Articles producció científica> Medicina i Cirurgia

A Metabolites Merging Strategy (MMS): Harmonization to Enable Studies’ Intercomparison

  • Identification data

    Identifier: imarina:9333910
    Authors:
    Villalba, HLlambrich, MGumà, JBrezmes, JCumeras, R
    Abstract:
    Metabolomics encounters challenges in cross-study comparisons due to diverse metabolite nomenclature and reporting practices. To bridge this gap, we introduce the Metabolites Merging Strategy (MMS), offering a systematic framework to harmonize multiple metabolite datasets for enhanced interstudy comparability. MMS has three steps. Step 1: Translation and merging of the different datasets by employing InChIKeys for data integration, encompassing the translation of metabolite names (if needed). Followed by Step 2: Attributes’ retrieval from the InChIkey, including descriptors of name (title name from PubChem and RefMet name from Metabolomics Workbench), and chemical properties (molecular weight and molecular formula), both systematic (InChI, InChIKey, SMILES) and non-systematic identifiers (PubChem, CheBI, HMDB, KEGG, LipidMaps, DrugBank, Bin ID and CAS number), and their ontology. Finally, a meticulous three-step curation process is used to rectify disparities for conjugated base/acid compounds (optional step), missing attributes, and synonym checking (duplicated information). The MMS procedure is exemplified through a case study of urinary asthma metabolites, where MMS facilitated the identification of significant pathways hidden when no dataset merging strategy was followed. This study highlights the need for standardized and unified metabolite datasets to enhance the reproducibility and comparability of metabolomics studies.
  • Others:

    Author, as appears in the article.: Villalba, H; Llambrich, M; Gumà, J; Brezmes, J; Cumeras, R
    Department: Enginyeria Electrònica, Elèctrica i Automàtica Medicina i Cirurgia
    URV's Author/s: Brezmes Llecha, Jesús Jorge / Cumeras Olmeda, Raquel / Gumà Padró, José / Llambrich Rodriguez, Maria
    Keywords: Studies intercomparison Metabolomics Metabolites Merging Inchikey Harmonization studies intercomparison standards merging inchikey harmonization
    Abstract: Metabolomics encounters challenges in cross-study comparisons due to diverse metabolite nomenclature and reporting practices. To bridge this gap, we introduce the Metabolites Merging Strategy (MMS), offering a systematic framework to harmonize multiple metabolite datasets for enhanced interstudy comparability. MMS has three steps. Step 1: Translation and merging of the different datasets by employing InChIKeys for data integration, encompassing the translation of metabolite names (if needed). Followed by Step 2: Attributes’ retrieval from the InChIkey, including descriptors of name (title name from PubChem and RefMet name from Metabolomics Workbench), and chemical properties (molecular weight and molecular formula), both systematic (InChI, InChIKey, SMILES) and non-systematic identifiers (PubChem, CheBI, HMDB, KEGG, LipidMaps, DrugBank, Bin ID and CAS number), and their ontology. Finally, a meticulous three-step curation process is used to rectify disparities for conjugated base/acid compounds (optional step), missing attributes, and synonym checking (duplicated information). The MMS procedure is exemplified through a case study of urinary asthma metabolites, where MMS facilitated the identification of significant pathways hidden when no dataset merging strategy was followed. This study highlights the need for standardized and unified metabolite datasets to enhance the reproducibility and comparability of metabolomics studies.
    Thematic Areas: Molecular biology Medicina ii Farmacia Endocrinology, diabetes and metabolism Ciências biológicas ii Ciências biológicas i Biotecnología Biochemistry & molecular biology Biochemistry
    licence for use: https://creativecommons.org/licenses/by/3.0/es/
    Author's mail: raquel.cumeras@urv.cat jose.guma@urv.cat jesus.brezmes@urv.cat maria.llambrich@urv.cat
    Author identifier: 0000-0003-4663-4247 0000-0001-7541-9832 0000-0002-7704-8550 0000-0001-8418-0982
    Record's date: 2024-01-13
    Papper version: info:eu-repo/semantics/publishedVersion
    Link to the original source: https://www.mdpi.com/2218-1989/13/12/1167
    Papper original source: Metabolites. 13 (12):
    APA: Villalba, H; Llambrich, M; Gumà, J; Brezmes, J; Cumeras, R (2023). A Metabolites Merging Strategy (MMS): Harmonization to Enable Studies’ Intercomparison. Metabolites, 13(12), -. DOI: 10.3390/metabo13121167
    Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
    Article's DOI: 10.3390/metabo13121167
    Entity: Universitat Rovira i Virgili
    Journal publication year: 2023
    Publication Type: Journal Publications
  • Keywords:

    Biochemistry,Biochemistry & Molecular Biology,Endocrinology, Diabetes and Metabolism,Molecular Biology
    Studies intercomparison
    Metabolomics
    Metabolites
    Merging
    Inchikey
    Harmonization
    studies intercomparison
    standards
    merging
    inchikey
    harmonization
    Molecular biology
    Medicina ii
    Farmacia
    Endocrinology, diabetes and metabolism
    Ciências biológicas ii
    Ciências biológicas i
    Biotecnología
    Biochemistry & molecular biology
    Biochemistry
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