Beyond the clause: extraction of phosphorylation information from medline abstracts

Motivation: Phosphorylation is an important biochemical reaction that plays a critical role in signal transduction pathways and cell-cycle processes. A text mining system to extract the phosphorylation relation from the literature is reported. The focus of this paper is on the new methods developed...

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Bibliographic Details
Published in:Bioinformatics 2005-06, Vol.21 (suppl-1), p.i319-i327
Main Authors: Narayanaswamy, M., Ravikumar, K. E., Vijay-Shanker, K.
Format: Article
Language:English
Subjects:
Artificial Intelligence
Computational Biology - methods
Database Management Systems
Databases, Protein
Humans
MEDLINE
Natural Language Processing
Pattern Recognition, Automated
Phosphorylation
Proteomics - methods
Signal Transduction
Software
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Summary:Motivation: Phosphorylation is an important biochemical reaction that plays a critical role in signal transduction pathways and cell-cycle processes. A text mining system to extract the phosphorylation relation from the literature is reported. The focus of this paper is on the new methods developed and implemented to connect and merge pieces of information about phosphorylation mentioned in different sentences in the text. The effectiveness and accuracy of the system as a whole as well as that of the methods for extraction beyond a clause/sentence is evaluated using an independently annotated dataset, the Phospho.ELM database. The new methods developed to merge pieces of information from different sentences are shown to be effective in significantly raising the recall without much difference in precision. Contact: vijay@cis.udel.edu
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/bti1011