Upload
silvia-fisher
View
214
Download
0
Tags:
Embed Size (px)
Citation preview
All Rights Reserved, Duke Medicine 2007
Duke Cancer InstituteInvolvement with
Data Standards and Semantics(May 6, 2011)
Salvatore MungalDuke Bioinformatics Shared Resources (DBSR)Duke Cancer Institute (DCI)
All Rights Reserved, Duke Medicine 2007
Agenda• Background:
– The Promise of Interoperability– The caBIG Initiative– Interoperability Fundamentals
• Groups of Standards• Standards at Duke• caBIG Interoperability Development• Benefits of caBIG Interoperability Adoption• Building Blocks/Development• caBIG Implementation Framework at Duke• Benefits of caBIG Adoption with Data Standards• Current Pilot• Under Development• Future Plans
All Rights Reserved, Duke Medicine 2007
The Promise of Interoperability• Interoperability is based on common data standards and is a
pre-requisite for the aggregation and sharing of data• Interoperability in Life Sciences research can lead to faster
conclusions via analysis of shared/aggregated data • In health care, widespread interoperability can lead to better
outcomes in many areas ranging from high quality care, individual patient safety during treatment, to population safety from epidemics, to the everyday chronic and acute care of millions of citizens, irrespective of location
• Currently, vendor systems are not interoperable, institutional systems are not interoperable, and enterprises are not interoperable.
• Interoperability is the future
Published with permission
All Rights Reserved, Duke Medicine 2007
Background: The caBIG Initiative
• In 2003 Dr. Andrew von Eschenbach set the caBIG initiative in motion
• Sharing and expanding interoperable datasets for analysis - a crucial goal
• Accelerated research, cures and better outcomes• The success of this initiative relies on the incorporation of
standard datatypes, semantics, and software systems i.e. the semantic and syntactic - all working in harmony
• Interoperability is the future and caBIG leads the charge
All Rights Reserved, Duke Medicine 2007
Background: Interoperability Fundamentals• The fundamental unit of interoperability is the data standard (HL7
BRIDG, LS_DAM etc.)• The fundamental unit in caBIG data standards currently is the
Common Data Element (CDE) which uses ISO 11179 that incorporates standard semantics (vocabularies, terminologies etc.) and standard value domains/datatypes in it’s metadata (mapping of ISO 11179 to 21090)
• caBIG uses CDEs in Clinical/Life Sciences research/studies• In a Yin/Yang relationship (syntactic/semantic), software
encapsulates data and their CDEs (metadata) to facilitate data sharing - automated interoperability could be realized
• Other groups are creating their own data standards and are willing to use caBIG as a model
All Rights Reserved, Duke Medicine 2007
GROUPS OF STANDARDS
• GENERIC, BROAD USEXML, TCP/IP, Web services, OCL, CCOW, SECURITY, GIS, etc.W3C, IETF, OMG, HL7 others.
