CDISC Protocol → TLF Pipeline

An end-to-end run of the clinical reporting pipeline on the CDISC Pilot study (LZZT / CDISCPILOT01) — "Safety and Efficacy of the Xanomeline Transdermal Therapeutic System (TTS) in Patients with Mild to Moderate Alzheimer's Disease".

The pipeline takes a study definition plus its SDTM data and produces the full reporting package: a TLF plan, analysis/ADaM specs, derived ADaM datasets, the Tables/Listings/Figures themselves, and an interactive traceability explorer.

Pipeline stages

USDM + SDTM  →  TLF plan  →  analysis/ADaM spec  →  ADaM  →  TLF  →  traceability

Layout

inputs/                  # NOT committed — see "Getting the input data" below
  usdm.json              # study definition (CDISC USDM 4.0.0)
  sdtm/                  # SDTM datasets (*.xpt + *.json) + define.xml
outputs/
  tlf-plan/              # study model, TLF index/plan, analysis + adam specs
  adam/                  # derived ADaM datasets, admiral code, QC reports
  tlf/                   # generated Tables/Listings/Figures + ARD
  traceability/          # standalone HTML traceability explorer

Getting the input data

The inputs/ directory is git-ignored and must be populated locally. Both sources are the public CDISC Pilot study (CDISCPILOT01 / LZZT):

• inputs/usdm.json — protocol / study definition in CDISC USDM (Unified Study Definitions Model) format, from the CDISC DDF Reference Architecture: https://github.com/cdisc-org/DDF-RA/tree/main/Documents/Examples/CDISC_Pilot
• inputs/sdtm/ — SDTM datasets (.xpt/.json) and define.xml from the CDISC SDTM/ADaM Pilot Project submission package: https://github.com/cdisc-org/sdtm-adam-pilot-project/tree/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01 (this package also contains the reference ADaM datasets for the same study).

Place these files under inputs/ matching the layout above before running the pipeline.