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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: build the laboratory domain with one record per subject for
glucose and one for creatinine, each with its result in standard units
(LBSTRESN) and the metadata a data definition describes it by.
Input: laboratory results delivered by the vendor, one record per
subject, with glucose in mmol/L (GLUC) and creatinine in mg/dL
(CREATMG).
Variables:
DOMAINisLBon every record.LBTESTCDwould beGLUCorCREAT.LBSTRESNwould be the glucose as delivered, and the creatinine converted to micromoles per litre (multiplied by 88.42).
Note: the result of each test is described as delivered by the vendor. The creatinine result is converted here before it is submitted, so it did not arrive as it stands, and its description contradicts how the value is made; the run is rejected before any data is read and no artifact is accepted.
How to fix
Describe the converted creatinine result as derived by the sponsor, and keep the delivered glucose result as collected:
- id: CREAT
where: {LBTESTCD: [CREAT]}
origins:
- type: Derived
source: Sponsor
method: Creatinine in mg/dL multiplied by 88.42
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- validation
- condition
- refuted_value_origin
- rule
- SUB-13
expected/error.yaml
phase: validation
condition: refuted_value_origin
spec_paths:
- columns.LBSTRESN.submission.value_level.CREAT
rule: SUB-13
context:
column: LBSTRESN
entry: CREAT
origin_type: Collected
Inputs
Under review1 source fileinput/lab.csv
Edit2 rows| STUDYID | USUBJID | GLUC | CREATMG |
|---|---|---|---|
| YAMAA-01 | 5.4 | 0.9 | |
| YAMAA-01 | 6.1 | 1.2 |
Unexpected Output
Under reviewNo artifact is producedNo fixture files in this directory.
Human review and assessment
| Variable Name | Variable Label | Type | Length | Controlled Terms or Format | Origin | Core | Conversion Definition | Variable Type | Variable Order | Comments for Define |
|---|---|---|---|---|---|---|---|---|---|---|
| DOMAIN | Domain Abbreviation | Char | 2 | Assigned | Req | Set constant value "LB". | SDTM | 1 | ||
| STUDYID | Study Identifier | Char | 8 | Protocol | Req | Copy value from LAB.STUDYID. | SDTM | 2 | ||
| USUBJID | Unique Subject Identifier | Char | 12 | Assigned | Req | Copy value from LAB.USUBJID. | SDTM | 3 | ||
| LBTESTCD | Lab Test or Examination Short Name | Char | 5 | Assigned | Req | Set per constructed row; see the Row construction sheet. | SDTM | 4 | ||
| LBSTRESN | Numeric Result/Finding in Standard Units | Num | 8 | Derived | Exp | Result in standard units | SDTM | 5 |
| Template | Include when | LBTESTCD | LBSTRESN |
|---|---|---|---|
| glucose | Constant "GLUC" | Copy LAB.GLUC | |
| creatinine | Constant "CREAT" | Compute LAB.CREATMG * 88.42 |
| Version | Date | Author | Description | Reviewer | Sign-off |
|---|---|---|---|---|---|
| 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 |