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Information Extraction of Protein Phosphorylation from Biomedical Literature
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Author(s): M. Narayanaswamy (Anna University, India), K. E. Ravikumar (Anna University, India), Z. Z. Hu (Georgetown University Medical Center, USA), K. Vijay-Shanker (University of Delaware, USA)and C. H. Wu (Georgetown University Medical Center, USA)
Copyright: 2009
Pages: 14
Source title:
Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration
Source Author(s)/Editor(s): Violaine Prince (University Montpellier 2, France)and Mathieu Roche (University Montpellier 2, France)
DOI: 10.4018/978-1-60566-274-9.ch009
PurchaseView on the publisher's website for pricing and purchasing information.
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Abstract
Protein posttranslational modification (PTM) is a fundamental biological process, and currently few text mining systems focus on PTM information extraction. A rule-based text mining system, RLIMS-P (Rule-based LIterature Mining System for Protein Phosphorylation), was recently developed by our group to extract protein substrate, kinase and phosphorylated residue/sites from MEDLINE abstracts. This chapter covers the evaluation and benchmarking of RLIMS-P and highlights some novel and unique features of the system. The extraction patterns of RLIMS-P capture a range of lexical, syntactic and semantic constraints found in sentences expressing phosphorylation information. RLIMS-P also has a second phase that puts together information extracted from different sentences. This is an important feature since it is not common to find the kinase, substrate and site of phosphorylation to be mentioned in the same sentence. Small modifications to the rules for extraction of phosphorylation information have also allowed us to develop systems for extraction of two other PTMs, acetylation and methylation. A thorough evaluation of these two systems needs to be completed. Finally, an online version of RLIMSP with enhanced functionalities, namely, phosphorylation annotation ranking, evidence tagging, and protein entity mapping, has been developed and is publicly accessible.
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