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Predicting the Extension of Biomedical Ontologies 英文参考文献.doc

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Predicting the Extension of Biomedical Ontologies 英文参考文献

PredictingtheExtensionofBiomedicalOntologies CatiaPesquita*,FranciscoM.Couto FacultyofSciences,UniversityofLisboa,Lisboa,Portugal Abstract Developingandextendingabiomedicalontologyisaverydemandingtaskthatcanneverbeconsideredcompletegiven ourever-evolvingunderstandingofthelifesciences.Extensioninparticularcanbenefitfromtheautomationofsomeofits steps,thus releasingexpertstofocuson hardertasks.Herewepresentastrategy tosupport theautomationofchange capturingwithinontologyextensionwheretheneedfornewconceptsorrelationsisidentified.Ourstrategyisbasedon predicting areas of an ontology that will undergo extension in a future version by applying supervised learning over featuresofpreviousontologyversions.WeusedtheGeneOntologyasourtestbedandobtainedencouragingresultswith averagef-measurereaching0.79forasubsetofbiologicalprocessterms.Ourstrategywasalsoabletooutperformstateof the art change capturing methods. In addition we have identified several issues concerning prediction of ontology evolution,andhavedelineatedageneralframeworkforontologyextensionprediction.Ourstrategycanbeappliedtoany biomedicalontologywithversioning,tohelpfocuseithermanualorsemi-automatedextensionmethodsonareasofthe ontologythatneedextension. Citation:PesquitaC,CoutoFM(2012)PredictingtheExtensionofBiomedicalOntologies.PLoSComputBiol8(9):e1002630.doi:10.1371/journal.pcbi.1002630 Editor:K.BretonnelCohen,UniversityofColoradoSchoolofMedicine,UnitedStatesofAmerica ReceivedDecember20,2011;AcceptedJune11,2012;PublishedSeptember13,2012 Copyright: ?2012 Pesquita,Couto. This is an open-access articledistributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:ThisworkwassupportedbythePortugueseFundac?a?o paraaCie?nciaeTecnologiathroughtheMultiannualFundingProgramme,andthegrantref. SFRH/BD/42481/2007.TheauthorsalsowishtothanktheEuropeanCommissionforthefinancialsupportofth