title: HiPub: translating PubMed and PMC texts to networks for knowledge discovery.
abstract: We introduce HiPub, a seamless Chrome browser plug-in that automatically recognizes, annotates and translates biomedical entities from texts into networks for knowledge discovery. Using a combination of two different named-entity recognition resources, HiPub can recognize genes, proteins, diseases, drugs, mutations and cell lines in texts, and achieve high precision and recall. HiPub extracts biomedical entity-relationships from texts to construct context-specific networks, and integrates existing network data from external databases for knowledge discovery. It allows users to add additional entities from related articles, as well as user-defined entities for discovering new and unexpected entity-relationships. HiPub provides functional enrichment analysis on the biomedical entity network, and link-outs to external resources to assist users in learning new entities and relations.
  
  
  
  HiPub and detailed user guide are available at http://hipub.korea.ac.kr
  
  
  
  kangj@korea.ac.kr, aikchoon.tan@ucdenver.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Science and Engineering, Korea University, Seoul, Korea.
authors.forename: Kyubum
authors.initials: K
authors.lastname: Lee
authors.affiliation: Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul, Korea.
authors.forename: Wonho
authors.initials: W
authors.lastname: Shin
authors.affiliation: Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul, Korea.
authors.forename: Byounggun
authors.initials: B
authors.lastname: Kim
authors.affiliation: Department of Computer Science and Engineering, Korea University, Seoul, Korea.
authors.forename: Sunwon
authors.initials: S
authors.lastname: Lee
authors.affiliation: Department of Computer Science and Engineering, Korea University, Seoul, Korea.
authors.forename: Yonghwa
authors.initials: Y
authors.lastname: Choi
authors.affiliation: Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul, Korea.
authors.forename: Sunkyu
authors.initials: S
authors.lastname: Kim
authors.affiliation: Department of Computer Science and Engineering, Korea University, Seoul, Korea.
authors.forename: Minji
authors.initials: M
authors.lastname: Jeon
authors.affiliation: Translational Bioinformatics and Cancer Systems Biology Laboratory, Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
authors.forename: Aik Choon
authors.initials: AC
authors.lastname: Tan
authors.affiliation: Department of Computer Science and Engineering, Korea University, Seoul, Korea Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul, Korea.
authors.forename: Jaewoo
authors.initials: J
authors.lastname: Kang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D066289:Data Curation; D016208:Databases, Factual; D005796:Genes; D006801:Humans; D010363:Pattern Recognition, Automated; D004364:Pharmaceutical Preparations; D011506:Proteins; D039781:PubMed; D057386:Search Engine
chemical_list: D004364:Pharmaceutical Preparations; D011506:Proteins