NDDRF: A risk factor knowledgebase for personalized prevention of neurodegenerative diseases.

INTRODUCTION: Neurodegenerative diseases (NDDs) are a series of chronic diseases, which are associated with progressive loss of neuronal structure or function. The complex etiologies of the NDDs remain unclear, thus the prevention and early diagnosis of NDDs are critical to reducing the mortality and morbidity of these diseases. OBJECTIVES: To provide a systematic understanding of the heterogeneity of the risk factors associated with different NDDs (pan-neurodegenerative diseases or pan-NDDs), the knowledgebase is established to facilitate the personalized and knowledge-guided diagnosis, prevention and prediction of NDDs. METHODS: Before data collection, the medical, lifescienceand informatics experts as well as the potential users of the database were consulted and discussed for the scope of data and the classification of risk factors. The PubMed database was used as the resource of the data and knowledge extraction. Risk factors of NDDs were manually collected from literature published between 1975 and 2020. RESULTS: The comprehensive risk factors database for NDDs (NDDRF) was established including 998 single or combined risk factors, 2293 records and 1071 articles relevant to the 14 most common NDDs. The single risk factors are classified into 3 categories, i.e. epidemiological factors (469), genetic factors (324) and biochemical factors (153). Among all the factors, 179 factors are positive and protective, while 880 factors have negative influence for NDDs. The knowledgebase is available at http://sysbio.org.cn/NDDRF/. CONCLUSION: NDDRF provides the structured information and knowledge resource on risk factors of NDDs. It could benefit the future systematic and personalized investigation of pan-NDDs genesis and progression. Meanwhile it may be used for the future explainable artificial intelligence modeling for smart diagnosis and prevention of NDDs.

Quantitative Data Integration Analysis Method for Cross-Studies: Obstructive Sleep Apnea as an Example.

Objective: In recent years, the prevalence of obstructive sleep apnea (OSA) has gradually increased. The diagnosis of this multiphenotypic disorder requires a combination of several indicators. The objective of this study was to find significant apnea monitor indicators of OSA by developing a strategy for cross-study screening and integration of quantitative data. Methods: Articles related to sleep disorders were obtained from the PubMed database. A sleep disorder dataset and an OSA dataset were manually curated from these articles. Two evaluation indexes, the indicator coverage ratio (ICR) and the study integrity ratio (SIR), were used to filter out OSA indicators from the OSA dataset and create profiles including different numbers of indicators and studies for analysis. Data were analyzed by the meta 4.18-0 package of R, and the p value and standard mean difference (SMD) values were calculated to evaluate the change of each indicator. Results: The sleep disorder dataset was constructed based on 178 studies from 119 publications, the OSA dataset was extracted from 89 studies, 284 sleep-related indicators were filtered out, and 22 profiles were constructed. Apnea hypopnea index was significantly decreased in all 22 profiles. Total sleep time (TST) (min) showed no significant differences in 21 profiles. There were significant increases in rapid eye movement (REM) (%TST) in 18 profiles, minimum arterial oxygen saturation (SaO2) in 9 profiles, REM duration in 3 profiles, and slow wave sleep duration (%TST) and pulse oximetry lowest point in 2 profiles. There were significant decreases in apnea index (AI) in 14 profiles; arousal index and SaO2 < 90 (%TST) in 8 profiles; N1 stage (%TST) in 7 profiles; and hypopnea index, N1 stage (% sleep period time (%SPT)), N2 stage (%SPT), respiratory arousal index, and respiratory disorder index in 2 profiles. Conclusion: The proposed data integration strategy successfully identified multiple significant OSA indicators.

Translational Informatics for Parkinson's Disease: from Big Biomedical Data to Small Actionable Alterations.

Parkinson's disease (PD) is a common neurological disease in elderly people, and its morbidity and mortality are increasing with the advent of global ageing. The traditional paradigm of moving from small data to big data in biomedical research is shifting toward big data-based identification of small actionable alterations. To highlight the use of big data for precision PD medicine, we review PD big data and informatics for the translation of basic PD research to clinical applications. We emphasize some key findings in clinically actionable changes, such as susceptibility genetic variations for PD risk population screening, biomarkers for the diagnosis and stratification of PD patients, risk factors for PD, and lifestyles for the prevention of PD. The challenges associated with the collection, storage, and modelling of diverse big data for PD precision medicine and healthcare are also summarized. Future perspectives on systems modelling and intelligent medicine for PD monitoring, diagnosis, treatment, and healthcare are discussed in the end.

iT2DM Project: A Framework for Secondary Use of EHR Data for High-Throughput Phenotyping in Diabetes.

Diabetes is one of the major burdens in health care, but could be controlled if the relevant data are well-managed. Referring to current successful cases, we designed a framework for the interoperability and integration of medical data in compliance with both archetype and reference information model specification. The clinical data model (CDM) was designed on the basis of OpenEHR archetypes and self-made patient generated health data (PGHD). Integrating healthcare enterprise (IHE) protocol was taken into integrating different modality data. After terminology mapping, the personal health record could be transferred and shared in different clinical information vendors complying with HL7 standards. Many fragment data such as blood glucose and gene data were also integrated to system. Those patients suspected of higher risk of diabetic retinopathy (DR) were grouped as case and other patients could be filtered as control cohort. Furthermore, the framework could be further developed for precision medicine.