MicroRNA childhood cancer catalog (M3Cs): a resource for translational bioinformatics toward health informatics in pediatric cancer

Abstract

MicroRNA childhood Cancer Catalog (M3Cs) is a high-quality curated collection of published miRNA research studies on 16 pediatric cancer diseases. M3Cs scope was based on two approaches: data-driven clinical significance and data-driven human pediatric cell line models. Based on the translational bioinformatics spectrum, the main objective of this study is to bring miRNA research into clinical significance in both pediatric cancer patient care and drug discovery toward health informatics in childhood cancer. M3Cs development passed through three phases: 1. Literature Mining: It includes external database search and screening. 2. Data processing that includes three steps: (a) Data Extraction, (b) Data Curation and annotation, (c) Web Development. 3. Publishing: Shinyapps.io was used as a web interface for the deployment of M3Cs. M3Cs is now available online and can be accessed through https://m3cs.shinyapps.io/M3Cs/. For data-driven clinical significance approach, 538 miRNAs from 268 publications were reported in the clinical domain while 7 miRNAs from 5 publications were reported in the clinical & drug domain. For data-driven human pediatric cell line models approach, 538 miRNAs from 1268 publications were reported in the cell line domain while 211 miRNAs from 177 publications in the cell line & drug domain. M3Cs acted to fill the gap by applying translational bioinformatics general pathway to transfer data-driven research toward data-driven clinical care and/or hypothesis generation. Aggregated and well-curated data of M3Cs will enable stakeholders in health care to incorporate miRNA in the clinical policy. Database URL:https://m3cs.shinyapps.io/M3Cs/

A Standardized M3Cs clinical validity framework for microRNA data in microRNA databases with application to MicroRNA Childhood Cancer Catalog (M3Cs) version 2.0

“…As in M3Cs platform, M3Cs V.2.0 followed the same step of web development 3 . Shinyapps.io platform was used as a web interface for the deployment of the M3Cs V.2.0 application.…”

“…The catalog is a translational bioinformatics web tool for pediatric oncology researchers. In the clinical domain of M3Cs, the users can nd the role of miRNA under one or more of the following categories: diagnostic, prognostic, predictive, and susceptibility/risk biomarker 3 .…”

“…Second, we removed retracted papers. Third, we followed the same 3 steps of data processing in M3Cs with central validation at the end of each phase3 for studies published in 2023 as an update. In M3Cs V.2.0, we have added new features.…”

Childhood cancer data initiative: Status report

“…The CCDC is an open‐access, continuously growing inventory of pediatric databases and resources including registries, repositories (e.g., Genomic Data Commons 9 ), knowledge bases (e.g., Clinical Interpretation of Variants in Cancer: CIViC 10 ), and catalogs (e.g., MicroRNA Childhood Cancer Catalog 11 ). There are currently more than 45 resources and 220 datasets in the catalog.…”