Genes, Vol. 12, Pages 293: G2PMineR: A Genome to Phenome Literature Review Approach

Genes, Vol. 12, Pages 293: G2PMineR: A Genome to Phenome Literature Review Approach
Genes doi: 10.3390/genes12020293
Authors:
Wojahn
Galla
Melton
Buerki

There is a gap in the conceptual framework linking genes to phenotypes (G2P) for non-model organisms, as most non-model organisms do not yet have genomic resources readily available. To address this, researchers often perform literature reviews to understand G2P linkages by curating a list of likely gene candidates, hinging upon other studies already conducted in closely related systems. Sifting through hundreds to thousands of articles is a cumbersome task that slows down the scientific process and may introduce bias into a study. To fill this gap, we created G2PMineR, a free and open source literature mining tool developed specifically for G2P research. This R package uses automation to make the G2P review process efficient and unbiased, while also generating hypothesized associations between genes and phenotypes within a taxonomical framework. We applied the package to a literature review for drought-tolerance in plants. The analysis provides biologically meaningful results within the known framework of drought tolerance in plants. Overall, the package is useful for conducting literature reviews for genome-to-phenome projects, and also has broad appeal to scientists investigating a wide range of study systems as it can conduct analyses under the auspices of three different kingdoms (Plantae, Animalia, and...

Source: Genes - February 20, 2021 Category: Genetics & Stem Cells Authors: Wojahn Galla Melton Buerki Tags: Article Source Type: research