An ontology describing congenital heart defects data

Abstract

Congenital heart defects (CHDs) are a group of diseases characterized by a structural anomaly of the heart that is present at birth. They are considered as the commonest cause of childhood death in developed countries. The causes of congenital heart disease are still under investigation, but their strongly presumed to be genetic or a combination of genetic and environmental factors. In order to store the derived knowledge, a collaborative knowledge base called CHDWiki has been developed, which collects all the information about the genetic basis of CHDs. However, this dedicated web resource suffers the same problems with similar portals where heterogeneous information is hosted. Further steps should be taken in order to ensure the interoperability of the available data. Also, the hosted data should be offered in a machine-readable format in order to direct be used by other Bioinformatic tools. In order to solve these problems, the life science scientific community tends to use semantic web technologies, which have proved their efficiency through numerous examples including VariO ontology, Gene Ontology (GO), Orphanet Ontology of rare diseases (OntoOrpha) and many more.

In this contribution, we present an ontology, which describes CHD data, developed around three main data categories: genotype, phenotype (CHDs) and clinical reports. Retrieving data from CHDWiki, this ontology describes the relationships between genes and human phenotypes, derived from published data or single clinical cases, providing a useful tool to geneticists, molecular biologists and clinicians. This ontology hosts information about syndromic genes, chromosomal aberrations that may cause CHDs and associations between genes and CHDs. Further information is included such as structural variations and single point mutations.