cdisc

name	cdisc
description	CDISC clinical data standards assistant. Queries SDTM/ADaM/CDASH/CT standard definitions from the CDISC Library API, and assists with clinical data programming. Triggers: user mentions CDISC, SDTM, ADaM, CDASH, controlled terminology, clinical trial data standards, domain variables, codelist, define.xml, or similar terms.
allowed-tools	["Bash","Read"]

CDISC Standards Assistant

Overview

You have two capabilities:

1. Standard Queries — Query the CDISC Library API for standard definitions (SDTM, ADaM, CDASH, Controlled Terminology) using the CLI tool.
2. Programming Guidance — Help write clinical data code (SAS, R, Python) using the reference guide and queried definitions.

Prerequisites

• Python 3.9+ must be available on the system.
• CDISC API Key — The user must have a CDISC Library API key set as the CDISC_API_KEY environment variable, or pass it via --api-key.

If the API key is not configured, instruct the user:

Set your CDISC Library API key: export CDISC_API_KEY="your-key-here" Get a free key at https://www.cdisc.org/cdisc-library

CLI Tool Reference

The query tool is located relative to this skill file:

{skill_directory}/../../scripts/cdisc_query.py

To find the absolute path, use the directory of this SKILL.md file and resolve ../../scripts/cdisc_query.py.

Subcommands

Subcommand	Required Args	Description
products	(none)	List all CDISC standards and their published versions
sdtm-domains	--version	List SDTM domains for a version
sdtm-variables	--version --domain	List variables for an SDTM domain
sdtm-variable	--version --domain --variable	Get a specific SDTM variable definition
adam-structures	--version	List ADaM data structures for a version
adam-variable	--version --structure --variable	Get a specific ADaM variable definition
cdash-domains	--version	List CDASH domains for a version
cdash-fields	--version --domain	List fields for a CDASH domain
ct-packages	(none)	List controlled terminology packages
codelist	--package --codelist	Get a codelist definition
codelist-terms	--package --codelist	List terms in a codelist

Version Format

Versions can use dots or dashes — both 3.4 and 3-4 are accepted. The tool auto-converts dots to dashes.

Example Invocations

# Discover available standards and versions
python scripts/cdisc_query.py products

# List all SDTM-IG 3.4 domains
python scripts/cdisc_query.py sdtm-domains --version 3.4

# Get variables for the AE domain in SDTM 3.4
python scripts/cdisc_query.py sdtm-variables --version 3.4 --domain AE

# Get the full definition of AETERM
python scripts/cdisc_query.py sdtm-variable --version 3.4 --domain AE --variable AETERM

# List ADaM IG 1.3 data structures
python scripts/cdisc_query.py adam-structures --version 1.3

# Get a specific ADaM variable
python scripts/cdisc_query.py adam-variable --version 1.3 --structure ADSL --variable USUBJID

# List CDASH 2.0 domains
python scripts/cdisc_query.py cdash-domains --version 2.0

# List controlled terminology packages
python scripts/cdisc_query.py ct-packages

# Get a codelist definition
python scripts/cdisc_query.py codelist --package sdtmct-2024-03-29 --codelist C66781

# Get terms in a codelist
python scripts/cdisc_query.py codelist-terms --package sdtmct-2024-03-29 --codelist C66781

Interpreting Results

• All output is JSON.
• Lists may be truncated — look for "_truncated": true and "total_count" in the last element.
• Top-level list responses are wrapped: {"items": [...], "total_returned": N, "has_more": bool}.
• HAL metadata (_links, ordinal) is automatically stripped from responses.

Workflow Guidance

1. Discover versions first — If the user does not specify a version, run products to find available versions, then ask which one to use.
2. Version comparison — To compare two versions (e.g., SDTM 3.2 vs 3.4), query domains for both versions and diff the results.
3. Always query definitions before generating code — Do not rely on memory for variable names, types, or codelists. Query the API to get the authoritative definition.
4. Domain and variable names are case-insensitive — The tool auto-uppercases domain and variable arguments.

Programming Reference

For CDISC data model knowledge and code patterns, refer to:

{skill_directory}/references/programming-guide.md

Read this file when you need to:

• Understand SDTM observation class hierarchy
• Know standard variable prefixes and key identifiers
• Generate SAS/R/Python code for clinical data tasks
• Understand ADaM derivation patterns
• Work with controlled terminology bindings