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Wolfgang Kuchinke
TRANSFoRm Project Meeting
Standards for clinical research data:
Introduction to CDISC
– CDASH, PRM and BRIDG
Introduction
• The standards CDISC CDASH, SHARE, PRM and BRIDG
are described and introduced in terms of their abilities
to contribute to the development of a comprehensive
information model for clinical reserach (CRIM)
• In particular, the new clinical research information
model should allow the integrative usage of medical
care data together with clinical trial data
• The model should also support processes of the
Learning Health System
The standards that were evaluated
CDASH
●
Basic standard for the collection of clinical trial data
●
Identifies the basic data collection fields needed from a
clinical, scientific and regulatory perspective to enable more
efficient data collection at the Investigator sites
●
Sponsors will need to determine what additional data fields will
need to be added
●
Therapeutic area (TA) specific data fields
Clinical Data Acquisition Standards Harmonization
CDASH
• CDASH version 1.1 and CDASHUG V 1.0
• Public Review and Comment Period, comments until 14 May 2010
•Set of "content standards" (element name, definition, and
related metadata) for a basic set of data collection fields
•16 CRF content ‘safety data/domains’ that are common to
all therapeutic areas (Adverse Events, Concomitant
Medications, Comments, Demographics, Exposure,
Inclusion and Exclusion Criteria, Lab, Medical History, …)
•New version includes: conformance rules, explicit question
text, more information about collecting relative timing
variables, BRIDG annotations, as well as a few new
collection fields
Status
CDASH
• Purposes: CDASH (data collection) – SDTM (submission)
• Core description (three degrees: highly recommended,
recommended, optional)
• CDISC controlled term  link with spreadsheet
• CDASH / SDTM annotated CRF
• Best practice recommendations
• CDISC integration into the Oracle Clinical / Remote Data
Capture system (OC/RDC), SDTM conversion
•CDASH/SDTM compliant eCRF
•Metadata library within OC
• Creation of annotated CRF library
CDASH
• SDTM and the SDTMIG provide a standard for the
submission of data concerning data collected during
clinical trials
• CDASH data collection fields (or variables) can be mapped
to the SDTM structure
•When the data are identical between the two standards, the SDTMIG
variable names are presented in the CDASH domain tables
• Possible is the definition of own CDASH user domains (see
CDASH user guide) or customization of the 16 CDASH
domains
CDASH: Alignment with other standards
The Study Data Tabulation Model (SDTM)
W. Kuchinke
• Adverse Event – AE (Events)
• Comments – CO (Special Purpose)
• Prior and Concomitant Medications – CM (Interventions)
• Demographics – DM (Special Purpose)
• Disposition – DS (Events)
• Drug Accountability – DA (Findings)
CDASH
CDASH Domain Tables 1
W. Kuchinke
• Exposure – EX (Interventions)
• Medical History – MH (Events)
• Physical Examination – PE (Findings)
• Protocol Deviations – DV (Events)
• Subject Characteristics – SC (Findings)
• Substance Use – SU (Interventions)
• Vital Signs – VS (Findings)
CDASH:
CDASH Domain Tables 2
• SDTM Variable Name: Lists the SDTM-based variable
name defined in SDTMIG
• BRIDG: This column contains the BRIDG Release 3.0
classification
• Definition: Describes the purpose of the data collection
field. The text may or may not mirror the text in the
SDTMIG
• Core: Contains CDASH core designations for basic data
collection fields
CDASH
Table Headers
CDASH Domain Tables
Example: Exposure – EX (Interventions)
CDASH
Example: Best Practice Recommendations
W. Kuchinke
CDASH
Examle for linked terminology: CDASH Terminology 5-3-
2010
W. Kuchinke
SHARE
What is CDISC SHARE?
• A globally accessible electronic library built on
a common information model
• Enables precise and standardized data element
definitions that can be used in studies and
applications to improve biomedical research and
it’s link with healthcare
• SHARE is intended to be a healthcare‐biomedical research
enriched data dictionary built on the principles of
Computable Semantic Interoperability (CSI)
• It enables data reuse and data exchange that can be
interpreted between systems
• Supports
– Common information model (initially BRIDG)
– Strong data typing (ISO 21090)
– Common terminologies/value sets (CDISC, HL7, SNOMED, ICD, etc.)
– Processes supporting exchange of information
Aims of SHARE
SHARE
W. Kuchinke
CDISC-NCI partnership
•NCI has hosted the CDISC terminology through its
Enterprise Vocabulary Services (EVS) since early
2003
•NCI is migrating to new tools for semantic
management including a metadata repository (MDR)
•NCI has offered to include all CDISC requirements
for SHARE in its repository development process
–Support for tools that use SHARE that will be customizable,
global, and cover all therapeutic areas
Terminology
• Between 1 January and 31 March 2010, 46 terminology
requests were submitted through the Terminology
Request Page. The requests have been assessed,
addressed and answered
• New terms from CDISC Package 4 have been reviewed
by the terminology group, and have been updated
• These terms are now available for use in NCI EVS (April
2010)
• Links to three sets of terminology: usual set of
terminology for SDTM, link to a separate spreadsheet of
controlled terminology for ADaM and separate link to
CDASH terminology
W. Kuchinke
Terminology
• Example:
– 1200 terms for pilot from SEND (animal data)
– Position code list (vital signs)  harmonized
with HL7
• Sitting, standing, supine,…
• SDTMIG 3.1.2 links to terminology
– Interventions, events, findings,…
• Using SDTM to map Alzheimer data
• PKD foundation (kidney disease data)
W. Kuchinke
Terminology
• Example:
– 1200 terms for pilot from SEND (animal data)
– Position code list (vital signs)  harmonized
with HL7
• Sitting, standing, supine,…
• SDTMIG 3.1.2 links to terminology
– Interventions, events, findings,…
• Using SDTM to map Alzheimer data
• PKD foundation (kidney disease data)
W. Kuchinke
PRM
• Protocol Representation Model Version 1.0 final version is available
• Focus on the characteristics of a study and the definition and
association of activities within the protocols (e.g. "arms" and
"epochs“)
• Identifies, defines, and describes a set of over 100 common protocol
elements
• Includes the definitions of the roles that participate in those activities,
and protocol content including Study Design, Eligibility Criteria, and
the requirements from the ClinicalTrials.gov and World Health
Organization (WHO) registries
• PRM V1.0 is based on the BRIDG Release 3.0 Protocol Represen-
tation sub-domain. It includes all classes in the BRIDG Protocol
Representation sub-domain plus some classes from other BRIDG sub-
domains
Protocol Representation Model
PRM
• The PRM elements were developed so that protocol
information could be reused and repurposed across multiple
documents, databases, and systems
• PRM is not a specific protocol template
• Use of the PRM common elements enables and facilitates
information reuse without constraining the design of the study
or the style of the document
• PRM is now embedded within the BRIDG model, and can be
considered a subset of the BRIDG model
Uses
PRM
• Clinical Trial / Study Registry: elements related to the
background information of a study, based on the
requirements from WHO and Clintrials.gov.
