Interactive Visualization of BioMedical Data

Public databases such as the NCBI Gene Expression Omnibus (GEO) house millions of experimental gene expression datasets invaluable for transcriptome meta-analysis, enabling researchers to identify genes, pathways, and biomarkers with enhanced accuracy. However, while these datasets offer great potential, finding relevant biological pathways in disease-related contexts remains challenging. To address this, we introduce a web-based visualization tool that utilizes PubMed abstracts to extract key biomedical entities, such as genes, pathways, diseases, species, and chemicals, and represent their relationships through an interactive graph. By leveraging PubMed’s annotated MeSH terms, our tool allows users to explore the literature more intuitively, bypassing traditional dataset search limitations and focusing on published results. The tool transforms complex query outputs into a graph-based network, providing a visual interface for navigating connections between biological entities. This interactive approach helps researchers to analyze relationships within large-scale biomedical data and uncover potential pathways for drug repurposing and disease understanding. We discuss the tool’s design using D3.js, its application in biomedical research, and the challenges faced when visualizing large datasets, offering new insights for improved data interpretation and exploration.