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dc.contributor.authorLi, Chuanxi
dc.contributor.authorChen, Peng
dc.contributor.authorWang, Rujing
dc.contributor.authorWang, Xiujie
dc.contributor.authorSu, Yaru
dc.contributor.authorLi, Jinyan
dc.date.accessioned2015-08-03T11:43:26Z
dc.date.available2015-08-03T11:43:26Z
dc.date.issued2014
dc.identifier.issn17485673
dc.identifier.doi10.1504/IJDMB.2014.062890
dc.identifier.urihttp://hdl.handle.net/10754/563219
dc.description.abstractMining Protein-Protein Interactions (PPIs) from the fast-growing biomedical literature resources has been proven as an effective approach for the identifi cation of biological regulatory networks. This paper presents a novel method based on the idea of Interaction Relation Ontology (IRO), which specifi es and organises words of various proteins interaction relationships. Our method is a two-stage PPI extraction method. At fi rst, IRO is applied in a binary classifi er to determine whether sentences contain a relation or not. Then, IRO is taken to guide PPI extraction by building sentence dependency parse tree. Comprehensive and quantitative evaluations and detailed analyses are used to demonstrate the signifi cant performance of IRO on relation sentences classifi cation and PPI extraction. Our PPI extraction method yielded a recall of around 80% and 90% and an F1 of around 54% and 66% on corpora of AIMed and Bioinfer, respectively, which are superior to most existing extraction methods. Copyright © 2014 Inderscience Enterprises Ltd.
dc.description.sponsorshipWe thank the anonymous reviewers for their constructive comments on the paper. This research was supported in part by the National Natural Science Foundation of China (No. 60774096) and the National Key Technology R&D Program of China (No. 2008BAK49B05). This work was also supported in party by the National Science Foundation of China (No. 60803107).
dc.publisherInderscience Publishers
dc.subjectBioinformatics
dc.subjectInformation extraction
dc.subjectInteraction relation ontology
dc.subjectProtein-protein interaction
dc.subjectRelation extraction
dc.subjectRelation word
dc.subjectSentence typed dependency
dc.subjectText mining
dc.titlePPI-IRO: A two-stage method for protein-protein interaction extraction based on interaction relation ontology
dc.typeArticle
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.identifier.journalInternational Journal of Data Mining and Bioinformatics
dc.contributor.institutionInstitute of Intelligent Machines, Chinese Academy of Sciences, Hefei 230031, China
dc.contributor.institutionSchool of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China
dc.contributor.institutionState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
dc.contributor.institutionAdvanced Analytics Institute, University of Technology Sydney, Australia
kaust.personChen, Peng


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