RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information

M. Torii, G. Li, Z. Li, R. Oughtred, F. Diella, I. Celen, C. N. Arighi, H. Huang, K. Vijay-Shanker, C. H. Wu
2014 Database: The Journal of Biological Databases and Curation  
These authors contributed equally to this work. Citation details: Torii,M., Li,G., Li,Z., et al. RLIMS-P: an online text mining tool for literature-based extraction of protein phosphorylation information. Abstract Protein phosphorylation is central to the regulation of most aspects of cell function. Given its importance, it has been the subject of active research as well as the focus of curation in several biological databases. We have developed Rule-based Literature Mining System for protein
more » ... osphorylation (RLIMS-P), an online text-mining tool to help curators identify biomedical research articles relevant to protein phosphorylation. The tool presents information on protein kinases, substrates and phosphorylation sites automatically extracted from the biomedical literature. The utility of the RLIMS-P Web site has been evaluated by curators from Phospho.ELM, PhosphoGRID/BioGrid and Protein Ontology as part of the BioCreative IV user interactive task (IAT). The system achieved F-scores of 0.76, 0.88 and 0.92 for the extraction of kinase, substrate and phosphorylation sites, respectively, and a precision of 0.88 in the retrieval of relevant phosphorylation literature. The system also received highly favorable feedback from the curators in a user survey. Based on the curators' suggestions, the Web site has been enhanced to improve its usability. In the RLIMS-P Web site, phosphorylation information can be retrieved by PubMed IDs or keywords, with an option for selecting targeted species. The result page displays a sortable table with phosphorylation information. The text evidence page displays the abstract with color-coded entity mentions and includes links to UniProtKB entries via normalization, i.e. the linking of entity mentions to database identifiers, V C The Author(s)
doi:10.1093/database/bau081 pmid:25122463 pmcid:PMC4131691 fatcat:ptfbobrhkbdrbovnwydi3t6pbu