– Examples: Study Type, Registration ID, Sponsors, and Date of first enrollment.
• Eligibility: elements related to eligibility criteria
– Examples: minimum age, maximum age, and subject, ethnicity.
• Study Design Part 1: Elements related to a study’s
experimental design
– Examples: minimum age, maximum age, and subject, ethnicity.
• Study Design Part 2: Elements related to a study’s Schedule
of Events and Activities
Four major components (four major areas of a protocol)
PRM
• The CDISC Study Data Tabulation Model (SDTM) includes
datasets that describe aspects of study plans that are part of
the protocol
• These datasets, called the Trial Design Model (TDM) were
used as a source of elements for the PRM and BRIDG
• Elements from the vocabulary for the Trial Summary SDTM
dataset were referenced in the Clinical Trial Registry portion
of the PRM
The PRM’s relationship to SDTM
PRM
W. Kuchinke
• A common structure for protocols
• Domain Analysis Model
• Contains the definition of objects (classes, attributes,
relationships)  UML Model (class diagram)
• Complete PRM  Excel file and EA file (enterprise
architect)
Class diagram
PRM
W. Kuchinke
• PRM is now embedded within the BRIDG model and can
be considered a subset of BRIDG
• The BRIDG model was transformed by focusing specifically
on incorporating elements from the PR Elements
Spreadsheet and representing them in the BRIDG
• As of 2009, most of the elements of the PR Elements
Spreadsheet with their attributes and appropriate
relationships have been represented in BRIDG
The PRM’s relationship to BRIDG
PRM
W. Kuchinke
Protocol Representation Model in UML
The Complete Protocol Representation Model in UML
Sample view of how the PRM is actually a subset of the BRIDG model
W. Kuchinke
Adverse Event Sub-Domain: AdverseEvent
The Complete Protocol Representation Model in UML
Study Lifecycle and the Temporal Grouping of Activities into “Pillars”
• Study activities can be defined once and referenced in many different
studies to save the time and effort of re-entering data
• Make semantic connections between an activity being used in two
different studies or at two different points in the same study
• This notion of activities being defined once and referenced in many
studies is the core idea of the DefinedActivity class and its subclasses
• These are reusable concepts that essentially form a global library of
activities that can be referenced in studies
• This part of the model is what the BRIDG SCC calls the “Defined Pillar”
W. Kuchinke
• CDISC SDTM (partly)
• CDISC ODM Study Design Extension
• HL7 Clinical Trial Registration message
• HL7 Study Design message
• caBIG PSC
– Scheduling system, implementation of PRM epochs, segments, activities,…)
– XML export/import, but: no periods in PRM (ODM), time duration: smallest unit is a day
– ODM for PSC import, 1 segment = 1 period, add scheduling activities to each segment
• IHE - Retrieve Protocol for Execution
– mechanism for an Electronic Health Record (EHR) to retrieve a complex set of clinical
research instructions (Protocol Definition) from an Electronic Data Capture (EDC) system
to execute within the EHR.
Implementations of the model
PRM
W. Kuchinke
BRIDG
• BRIDG R3.0.1 CDISC ISO JIC Review period
• Release 3.0.1 is being balloted through the ISO Joint
Initiative Council (JIC) process
• Includes HL7 and ISO ballots as well as another CDISC review and
comment cycle
• BRIDG as a global standard
Status
BRIDG
W. Kuchinke
• The BRIDG Model is an instance of a construct referred to as
Domain Analysis Model (DAM) or “problem space model.”
• The term “analysis” refers to the fact that the model is
specifically constructed to be implementation-independent
• The semantics of the model are restricted to those that
characterize the “problem domain” as described by domain
experts
• In particular, a DAM specifically excludes semantics that are
introduced based on a particular “solution space” that can be
built to solve the stated problem
Definition of BRIDG Model Domain of Interest
BRIDG
W. Kuchinke
• A dynamic component contains the Storyboards, Activity
Diagrams, State Diagrams, Sequence Diagrams, etc. and
defines the various processes and dynamic behaviour of the
domain
• A static component contains the Class Diagrams and
Instance Diagrams and describes the concepts, attributes,
and relationships of the static constructs which collectively
define a domain-of-interest (e.g. data, information, roles, etc.)
Representing static and dynamic content in the BRIDG Model
BRIDG
W. Kuchinke
• 3 layers
– Domain-friendly business model
– Domain analysis model in OWL
– RIM-based model (mapping mode – HL7)
• e.g.: AE sub-domain, class: study subject / investigational subject
BRIDG overview
BRIDG
W. Kuchinke
BRIDG: BRIDG Release 3.0+ approach
• A Domain Analysis Model (DAM) is a conceptual model
used to depict the behavioural and static semantics of the
domain of interest.
