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Reference: Ono T, et al. (2001) Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics 17(2):155-61

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Abstract


MOTIVATION: To understand biological process, we must clarify how proteins interact with each other. However, since information about protein-protein interactions still exists primarily in the scientific literature, it is not accessible in a computer-readable format. Efficient processing of large amounts of interactions therefore needs an intelligent information extraction method. Our aim is to develop an efficient method for extracting information on protein-protein interaction from scientific literature. RESULTS: We present a method for extracting information on protein-protein interactions from the scientific literature. This method, which employs only a protein name dictionary, surface clues on word patterns and simple part-of-speech rules, achieved high recall and precision rates for yeast (recall = 86.8% and precision = 94.3%) and Escherichia coli (recall = 82.5% and precision = 93.5%). The result of extraction suggests that our method should be applicable to any species for which a protein name dictionary is constructed. AVAILABILITY: The program is available on request from the authors.

Reference Type
Journal Article | Research Support, Non-U.S. Gov't
Authors
Ono T, Hishigaki H, Tanigami A, Takagi T
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Interaction Annotations


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Interactor Interactor Type Assay Annotation Action Modification Phenotype Source Reference

Gene Ontology Annotations


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Gene Gene Ontology Term Qualifier Aspect Method Evidence Source Assigned On Annotation Extension Reference

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Gene Phenotype Experiment Type Mutant Information Strain Background Chemical Details Reference

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Regulator Target Experiment Assay Construct Conditions Strain Background Reference