ODAMNet: A Python package to identify molecular relationships between chemicals and rare diseases using overlap, active module and random walk approaches

Abstract

Environmental factors are external conditions that can affect the health of living organisms. For a number of rare genetic diseases, an interplay between genetic and environmental factors is known or suspected. However, the studies are limited by the scarcity of patients and the difficulties in gathering reliable exposure information.In order to aid in fostering research between environmental factors and rare diseases, we propose ODAMNet, a Python package to investigate the possible relationships between chemicals, which are a subset of environmental factors, and rare diseases. ODAMNet offers three different and complementary bioinformatics approaches for the exploration of relationships: overlap analysis, active module identification and random walk with restart. ODAMNet allows systematic analysis of chemical - rare disease relationships and generation of hypotheses for further investigation of effect mechanisms.

Keywords

• Rare disease
• Chemical
• Environmental factor
• Overlap analysis
• Random walk with restart
• Active module identification