• A DAM provides an opportunity for subject matter experts
within a particular domain to integrate and harmonize their
perspectives regarding the use cases, activities, and
information needs
• A DAM is particularly useful when used in a domain with
broad interests and a diverse population of experts
BRIDG Project Domain Analysis Modeling
BRIDG
From: C Cain. CDISC BRIDG Training Nov. 2009
• StudyDocument
• Study
• Amendment
• StudyEvent
• Arm
• SupplementalMaterial
• StudyObligation
• Patient
• Person
• DesignCharacteristics
• Outcome
• StudyObjective
• ProtocolReview
• PlannedIntervention
BRIDG Model Major Classes, examples
BRIDG
CTRR HL7 RIM Specification → graphic view
BRIDG
From: C Cain. CDISC BRIDG Training, Nov. 2009
DocumentEvent
ClinicalTrialIntent
StudyOverall
Status
DocumentEvent
ClinicalTrialIntent
Subject
• The Protocol Representation sub-domain is intended for
involvement in the planning and design of a research
protocol
– The majority of business requirements comes from clinical trial
protocols
• Focus on the characteristics of a study and the definition
and association of activities within the protocols
• Including "arms" and "epochs"
• It also includes the definitions of the roles participating in
those activities
Protocol representation sub-domain model
BRIDG
W. Kuchinke
BRIDG: relationship Common Sub-domain Document and Study Protocol Document
PR-SD
Study protocol
document
• Separation of domain-friendly UML-based model from a new, fully
specified RIM-based model
• Divide UML model into topical sub-domains:
– Common, Protocol Representation, Study Conduct, Adverse Event, Regulatory
• Improved UML model:
– Update or simplify parts of model for clarity
– Add tags to UML model elements to indicate source model element mappings
– Clean up diagrams – business rules become constraints, better association labels, etc.
Approach for Release 3.0
BRIDG
W. Kuchinke
• The three layer architecture includes the concept of independently developed
subdomain specific business models developed with Enterprise Architect (EA)
modeling tool as separate EA files for each sub-domain
• The sub-domains are harmonized with BRIDG to form a single comprehensive
enterprise view of the domain of clinical and pre-clinical protocol-driven research and its
associated regulatory artifacts
• The enterprise view is transformed into an OWL-DL expression that is used to facilitate
semantic validation of the UML expression and to enable semantic reasoning
• Layer three of the BRIDG architecture is a re-expression of the BRIDG semantics using
the Health Level Seven (HL7) Reference Information Model (RIM)
• This RIM-based BRIDG model is built using HL7’s proprietary notation
• It forms a linkage between semantics represented in the BRIDG enterprise domain
analysis static model and HL7 interoperability specifications (messages, documents, and
services)
Three layer architecture BRIDG
BRIDG
W. Kuchinke
CTRR Activity Diagram: Clinical Trial Registration
BRIDG, example CT registration
From: C Cain. CDISC BRIDG Training Nov. 2009
Mapping of BRIDG to HL7 RIM
BRIDG
From: C Cain. CDISC BRIDG Training Nov. 2009
CTRR HL7 RIM Specification
BRIDG
From: C Cain. CDISC BRIDG Training, Nov. 2009
subject
Relationship: Protocol Representation Sub-Domain
Study
• During the CDISC SHARE pilot, BRIDG was used to organize and define
data elements from several sources
• The BRIDG mapping helps answer questions about the variables
• BRIDG also helps with understanding relationships between variables
BRIDG and CDISC SHARE
BRIDG
W. Kuchinke
• This specification is a style guide for development of well-formed
Domain Analysis Static Models using the Unified Modeling Language
(UML) as implemented by the Enterprise Architect (EA)
• This specification was developed specifically for the Biomedical
Research Integrated Domain Group (BRIDG) project
• The BRIDG model is an instance of a Domain Analysis Model (DAM)
– A DAM is a conceptual model used to depict the behavioral and static
semantics of a domain of interest
– A DAM is an unambiguous expression of semantics
BRIDG DOMAIN ANALYSIS STATIC MODEL STYLE GUIDE
RELEASE 002, JANUARY 29, 2010
BRIDG
W. Kuchinke
• A domain analysis model is used as reference for the development of
information system interoperability specifications such as messages,
documents, and services as well as design specifications of information
system components such as databases, system objects, and application
logic
• The DAM is a source of requirement specifications and is the primary
artifact from which platform independent information system design
specifications are derived
• The preferred language of a domain analysis model is UML
• The static portion of a UML domain analysis model, in particular the class
diagram
• It sets forth principles, guidelines, and rules for the creation of well-formed
static models and static model diagrams
Domain Analysis Model (DAM)
BRIDG
Static Model Class Diagram (class, classifier,
relationship,…)
• Guidance to developers of domain analysis models which contribute to
and are harmonized with the BRIDG Static Model
• Guidance to the BRIDG Semantic Coordination Committee (SCC) for use
in developing the BRIDG Static Model
• Serve as a set of rules by which the BRIDG and contributing sub-domain
models can be assessed for well-formness
• Motivation for this specification emerged from a decision made by the
BRIDG project to adopt a three-layer architecture for the BRIDG model
Purpose of the BRIDG Domain Analysis Model
BRIDG
W. Kuchinke
• This document provides an overview of the artifacts provided with the BRIDG model that
describe how the semantics of BRIDG can be expressed in terms of the HL7 v3
Reference Information Model
• It includes a listing of artifacts, a short explanation of how to interpret these artifacts
• The BRIDG model is a domain‐friendly information model reflecting the content of
clinical trials and related areas
• HL7 would refer to it as a Domain Analysis Model (DAM)
• Mapping exists of all the classes, attributes and associations from BRIDG using HL7’s
RIM
• This mapping is not intended to produce implementable HL7 artifacts
BRIDG RIM Representation
BRIDG
W. Kuchinke
• Though the BRIDG RIM mapping models are not intended for use as
design models, it is completely possible to create HL7 v3 implementation
models that realize BRIDG semantics
• The availability of mappings from BRIDG into RIM‐based models eases
the process of developing or adapting standards to be “BRIDG compliant”
Use of the BRIDG RIM mappings
BRIDG
W. Kuchinke
• There is not a one‐to‐one mapping between each attribute, association or
class in the BRIDG and a corresponding attribute, association or class in
the RIM representation
• Often a single class in BRIDG may require 20 or 30 RIM classes with
various associations in order to represent the attributes in a single BRIDG
class
• In other cases, multiple distinct BRIDG classes may be represented within
a single RIM model class
• The intention is to ensure that the RIM representation is capable of
expressing the same semantics and variations as would be possible with
the BRIDG UML model
No direct alignment
BRIDG
• This view provides a rendered HTML representation of each of the models
• It lists all of the tables and for each table provides a listing of the attributes
and outbound associations
• Descriptive elements that are not present in the graphical view
• Table views are provided for each of the “source” models as well as auto‐
generated “serializations” of the source models, one for each model entry
