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MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles.

Ferry-Dumazet H, Gil L, Deborde C, Moing A, Bernillon S, Rolin D, Nikolski M, de Daruvar A, Jacob D - BMC Plant Biol. (2011)

Bottom Line: Improvements in the techniques for metabolomics analyses and growing interest in metabolomic approaches are resulting in the generation of increasing numbers of metabolomic profiles.Various databases have been created, including organism-specific knowledgebases and analytical technique-specific spectral databases.MeRy-B manages all the data generated by NMR-based plant metabolomics experiments, from description of the biological source to identification of the metabolites and determinations of their concentrations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Université de Bordeaux, Centre de Bioinformatique de Bordeaux, Génomique Fonctionnelle Bordeaux, F-33076 Bordeaux, France.

ABSTRACT

Background: Improvements in the techniques for metabolomics analyses and growing interest in metabolomic approaches are resulting in the generation of increasing numbers of metabolomic profiles. Platforms are required for profile management, as a function of experimental design, and for metabolite identification, to facilitate the mining of the corresponding data. Various databases have been created, including organism-specific knowledgebases and analytical technique-specific spectral databases. However, there is currently no platform meeting the requirements for both profile management and metabolite identification for nuclear magnetic resonance (NMR) experiments.

Description: MeRy-B, the first platform for plant (1)H-NMR metabolomic profiles, is designed (i) to provide a knowledgebase of curated plant profiles and metabolites obtained by NMR, together with the corresponding experimental and analytical metadata, (ii) for queries and visualization of the data, (iii) to discriminate between profiles with spectrum visualization tools and statistical analysis, (iv) to facilitate compound identification. It contains lists of plant metabolites and unknown compounds, with information about experimental conditions, the factors studied and metabolite concentrations for several plant species, compiled from more than one thousand annotated NMR profiles for various organs or tissues.

Conclusion: MeRy-B manages all the data generated by NMR-based plant metabolomics experiments, from description of the biological source to identification of the metabolites and determinations of their concentrations. It is the first database allowing the display and overlay of NMR metabolomic profiles selected through queries on data or metadata. MeRy-B is available from http://www.cbib.u-bordeaux2.fr/MERYB/index.php.

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The MeRy-B card. The MeRy-B card displays all public data stored in the MeRy-B knowledgebase for a given compound. For each species and tissue in which a given compound is found, this card displays data concerning 1H-NMR chemical shifts, multiplicity and quantification. Data may be filtered and sorted by species and/or tissue.
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Figure 4: The MeRy-B card. The MeRy-B card displays all public data stored in the MeRy-B knowledgebase for a given compound. For each species and tissue in which a given compound is found, this card displays data concerning 1H-NMR chemical shifts, multiplicity and quantification. Data may be filtered and sorted by species and/or tissue.

Mentions: The "Search compound" tool enables users to carry out searches of previously detected compounds stored in the MeRy-B knowledgebase. Three types of search may be carried out: (i) a compound search (by name, synonym or elemental formula, according to Hill notation), (ii) a chemical shift search for 1H-NMR data (by chemical shift +/- tolerance, multiplicity, pH, solvent) after the selection of the 1H NMR technique and (iii) advanced searches corresponding to a combination of both these types of search. For example, a new user observes a singlet at 9.08 ppm in tomato at pH 6. He or she then tries to identify this compound by looking for identified compounds described in the MeRy-B knowledgebase as a singlet close to 9.08 ppm ± 0.2. The search returns one compound: trigonelline, with an external link to the KEGG compound card. The user can then check whether the other three chemical shifts of trigonelline were also detected on his/her NMR spectrum. In addition, another link provides all the information available about each compound in MeRy-B via a "MeRy-B card" (MBC) (Figure 4). Chemical Translation Service (CTS, [53]) and HMDB IDs are also provided when available. For a given compound, the "MeRy-B card" displays the list of experiments in which it was detected and, for each experiment, additional metadata are listed (species, tissue/organ, and project name), together with a summary of the analytical results (e.g. for 1H-NMR: chemical shift, multiplicity, minimum and maximum values for quantification). This card also highlights quantitative differences between species, tissues, organs or experiments for a given compound. One or several "MeRy-B cards" are returned for each chemical shift and/or compound search. Comparisons must take into account the possible use of different quantification units. Units are always provided on MeRy-B cards to prevent inappropriate comparisons.


MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles.

