Transcript SALUSProjectOverview_ABM_Milan

SALUS - Scalable, Standard based
Interoperability
Framework for Sustainable Proactive
Post Market Safety Studies
A general overview
January 2015
SALUS Consortium
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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SALUS: Scalable, Standard based Interoperability
Framework for Sustainable Proactive Post Market Safety
Studies (http://www.salusproject.eu/)
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A STREP funded under Objective ICT-2011.5.3b) Tools and
environments enabling the re-use of electronic health records which
aims to
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Enable effective integration and utilization of electronic health record
(EHR) data to improve post-market safety activities
Pilots in Lombardy Region (Italy) and Eastern Saxony (Germany)
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WHO-UMC and ROCHE is actively involved in pilot studies
Partners
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SRDC Ltd, Turkey
(coordinator)
EUROREC, France
WHO- UMC, Sweden
OFFIS, Germany
AGFA Healthcare, Belgium
January 22, 2015
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ERS, Netherlands
LISPA, Italy
INSERM, France
TUD, Germany
ROCHE, Switzerland
SALUS 2nd Advisory Board Meeting, Milan
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Motivation
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Clinical trials are focused and not adequate to ensure
comprehensive drug safety
Post market safety studies address this problem, but
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Reactive based on spontaneous case safety reports
It is estimated that medical practitioners report only
about 5% of harmful drug side effects
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Medical professionals do not always see reporting a priority
Detecting adverse events may not always be straightforward
ADRs are the fifth most common cause of hospital deaths
Approximately 5% of all hospital admissions in Europe are due to an
adverse drug reaction (ADR)
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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Objectives
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Enable effective integration and utilization of electronic
health record (EHR) data to improve post-market safety
activities on a proactive basis
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EHR covers extended parts of the underlying medical histories,
include more complete information on potential risk factors,
and not restricted to patients who have experienced a
suspected ADE
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Denominator is missing in SRS data
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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How SALUS extends current spontaneous reporting
system to seamlessly exploit the already existing clinical
data at EHRs
Use Case:
Enabling
Notification
of Suspected
ADEs
External ADE
Detection Tool
Use Case:
Semiautomatic
ADE
Reporting
Secure Functional and semantic
Interoperability profiles enabling
ADE detection monitors to easily
deployed on top of existing EHRs
ADE Signals
detected through
mining case
reports
Secure Functional and semantic
Interoperability profiles enabling filling
individual case reports by extracting
available information from EHRs
Secure Functional and semantic
Interoperability profiles for tracing back
case reports to EHRs to retrieve
additional clinical context
B
A
Signal Follow up
Studies
C
Suspected ADE
detected semiautomatically
EHR System used
in clinical care
EHR System used
in clinical care
EHR System used
in clinical care
An ideal system for ADR surveillance would combine the
strengths of case reports with those of EHRs
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
Use Case:
Clinical
Review of
Patient
History
Use Case:
Temporal
Pattern
Characteriza
tion
Use Case:
Case-Series
Characteriza
tion
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How SALUS enables exploratory/confirmatory
signal detection and epidemiological research
studies on top of heterogeneous EHRs
Use Case: Temporal
association screening
on EHRs:
-Open ended analysis,
no prior hypothesis
-Generates
associations that
might become signals
Use Case: Using
EHRs as secondary
use data sources for
Post Marketing
safety studies:
ROCHE Estimate
incidence rates of
CHF in diabetic
patients with a
recent acute
coronary syndrome
(ACS) event
•Screening of heterogeneous EHR data for adverse event signals detection
•Carrying out outcome research to identify long term effects of drugs
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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Project timeline
M40
Extension
4 Months
WP3
WP4
WP5
WP6
WP7
WP3
WP7
WP8
WP1
WP2
Month
36
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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4 Months of project extension
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Deployment and Validation activities delayed in TUD because of the delay in
the data access agreement by the ethical board of UKD (The university
hospital of the Technical University of Dresden)
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UKD board signed the agreement in June 2014 [M29]
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Technical arrangements on TUD took some time for establishing the secure
authentication mechanisms for remote access and establishment of the
connection between SALUS server and TUD’s TST1 database
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 4 Months extension has been requested from the EC
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which includes a copy of TUD’s production database.
Accepted
All deployment and validation activities have been carried out as planned in
LISPA settings.
