组会汇报（2011-08-01）-HomeTheNational.ppt

1、Lei Liu, Ph.D.,The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China,Biomedical Data Integration and Knowledgebase,Shanghai Center for Bioinformation TechnologyAndShanghai Institutes for Biological Sciences, CAS,Part 1: Ontology,Knowledge ManagementData Int

2、egration and ExchangeSemantic InteroperabilityDecision Support and Reasoning,Knowledge Management,Annotating Data and ResourcesAccessing Biomedical InformationMapping across Biomedical Ontologies,Ontology,Data Exchange &Semantic Interoperability,Information and Data IntegrationSemantic Interoperabil

3、ity,Ontology,Decision Support and Reasoning,Data SelectionData AggregationDecision SupportNatural Language Processing ApplicationsKnowledge Discovery,Ontology,Example: Ontology Server,Example: Building Knowledge Base,Edit,Example: Building Knowledge Base,Search tool,Part 2: SNOMED CT,Systematized No

4、menclature of MedicineReference Terminology(SNOMED RT),Clinical Terms(CT),SNOMED CT,CAP,NHS,CAP: College of American PathologistsNHS: National Health ServiceIHTSDO: International Health Terminology Standards Development Organization,Core contents,SNOMED CT,Applications,Electronic Health Record Syste

5、ms Computerized Provider Order Entry(CPOE)Knowledge databases used in clinical decision support systems(CDSS) Remote Intensive Care Unit Monitoring Laboratory Reporting Cancer Reporting Genetic Databases,SNOMED CT,Medical domains of the 100 Medline indexed papers in which a specific medical domain h

6、as been described. (BMC Medical Informatics and Decision Making 2008, 8(Suppl 1):S2),SNOMED CT,Example: Mapping,Example: Encoding,Example: Standardization of Terminology,Part 3: OpenEHR,Objectives,Promote and publish formal specification,Promote and publish EHR architectures and models,Interoperable

7、 health informatics system,Maintain open source “reference” implementation,Implement EHR architectures into clinical use,Work closely with standards bodies,openEHR introduction,Definition: openEHR is an open standard specification in health informatics that describes the management and storage, retr

8、ieval and exchange of health data in electronic health records (EHRs)Features:Patient-centricLifelongVendor-independent,Architecture of OpenEHR,OpenEHR Release 1.0.2,Two-level modeling of openEHR,openEHR EHR system implementation,applicability,ApplyStore dataSearch dataShare dataNot applyControl the

9、 exchanging flow,Integration of SNOMED CT into OpenEHR,HL7 v3 introduction,mission: provides standards for interoperabilityFeaturesstandard data, use reference information model (RIM)CDA, standardize clinical documents for exchange support healthcare workflows (V3 messaging),RIM,applicability,Applye

10、xchange informationControl the exchanging flowControl the exchanging datas sizeNot applyStore data (we can store CDAs, but its not a best practice)Search data,Ongoing Biomedical Informatics Projects,Clinical Data and Sample is at the Core of Translational Medicine,Clinical Data,Clinical Practice,Bio

11、marker,Biospecimen,Clinical Trial,LIMS,Genotypes,Domain Workspaces,Cross Cutting & Strategic Workspaces,Clinical Trials Management Systems (CTMS，临床实验管理系统)https:/cabig.nci.nih.gov/workspaces/CTMS/,Integrative Cancer Research (ICR，综合肿瘤研究)https:/cabig.nci.nih.gov/workspaces/ICR,Tissue Banks & Pathology

12、 Tools (TBPT，组织库&病理学工)https:/cabig.nci.nih.gov/workspaces/TBPT,In Vivo Imaging（Vivo成像）https:/cabig.nci.nih.gov/workspaces/Imaging,Vocabularies&Common Data Elements (VCDE，词汇&公共数据元素)https:/cabig.nci.nih.gov/workspaces/VCDE,Architecture(体系构架)https:/cabig.nci.nih.gov/workspaces/Architecture,Data Sharing

13、 & Intellectual Capital (DSIC，数据共享&智能财产)https:/cabig.nci.nih.gov/working_groups/DSIC_SLWG,Documentation & Training (D&T，文件&培训)https:/cabig.nci.nih.gov/working_groups/Training_SLWG,caBIG Workspaces,References and Standards,References used: caCORE (Cancer Common Ontologic Representation Environment):

14、caDSR (Cancer Data Standards Repository) NCI CBIIT (National Cancer institute Center for Biomedical Informatics and Information Technology),Collaboration with NCI and caBIG:Attended the caBIG annual meeting and visited caBIG in 2008Two people from our center attended the Boot Camp,Tissue Bank Inform

