生物医学领域本体开发项目比较研究

研究与探讨,,,,[]介绍了国际上发展较好的四类生物医学领域本体,从开发时间目的覆盖内容结构等方面进行了深入比较,总结出目前本体开发中存在的同义词与术语表达对应关系与间隔尺度等主要问题[]生物医学;本体;UMLS;OBO;OpenGALEN;OBI[]R318[]A[]1671-3982(2010)05-0016-04ComparativestudyonontologyprojectsinbiomedicalfieldWUZheng-jing,HUANGWe,iMUDong-me,iZHUJing,LIMeng(CollegeofPublicHealth,JilinUniversity,Changchun130021,JilinProvince,China)[Abstract]Fourtypesofwell-developedinternationalontologyinbiomedicalfieldwereintroduced.Themajorproblemsindevelopmentofontologyweresummarizedincludingtheexpressionofsynonymsandtermsaswellascorrespondenceandintervalmeasurebycomparingtheirdevelopmenttime,objective,coverageandstructure.[Keywords]biomedicine;ontology;unifiedmedicallanguagesystem;openbiomedicalontology;OpenGALEN;ontologyforbiomedicalinvestigations[](:07JA870001),(:2008Z020)[],130021[](1962-),,,,,40(SemanticWeb),,1,41.1基于医学信息检索的本体类型(unifiedmedicallanguagesystem,UMLS),1986,UMLS(UMLSknowledgesource)[1]UMLS(metathesaureus)(semanticnetwork)(specialistlexicon)UMLS,1.2基于生物医学数据的本体类型(openbiomedicalontology,OBO),[2],OBO,(NIH),,OBOFoundry![3]OBOGO(geneontology,)[4],CT(celltype,)[5],PO(plantontology,)[6],SO(sequenceontology,)[7]OBO1620105195ChinJMedLibrInfSc,iVo.l19No.5May.2010-Edit,OBO[8]1.3基于临床医学的本体类型OpenGALEN[9],GALEN(generalisedarchitectureforlanguages,encyclopaediasandnomenclaturesinmedicine)[10]2738,,OpenGALEN,GRAIL(GALENrepresentationandIntergrationlanguage)GALENGRAIL(),GALEN[11]1.4基于医学调查的本体类型(ontologyforbiomedicalinvestigations,OBI)OBI,(FuGO)OBI[12],,,()()[13]2,,,42.1开发时间与研究规模UMLS(1986),OpenGALEN2080,OBO21OBI,OBO,OBO4(1),UMLS14()UMLS1986,[14]Open-GALEN1999GALENOBO200160OBI200625,UMLS,OBO,,OpenGALENOBI25,UMLSOBO2.2覆盖领域与本体结构比较4UMLS,100OpenGALEN,GALEN1720105195ChinJMedLibrInfSc,iVo.l19No.5May.2010OBO42UMLS,OBO,,OpenGALENOBI,24UMLS,:,,,,,50010054OpenGALEN25000[17]925[19]OBOOBOOBO[15]OBO74,899734OBOOBO13[20]OBI,,,,(),[16]OBI661[18]OBI3:∀(RO)#(RO-proposed)∃OBI(Relations.owl)[21]2.3开发工具比较UMLSOBOOBO-Edi,tJava,(DAML+OIL)OpenGALENGALENGRAILGRAILGALEN,GALENUMLS(),UMLS,,UMLS,15UMLS99.5%OBODAG-EditOWL,,(relationship)(),[22]GALEN,()[23]3,,3.1同义词与术语表达问题,,,()()3.2对应关系与间隔尺度问题,,1820105195ChinJMedLibrInfSc,iVo.l19No.5May.2010UniProt(),,,,[24]4(NKI)(NKIMed),%&,[25],,,,,,∋([1]UnifiedMedicalLanguageSystem[EB/OL].[2008-10-10].[2]OpenBiomedicalOntologies[EB/OL].[2008-10-10].[3]AbouttheOBOFoundry[EB/OL].[2008-10-10].[4]AshburnerM,BallCA,BlakeJA,etal.GeneOntology:ToolfortheUnificationofBiology[J].NaGenet(S1061-4036),2000,25(1):25-29.[5]BardJ,RheeSY,AshburnerM.Anontologyforcelltypes[J].GenomeBiol(S1465-6906),2005,6(2):21.[6]PlantOntologyConsortium.ThePlantOntologyConsortiumandplantontologies[J].CompFunctGenomics(S1531-6912),2002,3(2):137-142.[7]EilbeckK,LewisSE,MungallCJ,etal.TheSequenceOntology:aToolfortheUnificationofGenomeAnnotations[J].GenomeBio(S1465-6906),2005,6(5):44.[8]OBO-Edit[EB/OL].[2008-12-01].[9].[EB/OL].[2008-12-01].[10]OpenGALEN[EB/OL].[2008-12-01].[11]OpenGALEN[EB/OL].[2008-12-01].[12]ChristineGolbreich,MatthewHorridge,IanHorrocks,etal.OBOandOWL:LeveragingSemanticWebTechnologiesfortheLifeSciences[EB/OL].[2008-12-01].[13]OntologyforBiomedicalInvestigations[EB/OL].[2008-12-01].[14][EB/OL].[2009-09-16].[15]OLS-Ontology[EB/OL].[2009-09-29].[16]BranchDevelopment[EB/OL].[2009-09-29].[17].[D].:,,2008.[18]Coreterms[EB/OL].[2009-09-29].[19].[EB/OL].[2009-09-29].[20]OBOFoundrycandidateontologies[EB/OL].[2009-09-29].[21]ListofRalations[EB/OL].[2009-09-29].[22].[J].,2006,27(2):81-84.[23]RectorAL,RogersJE,ZanstraPE,etal.OpenGALEN:OpenSourceMedicalTerminologyandTools[C].AMIAAnnuSympProc.2003:982.[24]Kei-HoiCheung,SmithAK,KevinY.L.Yip,etal.SemanticWebApproachtoDatabaseintheLifeScience[M].NewYork,NY:SpringerUS,2007:11-30.[25],.[J].,2007,20(7):1106-1110.[:2009-09-08][本文编辑:吕婷]1920105195ChinJMedLibrInfSc,iVo.l19No.5May.2010