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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SALUS Development
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Latest development technologies
Client – Server architecture
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Git repository
SALUS as a single Apache Maven project
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web based GUIs
ubiquitous access
~60 different modules
Build with a single command
Configurable
Java + Javascript
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RESTful service communication
Direct Java calls
XML SOAP communication
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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Integrated SALUS Components
Audit
Services
Authentication
Services
Deidentification &
Pseudonymization
Services
Termino logy
Server
Java
REST
REST
REST
Temporal
Association
Screening Tool
Temporal Pattern
Characterization
Tool
Post Market
Safety Study
Tool
Patient
History Tool
Existing EHR
Source
Mechanisms
Case Series
Characterization
Tool
ADE
Notification
Tool
REST
ICSR
Reporting
Tool
REST
Safety Analysis
Query Manager
SIL Data
Service
REST
REST
Java
Web Service
OMOP
Converter
January 22, 2015
Content
Formatter
SALUS 2nd Advisory Board Meeting, Milan
Technical
Interoperability
Layer
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Deployed SALUS Components
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Care Zone
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Servlets ready to be deployed after
automatic build
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Deployment scripts
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Java code: 535,453
Javascript code: 658,139 (includes
external libraries like jquery.js)
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Research Zone
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athena.war
qedext-ws.war
silds.war (tud)
sildslispa.war
deidentification.war
safetyanalysisquerymanager.war
irt.war
ant.war
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csct.war
pht.war
pmsst.war
tpt.war
Web Cloud
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terminologyserver.war
semanticmdr.war
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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SALUS Tools
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The web based tools which are used directly by the endusers
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Care Zone
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ADE Notification Tool
ICSR Reporting Tool
Research Zone
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Case Series Characterization Tool
Temporal Association Screening Tool
Temporal Pattern Characterization Tool
Post Marketing Safety Study Tool
Patient History Tool
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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SALUS Tools
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The services consumed by other SALUS components
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Terminology Server
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ATC, MedDRA, SNOMED-CT, ICD-10, ICD-10-GM, ICD-9-CM,
LOINC, TUD Local Coding System (partly)
CDE Repository (SemanticMDR based)
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163 SALUS Common Data Elements
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SPARQL Scripts (Extraction Specifications  IHE DEX Profile)
CDE mappings
 CDASH – HITSP C154
 OMOP CDM – HITSP C154
 BRIDG – HITSP C154 (partly)
 SALUS CIM – HITSP C154
 SDTM – SALUS CIM
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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Terminology Mappings in SALUS
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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Semantic/Technical
Interoperability Layers
Tool
Calculate
Query
Result
Calculator
Query
Manager
RDF HQMF query or GET entity
Convert terms
SALUS CIM
Ontology
SIL-DS
(TUD)
SIL-DS
SIL-DS
(LISPA)
Query
ORBIS SPARQL
Endpoint
Query
ORBIS DB
January 22, 2015
Terminology
Service
Query
TIL
Query
•IHE QED
•IHE CM
•HL7 HQMF
LISPA DWH
SALUS 2nd Advisory Board Meeting, Milan
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SALUS Security Architecture
•Pommerenning approach
•IHE ATNA Profile
•Audit Record Repository
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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SALUS Subscription Mechanism
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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Open Source Tools
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We support the community and created standalone open-source
tools and published on GitHub
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ontmalizer: create RDF/OWL representation of XML Schemas, and XML
instances that comply with such XML Schemas
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semanticMDR: ISO/IEC 11179 implementation with a complete set of
additional semantic capabilities.
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https://github.com/srdc/virt-jena
triplestore: a unified interface – JenaStore – which allows to use either
Virtuoso Quad Store or Jena TDB
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https://github.com/srdc/semanticMDR
virt-jena: fully operational Native Graph Model Storage Provider for the
Jena Framework on Virtuoso Servers
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https://github.com/srdc/ontmalizer
https://github.com/srdc/triplestore
the EYE Reasoner: Euler Yet another proof Engine.
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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At Month 36
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Validation is about to finish in LISPA settings.
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2 different databases for validation
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DWH
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DWH2
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16 million patients: ~500 million ambulatory, ~30 million hospitalization, ~ 275
million prescriptions, ~ 35 million vaccinations, ~1 million pregnancies
1 million patients
Database update for Subscription – Monthly
 PATIENT:
200.000 records
 HOSPITALIZATION:
133.000 records
 DRUGS:
7.500.000 records
 AMBULATORY:
14.100.000 records
 VACCINATION:
100.000 records
 CONDITION:
10.000.000 records (yearly)
 PREGNANCY
80.000 (yearly)
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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At Month 36
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Deployment is completed in TUD
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Research Zone access is established
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through secure VPN connections
Validation has started
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TST1: 1 million patients
TUD and Roche
Care Zone validation will be carried out internally in TUD
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ANT has been executed and a list of notifications have already been
created
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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SALUS Channels
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Publications
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2 PhD Thesis
5 published journal papers and book chapters
~20 conference presentations
awaiting and planned submissions…
Screencasts
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Tutorials
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Blog
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blog.salusproject.eu
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i.e. http://www.salusproject.eu/screencast/pmsst/1
27 blog posts
Twitter account
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@SALUSProject_EU
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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Results in summary
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Using the SALUS system, it is now possible to
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detect Adverse Drug Events on patient summaries
prefill Individual Case Safety Reports (ICSRs) with available
patient data
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submit ICH E2B based case safety reports to regulatory bodies
perform effectiveness studies on available EHR data by
submitting various queries for different purposes such as case
series characterization and temporal association screening
perform post market drug surveillance on selected cohorts
coming from different EHR sources and make analytical
calculations
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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Conclusions
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All the contractual obligations have been delivered on
time
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Up to now [M36]
Dissemination efforts
Collaboration with standardization bodies and other
projects
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A new Interoperability profile is published
SALUS MDR has attracted a lot of attention
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discussion with NCI for a replacement of caDSR tool set
Support to open-source community
SALUS Tools are ready and in use
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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Challenges and lessons learned
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Interoperability Challenge
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Accessing EHR Sources for secondary use
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Profiling approach
Selected use cases
SALUS provides the facilities to achieve interoperability &
demonstrates its applicability through selected use cases
Even at analysis time, we encountered problems
There should be clear incentives for Hospitals
Performance Challenge
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Dealing with real data of millions of people is not the same with
testing the system with test data
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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Thank you for
listening…
Questions
A. Anil SINACI
January 22, 2015
SALUS 2nd Advisory Board Meeting, Milan
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