title: ProNormz--an integrated approach for human proteins and protein kinases normalization.
abstract: The task of recognizing and normalizing protein name mentions in biomedical literature is a challenging task and important for text mining applications such as protein-protein interactions, pathway reconstruction and many more. In this paper, we present ProNormz, an integrated approach for human proteins (HPs) tagging and normalization. In Homo sapiens, a greater number of biological processes are regulated by a large human gene family called protein kinases by post translational phosphorylation. Recognition and normalization of human protein kinases (HPKs) is considered to be important for the extraction of the underlying information on its regulatory mechanism from biomedical literature. ProNormz distinguishes HPKs from other HPs besides tagging and normalization. To our knowledge, ProNormz is the first normalization system available to distinguish HPKs from other HPs in addition to gene normalization task. ProNormz incorporates a specialized synonyms dictionary for human proteins and protein kinases, a set of 15 string matching rules and a disambiguation module to achieve the normalization. Experimental results on benchmark BioCreative II training and test datasets show that our integrated approach achieve a fairly good performance and outperforms more sophisticated semantic similarity and disambiguation systems presented in BioCreative II GN task. As a freely available web tool, ProNormz is useful to developers as extensible gene normalization implementation, to researchers as a standard for comparing their innovative techniques, and to biologists for normalization and categorization of HPs and HPKs mentions in biomedical literature. URL: http://www.biominingbu.org/pronormz.
authors.affiliation: Data Mining and Text Mining Laboratory, Department of Bioinformatics, School of Life Sciences, Bharathiar University, Coimbatore 641 046, India. Electronic address: sureshsubramani@hotmail.com.
authors.forename: Suresh
authors.initials: S
authors.lastname: Subramani
authors.affiliation: Data Mining and Text Mining Laboratory, Department of Bioinformatics, School of Life Sciences, Bharathiar University, Coimbatore 641 046, India. Electronic address: kalpana.rajaa@gmail.com.
authors.forename: Kalpana
authors.initials: K
authors.lastname: Raja
authors.affiliation: Data Mining and Text Mining Laboratory, Department of Bioinformatics, School of Life Sciences, Bharathiar University, Coimbatore 641 046, India. Electronic address: n.jeyakumar@yahoo.co.in.
authors.forename: Jeyakumar
authors.initials: J
authors.lastname: Natarajan
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D010766:Phosphorylation; D011494:Protein Kinases / Q000737:chemistry*; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry*; D012660:Semantics; D012984:Software
chemical_list: D011506:Proteins; D011494:Protein Kinases
keywords: Biomedical informatics; Gene name finding; Human protein normalization; Protein kinase tagging; Text mining