Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011,...

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Lei Liu, Ph.D. 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 Technology And Shanghai Institutes for Biological Sciences, CAS

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Page 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.

Lei Liu, Ph.D.Lei Liu, Ph.D.Lei Liu, Ph.D.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 TechnologyAnd

Shanghai Institutes for Biological Sciences, CAS

Page 2: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Part 1: Ontology

Knowledge Management

Data Integration and Exchange

Semantic Interoperability

Decision Support and Reasoning

Page 3: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Knowledge Management

Annotating Data and Resources

Accessing Biomedical Information

Mapping across Biomedical Ontologies

Ontology

Page 4: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Data Exchange &Semantic Interoperability

Information and Data Integration

Semantic Interoperability

Ontology

Page 5: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Decision Support and Reasoning

Data Selection

Data Aggregation

Decision Support

Natural Language Processing Applications

Knowledge DiscoveryOntology

Page 6: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Example: Ontology Server

Page 7: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Example: Building Knowledge Base

Edit

Page 8: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Example: Building Knowledge Base

Search tool

Page 9: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Part 2: SNOMED CT

Systematized Nomenclature of Medicine—Reference

Terminology(SNOMED RT)

Clinical Terms(CT)

SNOMED CT

CAP

NHS CAP: College of American PathologistsNHS: National Health ServiceIHTSDO: International Health Terminology Standards Development Organization

Page 10: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Core contents

SNOMED CT

Page 11: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Applications

Electronic Health Record Systems 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

Page 12: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Medical domains of the 100 Medline indexed papers in which a specific medical domain has been described. (BMC Medical Informatics and Decision Making 2008, 8(Suppl 1):S2)

SNOMED CT

Page 13: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Example: Mapping

Page 14: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Example: Encoding

Page 15: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Example: Standardization of Terminology

Page 16: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Part 3: OpenEHR

Objectives

Promote and publish formal specification

Promote and publish EHR

architectures and models

Interoperable health informatics

system

Maintain open source “reference”

implementation

Implement EHR architectures into

clinical use

Work closely with standards bodies

Page 17: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

openEHR introduction

• Definition: – openEHR is an open standard specification in

health informatics that describes the management and storage, retrieval and exchange of health data in electronic health records (EHRs)

• Features:– Patient-centric– Lifelong– Vendor-independent

Page 18: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Architecture of OpenEHR

OpenEHR Release 1.0.2

Page 19: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Two-level modeling of openEHR

Page 20: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

openEHR EHR system implementation

Page 21: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

applicability

• Apply– Store data– Search data– Share data

• Not apply– Control the

exchanging flow

Page 22: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Integration of SNOMED CT into OpenEHR

Page 23: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

HL7 v3 introduction

• mission: provides standards for interoperability

• Features– standard data, use reference information model

(RIM)• CDA, standardize clinical documents for exchange

– support healthcare workflows (V3 messaging)

Page 24: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

RIM

Page 25: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

applicability

• Apply– exchange information– Control the exchanging flow– Control the exchanging data’s size

• Not apply– Store data (we can store CDAs, but it’s not a best

practice)– Search data

Page 26: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Ongoing Biomedical Informatics Projects

Clinical Decision Support

Medical Natural Language Processing

Synchronous Liver Metastasis Model

Drug Knowledge Base

Data SharingData Sharing＋＋

Decision SupportDecision Support

Data SharingData Sharing＋＋

Decision SupportDecision Support

Others

Medical Channel

Common Data Element Editor

Research Data Entry System

CDA Transfer Engine

HL7 V3 Message Model

Tissue Bank Annotation

Medical Terminology Service

Clinical Data Warehouse

Clinical Guideline Computerization

Page 27: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Clinical Data and Sample is at the Core Clinical Data and Sample is at the Core of Translational Medicineof Translational Medicine

Clinical Data

Clinical Practice

Biomarker

Biospecimen

Clinical Trial

LIMS

Genotypes

Page 28: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

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/

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

Integrative Cancer Research (ICR ，综合肿瘤研究 )

https://cabig.nci.nih.gov/workspaces/ICR

Tissue Banks & Pathology Tools (TBPT ，组织库 & 病理学工 )

https://cabig.nci.nih.gov/workspaces/TBPT

Tissue Banks & Pathology 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

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

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

Architecture( 体系构架 )

https://cabig.nci.nih.gov/workspaces/Architecture

Data Sharing & Intellectual Capital (DSIC ，数据共享 & 智能财产 )

https://cabig.nci.nih.gov/working_groups/DSIC_SLWG

Data Sharing & 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

Documentation & Training (D&T ，文件 & 培训 )

https://cabig.nci.nih.gov/working_groups/Training_SLWG

caBIG® WorkspacescaBIG® Workspaces

https://cabig.nci.nih.gov/workspaces/CTMS/
https://cabig.nci.nih.gov/workspaces/CTMS/
https://cabig.nci.nih.gov/workspaces/ICR
https://cabig.nci.nih.gov/workspaces/ICR
https://cabig.nci.nih.gov/workspaces/Imaging
https://cabig.nci.nih.gov/workspaces/Imaging
Page 29: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

References and StandardsReferences and Standards

References used: ① caCORE (Cancer Common Ontologic Representation Environment): ② caDSR (Cancer Data Standards Repository) ③ 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 2008•Two people from our center attended the Boot Camp

Page 30: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Tissue Bank Information Management System