point
Table View
BRIDG
• These files are a rendering of the HL7‐style model diagrams as
constructed in Visio
• Exposes the classes, attributes and associations used as well as their
relationship to the HL7 RIM
Graphical View
BRIDG
W. Kuchinke
Example - Study subject: graphic view
W. Kuchinke From CDISC.com
Research
Subject
Example - Study site: graphic view
From CDISC.com
Consequences for developing the Clinical Research
Information Model (CRIM) for the Learning Health
System of the TRANSFoRm project
TRANSFoRm project: Translational research
and patient safety in Europe
• TRANSFoRm project developed technology that
facilitates a Learning Health System (LHS)
• Building on existing work at international level in
clinical trial information models (BRIDG and
PCROM), service-based approaches to semantic
interoperability and data standards (ISO11179 and
controlled vocabulary), data discovery, machine
learning and electronic health records based on
open standards (openEHR)
• Interaction with individual eHR systems as well as
operation within the patient consultation provides
both diagnostic support and support for the
identification and follow up of subjects for research
TRANSFoRm project: Translational research
and patient safety in Europe
• During Randomised Controlled Trials, researchers are able to
manage the whole RCT lifecycle via electronic health record
systems of general practitioners
– This includes feasibility and recruitment, including
consultation, recruitment on incident criteria, live flagging
of follow up requirements, semantically integrated
electronic case report forms deployed within the EHR
system and smart-phone and web-captured patient
related outcome measures
• Data provenance and data privacy are handled by the
TRANSFoRm system
• For knowledge translation a prototype system to interact
with the EHR system during the consultation between GP and
patient was developed
TRANSFoRm project: Translational research
and patient safety in Europe
• Requirements for interoperability, semantically aware,
dynamic interfaces and a rich ontology are common to all
elements of research and knowledge translation
• TRANSFoRm supports clinical studies with potential patient
safety value and directly support the use of evidence for
diagnosis
• The three clinical use cases are representative of the two
types of translational research
– genotype=phenotype studies and RCTs and one form of
knowledge translation by diagnostic decision support
• The clinical use cases were used to generate highly detailed
user requirements specifications in legal, privacy and data
security, and regarding decision support rules
• Based on the detailed requirements information models and
data standards for clinical concepts were developed
How to develop a suitable information model
• Use of activity models and use cases
• Search for a suitable information model consisting of
objects and/or classes and their associations
• The purpose of the resulting model
– Act as CRIM that specifies the necessary information
objects, their relationships and associated activities
– required to fully support the development of
TRANSFoRm tools for the Learning Health System
• All activity objects of the workflows were defined and
characterized according to their data requirements and
information needs and mapped to the concepts of
established information models
– PCROM
– BRIDG
– SDM
– CTOM
– OpenEHR
– HL7 RM
Result of the evaluation of the information
objects required by our use cases
• The best mapping results were achieved with PCROM and
it was decided to use PCROM as basis for the
development of CRIM
• Comparison of PCROM to BRIDG found a significant
overlap of concepts but also several areas important to
research that were either not yet represented or
represented quite differently in BRIDG
• The comparison between PCROM and BRIDG showed that
PCROM is an easier representation of RCT than BRIDG
and can easier support the interoperability needs arising
from the development of electronic clinical trials systems
• Thus the CRIM we developed will be superior for
representing information objects in the Leraning Health
System
Domain and information objects identified in two clinical use case workflows and their
relation to PCROM and BRIDG (part of the full table)
Treatment of information objects during
model building
• Class/Domain Objects were mapped to the
corresponding information objects in PCROM and
BRIDG
• Objects that could not be mapped are classified as
belonging to the data model or being a process
activity
– These objects were not considered for the
information model but were relevant for the
data model of TRANSFoRm
• All objects that were used for evaluation of the
model
W. Kuchinke
Information objects related to BRIDG that
were considered for the CRIM
• DefinedAdverseEvent,
AdverseEvent,
• (AdverseEventActionTakenRelations
hip,
• AdverseEventOutcomeAssessment,
• AdverseEventOutcomeResult,
• AdverseEventSeriousness)
• StudyActivity (DefinedActivity)
• Document (DocumentAuthor)
• HealthCareProvider
• DefinedEligibilityCriterion,
• DefinedInclusionCriterion,
• DefinedExclusionCriterion
• StudySubject, StudyProtocol (not
directly displayed)
• StudyAgent (Product, Drug)
• StudySubject (as result)
• RandomizationBookEntry
• DefinedNotification,
PlannedNotification,
• NotificationReceiver
• StudyObjective
• DefinedObservation result
• DefinedObservation
• DefinedEligibilityCriterion,
• DefinedInclusionCriterion,
• DefinedExclusionCriterion
• StudySubject, StudyProtocol (not
directly displayed)
• Subject
• Activity
• QualifiedPerson, ResearchStaff,
• ResearchOrganization
• DefinedObservation result
W. Kuchinke
Reference for CRIM
• Kuchinke W, Karakoyun T, Ohmann C, Arvanitis TN, Taweel A, Delaney BC,
Speedie SM. Extension of the primary care research object model (PCROM)
as clinical research information model (CRIM) for the "learning healthcare
system". BMC Med Inform Decis Mak. 2014 Dec 18;14:118
• doi: 10.1186/s12911-014-0118-2
• PMID: 25519481; PMCID: PMC4276023
W. Kuchinke
Creation of the Information model for clinical
research (CRIM)
• Workflow descriptions and data objects of two clinical use
cases (Gastro-Oesophageal Reflux Disease and Type 2
Diabetes) were described in UML activity diagrams
• The components of activity diagrams were mapped to
information objects of PCROM (Primary Care Research Object
Model) and BRIDG (Biomedical Research Integrated Domain
Group)
• Evaluation of the models
• The class diagram of PCROM was adapted to comply with
workflow descriptions more smoothly
• PCROM is a primary care information model already used for
clinical trials and therefore suitable for the LHS
• It can act as an information model for TRANSFoRm
• Adaption of PCROM by adding 14 new information object types
from BRIDG, two extensions of existing objects and the
introduction of two new high-ranking concepts (CARE area and
ENTRY area)
The Clinical Resarch Information Model - CRIM
From: Kuchinke et.al.: Extension of the primary care research object model
W. Kuchinke
Contact
Presentation was presented partly at the: ePCRN – TRANSFoRm Meeting, 13 May 2010,
Minneapolis, USA. This presentation contains additional material
More information:
www.learninghealthcareproject.org/publication/5/104/the-transform-project
Wolfgang Kuchinke
UDUS, Duesseldorf, Germany
wolfgang.kuchinke@uni-duesseldorf.de
wokuchinke@outlook.de

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Standards for clinical research data - steps to an information model (CRIM).

