BRIDG Basics 1. What is BRIDG? Biomedical Research Integrated Domain Group A formal model A...
-
Upload
jacob-archer -
Category
Documents
-
view
221 -
download
2
Transcript of BRIDG Basics 1. What is BRIDG? Biomedical Research Integrated Domain Group A formal model A...
BRIDG Basics
1
What is BRIDG?Biomedical Research Integrated Domain Group
• A formal model
• A communication bridge
• An open community of stakeholders
• The semantic foundation for application and message development
2
How did BRIDG get started? • Four important streams of development came together
– CDISC: In early 2004, CDISC started constructing a Domain Analysis Model to support harmonization of their standards for clinical research as well as with the Health Level Seven (HL7) healthcare standard.
– NCI: In late 2004, NCI's Cancer Biomedical Informatics Grid (caBIG™) initiative joined the CDISC BRIDG efforts to construct a structured protocol representation for its Clinical Trials Management Systems (CTMS) Workspace, in order to further interoperability among clinical trials research in cancer.
– HL7: In 2005, the BRIDG model was adopted by the HL7 Regulated Clinical Research Information Management (RCRIM) Technical Committee as the RCRIM Domain Analysis Model.
– FDA: In 2007, the US Food and Drug Administration included BRIDG in their 5 year IT Plan as a foundation for several projects.
3
BRIDG Scope
BRIDG Scope: Protocol-driven research and its associated regulatory artifacts,
i.e. the data, organization, resources, rules, and processes involved in the formal assessment of the utility, impact, or other pharmacological, physiological, or psychological effects of a drug, procedure, process, subject characteristic, biologic, cosmetic, food or device on a human, animal, or other subject or substance plus all associated regulatory artifacts required for or derived from this effort, including data specifically associated with post-marketing adverse event reporting.
4
BRIDG Governance
5
•BRIDG Board of Directors
•BRIDG Semantic Coordination Committee
Current Governance of the BRIDG Model BRIDG Board of Directors
• BRIDG Board of Directors– Representation from the current stakeholders– Helps to set priorities and identify resources
6
BRIDGBoard of Directors
NCI
Academia
Pharma Industry
CDISC
HL7FDA
Source: Doug Fridsma
7
BRIDG Board of Directors
7
Appointed Members
Charlie Mead NCIBron Kisler CDISCChuck Jaffe HL7Jay Levine FDA
At Large Members Term Expiration
Becky Kush* 2011John Speakman 2013Jack Jones 2011Cecil Lynch 2012AbdulMalik Shakir 2012Diane Wold 2013Sub Dubman 2013
* Chair
Current Organization of the BRIDG SCC
• Semantic Coordination Committee (SCC)– Responsible for ongoing model maintenance– Harmonizes subdomain projects into the main model
8
BRIDGSemantic Coordination Committee
caBIG HL7CDISC FDA
Source: Doug Fridsma
99
Semantic Coordination Committee (SCC)
Name Affiliation
Charlie Mead NCI / Booz & CompanySteve Sandberg NCI / ScenPro, Inc.Mike Woodcock NCI / Mayo ClinicSmita Hastak NCI / ScenPro, Inc.Wendy Ver Hoef NCI / ScenPro, Inc.Becky Angeles NCI / ScenPro, Inc.Julie Evans CDISCLloyd McKenzie NCI / Gordon Point Informatics
The BRIDG Model
10
Perspectives of BRIDG
11
Perspectives of BRIDG
• Recognize and support the different types of BRIDG users
• Each perspective is intended for a different audience
• Each perspective is a representation of the same semantics
12
BRIDG Canonical Perspective
• Comprehensive Domain Analysis Model (DAM)
• Intended for information analysts• Single UML model• Modeled and managed in Enterprise Architect
13
BRIDG Canonical PerspectiveModel of Subject
class BRIDG Domain Analysis Mo...
