An online literature mining tool for protein phosphorylation

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...

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Bibliographic Details
Published in:Bioinformatics 2006-07, Vol.22 (13), p.1668-1669
Main Authors: Yuan, X., Hu, Z. Z., Wu, H. T., Torii, M., Narayanaswamy, M., Ravikumar, K. E., Vijay-Shanker, K., Wu, C. H.
Format: Article
Language:English
Subjects:
Animals
Biological and medical sciences
Computational Biology - methods
Databases, Bibliographic
Databases, Factual
Databases, Protein
Fundamental and applied biological sciences. Psychology
General aspects
Humans
Information Storage and Retrieval
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Phosphorylation
Proteins - chemistry
PubMed
Software
User-Computer Interface
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Description
Summary: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 Contact:zh9@georgetown.edu Supplementary Information:
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btl159