Automated Recommendation of Research Keywords from PubMed That Suggest the Molecular Mechanism Associated with Biomarker Metabolites

• Published in: Metabolites Vol. 12; no. 2; p. 133
• Main Authors: Kanazawa, Shinji, Shimizu, Satoshi, Kajihara, Shigeki, Mukai, Norio, Iida, Junko, Matsuda, Fumio
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 01.02.2022; MDPI
• Subjects: Amino acids; Association analysis; Automation; biomarker discovery; Biomarkers; Carbon; Connectivity; Dehydrogenases; Diabetes; Disease; keyword recommendation; Keywords; Knowledge; Medical Subject Headings terms; MeSH co-occurrence; Metabolism; Metabolites; Metabolomics; Methods; Molecular modelling; Prostate cancer; Signal transduction; Software; Tumors; Medical Subject Headings terms; association analysis; biomarker discovery; keyword recommendation; MeSH co-occurrence
• ISSN: 2218-1989; 2218-1989
• DOI: 10.3390/metabo12020133

Metabolomics can help identify candidate biomarker metabolites whose levels are altered in response to disease development or drug administration. However, assessment of the underlying molecular mechanism is challenging considering it depends on the researcher’s knowledge. This study reports a novel method for the automated recommendation of keywords known in the literature that may be overlooked by researchers. The proposed method aided in the identification of Medical Subject Headings (MeSH) terms in PubMed using MeSH co-occurrence data. The intended users are biocurators who have identified specific biomarker metabolites from a metabolomics study and would like to identify literature-reported molecular mechanisms that are associated with both the metabolite and their research area of interest. The proposed method finds MeSH terms that co-occur with a MeSH term of the candidate biomarker metabolite as well as a MeSH term of a researcher’s known keyword, such as the name of a disease. The connectivity score S was determined using association analysis. Pilot analyses demonstrated that, while the biological significance of the obtained MeSH terms could not be guaranteed, the developed method can be useful for finding keywords to further investigate molecular mechanisms in association with candidate biomarker molecules.