15、ation Management System,样本数据库信息管理系统全面解决方案,Biobank Information Management Platform,Use Cases,Combined Tissue Bank Annotation from Operation Summary and Pathology Report,Medical Natural Language Processing,Difficulties of acquiring data and multiple times of entering,Direct connection to HIS、LIS and E

16、MRAutomatic transferring of data without entering by staffsActive reminding system for follow-upAutomatic Data Query and Extraction Across Systems,Molecular classification database,Diagnostic testsdatabase,Patients situation of treatment database,Patient follow-updatabase,Sample database,Personalize

17、d treatment procedures,Clinical Information Enquiry System: The overall framework and subsystems,HISdatabase,LISdatabase,General enquiries,PACSdatabase,D-QISdatabase,Clinical Information Enquiry System,Clinical Data Warehouse,R-MIM Model,Database Structure,Clinical Document（XML）,Database Records,SOA

18、 Service Bus,Clinical Data Warehouse,Clinical Document CDA Transfer Engine,Schema for Clinical Document,HL7 CDA Schema,Transfer Engine,Discharge Summary,CDA File,Mapping,Common Medical Terminology Service,Difficulties of Extracting Data,METHODS,Models Performance,Models Performance,AUC(Lymphadenecta

19、sis):0.9517,AUC(Tumor Boundary):0.995,Models Performance,Biomedical Data Integration and Mining,Integration,Data Mining,Personalized Medicine Databases,Personalized Medicine Decision Support System,Medical Informatic,Bioinformatics,Translational Medicine,Genomics,Disease and Gene Integration,GAD,COS

20、MIC,Data Integration,Gene2Disease Databases,Genetic Polymorphisms 39910Gene Mutations 150654519 Major DiseasesStructured Gene Information 31412,Drug and Drug metabolism Study,Drug-Target-SNP Integration and Databases,SNP,Drug,Data Integration,Drug-Target Polymorphism Databases,dbSNP,HapMap,Query Dru

21、g-Target-SNP,Drug Info,Target Info,SNP Info,Drug Metabolism,Mutation Information Integration,Extraction from Locus-specific databases,LSDB Addresses,Using WiKi Collect LSDB Addresses1300 LSDB Classification of Genes link to OMIM Database,http:/129.89.44.120/twiki/bin/view,Mutation Information Extrac

22、tion,Natural Language ProcessingTwo LSDB Data ExtrationAlzheimer Disease & Frontotemporal Dementia Mutation DatabaseSarcomere Protein Gene Mutation Database1725 mutation records,Mutation Association with Disease PhenotypesStandardsGene Names - HUGODiseases（ICD-10）Mapping ICD-10 and MeSH, using keywo

23、rd searchAdopt SNOMED CT，Build Disease Ontologies,映射后的ICD-10疾病词汇表,Mutation Information Integration,Disease Related Unique Mutation Search Engine，DRUMS,Query,Genes, Diseases, Mutations, Sequences,More than 170,000Mutations, 6000 genes,External Links,Documents upload,By GenesBy DiseasesBy Mutation typ

24、es,http:/www.scbit.org/glif,Mutation Information Integration,DRUMS Query Results,Mutation Information Integration,Biomedical Informatics Systems for Translational Research,BioBank,EMR for Research EMR for Clinical TrialFollow-up Information Systems,Omic DatabasesLIMSBioinformatics Analysis Platform,

25、Database Establishment for Translational Research,DE-IDENTIFICATION,One way hash,Data Parsing,Data Parsing,Information collected during clinical care,Restructuring for research,Data export,SD Database,Access through secured online application,Informatics in EMR-based PGx Studies,Natural language pro

26、cessing (NLP)Machine learning & data mining,DNA Biobank,EMR,Informatics Approaches,Information Flow in Translational Medicine,New Therapeutic knowledge,Clinical Practice,Biospecimen,Clinical Data,High Throughput Research,CODATA Task Group of Biomedical Ontology,提出生物医学数据互操作中的最关键问题提出研究的重点方向提出研究的思路与可能的技术路线研讨预期的研究结果和可能的应用研讨此研究的立项可能The interoperability of Biomedical DataOntology Building PrinciplesData Sharing StrategiesTechnical RoadmapExpected Achievements Plan to make the first Discussion Meeting in 20112011 年内召开第一次研讨会，提出研究思路，形成核心团队，制定研究计划。,