RIDAB: Electronic medical record-integrated real world data platform for predicting and summarizing interactions in biomedical research from heterogeneous data resources. (June 2022)

• Record Type: Journal Article
• Authors: Kim, Yunha; Ahn, Imjin; Cho, Ha Na; Gwon, Hansle; Kang, Hee Jun; Seo, Hyeram; Choi, Heejung; Kim, Kyu-Pyo; Jun, Tae Joon; Kim, Young-Hak
• Is Part Of: Computer methods and programs in biomedicine. Volume 221(2022)
• Publication Date: 2022-06
• Subjects: Real world data -- Electronic medical records -- Biological database -- Graph representation learning -- Drug repositioning; Medicine -- Computer programs -- Periodicals; Biology -- Computer programs -- Periodicals; Computers -- Periodicals; Medicine -- Periodicals; Médecine -- Logiciels -- Périodiques; Biologie -- Logiciels -- Périodiques; Biology -- Computer programs; Medicine -- Computer programs; Periodicals; Electronic journals; 610.28
• DOI: 10.1016/j.cmpb.2022.106866
• Languages: English
• ISSNs: 0169-2607

Abstract

Highlights: Retrospective feature for deep leaning is implied in electronic medical record (EMR). Method suggested to integrate EMR data into biomedical networks to reflect real world. EMR constructed into network structure to correspond with biomedical network. Drug repositioning prediction improved when network integrated both database. Graphical abstract: Abstract: Background and objective: With the advent of bioinformatics, biological databases have been constructed to computerize data. Biological systems can be described as interactions and relationships between elements constituting the systems, and they are organized in various biomedical open databases. These open databases have been used in approaches to predict functional interactions such as protein-protein interactions (PPI), drug-drug interactions (DDI) and disease-disease relationships (DDR). However, just combining interaction data has limited effectiveness in predicting the complex relationships occurring in a whole context. Each contributing source contains information on each element in a specific field of knowledge but there is a lack of inter-disciplinary insight in combining them. Methods: In this study, we propose the RWD Integrated platform for Discovering Associations in Biomedical research (RIDAB) to predict interactions between biomedical entities. RIDAB is established as a graph network to construct a platform that predicts the interactions of target entities. Biomedical open database is combined with EMRs each representing a biomedical network and a real-world data. To integrate databases from different domains to build the platform, mapping of the vocabularies was required. In addition, the appropriate structure of the network and the graph embedding method to be used were needed to be selected to fit the tasks. Results: The feasibility of the platform was evaluated using node similarity and link prediction for drug repositioning task, a commonly used task for biomedical network. In addition, we compared the US Food and Drug Administration (FDA)-approved repositioned drugs with the predicted result. By integrating EMR database with biomedical networks, the platform showed increased f1 score in predicting repositioned drugs, from 45.62% to 57.26%, compared to platforms based on biomedical networks alone. Conclusions: This study demonstrates that the elements of biomedical research findings can be reflected by integrating EMR data with open-source biomedical networks. In addition, showed the feasibility of using the established platform to represent the integration of biomedical networks and reflected the relationship between real world networks.