title: HPIminer: A text mining system for building and visualizing human protein interaction networks and pathways.
abstract: The knowledge on protein-protein interactions (PPI) and their related pathways are equally important to understand the biological functions of the living cell. Such information on human proteins is highly desirable to understand the mechanism of several diseases such as cancer, diabetes, and Alzheimer's disease. Because much of that information is buried in biomedical literature, an automated text mining system for visualizing human PPI and pathways is highly desirable. In this paper, we present HPIminer, a text mining system for visualizing human protein interactions and pathways from biomedical literature. HPIminer extracts human PPI information and PPI pairs from biomedical literature, and visualize their associated interactions, networks and pathways using two curated databases HPRD and KEGG. To our knowledge, HPIminer is the first system to build interaction networks from literature as well as curated databases. Further, the new interactions mined only from literature and not reported earlier in databases are highlighted as new. A comparative study with other similar tools shows that the resultant network is more informative and provides additional information on interacting proteins and their associated networks.
authors: Data Mining and Text Mining Laboratory, Department of Bioinformatics, School of Life Sciences, Bharathiar University, Tamil Nadu, India. Electronic address: sureshsubramani@hotmail.com.
authors: Suresh
authors: S
authors: Subramani
authors: Data Mining and Text Mining Laboratory, Department of Bioinformatics, School of Life Sciences, Bharathiar University, Tamil Nadu, India. Electronic address: kalpana.rajaa@gmail.com.
authors: Raja
authors: R
authors: Kalpana
authors: Department of Computer Science, Bharathiar University, Coimbatore, Tamil Nadu, India. Electronic address: pankajmoses@hotmail.com.
authors: Pankaj Moses
authors: PM
authors: Monickaraj
authors: Data Mining and Text Mining Laboratory, Department of Bioinformatics, School of Life Sciences, Bharathiar University, Tamil Nadu, India. Electronic address: n.jeyakumar@yahoo.co.in.
authors: Jeyakumar
authors: J
authors: Natarajan
mesh_terms: D000544:Alzheimer Disease / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D057225:Data Mining / Q000379:methods*; D006801:Humans; D007091:Image Processing, Computer-Assisted; D008962:Models, Theoretical; D025941:Protein Interaction Mapping / Q000379:methods*; D014584:User-Computer Interface
keywords: Biomedical informatics; Information extraction; Knowledge discovery; Network visualization; Pathway visualization; Protein–protein interactions; Text mining