MetaboMiner protocols

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MetaboMiner statistics

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MetaboMiner specifications

Information


Unique identifier OMICS_02847
Name MetaboMiner
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jianguo Xia <>

Publication for MetaboMiner

MetaboMiner in pipelines

 (2)
2017
PMCID: 5312079
PMID: 28196956
DOI: 10.1128/mBio.01434-16

[…] for riken metabolomics (prime; http://prime.psc.riken.jp/) (), human metabolome database (hmdb; http://www.hmdb.ca/) (), madison metabolomics consortium database (http://mmcd.nmrfam.wisc.edu/) (), metabominer (http://wishart.biology.ualberta.ca/metabominer/) (), and biomagresbank (bmrb; http://www.bmrb.wisc.edu//) () with error tolerances of 0.08 ppm and 0.25 ppm for 1h and 13c chemical […]

2017
PMCID: 5539425
PMID: 28765220
DOI: 10.1128/mBio.00887-17

[…] 1h and 13c chemical shifts to the metabolite reference data from the platform for riken metabolomics (prime) (), human metabolome database (hmdb) (), madison metabolomics consortium database (), metabominer (), and biomagresbank (bmrb) () with error tolerances of 0.08 ppm and 0.25 ppm for 1h and 13c chemical shifts, respectively. the relative intensity (i.e., concentration) […]


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MetaboMiner in publications

 (9)
PMCID: 5539425
PMID: 28765220
DOI: 10.1128/mBio.00887-17

[…] 1h and 13c chemical shifts to the metabolite reference data from the platform for riken metabolomics (prime) (), human metabolome database (hmdb) (), madison metabolomics consortium database (), metabominer (), and biomagresbank (bmrb) () with error tolerances of 0.08 ppm and 0.25 ppm for 1h and 13c chemical shifts, respectively. the relative intensity (i.e., concentration) […]

PMCID: 5312079
PMID: 28196956
DOI: 10.1128/mBio.01434-16

[…] for riken metabolomics (prime; http://prime.psc.riken.jp/) (), human metabolome database (hmdb; http://www.hmdb.ca/) (), madison metabolomics consortium database (http://mmcd.nmrfam.wisc.edu/) (), metabominer (http://wishart.biology.ualberta.ca/metabominer/) (), and biomagresbank (bmrb; http://www.bmrb.wisc.edu//) () with error tolerances of 0.08 ppm and 0.25 ppm for 1h and 13c chemical […]

PMCID: 5109290
PMID: 27845374
DOI: 10.1038/srep36833

[…] like principal component analysis (pca), partial least squares discriminant analysis (pls-da) were performed. the nmr peaks found to be significantly modulated were annotated using colmar and metabominer web servers. these servers perform the search for the peaks in metabolome data bank (www.hmdb.ca) and annotate the peaks by identifying the corresponding metabolites. the significant […]

PMCID: 5064370
PMID: 27739464
DOI: 10.1038/srep35309

[…] them with the chemical shifts available in the database library of chenomx profiler (nmr suite, v8.1, chenomx inc., edmonton, canada) and further validated (a) using the freely available software metabominer, (b) performing spiking experiments using standard chemicals (see , and ) and (c) also using other existing databases and literature reports., the multivariate data analysis […]

PMCID: 4340359
PMID: 25333826
DOI: 10.1021/cb5006382

[…] are the bmrb (biological magnetic resonance data bank), hmdb (human metabolome database), mmcd (madison metabolomics consortium database), prime (platform for riken metabolomics) database, and the metabominer database. all of these databases were compiled by recording the 2d 13c–1h hsqc spectra of solutions of isolated (pure) compounds and they all perform cross-peak by cross-peak matching […]


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MetaboMiner institution(s)
Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada

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