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Bioinformatics Advance Access originally published online on April 27, 2006
Bioinformatics 2006 22(13):1668-1669; doi:10.1093/bioinformatics/btl159
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

An online literature mining tool for protein phosphorylation

X. Yuan 1,{dagger}, Z. Z. Hu 1,*,{dagger}, H. T. Wu 1, M. Torii 2, M. Narayanaswamy 3, K. E. Ravikumar 3, K. Vijay-Shanker 2 and C. H. Wu 1

1 Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center Washington, DC 20007, USA
2 Department of Computer and Information Sciences, University of Delaware Newark, DE 19716, USA
3 AU-KBC Research Centre, Anna University Chennai, India

*To whom correspondence should be addressed.

A web-based version of the RLIMS-P literature mining system was developed for online mining of protein phosphorylation information from MEDLINE abstracts. The online tool presents extracted phosphorylation objects (phosphorylated proteins, phosphorylation sites and protein kinases) in summary tables and full reports with evidence-tagged abstracts. The tool further allows mapping of phosphorylated proteins to protein entries in the UniProt Knowledgebase based on PubMed ID and/or protein name. The literature mining, coupled with database association, allows retrieval of rich biological information for the phosphorylated proteins and facilitates database annotation of phosphorylation features.

Availability: The online RLIMS-P is freely accessible at http://pir.georgetown.edu/iprolink/rlimsp

Contact: zh9{at}georgetown.edu

Supplementary Information: http://pir.georgetown.edu/iprolink/rlimsp/supplement/

Received on February 3, 2006; revised on March 21, 2006; accepted on April 21, 2006

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