title: 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 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 available through the PIR text mining portal (proteininformationresource.org/iprolink/).
authors.affiliation: Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, United States of America.
authors.forename: Ruoyao
authors.initials: R
authors.lastname: Ding
authors.affiliation: Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, United States of America; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, United States of America.
authors.forename: Cecilia N
authors.initials: CN
authors.lastname: Arighi
authors.affiliation: Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, United States of America.
authors.forename: Jung-Youn
authors.initials: JY
authors.lastname: Lee
authors.affiliation: Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, United States of America; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, United States of America.
authors.forename: Cathy H
authors.initials: CH
authors.lastname: Wu
authors.affiliation: Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, United States of America.
authors.forename: K
authors.initials: K
authors.lastname: Vijay-Shanker
mesh_terms: D057225:Data Mining / Q000379:methods*; D030541:Databases, Genetic; D017343:Genes, Plant; D058977:Molecular Sequence Annotation; D009323:Natural Language Processing; D010940:Plant Proteins / Q000235:genetics*; D010944:Plants / Q000235:genetics*; D012015:Reference Standards; D012984:Software; D009626:Terminology as Topic
chemical_list: D010940:Plant Proteins