NDLI: Improving Protein-Protein Interaction Pair Ranking with an Integrated Global Association Score

Content Provider	ACM Digital Library
Author	Tsai, Richard Tzong-Han
Abstract	Protein-protein interaction (PPI) database curation requires text-mining systems that can recognize and normalize interactor genes and return a ranked list of PPI pairs for each article. The order of PPI pairs in this list is essential for ease of curation. Most of the current PPI pair ranking approaches rely on association analysis between the two genes in the pair. However, we propose that ranking an extracted PPI pair by considering both the association between the paired genes and each of those genes' global associations with all other genes mentioned in the paper can provide a more reliable ranked list. In this work, we present a composite interaction score that considers not only the association score between two interactors (pair association score) but also their global association scores. We test three representative data fusion algorithms to estimate this global association score—two Borda-Fuse models and one linear combination model (LCM). The three estimation methods are evaluated using the data set of the BioCreative II.5 Interaction Pair Task (IPT) in terms of area under the interpolated precision/recall curve (AUC iP/R). Our experimental results indicate that using LCM to estimate the global association score can boost the AUC iP/R score from 0.0175 to 0.2396, outperforming the best BioCreative II.5 IPT system.
Starting Page	1690
Ending Page	1695
Page Count	6
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2012.99
Volume Number	9
Issue Number	6
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2012-11-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Accuracy,Databases,Training,Proteins,Mutual information,Bioinformatics,Protein engineering,bioinformatics databases,Text mining
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

Sl.	Authority	Responsibilities	Communication Details
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