Common Sub-Domain::StudySubject{leaf}
+ confidentialityIndicator: BL+ paymentMethodCode: CD+ statusCode: CD+ statusDate: TS.DATETIME::Subject+ state: ST+ actualIndicator: BL
Common Sub-Domain::StudySubjectIdentifier
+ identifier: II+ typeCode: CD+ effectiveDateRange: IVL<TS.DATETIME>
Common Sub-Domain::Subject{root}
+ state: ST+ actualIndicator: BL
+identifying
0..*
identifies
{is identified by}
+identified
1
14
15
BRIDG Comprehensive View – Canonical Perspective
Protocol Representation
Adverse Event
Study Conduct
Common Regulatory
BRIDG SME Perspective
• Domain-friendly layer• Intended for the subject matter experts (also
called business users or domain experts)• Multiple UML models, one for each sub-
domain• Modeled and managed in Enterprise Architect• Automatically generated from Canonical
Perspective
16
BRIDG SME PerspectiveAdverse Event Sub-Domain Model of
Subject
17
class View AE: Adv erse Ev ...
Common Sub-Domain::Investigativ eSubject
{root}
+ state: ST
constraints{Is a Function Performed By Exclusive Or}
Common Sub-Domain::StudySubject
{leaf}
+ confidentialityIndicator: BL+ paymentMethodCode: CD+ statusCode: CD+ statusDate: TS.DATETIME::InvestigativeSubject+ state: ST
BRIDG HL7 Perspective
• RIM-based model• Intended for message developers• Modeled in HL7 proprietary modeling
methodology and developed in Visio• Single DMIM-like model• Maps to UML-based model• Manually generated from Canonical
Perspective
18
BRIDG HL7 PerspectiveModel of Subject
19
BRIDG Semantic Perspective
• Several ontological representations• OWL-DL format• Intended for semantic validation and
inferencing
20
BRIDG Semantic PerspectiveModel of Subject
21
class View AE: Adv erse Ev ...
Common Sub-Domain::Investigativ eSubject
{root}
+ state: ST
constraints{Is a Function Performed By Exclusive Or}
Common Sub-Domain::StudySubject
{leaf}
+ confidentialityIndicator: BL+ paymentMethodCode: CD+ statusCode: CD+ statusDate: TS.DATETIME::InvestigativeSubject+ state: ST
BRIDG as a global, public standard
• CDISC Review and Comment Process resulted in BRIDG as a CDISC standard in January 2010
• ISO Joint Initiative Council (JIC) Ballot Process – first round in May 2010 – BRIDG passed the ballot in both ISO and HL7 – next round starts in December 2010– ISO– HL7– CDISC
22
23
BRIDG Content – 1(starting with most recent release)
Release Project Stakeholder
R3.0.3 Clinical Data Acquisition Standards Harmonization (CDASH) V1.1
CDISC
Study Data Tabulation Model (SDTM) V3.1.2 CDISC
Integrated Case Safety Report (ICSR) R2 FDA
R3.0.2 caBIG® Central Clinical. Participant Registry (C3PR) v2.9 NCI
Cancer Adverse Event Reporting System (caAERS) v2.2 NCI
Patient Study Calendar (PSC) v2.6 NCI
LabViewer v2.2 NCI
R3.0.1 Clinical Trials Registration and Results HL7 RCRIM
R3.0 (Architecture Redesign only)
24
Release Project StakeholderR2.2 CDISC HL7 Message Study Design (partial) FDA
CDISC HL7 Message Study Participation FDAR2.1 Clinical Trial Registry (COPPA, ct.gov, WHO, PRV1.0) CDISC, NCI
Protocol Abstraction (COPPA – Correlations, Organizations, People and Protocol Abstraction)
NCI
R2.0 Adverse Events CDISC, NCI, NIH, US Federal Gov’t, FDA
Player / Scoper for Person and Org NCI, CDISCPatient Registry (C3PR) NCI
R1.1 Study Data Tabulation Model (SDTM) CDISCTrial Design Model CDISC
R1.0 Regulated Product Submission (RPS) FDA/HL7 RCRIM Patient Study Calendar (PSC) NCIClinical Trial Object Model (CTOM) NCIcaXchange/LabHub NCI/HL7RCRIM TC/CDISC
BRIDG Content - 2
A Bit More About the Canonical and SME Perspectives
25
Unified Modeling Language
• Used in the BRIDG model via a modeling tool called Enterprise Architect
• The industry-standard language for specifying, visualizing, constructing, and documenting the requirements of software systems
• The BRIDG model uses these UML diagrams: – Class diagrams– Instance diagrams– State transition diagrams
26
UML Class Diagrams
class – a concept of primary importance the domain-of-interest, depicted as a rectangle labeled with the concept’s name
attribute (including datatype specification) – a descriptive feature of a class, depicted as being contained within the class
relationship – one of several types of “lines” between classes
27
28
Class diagram examplecd BRIDG Release 1.0
Employee
::Person- name: string
Company
- name: string
Person
- name: string
1..*
works for / employs
1
class
attribute
relationship
multiplicity
data type
BRIDG Class: StudyProtocolVersion
29
BRIDG Class Definition: StudyProtocolVersion
30
Definition of designConfigurationCode attribute
31
Instance Diagrams
• “Instances” of class diagrams use sample data values to illustrate specific representational constructs
32
33
class Adv erse Ev ent Sub-Dom...
