MeSHDbi

MeSHDbi is part of a framework designed to enhance over-representation analysis (ORA) in genome-wide studies using Medical Subject Headings (MeSH) terms. MeSH terms, which annotate PubMed documents, offer a comprehensive resource for extracting meaningful insights from gene lists, providing a broader biological context than traditional gene annotation resources. Recognizing the limitations of existing MeSH ORA software, the developers of MeSHDbi and its associated packages aim to provide a more exhaustive and user-friendly approach for ORA.

The framework consists of six types of R packages: MeSH.db, MeSH.AOR.db, MeSH.PCR.db, org.MeSH.XXX.db-type packages, MeSHDbi, and meshr. Together, these packages offer a complete solution for conducting MeSH-based ORA, enabling users to identify enriched MeSH terms associated with their gene lists and retrieve and save related PubMed documents locally. This comprehensive approach facilitates a deeper biological interpretation of gene lists generated from genome-wide studies, leveraging the extensive annotation and documentation available through MeSH terms.

By integrating MeSH ORA into their analysis, researchers can access an expansive and detailed annotation resource, enhancing their findings' biological relevance and understanding. MeSHDbi and its accompanying packages represent a significant advancement in bioinformatics. It offers a streamlined and efficient tool for exploring the connections between genes and broader biological themes documented in the scientific literature.