MeSHDbi

MeSHDbi performs MeSH-based over-representation analysis (ORA) of gene lists by integrating MeSH annotations and related R packages to support biological interpretation.

Key Features:

• MeSH-based ORA: Performs over-representation analysis (ORA) using Medical Subject Headings (MeSH) terms to identify enriched biological concepts from gene lists.
• Unified implementation: Consolidates functionalities of MeSH.db, MeSH.AOR.db, and MeSH.PCR.db for accessing and using MeSH annotations.
• Gene–MeSH package integration: Interfaces with MeSH.XXX.eg.db gene–MeSH mapping packages to associate genes with MeSH terms.
• SQLite database handling: Imports SQLite files and generates MeSH.XXX.eg.db databases for data management and retrieval.
• Comprehensive ORA framework: Operates within a suite that includes MeSH.db, MeSH.AOR.db, MeSH.PCR.db, org.MeSH.XXX.db-type packages, MeSHDbi, and meshr R packages.
• PubMed document retrieval: Uses enriched MeSH terms to retrieve related PubMed documents which can be saved locally.

Scientific Applications:

• Biological interpretation: Extracts broader biological meaning from gene lists through MeSH term enrichment.
• Exhaustive annotation resource: Provides an exhaustive MeSH-based annotation resource for ORA to address limitations of existing MeSH ORA platforms.
• Literature linkage: Enables linking enriched MeSH terms to relevant PubMed literature for downstream literature-based analyses.

Methodology:

Implements an original framework for MeSH-based ORA by integrating multiple R packages (MeSH.db, MeSH.AOR.db, MeSH.PCR.db, org.MeSH.XXX.db-type packages, MeSH.XXX.eg.db, MeSHDbi, meshr) and by importing SQLite files to generate MeSH.XXX.eg.db databases.