Reject a Coding Dictionary That Is Also a List of Terms

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Summary

EditUnder reviewWhat this benchmark means

README.md

Public entries: Python and R. Passing coverage requires an installed inventory.

Goal: build the adverse events domain with each event's dictionary-derived term (AEDECOD), coded with the study's medical dictionary.

Input: collected adverse events, one record per event, coded by the sponsor, and the study's codelists in the project file.

Variables:

DOMAIN is AE on every record.
AESEQ would be the collected sequence number of the event.
AETERM would be the event as the investigator reported it.
AEDECOD would be the dictionary term the event was coded to.

Note: the codelist both refers to the medical dictionary and lists two of its terms. A list of terms is the whole set of values a column may hold, while a dictionary reference defers that set to the dictionary, so the two contradict each other, and the run is rejected before any data is read; no artifact is accepted.

How to fix

Refer to the dictionary and its version alone, since a dictionary is too large to list:

- id: MEDDRA
  name: Medical Dictionary for Regulatory Activities
  external:
    dictionary: MedDRA
    version: "27.1"

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: codelist_shape_invalid
rule: CT-3

expected/error.yaml

phase: validation
condition: codelist_shape_invalid
spec_paths:
  - codelists[0].codelists[0]
rule: CT-3
context:
  codelist: MEDDRA

YAML specification

1 spec file

spec.yaml

Edit91 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: AE5keys: [STUDYID, USUBJID, AESEQ]6input:7  RAW: {path: input/ae_raw.csv, types: {AESEQ: int}}89output:10  path: ae.csv11  columns: [DOMAIN, STUDYID, USUBJID, AESEQ, AETERM, AEDECOD]1213columns:14  - name: DOMAIN15    type: str16    label: Domain Abbreviation17    derivation: "'AE'"18    submission:19      core: Req20      role: Identifier21      length: 222      origins:23        - type: Assigned24          source: Sponsor2526  - name: STUDYID27    type: str28    label: Study Identifier29    derivation: RAW.STUDYID30    submission:31      core: Req32      role: Identifier33      length: 834      origins:35        - type: Protocol36          source: Sponsor3738  - name: USUBJID39    type: str40    label: Unique Subject Identifier41    derivation: RAW.USUBJID42    submission:43      core: Req44      role: Identifier45      length: 1246      origins:47        - type: Assigned48          source: Sponsor4950  - name: AESEQ51    type: int52    label: Sequence Number53    derivation: RAW.AESEQ54    submission:55      core: Req56      role: Identifier57      length: 858      origins:59        - type: Assigned60          source: Sponsor6162  - name: AETERM63    type: str64    label: Reported Term for the Adverse Event65    derivation: RAW.AETERM66    submission:67      core: Req68      role: Topic69      length: 1270      origins:71        - type: Collected72          source: Investigator7374  - name: AEDECOD75    type: str76    label: Dictionary-Derived Term77    derivation: RAW.AEDECOD78    submission:79      core: Req80      role: Synonym Qualifier81      length: 882      codelist: MEDDRA83      origins:84        - type: Assigned85          source: Sponsor8687submission:88  label: Adverse Events89  class: EVENTS90  structure: One record per adverse event per subject91  repeating: true

Inputs

Under review1 source file

input/ae_raw.csv

Edit2 rows

input/ae_raw.csv
STUDYID	USUBJID	AESEQ	AETERM	AEDECOD
YAMAA-01		1	HEADACHE	Headache
YAMAA-01		1	FEELING SICK	Nausea

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Human review and assessment

Variable Name	Variable Label	Type	Length	Controlled Terms or Format	Origin	Core	Conversion Definition	Variable Type	Variable Order
DOMAIN	Domain Abbreviation	Char	2		Assigned	Req	Set constant value "AE".	SDTM	1
STUDYID	Study Identifier	Char	8		Protocol	Req	Copy value from RAW.STUDYID.	SDTM	2
USUBJID	Unique Subject Identifier	Char	12		Assigned	Req	Copy value from RAW.USUBJID.	SDTM	3
AESEQ	Sequence Number	Num	8		Assigned	Req	Copy value from RAW.AESEQ.	SDTM	4
AETERM	Reported Term for the Adverse Event	Char	12		Collected	Req	Copy value from RAW.AETERM.	SDTM	5
AEDECOD	Dictionary-Derived Term	Char	8	Medical Dictionary for Regulatory Activities (MedDRA, version 27.1)	Assigned	Req	Copy value from RAW.AEDECOD.	SDTM	6

Codelist ID	Name	Value	Decode	Codelist NCI alias	Value NCI alias	Extensible	Extended value	SAS format	Dictionary	Version
MEDDRA	Medical Dictionary for Regulatory Activities	Headache				No			MedDRA	27.1
MEDDRA	Medical Dictionary for Regulatory Activities	Nausea				No			MedDRA	27.1

Version	Date	Author	Description
1.7	2026-10-20	yamaa docs build	Read a specification in the 1.0 surface as its 0.5 counterpart; state that missing values stay missing where a mapping declares no missing handler, and leave out a declared missing answer that restates a handler's default
1.6	2026-10-17	yamaa docs build	Describe collected date parts written as ISO 8601 date text and times of day counted in seconds since midnight
1.5	2026-10-17	yamaa docs build	Name collected precision in words instead of letter codes; state imputation fallbacks, minimum source precision, bounds ignored outside the collected period, and invalid text with no handler as an error; describe date and datetime shifts, imputation flag codes, and partial text giving no date part
1.4	2026-10-15	yamaa docs build	State datetime precision codes through the hour and minute, and complete only the time parts a collected datetime lacks
1.3	2026-09-29	yamaa docs build	Show study codelist names, external dictionaries, and ISO 8601 formats in variable rows; list the document's codelist values and metadata
1.2	2026-09-29	yamaa docs build	Classify ADaM copies from a declared input as Predecessor and recodes as Derived, and SDTM recodes of locally derived columns as Derived
1.1	2026-09-29	yamaa docs build	Resolve lookups into the donor record they select, and give every derivation shape a plain-language rule instead of its raw YAML
1.0		yamaa docs build	Initial generation from spec.yaml

How to fix

input/ae_raw.csv

Your review

Mapping spec