Graph-based Tool for Exploring PubMed Knowledge Base

Abstract

Studies have shown that data retrieval and visualization tools can help health professionals to improve their understanding and communication with patients, their relationship with stakeholders, and their decision-making process. However, not many efforts have been made in this direction. In this paper, we present a prototype system for the indexing, annotation, and visualization of the PubMed knowledge base to enable the search and retrieval of health-related evidence. The proposed tool builds and keeps updated an enriched graph based on PubMed articles associating them with concepts extracted from the Unified Medical Language System (UMLS) Metathesaurus. Moreover, it allows a full-text search and graph-based navigation and supports an overview of concepts and related publications. The proposed architecture enables scale-up thanks to its containerized nature and parallelization capabilities. The code is open-source under the Apache V2 license.