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Bioinformatics Advance Access originally published online on April 6, 2005
Bioinformatics 2005 21(11):2759-2765; doi:10.1093/bioinformatics/bti390
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Literature mining and database annotation of protein phosphorylation using a rule-based system

Z. Z. Hu 1,*, M. Narayanaswamy 2, K. E. Ravikumar 2, K. Vijay-Shanker 3 and C. H. Wu 1

1Department of Biochemistry and Molecular Biology, Georgetown University Medical Center Washington, DC 20057, USA
2AU-KBC Research Centre, Anna University Chennai 600044, India
3Department of Computer and Information Sciences, University of Delaware Newark, DE 19716, USA

*To whom correspondence should be addressed.

Motivation: A large volume of experimental data on protein phosphorylation is buried in the fast-growing PubMed literature. While of great value, such information is limited in databases owing to the laborious process of literature-based curation. Computational literature mining holds promise to facilitate database curation.

Results: A rule-based system, RLIMS-P (Rule-based LIterature Mining System for Protein Phosphorylation), was used to extract protein phosphorylation information from MEDLINE abstracts. An annotation-tagged literature corpus developed at PIR was used to evaluate the system for finding phosphorylation papers and extracting phosphorylation objects (kinases, substrates and sites) from abstracts. RLIMS-P achieved a precision and recall of 91.4 and 96.4% for paper retrieval, and of 97.9 and 88.0% for extraction of substrates and sites. Coupling the high recall for paper retrieval and high precision for information extraction, RLIMS-P facilitates literature mining and database annotation of protein phosphorylation.

Availability: The program is available on request from the authors. The phosphorylation patterns and datasets used in this study are available at http://pir.georgetown.edu/iprolink/

Contact: zh9{at}georgetown.edu


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