pubmed2ensembl: A Resource for Mining the Biological Literature on Genes
Author Information
Author(s): Baran Joachim, Gerner Martin, Haeussler Maximilian, Nenadic Goran, Bergman Casey M.
Primary Institution: University of Manchester
Hypothesis
How can genomic data be systematically integrated with biological literature?
Conclusion
pubmed2ensembl helps biologists find relevant literature on specific genomic regions or sets of functionally related genes more easily.
Supporting Evidence
- pubmed2ensembl links over 2,000,000 articles to nearly 150,000 genes.
- Users can filter and combine different data sources for information extraction.
- The tool allows text-based queries against PubMed and PubMed Central documents.
Takeaway
This study created a tool that connects gene information with scientific articles, making it easier for scientists to find research about specific genes.
Methodology
Developed pubmed2ensembl, an extension to the BioMart system linking over 2,000,000 articles in PubMed to nearly 150,000 genes in Ensembl from 50 species.
Potential Biases
Potential biases in gene-PMID links due to reliance on automated text mining and curation processes.
Limitations
The integration is limited to certain species and relies on the availability of curated data.
Digital Object Identifier (DOI)
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