Biomedical Discovery Acceleration, with Applications to Craniofacial Development 英文参考文献.docVIP

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Biomedical Discovery Acceleration, with Applications to Craniofacial Development 英文参考文献.doc

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Biomedical Discovery Acceleration, with Applications to Craniofacial Development 英文参考文献

BiomedicalDiscoveryAcceleration,withApplicationsto CraniofacialDevelopment SoniaM.Leach1.¤,HannahTipney1.,WeiguoFeng2,WilliamA.BaumgartnerJr.1,PriyankaKasliwal1, RonaldP.Schuyler1,TrevorWilliams2,RichardA.Spritz3,LawrenceHunter1* 1CenterforComputationalPharmacology,UniversityofColoradoatDenver,Denver,Colorado,UnitedStatesofAmerica,2DepartmentofCraniofacialBiology,University ofColoradoatDenver,Denver,Colorado,UnitedStatesofAmerica,3HumanMedicalGeneticsProgram,UniversityofColoradoatDenver,Denver,Colorado,UnitedStates ofAmerica Abstract Theprofusionofhigh-throughputinstrumentsandtheexplosionofnewresultsinthescientificliterature, particularlyin molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientistscanbenefitfromcomputationaltoolsthathelpnavigatethisvastandrapidlyevolvingterrain.Inthispaper,we describeanovelcomputationalapproachtothischallenge,aknowledge-basedsystemthatcombinesreading,reasoning, and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or using biomedical language processing to extract information from unstructureddata,andtrackknowledgeprovenance.Reasoningmethodsenrichtheknowledgethatresultsfromreading by,forexample,notingtwogenesthatareannotatedtothesameontologytermordatabaseentry.Reasoningisalsoused tocombineallsourcesintoaknowledgenetworkthatrepresentstheintegrationofallsortsofrelationshipsbetweenapair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruentnetworkconstructedfromexperimentaldataandvisualizethecombinednetworkinatoolthatfacilitatesthe knowledge-based analysis ofthat data.An implementationof this approach, called theHanalyzer, is demonstratedon a large-scale gene expression array dataset relevant to craniofacial development. The use of the tool was critical in the creation of hypotheses regard