1. Data Integration and Clinical Decision Support for Personalized Medicine and Healthcare
Lei Liu, Ph.D.
Shanghai Center for Bioinformation Technology
and
Shanghai Institute for Biological Sciences, CAS
3/29/2010

2. Translational Medicine
Integration of Basic and Clinical Research
From Bench to Bedside
Clinical Research
Imaging
Presenter: “NCIA is one in a set of complementary tools called the “Life Science Bundle.” Like all of the caBIG™ tools, NCIA plays a specific role in the cancer research continuum – which can be loosely grouped into four categories - Clinical Research, Imaging, Pathology, and Molecular Biology.” (the last 4 correspond with animations in the figure, so click while speaking). NCIA supports the Imaging aspects of this research continuum.”
Presenter: “NCIA is ……. (read the text from the slide).”
From Introduction of caBIG
Molecular Biology
Pathology 2

3. How to deliver the right healthcare and medicine to the right people and at the right time?
Collection of personalized genetic and physiological information
Genome wide association studies, SNP, CNV…
Biosample Banking
Phenotypic data collection – CRF
Biosensor technology
Translated the information to clinical practice
Data integration and mining
Electronic Medical Record
Clinical Decision Support
The materialization of an emerging idea for personalized medicine – purported to apply the right drug in the right dose for the right person at the right time – relies critically on our ability to identify all relevant genetic variants in each patient and interpret this information in a clinically meaningful manner

4. Clinical Decision Support in Personalized Medicine
Gregory J Downing, et al. Information management to enable personalized medicine: stakeholder roles in building clinical decision support. BMC Medical Informatics and Decision Making, 2009,9:44
Gregory J Downing, et al. Information management to enable personalized medicine: stakeholder roles in building clinical decision support.
BMC Medical Informatics and Decision Making, 2009,9:44

5. Integrated Clinical Information Systems and Service Platform
Key city hospitals
Community hospitals
HL7
Non-HL7
Paper Record
Shanghai Public R&D
Service Platform
Clinical Data Repository
Tissue Bank
Genotype Data Repository
Integrated Bioinformatics Platform(IBP)
Comprehensive
Data-Warehouse

6. caBIG® Workspaces Domain Workspaces Clinical Trials Management Systems
(CTMS，临床实验管理系统)
Integrative Cancer Research
(ICR，综合肿瘤研究)
Domain Workspaces
Tissue Banks & Pathology Tools (TBPT，组织库&病理学工)
In Vivo Imaging （Vivo成像）
Vocabularies&Common Data Elements
(VCDE，词汇&公共数据元素)
Architecture (体系构架)
Cross Cutting & Strategic Workspaces
Data Sharing & Intellectual Capital (DSIC，数据共享&智能财产)
Documentation & Training
(D&T，文件&培训)

7. Ongoing Projects Data Sharing ＋ Decision Support Medical Channel
Clinical Data Warehouse
Medical Channel
Common Data Element Editor
Clinical Decision Support
Medical Natural Language Processing
Research Data Entry System
Data Sharing ＋
Decision Support
CDA Transfer Engine
Synchronous Liver Metastasis Model
Drug Knowledge Base
HL7 V3 Message Model
Clinical Guideline Computerization
Tissue Bank Annotation
Medical Terminology Service
Others 7

8. Clinical Data Warehouse
Registry Information Model (RIM) 8

9. Clinical Data Warehouse
R-MIM Model
Database Structure
SOA Service Bus
Clinical Document
（XML）
Database Records

10. MetaManager: Common Element Editor Data
Science Data Sharing Technology Standard（SDS/T ）
ISO/IEC 11179

11. Metamanager: Clinical Research Data Entry System
Automatic Tansfer
MetaManager 1.40

12. Clinical Document CDA Transfer Engine
HL7 CDA Schema
Schema for Clinical Document
Discharge Summary
Transfer Engine
Mapping
CDA File

13. Construction of HL7 V3 Message Model
V3Generator

14. Natural Language Processing
这张图是整个自然语言处理的流程
首先，看蓝色虚线部分，这是人工标注阶段。张韡德医生和我用protégé对一部分手术记录进行手工标注，标注的内容主要是医生感兴趣的内容，标注的方式是按照医生的思维，先找到表明该信息点整句话，然后找到查找词和答案，比如，我们以肿瘤大小为例。整句话为“大小约4.5*5*8cm”，查找词为“大小”，答案为4.5*5*8cm
（动画还没做，打算采用复制的办法）

