PGenN, a gene normalization tool for plant genes and proteins in scientific literature.

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 evaluate

SUBMITTER: Ding R 

PROVIDER: S-EPMC4530884 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature