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