.Unfortunately, analytical reference standards were not available for all of the above-suggested structures […]

library_books

Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data

2018
BMC Bioinformatics
PMCID: 5749025
PMID: 29291722
DOI: 10.1186/s12859-017-2006-0

[…] used serum/plasma biomarkers, results with other types of biological samples would have been similar. On one hand, metabolite disease sets are not up-to-date. For instance, MetaboAnalyst and MBRole (SMPDB and HMDB disease databases, respectively) base their searches of literature dated between 1975 and 2008, as stated in the outputs of these tools. Since 2008, advances in high-throughput techniqu […]

call_split

Differential prioritization of therapies to subtypes of triple negative breast cancer using a systems medicine method

2017
Oncotarget
PMCID: 5696233
PMID: 29190967
DOI: 10.18632/oncotarget.21669
call_split See protocol

[…] taset to be used. Integrated pathway databases include BioCarta [], Edinburgh Human Metabolic Network [], HumanCyc [], INOH [], KEGG [], PharmGKB [], NCI Pathway Interaction Database [], Reactome [], SMPDB [], and WikiPathways []. Functions were obtained from the Gene Ontology []. […]

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

[…] local database of MS-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 […]

library_books

Metabolic risk management, physical exercise and lifestyle counselling in low active adults: controlled randomized trial (BELLUGAT)

2017
BMC Public Health
PMCID: 5351047
PMID: 28292282
DOI: 10.1186/s12889-017-4144-8

[…] which uses retention times in a standardized chromatographic system as an orthogonal searchable parameter to complement accurate mass data (accurate mass retention time approach). In both cases, the SMPDB database [, ] will be used for querying metabolites obtained from the HMDB search, using a 0.05 Da M.W. tolerance and the Metaboanalyst platform [, ] for the determination of differential featur […]

Citations

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SMPDB institution(s)
Department of Computing Science, University of Alberta, Edmonton, AB, Canada; Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada; National Institute for Nanotechnology, Edmonton, AB, Canada

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