Tuyển tập báo cáo các nghiên cứu khoa học quốc tế ngành hóa học dành cho các bạn yêu hóa học tham khảo đề tài: Research Article Extraction of Protein Interaction Data: A Comparative Analysis of Methods in Use | Hindawi Publishing Corporation EURASIP Journal on Bioinformatics and Systems Biology Volume 2007 Article ID 53096 9 pages doi 2007 53096 Research Article Extraction of Protein Interaction Data A Comparative Analysis of Methods in Use Hena Jose Thangavel Vadivukarasi and Jyothi Devakumar Jubilant Biosys Ltd. 96 Industrial Suburb 2nd Stage Yeshwanthpur Bangalore 560 022 India Received 31 March 2007 Accepted 8 October 2007 Recommended by Z. Jane Wang Several natural language processing tools both commercial and freely available are used to extract protein interactions from publications. Methods used by these tools include pattern matching to dynamic programming with individual recall and precision rates. A methodical survey of these tools keeping in mind the minimum interaction information a researcher would need in comparison to manual analysis has not been carried out. We compared data generated using some of the selected NLP tools with manually curated protein interaction data PathArt and IMaps to comparatively determine the recall and precision rate. The rates were found to be lower than the published scores when a normalized definition for interaction is considered. Each data point captured wrongly or not picked up by the tool was analyzed. Our evaluation brings forth critical failures of NLP tools and provides pointers for the development of an ideal NLP tool. Copyright 2007 Hena Jose et al. This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. 1. INTRODUCTION Protein interactions represent the social networking that happens within a cell. Understanding these networks provide a snapshot to the regulatory mechanisms that operate within the cellular milieu. The advent of yeast 2 hybrid Y2H chromatin IP assay CHIP assay microarray serial analysis of gene expression SAGE and two-dimensional .
