Background: The complexity of the phenotypic characteristics and molecular bases of many rare human genetic diseases make the diagnosis of such diseases a challenge for clinicians. A map for visualizing, locating and navigating rare diseases based on similarity will help clinicians and researchers understand and easily explore these diseases.
Methods: By defining the quantitative distance among phenotypes and pathogenic genes based on corresponding ontology systems, the distance matrix of rare diseases included in Orphanet was calculated and mapped into Euclidean space. Enhanced by clustering classes and disease information, a rare disease map was developed based on ECharts.
Results: The rare disease map called RDmap was published at http://rdmap.nbscn.org. The phenotype-based map comprises 3,287 rare diseases and the gene-based map comprises 3,789 rare genetic diseases and they were bridged by 1,718 overlapping diseases. RDmap works similar to the widely used Google map and supports zooming and panning. The phenotype similarity base disease location function performed better than traditional keyword search in an in-silico evaluation and 20 published cases of rare diseases also demonstrated that RDmap can be used by clinicians to improve diagnosis.
Conclusion: RDmap is the first user-interactive map-style rare disease knowledgebase. It will help clinicians and researchers explore the increasing complicated rare genetic diseases.