Page 31: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

样本数据库信息管理系统样本数据库信息管理系统全面解决方案全面解决方案

Biobank Information Management PlatformBiobank Information Management Platform

Page 32: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Use Cases

Page 33: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Combined Tissue Bank Annotation from Operation Summary and Pathology Report

Medical Natural Language Processing

Page 34: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Difficulties of acquiring data and multiple times of entering

Direct connection to HIS 、 LIS and EMR

Automatic transferring of data without entering by staffs

Active reminding system for follow-up

Automatic Data Query and Extraction Across Systems

Page 35: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Molecular classification

database

Diagnostic tests

database

Patients‘ situation

of treatment database

Patient follow-updatabase

Sample database

Personalized treatment

procedures

Clinical Information Enquiry System: The overall framework and subsystems

HISdatabase

LISdatabase

General enquiries

PACSdatabase

D-QISdatabase

Page 36: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Clinical Information Enquiry System

Page 37: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Clinical Data Warehouse

Part to process RIM object（create, delete, update, query RIM boject）

RDB

Persistence layer（hibernate）

RIM processor（busyness layer）

TABLE

Javasig

CALL

RIM object

mif document

xmldocument

RIM database structure

Page 38: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

R-MIM ModelR-MIM Model Database StructureDatabase Structure

Clinical Document（ XML ）

Clinical Document（ XML ） Database RecordsDatabase Records

SOA Service BusSOA Service Bus

Clinical Data Warehouse

Page 39: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Clinical Document CDA Transfer Engine

Schema for Clinical Document HL7 CDA Schema

Transfer Engine

Discharge Summary

CDA File

MappingMapping

Page 40: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Common Medical Terminology Service

Page 41: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Difficulties of Extracting Data

Page 42: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

METHODS

Page 43: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Model's Performance

Page 44: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Model's Performance

Page 45: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Model's Performance

Page 46: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Biomedical Data Integration and Mining

Integration

Data Mining

Personalized Medicine Databases

Personalized Medicine Decision Support System

Medical Informatic

Bioinformatics

Translational Medicine

Genomics

Page 47: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Disease and Gene Integration

GAD COSMIC

Data Integration

Gene2Disease Databases

参考文献信息参考文献信息

试验样本信息试验样本信息

突变信息突变信息

疾病信息疾病信息

疾病分类信息疾病分类信息

基因信息基因信息

主表主表

Genetic Polymorphisms 39910Gene Mutations 150654519 Major DiseasesStructured Gene Information 31412

Page 48: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Drug and Drug metabolism Study

• Drug-Target-SNP Integration and Databases

SNP Drug

Data Integration

Drug-Target Polymorphism Databases

dbSNP

HapMap

Query Drug-Target-SNP

Data Tables Records

Enzymes 50

Drug Targets 3866

Drug-Enzymes relationship 4387

Drug Information 4414

Enzymes-SNP 9558

Drug-Target Information 12051

rsSNP 332476

GenBank_SNP 337259

ssSNP 1745368

Mutations from populations

1839782

Total 201MB

Drug Info

Target Info

SNP Info

Drug Metabolism

Page 49: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Mutation Information Integration

• Extraction from Locus-specific databasesLSDB AddressesLSDB Addresses

Using WiKi Collect LSDB Addresses1300 LSDB Classification of Genes link to OMIM Database

http://129.89.44.120/twiki/bin/view

Mutation Information ExtractionMutation Information Extraction

Natural Language ProcessingTwo LSDB Data Extration

Alzheimer Disease & Frontotemporal Dementia Mutation DatabaseSarcomere Protein Gene Mutation Database

1725 mutation records

Page 50: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

• Mutation Association with Disease Phenotypes• Standards

• Gene Names -- HUGO• Diseases （ ICD-10 ）

– Mapping ICD-10 and MeSH, using keyword search– Adopt SNOMED CT ， Build Disease Ontologies

映射后的 ICD-10 疾病词汇表

Mutation Information Integration

Page 51: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

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 types

http://www.scbit.org/glif

Mutation Information Integration

Page 52: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

• DRUMS Query Results

Mutation Information Integration

Page 53: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Biomedical Informatics Systems for Translational Research

BioBankBioBank•EMR for Research •EMR for Clinical Trial•Follow-up Information Systems

•EMR for Research •EMR for Clinical Trial•Follow-up Information Systems

•Omic Databases•LIMS•Bioinformatics Analysis Platform

•Omic Databases•LIMS•Bioinformatics Analysis Platform

Page 54: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Database Establishment for Translational Research

Star Server

EDW

HEO

DE-

IDEN

TIFI

CATI

ON

One way hashOne way hash

Dat

a Pa

rsin

gD

ata

Pars

ing

Information collected Information collected during clinical careduring clinical care

Restructuring for research

Data export

SD Database

Access through secured online application

Page 55: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Informatics in EMR-based PGx Studies

• Natural language processing (NLP)• Machine learning & data mining

DNA Biobank EMR Drug Exposure

Drug Response

Informatics Approaches

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Page 56: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

Information Flow in Translational Medicine

New Therapeutic knowledge

Clinical Practice

Biospecimen

Clinical Data

High Throughput

Research

Page 57: Lei Liu, Ph.D. The Fifth China-US Roundtable on Scientific Data Cooperation October 27-28, 2011, Beijing, China Biomedical Data Integration and Knowledgebase.

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 2011

2011 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。


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