pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature

Ruoyao Ding, Cecilia N. Arighi, Jung-Youn Lee, Cathy H. Wu, K. Vijay-Shanker, Willy John Wilbur
2015 PLoS ONE  
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
more » ... ies, 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 ( The annotated literature corpus is also publicly available through the PIR text mining portal ( The system accepts as input a single or multiple PMIDs. Although it can process any text as input, some of the rules for species assignment were developed specifically for abstracts. Given a list of PMIDs, the titles, abstract text, and the MeSH terms are extracted for each PMID. We use an in-house developed tool to split the abstract text into sentences and then tokenize the sentences. This tokenization is based entirely on orthographic features such as the combination of lower case followed by uppercase letters or presence of numerals and symbols.
doi:10.1371/journal.pone.0135305 pmid:26258475 pmcid:PMC4530884 fatcat:6gphkqhqnzfgbkzbzshp2ge4ha