Clinical & Medical Biochemistry

Abstract

RareDDB: An Integrated Catalog of Rare Disease Database

Hemant Gupta, Chandan Badapanda, Arpita Ghosh and Surendra Chikara

Background: RareDDB repository for rare disease or orphan disease (http://rareddb.xcelrislabs.com/) is a freely accessible web-based user friendly database which provides detailed information for different types of rare diseases with their associated genes, SNPs along with functional annotations and drug?s information. Method: The RareDDB database was developed using information from various databases such as Orphanet, GHR, OMIM, RDI and dbSNP database using in-house perl script. RareDDB has been implemented using three-tier architecture. Results: RareDDB contains 2,396 genes that are associated with 6,651 rare diseases and 379 drugs. RareDDB also contains 336,826 curated SNPs related to 1,553 rare diseases. Sequential BLAST homology of 2,396 genes resulted in total 5,900 Gene Ontology terms which includes 1,112 metabolic pathway terms. The orthologs analysis resulted in 849 common orthologs between mouse, yeast, zebra fish, Drosophila and worm using DIOPT server. RareDDB is also linked with databases such as PharmGKB, Drugbank, KEGG and Orphanet to provide comprehensive information about rare disease. In this study, we have also compared rare diseases and their genes between global populations and Indian sub-population which resulted in 521 and 431 common diseases and genes respectively. Conclusion: RareDDB is a secondary database made by integrating primary data resources such as Orphanet, GHR, OMIM, RDI and dbSNP and also has linked databases for providing detailed information regarding rare diseases. This database comprises dedicated information on rare diseases, orphan drugs, SNPs, genes with their GO terms, Gene location on the chromosomes and orthologs. RareDDB database has a user friendly interface for searching and browsing information related to rare diseases.