Search and visualization of gene-drug-disease interactions for pharmacogenomics and precision medicine research using GeneDive

• DOI: 10.1016/j.jbi.2021.103732
• Publication Date: 2021-03-18T19:23:12Z
• Authors: Mike Wong; Paul Previde; Jack Cole; Brook Thomas; Nayana Laxmeshwar; Emily Mallory; Jake Lever; Dragutin Petkovic; Russ B. Altman; Anagha Kulkarni
• Keywords: Pharmacogenomics; Personalized Medicine

Understanding the relationships between genes, drugs, and disease states is at core of pharmacogenomics. Two leading approaches for identifying these in medical literature are: human expert led manual curation efforts, modern data mining based automated approaches. The former generates small amounts high-quality data, latter offers large volumes mixed quality data. algorithmically extracted are often accompanied by supporting evidence, such as, confidence scores, source articles, surrounding contexts (excerpts) from that can be used as indicators. Tools leverage indicators to help user gain access larger needed.We introduce GeneDive, a web application pharmacogenomics researchers precision medicine practitioners makes gene, disease, drug interactions easily accessible usable. GeneDive designed meet three key objectives: (1) provide functionality manage information-overload problem facilitate easy assimilation (2) support longitudinal exploratory research investigations, (3) offer integration user-provided without requiring sharing.GeneDive multiple search modalities, visualizations, other features guide efficiently information their interest. To research, evidence context each interaction readily available allows threshold controlled per risk tolerance level. interactive search-visualization loop enables relationship discoveries diseases, drugs might not explicitly described but emergent corpus deductive reasoning. ability utilize user's either combination with native datasets or isolation promotes richer data-driven exploration discovery. These functionalities along GeneDive's applicability medicine, bringing knowledge contained biomedical bear on particular clinical situations improving patient care, illustrated through detailed use cases.GeneDive comprehensive, broad-use biological browser. about its underlying system architecture http://www.genedive.net. Docker image also download this URL, allowing users import own securely privately; generate test hypotheses across datasets.