PGxAssist: A Retrieval and Summarization System for Pharmacogenomics Articles


Meghana Dayananda

Oral Defence Date: 

Monday, March 12, 2018 - 10:15


TH 434


Asst. Prof. Anagha Kulkarni and Assoc. Prof. Hui Yang


Pharmacogenomics (PGx) and Precision Medicine are young, but rapidly evolving fields that are heralding development of tailored drugs. Knowing the impact of genetic variations on drug response, and other relevant information about the gene (structure, expression, function of its protein, interactions with other genes, drugs, and diseases) is invaluable to PGx researchers and practitioners. The VIP Summaries generated by PharmGKB curators provide exactly that for genes that have been identified as Very Important Pharmacogenes. Compiling these VIP summary articles, however, is a very expensive task. Even simply finding the scholarly articles that should be summarized in these articles is a difficult and time-consuming task due to the rate at which literature is growing. As a solution, we propose, PGxAssist, a retrieval system that is trained to identify articles that are relevant to a given gene in the context of Pharmacogenomics. Furthermore, PGxAssist generates extractive summary of the abstracts of selected articles, and identifies the appropriate article section that should include the generated summary. An end-to-end system that is complete with a web application has been developed for PGxAssist.


Pharmacogenomics, Article Classification, Information Retrieval, Biomedical Literature