• DATA ELEMENTSRIM, DATA ELEMENTS, DATA TYPES, TERMINOLOGY, TEMPLATES, CDAHL7, CEN, ISO, NCPDP, X12N, IEEE, SNOMED. LOINC, RXNORM, SPL
• DATA INTERCHANGEStructured and free form documents, imagesHL7 V2.N AND V3, DICOM, IEEE X73, ASTM, NCPDP, X12n and others
• KNOWLEDGE REPRESENTATIONGuidelines and Protocols, ARDEN SYNTAX, GLIF, GEM, PRODIOGY, PROTIGÉ, vMR, GELLO, othersHL7, ASTM, UK, others
• ELECTRONIC HEALTH RECORDFUNCTIONAL REQUIREMENTS, CONTENT DATA SETS, EHR MODEL, CCR, TRANSFER EHR, other HERHL7, ASTM, CEN, openEHR
• APPLICATION LEVEL SUPPORTIDENTIFIERS, RESOURCE REGISTRIES, TOOL SETS, CONFORMANCE AND IMPLEMENTATION MANUALSHIPAA, HL7, ASTM, ISO, CEN
Published with permission
All Rights Reserved, Duke Medicine 2007
Standards at Duke• Duke is facilitating several projects in HL7
– Cardiovascular DAM– Anesthesiology DAM– InfoButton Standard– Tuberculosis DAM
• The caBIG Standards– ISO 21090/11179, – HL7 – Semantics - Vocabularies, Terminologies and
Ontologies (LOINC etc.)• Several applications with standards (listed later)
All Rights Reserved, Duke Medicine 2007
DATA
KNOWLEDGE
PROCESS
STA
ND
AR
DS
Low cost
Accessible
Patient Safety
Quality
Analysis
Statistics
Research
Clinical Trials
EBM
Analysis
Statistics
Research
Clinical Trials
EBM
Analysis
Statistics
Research
Clinical Trials
EBM
Analysis
Statistics
Research
Clinical Trials
Surveillance
Analysis
Public/PrivatePartnership
Vendor/ProviderPartnership
Published with permission
Privacy, Security, Trust, Integrity
All Rights Reserved, Duke Medicine 2007
PreventiveCare
Acute Care ChronicCare
Data Data Data
DecisionSupport
Decision Support Decision Support
Norm
al
Concern
Abnorm
al
Outpatient
Specialty
Em
ergency
Hospital
Intensive
Control
Treatm
ent
Perform
ance
Sym
ptoms
Diagnoses
Treatm
ent
Outcom
es
Genom
ic Medicine
Nursing Homes, etc. Home Care
Published with permission
A view of the healthcare world
All Rights Reserved, Duke Medicine 2007
Where do standards start?• With the smallest element – the data element• If we define a structured set of any and all data
elements that might be contained within an electronic health record, and if
• we include precise and unambiguous definitions, data types, units, roles and use, and many other attributes, and if
• we define unique value sets for these data elements (single, integrated terminology)
• then we can achieve interoperability independently of how these data elements might be packaged for interchange.
Published with permission
All Rights Reserved, Duke Medicine 2007
EHR Interoperability Diagram
PatientEncounter
Provider EHR
Database
PersonalEHR
PopulationEHR
Profile
Profile
ProfileResearchDatabase
EnterpriseData
WarehousePersonal
EHR
Profile
Disease Registry
Profile Billing/Claims
Institution EHR
Database
ResearchDatabaseResearch
Database
Disease RegistryDisease
Registry
Derived from master data element registry
Published with permission
All Rights Reserved, Duke Medicine 2007
caBIG Interoperability Development at Duke• Cancer Central Participant Registry (C3PR)• caTRIP
– Many elements are part of other caBIG applications
• RProteomics• Duke Cancer Proteome Characterization Center
(proposal)• VCDE/Architecture Mentorship
All Rights Reserved, Duke Medicine 2007
caBIG Adoption at Duke• Flagship C3D implementation
– Many trials in production, many more in development (all CDE based)
• caAERS (CALGB and Duke) (in progress)• C3PR multi-center pilot • caGRID• RProteomics (soon to be in development)• caArray
All Rights Reserved, Duke Medicine 2007
Integration Hub
CTMS(eResearch)
CDMSC3D
(Oracle Clinical)
Safety Desk(ExtraView)
S/AE Reporting(caAERS)
API
Web Service
Pull Study Status/Agentfrom eResearch
MedWatch input from e-mail, fax, paper,
caAERS
Local investigator assessment for IRB
routing determination
Local IRB and/or affiliate sites
(FDA for SAEs)
MedWatch form generation for
Duke held IND/IDE
Promised API
Clinical Connector
eIRB(Click
Commerce)
Protocol #Short Title
Investigator nameStudy Status (initial)
Data Entity Overview
All Rights Reserved, Duke Medicine 2007
Integration Hub
CTMS(eResearch)
CDMSC3D
(Oracle Clinical)
Safety Desk(ExtraView)
S/AE Reporting(caAERS)
API
Web Service
Pull Study Status/Agentfrom eResearch
MedWatch input from e-mail, fax, paper,
caAERS
Local investigator assessment for IRB
routing determination
Local IRB and/or affiliate sites
(FDA for SAEs)
MedWatch form generation for
Duke held IND/IDE
Promised API
Clinical Connector
eIRB(Click
Commerce)
Protocol #Short Title
Investigator nameStudy Status (initial)
CDE BASED
Data Entity Overview CDE Based
All Rights Reserved, Duke Medicine 2007
Program Project (P01) Proposal
Data Export Process
Invoice
Velos eResearchClinical Trial Management System ( CTMS )
Protocol/ Patient Management
BudgetReport/Financial
Data
Investigator/ CRC
Regulatory DocsBudget
Trial Protocol Dev .