  • 1. Wolfgang Kuchinke TRANSFoRm Project Meeting Standards for clinical research data: Introduction to CDISC – CDASH, PRM and BRIDG
  • 2. Introduction • The standards CDISC CDASH, SHARE, PRM and BRIDG are described and introduced in terms of their abilities to contribute to the development of a comprehensive information model for clinical reserach (CRIM) • In particular, the new clinical research information model should allow the integrative usage of medical care data together with clinical trial data • The model should also support processes of the Learning Health System
  • 3. The standards that were evaluated
  • 5. ● Basic standard for the collection of clinical trial data ● Identifies the basic data collection fields needed from a clinical, scientific and regulatory perspective to enable more efficient data collection at the Investigator sites ● Sponsors will need to determine what additional data fields will need to be added ● Therapeutic area (TA) specific data fields Clinical Data Acquisition Standards Harmonization CDASH
  • 6. • CDASH version 1.1 and CDASHUG V 1.0 • Public Review and Comment Period, comments until 14 May 2010 •Set of "content standards" (element name, definition, and related metadata) for a basic set of data collection fields •16 CRF content ‘safety data/domains’ that are common to all therapeutic areas (Adverse Events, Concomitant Medications, Comments, Demographics, Exposure, Inclusion and Exclusion Criteria, Lab, Medical History, …) •New version includes: conformance rules, explicit question text, more information about collecting relative timing variables, BRIDG annotations, as well as a few new collection fields Status CDASH
  • 7. • Purposes: CDASH (data collection) – SDTM (submission) • Core description (three degrees: highly recommended, recommended, optional) • CDISC controlled term  link with spreadsheet • CDASH / SDTM annotated CRF • Best practice recommendations • CDISC integration into the Oracle Clinical / Remote Data Capture system (OC/RDC), SDTM conversion •CDASH/SDTM compliant eCRF •Metadata library within OC • Creation of annotated CRF library CDASH
  • 8. • SDTM and the SDTMIG provide a standard for the submission of data concerning data collected during clinical trials • CDASH data collection fields (or variables) can be mapped to the SDTM structure •When the data are identical between the two standards, the SDTMIG variable names are presented in the CDASH domain tables • Possible is the definition of own CDASH user domains (see CDASH user guide) or customization of the 16 CDASH domains CDASH: Alignment with other standards The Study Data Tabulation Model (SDTM) W. Kuchinke
  • 9. • Adverse Event – AE (Events) • Comments – CO (Special Purpose) • Prior and Concomitant Medications – CM (Interventions) • Demographics – DM (Special Purpose) • Disposition – DS (Events) • Drug Accountability – DA (Findings) CDASH CDASH Domain Tables 1 W. Kuchinke
  • 10. • Exposure – EX (Interventions) • Medical History – MH (Events) • Physical Examination – PE (Findings) • Protocol Deviations – DV (Events) • Subject Characteristics – SC (Findings) • Substance Use – SU (Interventions) • Vital Signs – VS (Findings) CDASH: CDASH Domain Tables 2
  • 11. • SDTM Variable Name: Lists the SDTM-based variable name defined in SDTMIG • BRIDG: This column contains the BRIDG Release 3.0 classification • Definition: Describes the purpose of the data collection field. The text may or may not mirror the text in the SDTMIG • Core: Contains CDASH core designations for basic data collection fields CDASH Table Headers
  • 12. CDASH Domain Tables Example: Exposure – EX (Interventions)
  • 13. CDASH Example: Best Practice Recommendations W. Kuchinke
  • 14. CDASH Examle for linked terminology: CDASH Terminology 5-3- 2010 W. Kuchinke
  • 15. SHARE
  • 16. What is CDISC SHARE? • A globally accessible electronic library built on a common information model • Enables precise and standardized data element definitions that can be used in studies and applications to improve biomedical research and it’s link with healthcare
  • 17. • SHARE is intended to be a healthcare‐biomedical research enriched data dictionary built on the principles of Computable Semantic Interoperability (CSI) • It enables data reuse and data exchange that can be interpreted between systems • Supports – Common information model (initially BRIDG) – Strong data typing (ISO 21090) – Common terminologies/value sets (CDISC, HL7, SNOMED, ICD, etc.) – Processes supporting exchange of information Aims of SHARE SHARE W. Kuchinke
  • 18. CDISC-NCI partnership •NCI has hosted the CDISC terminology through its Enterprise Vocabulary Services (EVS) since early 2003 •NCI is migrating to new tools for semantic management including a metadata repository (MDR) •NCI has offered to include all CDISC requirements for SHARE in its repository development process –Support for tools that use SHARE that will be customizable, global, and cover all therapeutic areas
  • 19. Terminology • Between 1 January and 31 March 2010, 46 terminology requests were submitted through the Terminology Request Page. The requests have been assessed, addressed and answered • New terms from CDISC Package 4 have been reviewed by the terminology group, and have been updated • These terms are now available for use in NCI EVS (April 2010) • Links to three sets of terminology: usual set of terminology for SDTM, link to a separate spreadsheet of controlled terminology for ADaM and separate link to CDASH terminology W. Kuchinke
  • 20. Terminology • Example: – 1200 terms for pilot from SEND (animal data) – Position code list (vital signs)  harmonized with HL7 • Sitting, standing, supine,… • SDTMIG 3.1.2 links to terminology – Interventions, events, findings,… • Using SDTM to map Alzheimer data • PKD foundation (kidney disease data) W. Kuchinke
  • 21. Terminology • Example: – 1200 terms for pilot from SEND (animal data) – Position code list (vital signs)  harmonized with HL7 • Sitting, standing, supine,… • SDTMIG 3.1.2 links to terminology – Interventions, events, findings,… • Using SDTM to map Alzheimer data • PKD foundation (kidney disease data) W. Kuchinke
  • 22. PRM
  • 23. • Protocol Representation Model Version 1.0 final version is available • Focus on the characteristics of a study and the definition and association of activities within the protocols (e.g. "arms" and "epochs“) • Identifies, defines, and describes a set of over 100 common protocol elements • Includes the definitions of the roles that participate in those activities, and protocol content including Study Design, Eligibility Criteria, and the requirements from the ClinicalTrials.gov and World Health Organization (WHO) registries • PRM V1.0 is based on the BRIDG Release 3.0 Protocol Represen- tation sub-domain. It includes all classes in the BRIDG Protocol Representation sub-domain plus some classes from other BRIDG sub- domains Protocol Representation Model PRM