Ferry-Dumazet H, Gil L, Deborde C, Moing A, Bernillon S, Rolin D, Nikolski M, de Daruvar A, Jacob D - BMC Plant Biol. (2011)

The MeRy-B card. The MeRy-B card displays all public data stored in the MeRy-B knowledgebase for a given compound. For each species and tissue in which a given compound is found, this card displays data concerning 1H-NMR chemical shifts, multiplicity and quantification. Data may be filtered and sorted by species and/or tissue.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3141636&req=5

Figure 4: The MeRy-B card. The MeRy-B card displays all public data stored in the MeRy-B knowledgebase for a given compound. For each species and tissue in which a given compound is found, this card displays data concerning 1H-NMR chemical shifts, multiplicity and quantification. Data may be filtered and sorted by species and/or tissue.
Mentions: The "Search compound" tool enables users to carry out searches of previously detected compounds stored in the MeRy-B knowledgebase. Three types of search may be carried out: (i) a compound search (by name, synonym or elemental formula, according to Hill notation), (ii) a chemical shift search for 1H-NMR data (by chemical shift +/- tolerance, multiplicity, pH, solvent) after the selection of the 1H NMR technique and (iii) advanced searches corresponding to a combination of both these types of search. For example, a new user observes a singlet at 9.08 ppm in tomato at pH 6. He or she then tries to identify this compound by looking for identified compounds described in the MeRy-B knowledgebase as a singlet close to 9.08 ppm ± 0.2. The search returns one compound: trigonelline, with an external link to the KEGG compound card. The user can then check whether the other three chemical shifts of trigonelline were also detected on his/her NMR spectrum. In addition, another link provides all the information available about each compound in MeRy-B via a "MeRy-B card" (MBC) (Figure 4). Chemical Translation Service (CTS, [53]) and HMDB IDs are also provided when available. For a given compound, the "MeRy-B card" displays the list of experiments in which it was detected and, for each experiment, additional metadata are listed (species, tissue/organ, and project name), together with a summary of the analytical results (e.g. for 1H-NMR: chemical shift, multiplicity, minimum and maximum values for quantification). This card also highlights quantitative differences between species, tissues, organs or experiments for a given compound. One or several "MeRy-B cards" are returned for each chemical shift and/or compound search. Comparisons must take into account the possible use of different quantification units. Units are always provided on MeRy-B cards to prevent inappropriate comparisons.

Bottom Line: Improvements in the techniques for metabolomics analyses and growing interest in metabolomic approaches are resulting in the generation of increasing numbers of metabolomic profiles.Various databases have been created, including organism-specific knowledgebases and analytical technique-specific spectral databases.MeRy-B manages all the data generated by NMR-based plant metabolomics experiments, from description of the biological source to identification of the metabolites and determinations of their concentrations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Université de Bordeaux, Centre de Bioinformatique de Bordeaux, Génomique Fonctionnelle Bordeaux, F-33076 Bordeaux, France.

ABSTRACT

Background: Improvements in the techniques for metabolomics analyses and growing interest in metabolomic approaches are resulting in the generation of increasing numbers of metabolomic profiles. Platforms are required for profile management, as a function of experimental design, and for metabolite identification, to facilitate the mining of the corresponding data. Various databases have been created, including organism-specific knowledgebases and analytical technique-specific spectral databases. However, there is currently no platform meeting the requirements for both profile management and metabolite identification for nuclear magnetic resonance (NMR) experiments.

Description: MeRy-B, the first platform for plant (1)H-NMR metabolomic profiles, is designed (i) to provide a knowledgebase of curated plant profiles and metabolites obtained by NMR, together with the corresponding experimental and analytical metadata, (ii) for queries and visualization of the data, (iii) to discriminate between profiles with spectrum visualization tools and statistical analysis, (iv) to facilitate compound identification. It contains lists of plant metabolites and unknown compounds, with information about experimental conditions, the factors studied and metabolite concentrations for several plant species, compiled from more than one thousand annotated NMR profiles for various organs or tissues.

Conclusion: MeRy-B manages all the data generated by NMR-based plant metabolomics experiments, from description of the biological source to identification of the metabolites and determinations of their concentrations. It is the first database allowing the display and overlay of NMR metabolomic profiles selected through queries on data or metadata. MeRy-B is available from http://www.cbib.u-bordeaux2.fr/MERYB/index.php.

Show MeSH