title: NTTMUNSW BioC modules for recognizing and normalizing species and gene/protein mentions.
abstract: In recent years, the number of published biomedical articles has increased as researchers have focused on biological domains to investigate the functions of biological objects, such as genes and proteins. However, the ambiguous nature of genes and their products have rendered the literature more complex for readers and curators of molecular interaction databases. To address this challenge, a normalization technique that can link variants of biological objects to a single, standardized form was applied. In this work, we developed a species normalization module, which recognizes species names and normalizes them to NCBI Taxonomy IDs. Unlike most previous work, which ignored the prefix of a gene name that represents an abbreviation of the species name to which the gene belongs, the recognition results of our module include the prefixed species. The developed species normalization module achieved an overall F-score of 0.954 on an instance-level species normalization corpus. For gene normalization, two separate modules were respectively employed to recognize gene mentions and normalize those mentions to their Entrez Gene IDs by utilizing a multistage normalization algorithm developed for processing full-text articles. All of the developed modules are BioC-compatible .NET framework libraries and are publicly available from the NuGet gallery.Database URL: https://sites.google.com/site/hjdairesearch/Projects/isn-corpus.
authors.affiliation: Department of Computer Science and Information Engineering, National Taitung University, Taitung, Taiwan Interdisciplinary Program of Green and Information Technology, National Taitung University, Taitung, Taiwan hjdai@nttu.edu.tw emilysu@tmu.edu.tw.
authors.forename: Hong-Jie
authors.initials: HJ
authors.lastname: Dai
authors.affiliation: Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
authors.forename: Onkar
authors.initials: O
authors.lastname: Singh
authors.affiliation: School of Public Health and Community Medicine, the University of New South Wales, Sydney, Australia Prince of Wales Clinical School, the University of New South Wales, Australia.
authors.forename: Jitendra
authors.initials: J
authors.lastname: Jonnagaddala
authors.affiliation: Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan hjdai@nttu.edu.tw emilysu@tmu.edu.tw.
authors.forename: Emily Chia-Yu
authors.initials: EC
authors.lastname: Su
mesh_terms: D000465:Algorithms; D000818:Animals; D002965:Classification; D057225:Data Mining / Q000379:methods*; D005796:Genes; D006801:Humans; D011506:Proteins
chemical_list: D011506:Proteins