  • 24. • The PRM elements were developed so that protocol information could be reused and repurposed across multiple documents, databases, and systems • PRM is not a specific protocol template • Use of the PRM common elements enables and facilitates information reuse without constraining the design of the study or the style of the document • PRM is now embedded within the BRIDG model, and can be considered a subset of the BRIDG model Uses PRM
  • 25. • Clinical Trial / Study Registry: elements related to the background information of a study, based on the requirements from WHO and Clintrials.gov. – Examples: Study Type, Registration ID, Sponsors, and Date of first enrollment. • Eligibility: elements related to eligibility criteria – Examples: minimum age, maximum age, and subject, ethnicity. • Study Design Part 1: Elements related to a study’s experimental design – Examples: minimum age, maximum age, and subject, ethnicity. • Study Design Part 2: Elements related to a study’s Schedule of Events and Activities Four major components (four major areas of a protocol) PRM
  • 26. • The CDISC Study Data Tabulation Model (SDTM) includes datasets that describe aspects of study plans that are part of the protocol • These datasets, called the Trial Design Model (TDM) were used as a source of elements for the PRM and BRIDG • Elements from the vocabulary for the Trial Summary SDTM dataset were referenced in the Clinical Trial Registry portion of the PRM The PRM’s relationship to SDTM PRM W. Kuchinke
  • 27. • A common structure for protocols • Domain Analysis Model • Contains the definition of objects (classes, attributes, relationships)  UML Model (class diagram) • Complete PRM  Excel file and EA file (enterprise architect) Class diagram PRM W. Kuchinke
  • 28. • PRM is now embedded within the BRIDG model and can be considered a subset of BRIDG • The BRIDG model was transformed by focusing specifically on incorporating elements from the PR Elements Spreadsheet and representing them in the BRIDG • As of 2009, most of the elements of the PR Elements Spreadsheet with their attributes and appropriate relationships have been represented in BRIDG The PRM’s relationship to BRIDG PRM W. Kuchinke
  • 30. The Complete Protocol Representation Model in UML Sample view of how the PRM is actually a subset of the BRIDG model W. Kuchinke
  • 32. The Complete Protocol Representation Model in UML Study Lifecycle and the Temporal Grouping of Activities into “Pillars” • Study activities can be defined once and referenced in many different studies to save the time and effort of re-entering data • Make semantic connections between an activity being used in two different studies or at two different points in the same study • This notion of activities being defined once and referenced in many studies is the core idea of the DefinedActivity class and its subclasses • These are reusable concepts that essentially form a global library of activities that can be referenced in studies • This part of the model is what the BRIDG SCC calls the “Defined Pillar” W. Kuchinke
  • 33. • CDISC SDTM (partly) • CDISC ODM Study Design Extension • HL7 Clinical Trial Registration message • HL7 Study Design message • caBIG PSC – Scheduling system, implementation of PRM epochs, segments, activities,…) – XML export/import, but: no periods in PRM (ODM), time duration: smallest unit is a day – ODM for PSC import, 1 segment = 1 period, add scheduling activities to each segment • IHE - Retrieve Protocol for Execution – mechanism for an Electronic Health Record (EHR) to retrieve a complex set of clinical research instructions (Protocol Definition) from an Electronic Data Capture (EDC) system to execute within the EHR. Implementations of the model PRM W. Kuchinke
  • 34. BRIDG
  • 35. • BRIDG R3.0.1 CDISC ISO JIC Review period • Release 3.0.1 is being balloted through the ISO Joint Initiative Council (JIC) process • Includes HL7 and ISO ballots as well as another CDISC review and comment cycle • BRIDG as a global standard Status BRIDG W. Kuchinke
  • 36. • The BRIDG Model is an instance of a construct referred to as Domain Analysis Model (DAM) or “problem space model.” • The term “analysis” refers to the fact that the model is specifically constructed to be implementation-independent • The semantics of the model are restricted to those that characterize the “problem domain” as described by domain experts • In particular, a DAM specifically excludes semantics that are introduced based on a particular “solution space” that can be built to solve the stated problem Definition of BRIDG Model Domain of Interest BRIDG W. Kuchinke
  • 37. • A dynamic component contains the Storyboards, Activity Diagrams, State Diagrams, Sequence Diagrams, etc. and defines the various processes and dynamic behaviour of the domain • A static component contains the Class Diagrams and Instance Diagrams and describes the concepts, attributes, and relationships of the static constructs which collectively define a domain-of-interest (e.g. data, information, roles, etc.) Representing static and dynamic content in the BRIDG Model BRIDG W. Kuchinke
  • 38. • 3 layers – Domain-friendly business model – Domain analysis model in OWL – RIM-based model (mapping mode – HL7) • e.g.: AE sub-domain, class: study subject / investigational subject BRIDG overview BRIDG W. Kuchinke
  • 39. BRIDG: BRIDG Release 3.0+ approach
  • 40. • A Domain Analysis Model (DAM) is a conceptual model used to depict the behavioural and static semantics of the domain of interest. • A DAM provides an opportunity for subject matter experts within a particular domain to integrate and harmonize their perspectives regarding the use cases, activities, and information needs • A DAM is particularly useful when used in a domain with broad interests and a diverse population of experts BRIDG Project Domain Analysis Modeling BRIDG From: C Cain. CDISC BRIDG Training Nov. 2009
  • 41. • StudyDocument • Study • Amendment • StudyEvent • Arm • SupplementalMaterial • StudyObligation • Patient • Person • DesignCharacteristics • Outcome • StudyObjective • ProtocolReview • PlannedIntervention BRIDG Model Major Classes, examples BRIDG
  • 42. CTRR HL7 RIM Specification → graphic view BRIDG From: C Cain. CDISC BRIDG Training, Nov. 2009 DocumentEvent ClinicalTrialIntent StudyOverall Status DocumentEvent ClinicalTrialIntent Subject
  • 43. • The Protocol Representation sub-domain is intended for involvement in the planning and design of a research protocol – The majority of business requirements comes from clinical trial protocols • Focus on the characteristics of a study and the definition and association of activities within the protocols • Including "arms" and "epochs" • It also includes the definitions of the roles participating in those activities Protocol representation sub-domain model BRIDG W. Kuchinke
