Articles producció científica> Medicina i Cirurgia

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

  • Datos identificativos

    Identificador: imarina:9333910
    Autores:
    Villalba, HLlambrich, MGumà, JBrezmes, JCumeras, R
    Resumen:
    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.
  • Otros:

    Autor según el artículo: Villalba, H; Llambrich, M; Gumà, J; Brezmes, J; Cumeras, R
    Departamento: Enginyeria Electrònica, Elèctrica i Automàtica Medicina i Cirurgia
    Autor/es de la URV: Brezmes Llecha, Jesús Jorge / Cumeras Olmeda, Raquel / Gumà Padró, José / Llambrich Rodriguez, Maria
    Palabras clave: Studies intercomparison Metabolomics Metabolites Merging Inchikey Harmonization studies intercomparison standards merging inchikey harmonization
    Resumen: 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.
    Áreas temáticas: Molecular biology Medicina ii Farmacia Endocrinology, diabetes and metabolism Ciências biológicas ii Ciências biológicas i Biotecnología Biochemistry & molecular biology Biochemistry
    Acceso a la licencia de uso: https://creativecommons.org/licenses/by/3.0/es/
    Direcció de correo del autor: raquel.cumeras@urv.cat jose.guma@urv.cat jesus.brezmes@urv.cat maria.llambrich@urv.cat
    Identificador del autor: 0000-0003-4663-4247 0000-0001-7541-9832 0000-0002-7704-8550 0000-0001-8418-0982
    Fecha de alta del registro: 2024-01-13
    Versión del articulo depositado: info:eu-repo/semantics/publishedVersion
    Enlace a la fuente original: https://www.mdpi.com/2218-1989/13/12/1167
    Referencia al articulo segun fuente origial: Metabolites. 13 (12):
    Referencia de l'ítem segons les normes 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
    URL Documento de licencia: https://repositori.urv.cat/ca/proteccio-de-dades/
    DOI del artículo: 10.3390/metabo13121167
    Entidad: Universitat Rovira i Virgili
    Año de publicación de la revista: 2023
    Tipo de publicación: Journal Publications
  • Palabras clave:

    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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