Semantic Similarity for Automatic Classification of Chemical Compounds 英文参考文献.docVIP

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Semantic Similarity for Automatic Classification of Chemical Compounds 英文参考文献.doc

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Semantic Similarity for Automatic Classification of Chemical Compounds 英文参考文献

SemanticSimilarityforAutomaticClassificationof ChemicalCompounds Joa?oD.Ferreira*,FranciscoM.Couto LaSIGE,UniversityofLisbon,Lisbon,Portugal Abstract With the increasing amount of data made available in the chemical field, there is a strong need for systems capable of comparingandclassifyingchemicalcompoundsinanefficientandeffectiveway.Thebestapproachesexistingtodayare basedonthestructure-activityrelationshippremise,whichstatesthatbiologicalactivityofamoleculeisstronglyrelatedto itsstructuralorphysicochemicalproperties.Thisworkpresentsanovelapproachtotheautomaticclassificationofchemical compounds by integrating semantic similarity with existing structural comparison methods. Our approach was assessed basedontheMatthewsCorrelationCoefficientfortheprediction,andachievedvaluesof0.810whenusedasapredictionof blood-brainbarrierpermeability,0.694forP-glycoproteinsubstrate,and0.673forestrogenreceptorbindingactivity.These resultsexposeasignificantimprovementoverthecurrentlyexistingmethods,whosebestperformanceswere0.628,0.591, and 0.647 respectively. It was demonstratedthat theintegration of semantic similarity is afeasible andeffective way to improveexistingchemicalcompoundclassificationsystems.Amongotherpossible uses,thistoolhelpsthestudyofthe evolutionofmetabolicpathways,thestudyofthecorrelationofmetabolicnetworkswithpropertiesofthosenetworks,or theimprovementofontologiesthatrepresentchemicalinformation. Citation:FerreiraJD,CoutoFM(2010)SemanticSimilarityforAutomaticClassificationofChemicalCompounds.PLoSComputBiol6(9):e1000937.doi:10.1371/ journal.pcbi.1000937 Editor:JohnB.O.Mitchell,UniversityofStAndrews,UnitedKingdom ReceivedApril18,2010;AcceptedAugust23,2010;PublishedSeptember23,2010 Copyright: ? 2010 Ferreira, Couto. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:Thisworkwassupportedb