Summarizing scientific articles: experiments with relevance and rhetorical status
Computational Linguistics - Summarization
Text Mining for Biology And Biomedicine
Text Mining for Biology And Biomedicine
Overview of BioNLP'09 shared task on event extraction
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
MinePhos: A Literature Mining System for Protein Phoshphorylation Information Extraction
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Overview of BioNLP Shared Task 2011
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
iSimp: A sentence simplification system for biomedicail text
BIBM '12 Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
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Literature-based annotation of protein phosphorylation is the focus of many biological databases, as phosphorylation is a global regulator of cellular activity. To speed up manual curation of phosphorylation information, text mining technology has been utilized. In this paper, we report our ongoing effort to enhance RLIMS-P, a rule-based information extraction (IE) system to identify protein phosphorylation information in scientific literature. Despite the high accuracy attained by RLIMS-P, the use of elaborated patterns and rules resulted in a substantial effort for system development and maintenance. To mitigate this challenge, we redesigned RLIMS-P and integrated new natural language processing (NLP) techniques. It has also been adapted to mine full-text articles and generalized to be able to exploit common features for different post-translational modifications (PTMs). The updated RLIMS-P (version 2.0) was evaluated on abstracts in the publicly available BioNLP GENIA event extraction (GE) corpus, and achieved F-scores of 0.92 and 0.96 for phosphorylation substrate and site, respectively. On a full-text corpus developed in-house, it achieved F-scores of 0.91 and 0.92 for substrate and site, and 0.88 for kinase. The system was applied to the PubMed Central (PMC) Open Access Subset, and promising results have been obtained in mining the full-text articles. RLIMS-P focuses on protein phosphorylation information, but its new design would be generalizable for other PTM types. RLIMS-P version 2.0 is available at: http://proteininformationresource.org/rlimsp/.