Adv erseEv ent{leaf}
+ gradeCode: CD+ severityCode: CD+ seriousnessCode: CD+ categoryCode: CD+ subcategoryCode: CD+ occurrencePatternCode: CD+ endRelativeToReferenceCode: CD+ unexpectedReasonCode: DSET<CD>+ expectedIndicator: BL+ hospitalizationRequiredIndicator: BL+ highlightedIndicator: BL+ duration: PQ.TIME+ onsetDate: TS.DATETIME+ resolutionDate: TS.DATETIME::PerformedObservationResult+ identifier: II+ typeCode: CD+ result: ANY+ resultCodeModifiedText: ST+ targetAnatomicSiteCode: CD+ confidentialityCode: CD+ uncertaintyCode: CD+ reportedDate: TS.DATETIME+ comment: ST
Common Sub-Domain::StudySubject{leaf}
+ confidentialityIndicator: BL+ paymentMethodCode: CD+ statusCode: CD+ statusDate: TS.DATETIME::Subject+ state: ST+ actualIndicator: BL
Protocol Representation Sub-Domain::Study{root}
+ acronym: ST+ phaseCode: CD+ primaryPurposeCode: CD+ purposeStatement: ST+ diseaseCode: DSET<CD>+ targetAnatomicSiteCode: DSET<CD>+ designConfigurationCode: CD+ studySchematic: ED+ populationDescription: ST+ studySubjectTypeCode: CD+ plannedStudySubjectExperience: ST+ targetAccrualNumberRange: URG<INT>+ periodicTargetAccrualNumber: RTO<INT,PQ>+ accrualReportingMethodCode: CD+ responsiblePartyCode: CD+ participatingOrganizationTypeCode: CD+ participatingCountryCode: DSET<CD>+ aeCodingSystem: II+ multiInstitutionIndicator: BL
Study Conduct Sub-Domain::PerformedObserv ation
{leaf}
+ methodCode: DSET<CD>+ bodyPositionCode: CD+ targetAnatomicSiteCode: CD+ targetAnatomicSiteLateralityCode: CD+ /focalDuration: PQ.TIME+ /focalDateRange: IVL<TS.DATETIME>::PerformedActivity+ actualDuration: PQ.TIME+ actualDateRange: IVL<TS.DATETIME>+ /delayDuration: PQ.TIME+ missedReason: DSET<SC>+ missedIndicator: BL+ statusCode: CD+ statusDate: TS.DATETIME::Activity+ identifier: II+ reasonCode: DSET<CD>+ comment: ST
Study Conduct Sub-Domain::PerformedObserv ationResult
+ identifier: II+ typeCode: CD+ result: ANY+ resultCodeModifiedText: ST+ targetAnatomicSiteCode: CD+ confidentialityCode: CD+ uncertaintyCode: CD+ reportedDate: TS.DATETIME+ comment: ST
Common Sub-Domain::Subject{root}
+ state: ST+ actualIndicator: BL
Common Sub-Domain::Activity
{root}
+ identifier: II+ reasonCode: DSET<CD>+ comment: ST
Study Conduct Sub-Domain::PerformedObserv ation::PerformedActiv ity
{leaf}
+ actualDuration: PQ.TIME+ actualDateRange: IVL<TS.DATETIME>+ /delayDuration: PQ.TIME+ missedReason: DSET<SC>+ missedIndicator: BL+ statusCode: CD+ statusDate: TS.DATETIME::Activity+ identifier: II+ reasonCode: DSET<CD>+ comment: ST
Study Conduct Sub-Domain::StudySite
+ identifier: II+ leadIndicator: BL+ targetAccrualNumberRange: URG<INT>+ accrualStatusCode: CD+ accrualStatusDate: TS.DATETIME+ dateRange: IVL<TS.DATETIME>+ statusCode: CD+ statusDate: TS.DATETIME
+resulted
0..*
is a result of
{results in}
+producing
1
+involving 0..*
is participated in by
{participates in}
+involved 0..1
+contained
0..*
occurs inthe contextof
{providescontext to}
+containing 0..1
+executing
0..*
executes
{is executed at}
+executes
1
+assigned
0..*
is assigned to
{is the assigned location for}
+assigning 1
34
class AE7 - Adv erse Ev e...
