yamaa As a clinical trial statistician or programmer, challenge anything in this benchmark: describe a problem in Comments, or propose a fix with the Edit button on any source file.
- Task: Is this a specification error a study team could realistically make, and should the build stop on it rather than continue?
- Inputs: Do they trigger the failure for the reason the summary gives?
- Expected failure: Is this the right error, raised at the right point, and would it tell the programmer what to fix?
The other tabs beside Comments are background for assessment, not under review.
Summary
EditUnder reviewWhat this benchmark meansREADME.mdGoal: show for each adverse event the reported term (AETERM),
the coded term (AEDECOD), and the two safety groupings
(SMQ01NAM, SMQ01CD, SMQ02NAM, SMQ02CD).
Input: collected adverse events carrying the reported term
(AETERM) and the coded term (AEDECOD), plus a query dictionary
carrying each coded term (TERM) under a grouping name (GRPNAME)
with code (GRPID) and place (PREFIX).
Variables:
SMQ01NAMwould be the name from the dictionary entry whose place isSMQ01and whose term matches the coded term; blank when no entry matches.SMQ01CDwould be the code from that sameSMQ01entry; missing when no entry matches.SMQ02NAMwould be the name from the dictionary entry whose place isSMQ02and whose term matches the coded term; blank when no entry matches.SMQ02CDwould be the code from that sameSMQ02entry; missing when no entry matches.
Note: one place holds one grouping. A coded term claimed by two dictionary entries in the same place has no single answer: choosing either entry would drop the other, and which one was dropped would depend on the order the dictionary happened to be stored in. The run is therefore rejected and no artifact is accepted.
How to fix
First decide how many queries the study reports. Every query the study
analyses needs a place of its own, so move the second query claiming the
term, Hypersensitivity, from SMQ01 to the next free place:
PREFIX,GRPNAME,GRPID,SCOPE,TERM
SMQ03,Hypersensitivity,20000214,BROAD,STEVENS-JOHNSON SYNDROME
A new place needs its own lookup and its own SMQ03NAM and SMQ03CD,
because how many groupings an artifact carries is fixed when the study rules
are written and not when the dictionary is read. Do not resolve the clash by
keeping whichever query is stored first: it answers with a query the study did
not choose, and it stops reporting the other one at all.
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- join
- condition
- multiple_matches
- requirement
- REQ-0127
expected/error.yaml
phase: join
condition: multiple_matches
spec_paths:
- intermediates[0]
requirement: REQ-0127
context:
intermediate: SMQ1
dataset: QUERY
key:
- TERM
intermediate_key:
TERM: STEVENS-JOHNSON SYNDROME
match_count: 2
keys:
- STUDYID: PILOT7
USUBJID: P7-601
AESEQ: 2
Inputs
Under review2 source filesinput/ae.csv
Edit3 rows| STUDYID | USUBJID | AESEQ | AETERM | AEDECOD |
|---|---|---|---|---|
| PILOT7 | 1 | Widespread rash | RASH | |
| PILOT7 | 2 | Severe skin blistering | STEVENS-JOHNSON SYNDROME | |
| PILOT7 | 1 | Jaundice and dark urine | HEPATITIS |
input/queries.csv
Edit4 rows| PREFIX | GRPNAME | GRPID | SCOPE | TERM |
|---|---|---|---|---|
| SMQ01 | Severe Cutaneous Adverse Reactions | 20000020 | BROAD | RASH |
| SMQ01 | Severe Cutaneous Adverse Reactions | 20000020 | NARROW | STEVENS-JOHNSON SYNDROME |
| SMQ01 | Hypersensitivity | 20000214 | BROAD | STEVENS-JOHNSON SYNDROME |
| SMQ02 | Hepatic Disorders | 20000006 | NARROW | HEPATITIS |
Unexpected Output
Under reviewNo artifact is producedNo fixture files in this directory.
Comments and assessment materials
| Dataset Name | Variable Name | Variable Label | Type | Codelist/Controlled Terms | Core | Computational Method | Origin |
|---|---|---|---|---|---|---|---|
| ADAE | STUDYID | Study Identifier | character | Copy value from AE.STUDYID. | Predecessor | ||
| ADAE | USUBJID | Unique Subject Identifier | character | Copy value from AE.USUBJID. | Predecessor | ||
| ADAE | AESEQ | Sequence Number | numeric | Copy value from AE.AESEQ. | Predecessor | ||
| ADAE | AETERM | Reported Term for the Adverse Event | character | Copy value from AE.AETERM. | Predecessor | ||
| ADAE | AEDECOD | Dictionary-Derived Term | character | Copy value from AE.AEDECOD. | Predecessor | ||
| ADAE | SMQ01NAM | Standardized MedDRA Query 01 Name | character | Take GRPNAME from the QUERY record whose TERM equals AEDECOD, where QUERY.PREFIX = 'SMQ01', and a row with no match is an error. | Derived | ||
| ADAE | SMQ01CD | Standardized MedDRA Query 01 Code | numeric | Take GRPID from the QUERY record whose TERM equals AEDECOD, where QUERY.PREFIX = 'SMQ01', and a row with no match is an error. | Derived | ||
| ADAE | SMQ02NAM | Standardized MedDRA Query 02 Name | character | Take GRPNAME from the QUERY record whose TERM equals AEDECOD, where QUERY.PREFIX = 'SMQ02', and a row with no match is an error. | Derived | ||
| ADAE | SMQ02CD | Standardized MedDRA Query 02 Code | numeric | Take GRPID from the QUERY record whose TERM equals AEDECOD, where QUERY.PREFIX = 'SMQ02', and a row with no match is an error. | Derived |
| Version | Date | Author | Description | Reviewer | Sign-off |
|---|---|---|---|---|---|
| 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 |
Comments
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