Bhavin and Jimmy 20 mins Bhavin, Prasanna & Stuart - cdisc.org
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1. Introduction, Future State, Process and Architecture of the PoC – Bhavin and Mikkel 2. PoC for Study Design and Configuration using CDISC 360 Concept-based Standards – Mikkel and Nicolas 3. Automation of SDTM & ADaM Generation and Artifacts using CDISC 360 Enriched Metadata – Bhavin and Jimmy 4. Automation of TFL Generation using CDISC 360 Enriched Metadata – Bhavin, Prasanna & Stuart 5. Concluding Remarks and Next Steps – Bhavin and Mikkel 6. Q & A session 10 mins 20 mins 20 mins 20 mins 5 mins 15 mins Speaker: Bhavin
Transcript of Bhavin and Jimmy 20 mins Bhavin, Prasanna & Stuart - cdisc.org
1. Introduction, Future State, Process and Architecture of the PoC – Bhavin and Mikkel
2. PoC for Study Design and Configuration using CDISC 360 Concept-based Standards –Mikkel and Nicolas
3. Automation of SDTM & ADaM Generation and Artifacts using CDISC 360 Enriched Metadata –Bhavin and Jimmy
4. Automation of TFL Generation using CDISC 360 Enriched Metadata – Bhavin, Prasanna & Stuart
5. Concluding Remarks and Next Steps –Bhavin and Mikkel
6. Q & A session
10 mins
20 mins
20 mins
20 mins
5 mins
15 mins
Speaker: Bhavin
Automation of SDTM & ADaM Generation and Artifacts using CDISC 360 Enriched Metadata
Bhavin Busa (Vita Data Sciences), Jianhui [Jimmy] Zhao (AbbVie)CDISC 2020 US InterchangeOctober 07, 2020
Agenda1. Process Flow for CDISC 360 Proof of Concept2. Machine-readable Mapping Specifications3. SDTM/ADaM Automation Engine – PoC Design4. SDTM/ADaM Automation Engine – Live Demo5. Learnings from CDISC 360 PoC
Speaker: Bhavin
Speaker: Bhavin
Study Specifications from WS4
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Formats:- XML- CSV- SAS
Speaker: Bhavin
Machine-readable Mapping Specifications
Speaker: Bhavin
Essential Elements for Machine-readable Mapping Specifications
We break down the essential elements in 2 dimensions to meet the 4 key aspects of the machine readability
Dimension 1• Source: location (library name), datasets, processing sequence
• Mapping: fields needed to describe how source transits to target
• Target: location (library name), datasets, processing sequence, attributes (label, class, structure, purpose, etc.)
Dimension 2• Dataset Level: Transit datasets from source to target
• Variable Level: Map variables from source to target
• Value Level: Map variables from source to target under different conditions
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Speaker: Jimmy
Mapping Specifications: Dimension 1
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Source Mapping Target
Speaker: Jimmy
Mapping Specifications: Dimension 2
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Source Mapping Target
Dataset Level
Variable Level
Value Level
Speaker: Jimmy
Mapping Specifications: Dataset Level
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data VS1;set CDASH.VS;/********variable level: Source Sequence = 1********/
run;
proc sort data=VS1; by SUBJID;proc sort data=CDAHS.DM OUT=DM2; by USUBJID;
data VS2;merge DM2(in=a) VS1(in=b);by USUBJID;if b;/********variable level: Source Sequence = 2********/
run;
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Speaker: Jimmy
❸❹❺... Sequence 3, 4, 5, 6 ❻
proc sort data=VS6; by USUBJID VSTESTCD VISITNUM VSDTC;
run;
data SDTM.VS;set VS6;by USUBJID VSTESTCD VISITNUM VSDTC;
/********variable level: Source Sequence = 5********/
run;
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Mapping Specifications: Variable Level
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data VS1;set CDASH.VS;
**** Variable level processing ;DOMAIN = 'VS';USUBJID = catx('.', STUDYID, SUBJID);VISITNUM = input(put(VISIT, $VISITNUM.), BEST.);
[origin = Predecessor, do nothing];
if not missing(VISDAT) thenVSDTC = put(VISDAT, E8601DA.);
else if not missing(VSDAT) thenVSDTC = put(VSDAT, E8601DA.);
if VISIT = "VISIT 2 (WEEK 0)" then VSBLFL = 'Y';run;
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Speaker: Jimmy
Mapping Specifications: Value Level
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data VS3;set CDASH.VS;
if DIABP_VSPREF = 'Y' then do;VSTESTCD = 'DIABP';VSORRES = DIABP_VSORRES;VSORRESU = DIABP_VSORRESU;VSSTRESN = 'mmHg';VSSTRESN = INPUT(VSORRES, BEST.);VSSTRESC = PUT(VSSTRESN, 4.0);VSPOS = DIABP_VSPOS;OUTPUT;
end;
*** CONTINUTE ***;
if HEIGHT_VSPREF = 'Y' then do;VSTESTCD = 'HEIGHT';VSORRES = HEIGHT_VSORRES;VSORRESU = HEIGHT_VSORRESU;VSSTRESN = 'm';VSSTRESN = INPUT(VSORRES, BEST.);VSSTRESC = PUT(VSSTRESN, 4.0);OUTPUT;
end;run;
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Speaker: Jimmy
SDTM/ADaM Automation Engine – Proof of Concept Design
Speaker: Bhavin
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CDISC 360 – SDTM/ADaM Automation Engine PoC Design
Study Level CDASH or
SDTM
CDISC 360 Enriched Mapping
Specifications
R Shiny (front-end) & SAS
Import Metadata
Review Data
Run SDTM/ADaM Automation Engine
Edit Metadata
Generate SAS Program
Review & Execute SAS Program
Generate Define.xml
Generate Target Dataset
Speaker: Bhavin
R-Shiny Front-end Interface: Automate Execution
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Speaker: Bhavin
R-Shiny Front-end Interface: Automate Execution
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Speaker: Bhavin
R-Shiny Front-end Interface: Automate Execution
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Speaker: Bhavin
SDTM/ADaM Automation Engine – Live Demo!
Speaker: Jimmy
Learnings from CDISC 360 PoCMachine-readable Metadata
Speaker: Bhavin
Machine-readable Metadata
• CDISC 360 Enriched Metadata = Structural + Conceptual + Semantic + Process [Key to Automation]
o Content is part of the standards (CDISC library)
o ETL Metadata (mapping inference & derivation)
• System agnostic standards, concepts and elementso Can be consumed by any tool
o Organization can build an automation engine their own way
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WS1 & WS2
WS4
WS5 & WS6
Biomedical ConceptsFoundational Standards
Speaker: Bhavin
Thank You!Bhavin Busa, Vita Data SciencesJianhui [Jimmy] Zhao, AbbVie
Courtesy: Mahi Busa