NABTC-06-02 :Study
Patient #7 :StudySubject
Extremity-lower :Adv erseEv ent
hospitalizationRequiredIndicator = NoonsetDate = 01/31/2008resolutionDate = 02/01/2008gradeCode.CD.code = 3gradeCode.CD.codeSystemVersion = 3.0gradeCode.CD.codeSystem = CTCAEactualDateRange.IVL<TS> = blankresult = Extremity-lower (gait/walking)
Muscle weakness :Adv erseEv ent
onsetDate = 01/31/2008resolutionDate = 02/01/2008gradeCode.CD.code = 3gradeCode.CD.codeSystem = CTCAEgradeCode.CD.codeSystemVersion = 3.0actualDateRange.IVL<TS>.high = blankresult = Muscle weakness, generalized or specific area
Death :Adv erseEv ent
hospitalizationRequiredIndicator = NoonsetDate = 02/12/2008resolutionDate = 02/12/2008gradeCode.CD.codeSystemVersion = 3.0gradeCode.CD.code = 5gradeCode.CD.codeSystem = CTCAEactualDateRange.IVL<TS>.high = blankresult = Death
NABTC 2 Pt 7 :StudySite
Assess symptom :PerformedObserv ation Assess symptom :PerformedObserv ation Assess symptom :PerformedObserv ation
Part of an Instance Diagram
State Transition Diagrams
• A State Transition Diagram illustrates how an element (often a Class) can move between states, classifying its behavior according to transition triggers and constraining guards.
• Also called State Machine Diagrams or State Charts
35
State Transition Diagram – Study Subject
36
stm Subject StateDiagr...
Potential Candidate Candidate
Eligible
On-Study
Off-Study
Ineligible
Initial
Final
Interv ention Observ ation
Withdraw consent (after on-study) typically would trigger a whole set of regulatuery related actions.
Follow-Up
Study defines the epochs and States define the transitions of the subject thru the study defined "epochs"
Screening
Pending On-Study
System Restriction: A regulatory problem is encountered if any data is captured on a person before informed consent is signed; so no research system would ever be allowed to capture people as Potential Candidates or Candiates - those are only logical states.
NOTE: We have not addressed the notion of minors. This may not change the diagram, it's just that consent is obtained from whoever has legal power to provide consent. Need to consider this.
Having the Intervention and Observation sub-states is helpful for reporting but may cause other problems. Observation may be called "short-term follow-up" at some institutions, i.e. they are coming back to the clinic for tests though they are no longer receiving the intervention.
