SNPMap

SNPMap integrates SNP-related information from LitVar, PubTator, and GWAS Catalog APIs and visualizes semantic relationships among SNP-associated keywords to support interpretation of single-nucleotide polymorphisms from next-generation sequencing data.

Key Features:

• Automated Data Integration: Periodically retrieves and curates SNP-related information from LitVar, PubTator, and GWAS Catalog APIs.
• Visualization of Semantic Relationships: Generates two types of graphs that represent keywords and their semantic relationships to each SNP, using node size and edge width to indicate significance.
• Prioritization of Related SNPs: Calculates and sorts the most related SNPs for each keyword appearing in the integrated database.

Scientific Applications:

• Disease Diagnosis: Aggregates SNP-associated evidence to support identification of genetic markers tied to diseases.
• Prognostic Assessment: Provides semantic relationships and ranked variant lists to inform assessment of variant implications for disease progression and patient outcomes.
• Research Efficiency: Automates retrieval and integrates heterogeneous SNP information to accelerate variant interpretation workflows from next-generation sequencing data.

Methodology:

Periodic automated retrieval from LitVar, PubTator, and GWAS Catalog APIs; extraction and integration of SNP-related data; generation of two graph types representing keywords and their semantic relationships with node size/edge width encoding significance; computation and ranking of SNPs related to each keyword.