Jun 2, 2016 - Loader. Quik2Code. Reporting. Services. SHARE API. Spec. Generator .... variables in data examples. Inputs
SHARE: The Road Ahead Metadata Repositories: Promises and Realities PhUSE SDE: Gaithersburg, MD June 02, 2016
[email protected]
© CDISC 2014
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SHARE: The Road Ahead Agenda 1. 2. 3. 4. 5. 6. 7. 8. 9.
SHARE Benefits available today The SHARE Ecosystem The SHARE API New Exports: RDF and SHARE-XML SHARE Model End-to-End Standards TA Standards and Specification Generation What’s next MDR Pains in the C43362
© CDISC 2014
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1. SHARE Benefits Available Today • Machine-readable standards as they’re published § EU Interchange SHARE Showcase examples
• One metadata repository, many possible outputs § Reports on the metadata across versions § SDTM Core values across standards and versions
• End-to-End standards support § Helps with quality, uniformity, and completeness of the standards
• Standards examples repository
© CDISC 2014
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1. SHARE Benefits Available Today
© CDISC 2014
Reporting Services
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1. SHARE Benefits Available Today Index by BC, Domains
Index by Variables
Example Registry – Sample Outputs © CDISC 2014
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2. SHARE Ecosystem eSHARE JIRA Governance
HCL Interface
Spec Generator
SHARE API
WIKI Authoring
SHARE MDR
Reporting Services
Diff Generator
Quik2Code Content Loader
© CDISC 2014
BCmap
Programmatic QC
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3. The SHARE API
Web Clients
AWS EC2 Cloud
The SHARE API provides programmatic access to machine-readable SHARE content for Metadata Repositories (MDR) and other software tools.
SHARE Repository
eSHARE
SHARE Metadata Services Bus Batch Load
External Terminologies & Models © CDISC 2014
SHARE API
Export
Validation Tools EDC Products
External Repositories
Sponsor MDR
3. A quick look at the API • RESTful API: uses HTTP requests to Get standards metadata § http://{system-endpoint}/{context-root}/rest/semantics/{library-name}/ {rest-api-name}/{rest-api-parameter}?{query-parameters}
• Standards metadata returned in the following formats: § SHARE-XML • Extended ODM v1.3.2 XML • Extended Define-XML v2.0
§ RDF (only available for top-level standards)
• rdf-xml • turtle • n-triples § JSON (experimental) © CDISC 2014
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3. A quick look at the API • Get Standards API - Example § https://smpoc3.akana.com/sm/rest/semantics/CDISCAPI/standards?userid=bus_user&encoding=identity&lifecycle-status=Approved%20Final
© CDISC 2014
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4. RDF and SHARE-XML Exports • SHARE API and Exports use the same code base • RDF exports have recently completed testing • SHARE-XML offers additional metadata available in SHARE as an extension to ODM or Define-XML § Can easily re-create the metadata spreadsheets from the XML § Includes additional information not available in the spreadsheets
• Coming to eSHARE soon
© CDISC 2014
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5. SHARE Model class CDISC Model-Current is a
CDISCVersionedStandard
Define-XML
is a
ODM
In SHARE: Asthma, Alzheimer’s, Virology, CV, Diabetes, Influenza, MS, QT, CHCV is a
Therapeutic Area Standard
requires is a
Dataset-XML
is a
Protocol
SDM-XML
BRIDG
is an implementation of is harmonized with
In SHARE: • BRIDG 3.2 • ISO 21090
is harmonized with
is used by is harmonized with
is a
In SHARE: • ADaM CT • ADaM 2.1 (for review) SDTMForHumanTrials
SEND
AssociatedPersons
In SHARE: • CDASH to SDTM Map for Review
MedicalDev ices
CDASHCRF
PGx
In SHARE: • CDASH 1.1 • CDASH CT
«NEW» BiomedicalConcept
SDTMStandardDomain is built from semantics of
is built from semantics of
CDASHField
is built from semantics of
© CDISC 2014
AnalysisVariableMetadata
ADaMControlledTerminology
TrialDesign
SDTMGeneralObserv ationClass
FindingsAbout
Findings
is built from semantics of uses
is based on
SDTModel
Interv entions
SpecialPurpose SDTMVariable 1
CDASHControlledTerminology
AnalysisResultsMetadata
Ev ents
CDASHDomain
may have
AnalysisParameterValueLev elMetadata
ADaM
aligns with is aligned with
Lab
AnalysisDatasetMetadata
is a
SDTMProductFamily CDASH
is composed of
may have 1..* SDTMControlledTerminology
In SHARE: • SDTM IG 3.3 (draft), 3.2, 3.1.3, 3.1.2 • SEND 3.0 • SEND IG Diffs • SDTM, SEND, QRS, COA, QS CT • SDTM IG Diffs
Relationship
Relrec Suppqual
Pooldef
6. End-to-End Standards • Integrated protocol objectives and endpoints in SHARE § BC model integrated with protocol objectives and endpoints § Links going from TA to objectives to endpoints to BCs to CDASH
• Identify the key protocol concepts for TransCelerate CPT and CDISC CTR § Deliverable is a protocol vocabulary that can be loaded into SHARE as part of the concept model
• PoC for end-to-end standards that includes protocol § Objectives, endpoints, biomedical concepts, CDASH, SDTM, ADaM
© CDISC 2014
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7. TA Standards and Specification Generation Norma=ve metadata in SHARE
Deter -mine status Inputs
Inputs
Inputs Domains, variables Proposed Governance dra4 in data requests examples standards
Versioned metadata compare logics
Outputs
Outputs
Domain Outputs specifica=on Variable specifica=on Summary report report report Metadata Error report Metadata Error report
Process for TA Specification Generation* To Automate ~90% of Entire Document * Normative section, excluding informative section such as comments © CDISC 2014
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8. What’s Next •
SHARE approach to standards development § §
•
Controlled Terminology improvements §
•
Formal sub-setting in SHARE & updated new term request system
Biomedical Concepts & VLM § §
•
Evolve foundational standards development Continue to innovate and accelerate TA standards development
Start loading TA BC content into SHARE Address BCs more broadly
Alignment with healthcare standards § §
Support for the use of EHRs in clinical research (HCL) SHARE on FHIR © CDISC 2014
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9. MDR Pains in the C43362 • MS Smart Quotes: bane of the machine world § ’ “ ” ‑
• Generating Define-XML datatypes from SDTM § Map Char & Num to… § Text, integer, float, datetime, time, partialDate, durationDateTime, etc.
• CDISC Notes and Definitions § Should be replaced by a formal, persistent definition
• Value list is used instead of Controlled Terminology codelist • Standards in silos instead of an end-to-end model § Core (mandatory vs. core) © CDISC 2014
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Thanks! Q & A
© CDISC 2011
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