DUKE Systems
caBIGTM
Applications
Invoice
Velos eResearchClinical Trial Management System ( CTMS )
Protocol/ Patient Management
BudgetReport/Financial
Data
Investigator/ CRC
Regulatory DocsBudget
Trial Protocol Dev .
DUKE Systems
caBIGTM
Applications
C3D Bladder (M-I)
Protocol
C3D BladderProtocol
Integration Hub
Reports
Analyses
Reports
Analyses
Via web service
iReviewTM
Query
Report Interface
iReviewTM
Query
Report Interface
Tool and Investigator
Report
Report
Report
Investigator
Report
Report
Report
caTissue
Web Service
Cancer Adverse Event Reporting System (caAERS)
ClinicalConnector
SAS Datasets
All Rights Reserved, Duke Medicine 2007
Program Project (P01) Proposal CDE Based
Data Export Process
Invoice
Velos eResearchClinical Trial Management System ( CTMS )
Protocol/ Patient Management
BudgetReport/Financial
Data
Investigator/ CRC
Regulatory DocsBudget
Trial Protocol Dev .
DUKE Systems
caBIGTM
Applications
Invoice
Velos eResearchClinical Trial Management System ( CTMS )
Protocol/ Patient Management
BudgetReport/Financial
Data
Investigator/ CRC
Regulatory DocsBudget
Trial Protocol Dev .
DUKE Systems
caBIGTM
Applications
C3D Bladder (M-I)
Protocol
C3D BladderProtocol
Integration Hub
Reports
Analyses
Reports
Analyses
Via web service
iReviewTM
Query
Report Interface
iReviewTM
Query
Report Interface
Tool and Investigator
Report
Report
Report
Investigator
Report
Report
Report
caTissue
Web Service
Cancer Adverse Event Reporting System (caAERS)
ClinicalConnector
SAS Datasets
CDE BASED
All Rights Reserved, Duke Medicine 2007
Duke Proteome Characterization Center (PCC)(Proposed)
Key: Red arrows indicate semantic involvement
All Rights Reserved, Duke Medicine 2007
Duke Proteome Characterization Characterization Center (PCC)(Proposed) CDE Based
CDE BASED
All Rights Reserved, Duke Medicine 2007
Benefits of caBIG Interoperability Adoption
• C3D– Top-shelf CDMS (with CBIIT tech. support)– Regulatory compliant (21 CFR Part 11)– Shared Global Library (parent-child)– caDSR-Direct (local curation ability)– Thousands of Common Data Elements– Development curve
• Less steep now, new trials up much faster• More cluster (brain, breast, etc) replication
All Rights Reserved, Duke Medicine 2007
Supported Projects on caBIG PlatformsGoal: All Investigator-initiated Clinical Trials (all CDE based)•Currently ~40 trials in production or development
– Single and multi-center– Both IND/IDE and Registry
•International– Launching first trial with Beijing Cancer
Hospital• …more to come
•Funding Mix – Gov’t – NIH (NCI, NINDS, etc) and DoD– Foundation (Komen, etc.)– Industry/Pharma
All Rights Reserved, Duke Medicine 2007
Supported Projects on caBIG Platforms CDE Based
Goal: All Investigator-initiated Clinical Trials (all CDE based)•Currently ~40 trials in production or development
– Single and multi-center– Both IND/IDE and Registry
•International– Launching first trial with Beijing Cancer
Hospital• …more to come
•Funding Mix – Gov’t – NIH (NCI, NINDS, etc) and DoD– Foundation (Komen, etc.)– Industry/Pharma
CDE BASED
All Rights Reserved, Duke Medicine 2007
Duke-Beijing Abraxane Trial CDE Based
