pubmed2ensembl

pubmed2ensembl links Ensembl BioMart genomic data with biomedical literature from PubMed and PubMed Central by integrating curated (Entrez Gene) and text-mined (MEDLINE) gene–publication associations across over 2 million PubMed articles and nearly 150,000 genes in 50 species.

Key Features:

• Extensive Database Linking: Connects over 2 million PubMed articles to nearly 150,000 Ensembl genes across 50 species.
• Curated and Automated Data Sources: Integrates curated links from Entrez Gene and automatically generated links from text-mining MEDLINE records.
• Customizable Data Filtering: Allows filtering and combination of multiple gene–publication data sources for targeted analyses.
• Text-based Literature–Genome Querying: Supports queries against PubMed and PubMed Central text combined with constraints on genomic features.
• Automated BioMart Construction Scripting Language: Provides a scripting language to automate construction and customization of BioMarts.

Scientific Applications:

• Literature retrieval for genomic regions: Retrieve publications linked to specific genomic regions or genes for functional interpretation.
• Gene-set literature aggregation: Aggregate and analyze publications associated with functionally related gene sets.
• Cross-species literature mapping: Map literature evidence to orthologous genes across 50 species in Ensembl for comparative studies.

Methodology:

Integrates curated Entrez Gene links and text-mined associations from MEDLINE, maps PubMed/PubMed Central publications to Ensembl gene identifiers across species, and extends Ensembl BioMart with publication links using an automated BioMart construction scripting language.