Ignet: A Web-Based Literature Mining System for Gene Interaction Networks

Biological systems' complexity is often represented through networks of genes, proteins, and metabolites. Ignet, a web-based database, facilitates the construction and exploration of gene interaction networks using PubMed abstracts. Ignet uniquely combines centrality- and ontology-based network analysis, calculating four centrality scores—degree, eigenvector, closeness, and betweenness—to assess gene importance within networks. Degree centrality highlights direct connections, while betweenness centrality identifies key bridging genes. Additionally, Ignet integrates Vaccine Ontology (VO) and Interaction Network Ontology (INO), enhancing interaction relevance. Its user-friendly interface supports domain-specific network construction, particularly for vaccine research. Ignet includes three applications: Ignet Gene, GenePair, and Dignet. Ignet Gene and GenePair facilitate searches for genes and gene pairs, while Dignet extracts gene interactions from PubMed studies. Vignet, a specialized tool, focuses on vaccine-related gene interactions. Updated with PubMed data until 2024, Ignet employs a BIOBERT-based model for real-time text analysis, improving gene interaction identification accuracy.