First CT collaboration
caTissue-based tumor registry
Future network in China
CDE BASED
All Rights Reserved, Duke Medicine 2007
C3PR Multi-center Pilot (Completed) CDE Based
• PANVAC multi-center vaccine study– Grid-enabled– Secure– Accessible– CDE based
Dorian
GTS
CDS
webSSO
caXchange
Key
IdP
Study ServiceRegistration
Service
XYZ Cancer Center
CDE BASED
All Rights Reserved, Duke Medicine 2007
Under Development• caTissue (works with annotated samples)
– Pilot implementation underway– Potential for broad institutional adoption
• caArray – Installed (annotation tool is very useful)– caGrid enabled
• Laboratory Information System (GE – in use)– Uses LOINC
• Data warehouse– Implements a text analytic tool using Radlex
All Rights Reserved, Duke Medicine 2007
Under Development (con’t)• DISCERN (in use)
– HL7 is part of the eBrowser (DSR)– Potential for broad institutional adoption (available
to all Duke Researchers)• caArray
– Installed (annotation tool is very useful)– caGrid enabled
• Laboratory Information System (GE – in use)– Uses LOINC
• Data warehouse (in use)– Implements a text analytic tool using RadLex
All Rights Reserved, Duke Medicine 2007
Under Development (con’t)
• Cardiovascular Data Standards (DCRI)– DAM has ~ 1285 CDEs (HL7 conversion next)– Country wide adoption expected
• Bioconductor (off site caBIG compatible app.) – Genomic analysis (heavy use)
• GenePattern (off site caBIG compatible app.)– Genomic analysis (heavy use)
All Rights Reserved, Duke Medicine 2007
Future Plans
• C3D (all CDE based)– Streamline trial start-up with eCRF
Harmonization– Exchange data with caAERS– Complete integration with Velos eResearch
• Expanded use of caARRAY by DBSR– Annotations
• China (all CDE/Forms based)– Set-up local Suite environment in Beijing– Build-out multi-center Chinese network
All Rights Reserved, Duke Medicine 2007
Future Plans (con’t)
• Proteomic Center (proposed)– Streamline all data collection and analysis
with annotation engine, Tranche– Integration of RProteomics for analysis
• Duke will continue their involvement with HL7 standards
• Continued expansion of CRF creation (CDE based) by other groups – caDSR-Direct (local curation ability)
All Rights Reserved, Duke Medicine 2007
Summary
• Duke is very involved with data standards• Interoperability is the future• Currently, vendor systems are not interoperable, institutional
systems are not interoperable, and enterprises are not interoperable
• The fundamental unit of interoperability is the data standard (HL7 BRIDG, LS_DAM etc.)
• The fundamental unit in caBIG data standards currently is the Common Data Element (CDE) which uses ISO 11179 that incorporates standard semantics (vocabularies, terminologies etc.) and standard value domains/datatypes in it’s metadata
• For data standards, start with the smallest element – the data element
All Rights Reserved, Duke Medicine 2007
Acknowledgements
• DBSRWilliam Barry, DirectorPankaj Agarwal
• DTMIW. Ed Hammond, DirectorAnita Walden
• CCISBob Annecharico, DirectorMohammad Farid
• DCRIBrian McCourt, Assoc. DirectorRebecca Wilgus