Extracting Interactions between Proteins from PubMedbstract
Date Issued
2008
Date
2008
Author(s)
Zheng, Jing-Xu
Abstract
With the rapid progress of biomedical science and large amounts of analysis methods, many researchers nowadays access knowledge about protein-protein interaction through PubMed abstracts, but the amount of biomedical literature is enormous and continues to grow at exponential rate. Therefore, the demand for automatic extraction of information from text has been increasing, using text mining tools to find knowledge such as protein-protein interactions, which is useful for specific analysis tasks has become critical.e develop a system which can automatically extracts protein-protein interactions from free text using a shallow parser and sentence structure analysis techniques. Our system matches sentences against syntax patterns typically describing protein-protein interactions. We design an efficient algorithm and develop a set of rules which extracts protein-protein interactions from their syntactic roles. Protein-protein interactions include ACTOR ( doner of action) and OBJECT (receiver of action).There are essential steps to accomplish our system which includes preprocessor, sentence splitting, tokenization, part-of-speech tagging, protein names recognition, interaction keywords , prepositions , conjunction tagging and protein-protein interactions extracting. Finally, we evaluate our system on two samples, one derived from the LLL05 challenge, the other from BioCreAtIvE-PPI.
Subjects
protein-protein interaction
text mining
syntax patterns
sentence splitting
tokenization
part-of-speech
protein names recognition
Type
thesis
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