VarfromPDB: An Automated and Integrated Tool to Mine Disease-Gene-Variant Relations from the Public Databases and Literature

Abstract

Background: The relationships among phenotypes, genes, and variants play a key role for monogenic disorders in the era of precision medicine. Information about this is erupting with the current rapid development of genomic technology. However, it is time-consuming and error-prone to manually capture the information from the literature. Thus, how to capture this information rapidly and accurately is a bottleneck to be solved. Results: Here, we present VarfromPDB, an automated and integrated method to mine the genes and variants related to a Mendelian disorder from multiple public curated databases and literature. To demonstrate the procedure, feasibility and application, we used a monogenic disorder, Joubert syndrome, as an example to capture the related genes from multiple sources including HPO, OrphaNet, ClinVar, UniProt and PubMed abstracts. The captured gene list is more comprehensive than that from DisGeNET and DISEASES databases. Conclusion: VarfromPDB is a an automated and integrated tool to compile the up-to-date disease-genevariant database with comprehensive. It is valuable for genetic researchers and has great potential in facilitating the application of genetic testing for precision medicine. The source code for VarfromPDB is freely available at https://CRAN.R-project.org/package=VarfromPDB.