NDLI: BioLMiner System: Interaction Normalization Task and Interaction Pair Task in the BioCreative II.5 Challenge

Content Provider	IEEE Xplore Digital Library
Author	Yifei Chen Feng Liu Manderick, B.
Copyright Year	2004
Abstract	This paper describes a Biological Literature Miner (BioLMiner) system and its implementation. BioLMiner is a text mining system for biological literature, whose purpose is to extract useful information from biological literature, including gene and protein names, normalized gene and protein names, and protein-protein interaction pairs. BioLMiner has three main subsystems in a pipeline structure: a gene mention recognizer (GMRer), a gene normalizer (GNer), and a protein-protein interaction pair extractor (PPIEor). All these subsystems are developed based on the machine learning techniques including support vector machines (SVMs) and conditional random fields (CRFs) together with carefully designed informative features. At the same time, BioLMiner makes use of some biological specific resources and existing natural language processing tools. In order to evaluate and compare BioLMiner, it is adapted to participate in two tasks of the BioCreative II.5 challenge: interaction normalization task (INT) using GNer and interaction pair task (IPT) using PPIEor. Our system is among the highest performing systems on the two tasks from which it can be seen that GMRer provides a good support for the INT and IPT although its performance is not evaluated, and the methods developed in GNer and PPIEor are extended well to the BioCreative II.5 tasks.
Sponsorship	IEEE Computer Society
Page Count	14
File Size	3334108
Starting Page	428
Ending Page	441
File Format	PDF
ISSN	15455963
Volume Number	7
Issue Number	3
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2010-07-01
Publisher Place	U.S.A.
Access Restriction	One Nation One Subscription (ONOS)
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Data mining Text mining Databases Machine learning Pipelines Support vector machines Natural language processing Performance evaluation Pressing BioCreactive II.5 challenge. machine learning interaction protein normalization interaction pair extraction
Content Type	Text
Resource Type	Article
Subject	Applied Mathematics Genetics Biotechnology

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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
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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