pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature
Date
2015-08-10
Journal Title
Journal ISSN
Volume Title
Publisher
PLOS (Public Library of Science)
Abstract
BACKGROUND
Automatically detecting gene/protein names in the literature and connecting them to databases
records, also known as gene normalization, provides a means to structure the information
buried in free-text literature. Gene normalization is critical for improving the
coverage of annotation in the databases, and is an essential component of many text mining
systems and database curation pipelines.
METHODS
In this manuscript, we describe a gene normalization system specifically tailored for plant
species, called pGenN (pivot-based Gene Normalization). The system consists of three
steps: dictionary-based gene mention detection, species assignment, and intra species normalization.
We have developed new heuristics to improve each of these phases.
RESULTS
We evaluated the performance of pGenN on an in-house expertly annotated corpus consisting
of 104 plant relevant abstracts. Our system achieved an F-value of 88.9%(Precision
90.9% and Recall 87.2%) on this corpus, outperforming state-of-art systems presented in
BioCreative III. We have processed over 440,000 plant-related Medline abstracts using
pGenN. The gene normalization results are stored in a local database for direct query from
the pGenN web interface (proteininformationresource.org/pgenn/). The annotated literature
corpus is also publicly
Description
Publisher's PDF.
Keywords
Citation
Ding R, Arighi CN, Lee J-Y, Wu CH, Vijay- Shanker K (2015) pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature. PLoS ONE 10(8): e0135305. doi:10.1371/journal. pone.0135305