NDLI: An information extraction system for protein function prediction

Content Provider	IEEE Xplore Digital Library
Author	Taha, K. Yoo, P.D.
Copyright Year	2015
Description	Author affiliation: Electr. & Comput. Eng. Dept., Khalifa Univ., Abu Dhabi, United Arab Emirates (Taha, K.) \|\| Fac. of Sci. & Technol., Bournemouth Univ., Bournemouth, UK (Yoo, P.D.)
Abstract	We present a Natural Language Processing extraction system called IESforPFP, which can retrieve useful information from biomedical abstracts. IESforPFP aims at enhancing the state of the art of biological text mining by applying novel linguistic computational technique. By retrieving significant patterns of associations between proteins and molecules from biomedical abstracts, IESforPFP can determine the functions of un-annotated proteins. The system determines the semantic relationship between each protein-molecule pair in sentences using novel semantic rules. It applies a semantic relationship extraction model that retrieves information from different structural forms of constituents in sentences. In the framework of IESforPFP, each protein p is represented by a vector of weights. Each weight reflects the significance of a molecule m in the biomedical abstracts associated with p. That is, each weight quantifies the likelihood of the association between m and p. IESforPFP determines the set of annotated proteins that is semantically similar to p by comparing their vectors. It then annotates p with the functions of these annotated proteins. We evaluated the quality of IESforPFP by comparing it experimentally with two other systems. Results showed marked improvement.
Starting Page	1
Ending Page	7
File Size	448650
Page Count	7
File Format	PDF
e-ISBN	9781479969265
DOI	10.1109/CIBCB.2015.7300300
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2015-08-12
Publisher Place	Canada
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Protein engineering Semantics Pragmatics Information retrieval Syntactics biomedical literature Dependency parser biological NLP information extraction Text mining
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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