CardioGraph: a platform to study variations associated with familiar cardiopathies

Abstract

Abstract Background Familiar cardiopathies are genetic disorders that affect the heart. Cardiologists face a significant problem when treating patients suffering from these disorders: most DNA variations are novel (i.e., they have not been classified before). To facilitate the analysis of novel variations, we present CardioGraph, a platform specially designed to support the analysis of novel variations and help determine whether they are relevant for diagnosis. To do this, CardioGraph identifies and annotates the consequence of variations and provides contextual information regarding which heart structures, pathways, and biological processes are potentially affected by those variations. Methods We conducted our work through three steps. First, we define a data model to support the representation of the heterogeneous information. Second, we instantiate this data model to integrate and represent all the genomics knowledge available for familiar cardiopathies. In this step, we consider genomic data sources and the scientific literature. Third, the design and implementation of the CardioGraph platform. A three-tier structure was used: the database, the backend, and the frontend. Results Three main results were obtained: the data model, the knowledge base generated with the instantiation of the data model, and the platform itself. The platform code has been included as supplemental material in this manuscript. Besides, an instance is publicly available in the following link: https://genomics-hub.pros.dsic.upv.es:3090 . Conclusion CardioGraph is a platform that supports the analysis of novel variations. Future work will expand the body of knowledge about familiar cardiopathies and include new information about hotspots, functional studies, and previously reported variations.

Keywords

• Familiar cardiopathies
• Novel variations
• Knowledge representation
• Conceptual modeling