  • 44. BRIDG: relationship Common Sub-domain Document and Study Protocol Document PR-SD Study protocol document
  • 45. • Separation of domain-friendly UML-based model from a new, fully specified RIM-based model • Divide UML model into topical sub-domains: – Common, Protocol Representation, Study Conduct, Adverse Event, Regulatory • Improved UML model: – Update or simplify parts of model for clarity – Add tags to UML model elements to indicate source model element mappings – Clean up diagrams – business rules become constraints, better association labels, etc. Approach for Release 3.0 BRIDG W. Kuchinke
  • 46. • The three layer architecture includes the concept of independently developed subdomain specific business models developed with Enterprise Architect (EA) modeling tool as separate EA files for each sub-domain • The sub-domains are harmonized with BRIDG to form a single comprehensive enterprise view of the domain of clinical and pre-clinical protocol-driven research and its associated regulatory artifacts • The enterprise view is transformed into an OWL-DL expression that is used to facilitate semantic validation of the UML expression and to enable semantic reasoning • Layer three of the BRIDG architecture is a re-expression of the BRIDG semantics using the Health Level Seven (HL7) Reference Information Model (RIM) • This RIM-based BRIDG model is built using HL7’s proprietary notation • It forms a linkage between semantics represented in the BRIDG enterprise domain analysis static model and HL7 interoperability specifications (messages, documents, and services) Three layer architecture BRIDG BRIDG W. Kuchinke
  • 47. CTRR Activity Diagram: Clinical Trial Registration BRIDG, example CT registration From: C Cain. CDISC BRIDG Training Nov. 2009
  • 48. Mapping of BRIDG to HL7 RIM BRIDG From: C Cain. CDISC BRIDG Training Nov. 2009
  • 49. CTRR HL7 RIM Specification BRIDG From: C Cain. CDISC BRIDG Training, Nov. 2009 subject
  • 51. • During the CDISC SHARE pilot, BRIDG was used to organize and define data elements from several sources • The BRIDG mapping helps answer questions about the variables • BRIDG also helps with understanding relationships between variables BRIDG and CDISC SHARE BRIDG W. Kuchinke
  • 52. • This specification is a style guide for development of well-formed Domain Analysis Static Models using the Unified Modeling Language (UML) as implemented by the Enterprise Architect (EA) • This specification was developed specifically for the Biomedical Research Integrated Domain Group (BRIDG) project • The BRIDG model is an instance of a Domain Analysis Model (DAM) – A DAM is a conceptual model used to depict the behavioral and static semantics of a domain of interest – A DAM is an unambiguous expression of semantics BRIDG DOMAIN ANALYSIS STATIC MODEL STYLE GUIDE RELEASE 002, JANUARY 29, 2010 BRIDG W. Kuchinke
  • 53. • A domain analysis model is used as reference for the development of information system interoperability specifications such as messages, documents, and services as well as design specifications of information system components such as databases, system objects, and application logic • The DAM is a source of requirement specifications and is the primary artifact from which platform independent information system design specifications are derived • The preferred language of a domain analysis model is UML • The static portion of a UML domain analysis model, in particular the class diagram • It sets forth principles, guidelines, and rules for the creation of well-formed static models and static model diagrams Domain Analysis Model (DAM) BRIDG
  • 54. Static Model Class Diagram (class, classifier, relationship,…)
  • 55. • Guidance to developers of domain analysis models which contribute to and are harmonized with the BRIDG Static Model • Guidance to the BRIDG Semantic Coordination Committee (SCC) for use in developing the BRIDG Static Model • Serve as a set of rules by which the BRIDG and contributing sub-domain models can be assessed for well-formness • Motivation for this specification emerged from a decision made by the BRIDG project to adopt a three-layer architecture for the BRIDG model Purpose of the BRIDG Domain Analysis Model BRIDG W. Kuchinke
  • 56. • This document provides an overview of the artifacts provided with the BRIDG model that describe how the semantics of BRIDG can be expressed in terms of the HL7 v3 Reference Information Model • It includes a listing of artifacts, a short explanation of how to interpret these artifacts • The BRIDG model is a domain‐friendly information model reflecting the content of clinical trials and related areas • HL7 would refer to it as a Domain Analysis Model (DAM) • Mapping exists of all the classes, attributes and associations from BRIDG using HL7’s RIM • This mapping is not intended to produce implementable HL7 artifacts BRIDG RIM Representation BRIDG W. Kuchinke
  • 57. • Though the BRIDG RIM mapping models are not intended for use as design models, it is completely possible to create HL7 v3 implementation models that realize BRIDG semantics • The availability of mappings from BRIDG into RIM‐based models eases the process of developing or adapting standards to be “BRIDG compliant” Use of the BRIDG RIM mappings BRIDG W. Kuchinke
  • 58. • There is not a one‐to‐one mapping between each attribute, association or class in the BRIDG and a corresponding attribute, association or class in the RIM representation • Often a single class in BRIDG may require 20 or 30 RIM classes with various associations in order to represent the attributes in a single BRIDG class • In other cases, multiple distinct BRIDG classes may be represented within a single RIM model class • The intention is to ensure that the RIM representation is capable of expressing the same semantics and variations as would be possible with the BRIDG UML model No direct alignment BRIDG
  • 59. • This view provides a rendered HTML representation of each of the models • It lists all of the tables and for each table provides a listing of the attributes and outbound associations • Descriptive elements that are not present in the graphical view • Table views are provided for each of the “source” models as well as auto‐ generated “serializations” of the source models, one for each model entry point Table View BRIDG
  • 60. • These files are a rendering of the HL7‐style model diagrams as constructed in Visio • Exposes the classes, attributes and associations used as well as their relationship to the HL7 RIM Graphical View BRIDG W. Kuchinke
  • 61. Example - Study subject: graphic view W. Kuchinke From CDISC.com Research Subject
  • 62. Example - Study site: graphic view From CDISC.com
  • 63. Consequences for developing the Clinical Research Information Model (CRIM) for the Learning Health System of the TRANSFoRm project
