HFIP: an integrated multi-omics data and knowledge platform for the precision medicine of heart failure.

Jing Wu,Chenghui Zhao,Zhilong Jia,Jinxiu Sun,Yuan Ni,Gui Lin,Min Zhao,Kunlun He,Tao Li,Chengliang Yin,Qi Chen,Jinlong Shi,Guotong Xie

doi:10.1093/database/baab076

Abstract

As the terminal clinical phenotype of almost all types of cardiovascular diseases, heart failure (HF) is a complex and heterogeneous syndrome leading to considerable morbidity and mortality. Existing HF-related omics studies mainly focus on case/control comparisons, small cohorts of special subtypes, etc., and a large amount of multi-omics data and knowledge have been generated. However, it is difficult for researchers to obtain biological and clinical insights from these scattered data and knowledge. In this paper, we built the Heart Failure Integrated Platform (HFIP) for data exploration, fusion analysis and visualization by collecting and curating existing multi-omics data and knowledge from various public sources and also provided an auto-updating mechanism for future integration. The developed HFIP contained 253 datasets (7842 samples), multiple analysis flow, and 14 independent tools. In addition, based on the integration of existing databases and literature, a knowledge base for HF was constructed with a scoring system for evaluating the relationship between molecular signals and HF. The knowledge base includes 1956 genes and annotation information. The literature mining module was developed to assist the researcher to overview the hotspots and contexts in basic and clinical research. HFIP can be used as a data-driven and knowledge-guided platform for the basic and clinical research of HF. Database URL: http://heartfailure.medical-bigdata.com

Highlights

Heart failure (HF), the terminal phenotype of many cardiovascular diseases, is a complex and heterogeneous syndrome [1]
We focused on HF and attempted to construct an integrated platform consisting of multi-omics data, easy-to-use tools and relevant molecular knowledge, namely the Heart Failure Integrated Platform (HFIP), by automatically collecting and manually organizing relevant datasets and knowledge, and performing intelligent matching analysis and visualization tools on selected datasets
In order to facilitate clinicians or researchers to quickly obtain HF-related genes, we systematically integrated gene– HF associations from Online Mendelian Inheritance in Man (OMIM), ClinVar, DisGeNET and other databases, as well as information from literature mining based on confirmed HF keywords

Summary

Introduction

Heart failure (HF), the terminal phenotype of many cardiovascular diseases, is a complex and heterogeneous syndrome [1]. A comprehensive data platform that contains datasets, knowledge and tools for HF is necessary To fill this gap, we focused on HF and attempted to construct an integrated platform consisting of multi-omics data, easy-to-use tools and relevant molecular knowledge, namely the Heart Failure Integrated Platform (HFIP), by automatically collecting and manually organizing relevant datasets and knowledge, and performing intelligent matching analysis and visualization tools on selected datasets. We focused on HF and attempted to construct an integrated platform consisting of multi-omics data, easy-to-use tools and relevant molecular knowledge, namely the Heart Failure Integrated Platform (HFIP), by automatically collecting and manually organizing relevant datasets and knowledge, and performing intelligent matching analysis and visualization tools on selected datasets

Methods and results

Literature discovery and recommendation

Discussion

Future work