Not Registered
Withdrawn
Study Subject Status DISCLAIMER: All state transition diagrams are rough and should be considered DRAFT.
screen failure
pooling
subject refusal
follow-up complete
death (adverse event)
study terminated
unable orunwill ing toparticipate
did not meet elig. criteria
study permanentlyclosed to accrual
enrolled or registered
withdraw consent
withdrawn consent
refuse consent
eliminate
informed consent signed
eliminate
inclusion
exclusion
enrolled or registered
eligible, butunable orunwill ing topariticpate:
pre-registered or slot reserved
exclusion
trt and/orobseravationcomplete
trt or obs complete
adverse event
non-compliance
subject refusal
adverse event
subject refusal
withdrawn consent
identification
Important Components of a Release
• The Model– UML Based Model in Enterprise Architect Model
– Sub-Domains and Comprehensive View
– RIM Based Model
• Users Guide and Release Notes• Change Lists• Mapping Spreadsheet
37
User’s Guide
38
• Section 1: Guide to the Reader• Section 2: Executive Summary• Section 3: The BRIDG Project and BRIDG Model• Section 4: The BRIDG Model: General
Considerations and Representational Conventions
• Section 5: Model Content• Section 6: Glossary• Section 7: Appendix
User’s Guide
39
Release Notes
40
Table of Contents1 Executive Summary1.1 BRIDG ISO Joint Initiative Council (JIC) Ballot1.2 BRIDG Definition1.3 BRIDG Project Stakeholders1.4 BRIDG Project Goals1.5 Definition of BRIDG Model Domain of Interest2 What’s New in Release 3.0.12.1 General changes in Release 3.0.12.2 Detailed Change Lists for Release 3.0.13 Files in R3.0.1 Package3.1 UML-Based Models3.2 RIM-based Models3.3 Report of Comprehensive UML-Based Model3.4 XMI of Comprehensive UML-Based Model3.5 Release Notes (this file)3.6 User’s Guide3.7 BRIDG Domain Analysis Static Model Style Guide3.8 BRIDG CDISC Comment Resolution Spreadsheet4 Known Issues
UML-based Model: Mappings to Source Projects Enterprise Architect
41
UML-Based ModelMappings to Source Projects
RTF Report
42
methodCode public :CD A coded value specifying the technique that is used to perform the procedure.For example, for a specimen collection, finger stick, veni puncture, Abdominal/ ascites effusion, Biopsy, Bronchial alveolar lavage (BAL), etc.For example, if procedure is cholecystectomy the method could be open or laparoscopic.
Map:CTOM = 'SpecimenAcquisition.methodCode'Map:Lab = 'SpecimenCollection.method'Map:SDTM IG = 'EG.EGMETHOD'Map:SDTM IG = 'LB.LBMETHOD'
Foundation of rigorously defined data types
• Simple vs Abstract• Simple: Character, String, Text, Numeric
• BRIDG uses ISO 21090 data type specification
43
Datatypes: Complex
44
ISO 21090: Healthcare Data TypesST = StringCD = Concept Descriptor (Coded Concept)DSET = unordered collection, unique valuesED = Encapsulated dataURG = Uncertain RangeRTO = RatioII = Instance Identifier
Some CD properties:•displayName•originalText•code•codeSystemName•codeSystemVersion•valueSet•And more
Interfacing with Controlled Vocabularies
• Plans to move BRIDG semantics into a controlled environment such as NCI’s EVS / caDSR
• BRIDG controlled vocabulary should integrate with existing stakeholder vocabulary
45
What’s the Process?
46
Project Team develops Domain Analysis Model, mapping spreadsheet, valid value listsProject Team involves BRIDG SCC early
Updated BRIDG Domain Analysis Model is created
Reps from project team meet with SCC toharmonize the project model into the BRIDG
The project to BRIDG mapping spreadsheet needs to be maintained
A Look at the Model in Enterprise Architect
• How to get to the version for review:http://www.cdisc.org/contentmgr/showdetails.php/
id/1938• How to get to the model on the internet
– www.bridgmodel.org– The gForge site:
• Release Files• News• Bug and enhancement trackers• Work in progress in Subversion
47
www.bridgmodel.org
48
A Look at the Model in Enterprise Architect
• How to open the model and look at basic components – Project Browser– Views– Class diagrams– State Transition Diagrams– Instance diagrams
49
Enterprise Architect – Project Browser
50
ProjectBrowser
Project Browser - Views
51
52
Protocol Representation View
53
Comprehensive View
Project Browser – State Transition Diagrams
54
55
Project Browser – Instance Diagrams
56
57