  • 64. TRANSFoRm project: Translational research and patient safety in Europe • TRANSFoRm project developed technology that facilitates a Learning Health System (LHS) • Building on existing work at international level in clinical trial information models (BRIDG and PCROM), service-based approaches to semantic interoperability and data standards (ISO11179 and controlled vocabulary), data discovery, machine learning and electronic health records based on open standards (openEHR) • Interaction with individual eHR systems as well as operation within the patient consultation provides both diagnostic support and support for the identification and follow up of subjects for research
  • 65. TRANSFoRm project: Translational research and patient safety in Europe • During Randomised Controlled Trials, researchers are able to manage the whole RCT lifecycle via electronic health record systems of general practitioners – This includes feasibility and recruitment, including consultation, recruitment on incident criteria, live flagging of follow up requirements, semantically integrated electronic case report forms deployed within the EHR system and smart-phone and web-captured patient related outcome measures • Data provenance and data privacy are handled by the TRANSFoRm system • For knowledge translation a prototype system to interact with the EHR system during the consultation between GP and patient was developed
  • 66. TRANSFoRm project: Translational research and patient safety in Europe • Requirements for interoperability, semantically aware, dynamic interfaces and a rich ontology are common to all elements of research and knowledge translation • TRANSFoRm supports clinical studies with potential patient safety value and directly support the use of evidence for diagnosis • The three clinical use cases are representative of the two types of translational research – genotype=phenotype studies and RCTs and one form of knowledge translation by diagnostic decision support • The clinical use cases were used to generate highly detailed user requirements specifications in legal, privacy and data security, and regarding decision support rules • Based on the detailed requirements information models and data standards for clinical concepts were developed
  • 67. How to develop a suitable information model • Use of activity models and use cases • Search for a suitable information model consisting of objects and/or classes and their associations • The purpose of the resulting model – Act as CRIM that specifies the necessary information objects, their relationships and associated activities – required to fully support the development of TRANSFoRm tools for the Learning Health System • All activity objects of the workflows were defined and characterized according to their data requirements and information needs and mapped to the concepts of established information models – PCROM – BRIDG – SDM – CTOM – OpenEHR – HL7 RM
  • 68. Result of the evaluation of the information objects required by our use cases • The best mapping results were achieved with PCROM and it was decided to use PCROM as basis for the development of CRIM • Comparison of PCROM to BRIDG found a significant overlap of concepts but also several areas important to research that were either not yet represented or represented quite differently in BRIDG • The comparison between PCROM and BRIDG showed that PCROM is an easier representation of RCT than BRIDG and can easier support the interoperability needs arising from the development of electronic clinical trials systems • Thus the CRIM we developed will be superior for representing information objects in the Leraning Health System
  • 69. Domain and information objects identified in two clinical use case workflows and their relation to PCROM and BRIDG (part of the full table)
  • 70. Treatment of information objects during model building • Class/Domain Objects were mapped to the corresponding information objects in PCROM and BRIDG • Objects that could not be mapped are classified as belonging to the data model or being a process activity – These objects were not considered for the information model but were relevant for the data model of TRANSFoRm • All objects that were used for evaluation of the model W. Kuchinke
  • 71. Information objects related to BRIDG that were considered for the CRIM • DefinedAdverseEvent, AdverseEvent, • (AdverseEventActionTakenRelations hip, • AdverseEventOutcomeAssessment, • AdverseEventOutcomeResult, • AdverseEventSeriousness) • StudyActivity (DefinedActivity) • Document (DocumentAuthor) • HealthCareProvider • DefinedEligibilityCriterion, • DefinedInclusionCriterion, • DefinedExclusionCriterion • StudySubject, StudyProtocol (not directly displayed) • StudyAgent (Product, Drug) • StudySubject (as result) • RandomizationBookEntry • DefinedNotification, PlannedNotification, • NotificationReceiver • StudyObjective • DefinedObservation result • DefinedObservation • DefinedEligibilityCriterion, • DefinedInclusionCriterion, • DefinedExclusionCriterion • StudySubject, StudyProtocol (not directly displayed) • Subject • Activity • QualifiedPerson, ResearchStaff, • ResearchOrganization • DefinedObservation result W. Kuchinke
  • 72. Reference for CRIM • Kuchinke W, Karakoyun T, Ohmann C, Arvanitis TN, Taweel A, Delaney BC, Speedie SM. Extension of the primary care research object model (PCROM) as clinical research information model (CRIM) for the "learning healthcare system". BMC Med Inform Decis Mak. 2014 Dec 18;14:118 • doi: 10.1186/s12911-014-0118-2 • PMID: 25519481; PMCID: PMC4276023 W. Kuchinke
  • 73. Creation of the Information model for clinical research (CRIM) • Workflow descriptions and data objects of two clinical use cases (Gastro-Oesophageal Reflux Disease and Type 2 Diabetes) were described in UML activity diagrams • The components of activity diagrams were mapped to information objects of PCROM (Primary Care Research Object Model) and BRIDG (Biomedical Research Integrated Domain Group) • Evaluation of the models • The class diagram of PCROM was adapted to comply with workflow descriptions more smoothly • PCROM is a primary care information model already used for clinical trials and therefore suitable for the LHS • It can act as an information model for TRANSFoRm • Adaption of PCROM by adding 14 new information object types from BRIDG, two extensions of existing objects and the introduction of two new high-ranking concepts (CARE area and ENTRY area)
  • 74. The Clinical Resarch Information Model - CRIM From: Kuchinke et.al.: Extension of the primary care research object model W. Kuchinke
  • 75. Contact Presentation was presented partly at the: ePCRN – TRANSFoRm Meeting, 13 May 2010, Minneapolis, USA. This presentation contains additional material More information: www.learninghealthcareproject.org/publication/5/104/the-transform-project Wolfgang Kuchinke UDUS, Duesseldorf, Germany wolfgang.kuchinke@uni-duesseldorf.de wokuchinke@outlook.de