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Information Extraction of Protein Phosphorylation from Biomedical Literature

Information Extraction of Protein Phosphorylation from Biomedical Literature

M. Narayanaswamy, K. E. Ravikumar, Z. Z. Hu, K. Vijay-Shanker, C. H. Wu
Copyright: © 2009 |Pages: 14
ISBN13: 9781605662749|ISBN10: 1605662747|ISBN13 Softcover: 9781616925284|EISBN13: 9781605662756
DOI: 10.4018/978-1-60566-274-9.ch009
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MLA

Narayanaswamy, M., et al. "Information Extraction of Protein Phosphorylation from Biomedical Literature." Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration, edited by Violaine Prince and Mathieu Roche, IGI Global, 2009, pp. 163-176. https://doi.org/10.4018/978-1-60566-274-9.ch009

APA

Narayanaswamy, M., Ravikumar, K. E., Hu, Z. Z., Vijay-Shanker, K., & Wu, C. H. (2009). Information Extraction of Protein Phosphorylation from Biomedical Literature. In V. Prince & M. Roche (Eds.), Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration (pp. 163-176). IGI Global. https://doi.org/10.4018/978-1-60566-274-9.ch009

Chicago

Narayanaswamy, M., et al. "Information Extraction of Protein Phosphorylation from Biomedical Literature." In Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration, edited by Violaine Prince and Mathieu Roche, 163-176. Hershey, PA: IGI Global, 2009. https://doi.org/10.4018/978-1-60566-274-9.ch009

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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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