15. Information Retrieval
自然语言处理模块已经整合到临床数据收集系统Clindata Express中 15

16. Common Medical Terminology Service16

17. Integration of Drugs and Genetic Information
dbSNP
Gene Functions
整合后的数据库关系图
Drug Information
SNP

18. Integration of Disease and Gene Mutation Information
Disease Information
Literatures Support
Disease Classification
Main Table
整合后的数据库包括：
主表。基因信息表。实验（文章）信息表。疾病信息表。疾病分类表
主表： HGNC ID 基因相关
Association ID 疾病相关
Submitter
基因信息表： HGNC ID
Approved Symbol
Approved Name
Status
Previous Symbols
Previous Names
Aliases
Name Aliases
Chromosome
Accession Numbers
Pubmed IDs
Gene Family Name
Locus Specific Databases
GDB ID (mapped data)
Entrez Gene ID
OMIM ID
RefSeq
UniProt ID
Ensembl ID
UCSC ID
实验（文章）信息表：Association ID
Reference
Pubmed ID
Disease ID
Sample ID
Allele Author Discription
Allele Functional Effects
Population
Method
疾病信息表： Disease ID
Disease name
Disease Aliases
Disease Class ID
Disease Phenotype
疾病分类表： Disease Class ID
Disease Class
Disease Class Code
样品信息：Sample ID
HGNC ID
Association ID
Mutation ID
Narrow Phenotype
Sample gender
Sample age
Sample geographical location
Sample parent tested
Sample environment variables
突变信息： Mutation ID
Mutation type
Mutation intron
Mutation exon
Mutation DNA location
Mutation DNA change
Mutation RNA location
Mutation RNA change
Mutation protein location
Mutation protein change
Experiment Samples
Gene Functions
Mutations

19. GAD
COSMIC
Catalogue Of Somatic Mutations In Cancer

20. Disease Orientated Text Mining
5445 Full articles， Abstracts on colon cancer
Interaction networks among proteins,genes and drugs
所有摘要中基因、蛋白质与药物相互作用网络，其中红色的点代表药物，蓝色的点代表基因或蛋白质

21. Text Mining
MLH1and MSH2
与5-氟尿嘧啶相关的基因或蛋白质

22. Rate of Occurring of Colorectal Cancer in Shanghai

23. Study of HNPCC Related Gene Mutation in Chinese Population
98 suspected HNPCC patients
hMSH2 and hMLH1 genes
Patient DNA
PCR
Sequencing
Mutation Analysis

24. HNPCC Database Clinical Information Pathology Family History Mutation
Follow Ups

25. Hereditary Gene Mutation Screening Platform
(HNPCC)
Genetic Mutation
Doctor
Registry
Blood
Self-Update
Clinical Data
microsatellite instability
Patients
Screen Model
Screen Model
Follow Up Data
CRC - Colorectal Cancer

26. Prognostic Effect of Biomarkers in Colorectal Cancer Patients with Synchronous Liver Metastasis
Prediction Model with
Multiple biomarkers
New Medical Knowledge
Provide a Web-based tool
for clinical decision support

27. Colon Cancer Patients at Shanghai Tumor Hospital from 2000 to 2005
Prognostic Effect of Biomarkers in Colorectal Cancer Patients with Synchronous Liver Metastasis
Colon Cancer Patients at Shanghai Tumor Hospital from 2000 to 2005
training
validation
Liver metastasis
No liver
metastasis
Liver
Number of subject 81
657 26
335
age
58.91±12.00
57.53±13.58
55±12.00
58.33±12.76
Gender(male)
60.5%(49)
56.9%(374)
61.5%(16)
54.3%(182)

28. Feature Extraction Ranked score attributes 0.11024461 CEA_before
CA50
CA19-9
max_diamete
rectum
abdominal_mass
hepatic_flexure
bellyache
hemafecia
straining_feeling_in_anus
sigmoid_colon
tenesmus_stool
hypodynamia
excrement_frequency_more_than_10
appendix

29. Prediction results for 152 patients in 2006：
Prognostic Effect of Biomarkers in Colorectal Cancer Patients with Synchronous Liver Metastasis
Prediction results for 152 patients in 2006：
Sensitivity：62.5%
Specificity：91.7%
Accuracy：90.1%
ROC：0.85

30. TissBank Information System

31. Combined Tissue Bank Annotation from Operation Summary and Pathology Report
Medical Natural Language Processing 31

32. Rule-based Clinical Decision Support
Expert Knowledge
Medical Logic Module ——MLM
Input

33. Computerization of Clinical Guidelines
Arden Syntax

34. Clinical Decision Support

35. Medical Channel——Orthopedic
电子病历设计 35

36. Medical Channel——Orthopedic

37. Summary

38. Shanghai Public Center for Healthcare
Acknowledgement
上海公共卫生中心
Shanghai Public Center for Healthcare

39. Thank you!