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A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction
Joint Authors
Munkhdalai, Tsendsuren
Yu, Xiuming
Li, Meijing
Ryu, Keun Ho
Source
Mathematical Problems in Engineering
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-10, 10 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-10-19
Country of Publication
Egypt
No. of Pages
10
Main Subjects
Abstract EN
Many researchers focus on developing protein-named entity recognition (Protein-NER) or PPI extraction systems.
However, the studies about these two topics cannot be merged well; then existing PPI extraction systems’ Protein-NER still needs to improve.
In this paper, we developed the protein-protein interaction extraction system named PPIMiner based on Support Vector Machine (SVM) and parsing tree.
PPIMiner consists of three main models: natural language processing (NLP) model, Protein-NER model, and PPI discovery model.
The Protein-NER model, which is named ProNER, identifies the protein names based on two methods: dictionary-based method and machine learning-based method.
ProNER is capable of identifying more proteins than dictionary-based Protein-NER model in other existing systems.
The final discovered PPIs extracted via PPI discovery model are represented in detail because we showed the protein interaction types and the occurrence frequency through two different methods.
In the experiments, the result shows that the performances achieved by our ProNER and PPI discovery model are better than other existing tools.
PPIMiner applied this protein-named entity recognition approach and parsing tree based PPI extraction method to improve the performance of PPI extraction.
We also provide an easy-to-use interface to access PPIs database and an online system for PPIs extraction and Protein-NER.
American Psychological Association (APA)
Li, Meijing& Munkhdalai, Tsendsuren& Yu, Xiuming& Ryu, Keun Ho. 2015. A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction. Mathematical Problems in Engineering،Vol. 2015, no. 2015, pp.1-10.
https://search.emarefa.net/detail/BIM-1075132
Modern Language Association (MLA)
Li, Meijing…[et al.]. A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction. Mathematical Problems in Engineering No. 2015 (2015), pp.1-10.
https://search.emarefa.net/detail/BIM-1075132
American Medical Association (AMA)
Li, Meijing& Munkhdalai, Tsendsuren& Yu, Xiuming& Ryu, Keun Ho. A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction. Mathematical Problems in Engineering. 2015. Vol. 2015, no. 2015, pp.1-10.
https://search.emarefa.net/detail/BIM-1075132
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1075132