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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: build one Analysis Dataset for Adverse Events (ADAE) row per serious adverse event from a named selection of the collected events, and complete every row's dictionary term, actual treatment, customized query name and source domain from values stated once for each column.
Input: one spec.yaml over the collected adverse events
(input/ae.csv: study, subject, sequence, dictionary term and
seriousness), the subject-level file (input/adsl.csv: actual
treatment) and the sponsor's customized query (input/cqterm.csv: the
query name and the dictionary terms it collects).
Variables:
AEDECOD: the dictionary term collected for the serious event that built the row.TRTA: the actual treatment of the event's subject, matched on study and subject.CQ01NAM: the name of the customized query that collects the event's dictionary term; blank when no query collects it.SRCDOM:AE, the domain every row comes from.
Note: the row template states only the keys; every other column is stated once and evaluated for each row the template builds. A value read through the selection's name comes from the very event that built the row, a subject-level value is matched on the keys its file carries, and the query is looked up by the term already completed on the row. A non-serious event, or one whose seriousness was never recorded, leaves no row.
Inputs
Under review3 source filesinput/adsl.csv
Edit3 rows| STUDYID | USUBJID | TRT01A |
|---|---|---|
| YAMAA-01 | Placebo | |
| YAMAA-01 | Drug A | |
| YAMAA-01 | Drug A |
input/ae.csv
Edit5 rows| STUDYID | USUBJID | AESEQ | AEDECOD | AESER |
|---|---|---|---|---|
| YAMAA-01 | 1 | HEADACHE | N | |
| YAMAA-01 | 2 | PNEUMONIA | Y | |
| YAMAA-01 | 1 | SYNCOPE | Y | |
| YAMAA-01 | 2 | PNEUMONIA | Y | |
| YAMAA-01 | 1 | RASH | — |
input/cqterm.csv
Edit1 row| CQNAM | AEDECOD |
|---|---|
| Serious Infections | PNEUMONIA |
Expected output
Under review3 expected rowsexpected/adae.csv
Edit3 rows| STUDYID | USUBJID | AESEQ | AEDECOD | TRTA | CQ01NAM | SRCDOM |
|---|---|---|---|---|---|---|
| YAMAA-01 | 2 | PNEUMONIA | Placebo | Serious Infections | AE | |
| YAMAA-01 | 1 | SYNCOPE | Drug A | — | AE | |
| YAMAA-01 | 2 | PNEUMONIA | Drug A | Serious Infections | AE |
Human review and assessment
| Dataset Name | Variable Name | Variable Label | Type | Codelist/Controlled Terms | Core | Computational Method | Origin |
|---|---|---|---|---|---|---|---|
| ADAE | STUDYID | Study Identifier | character | Set per constructed row; see the Row construction sheet. | Derived | ||
| ADAE | USUBJID | Unique Subject Identifier | character | Set per constructed row; see the Row construction sheet. | Derived | ||
| ADAE | AESEQ | Sequence Number | numeric | Set per constructed row; see the Row construction sheet. | Derived | ||
| ADAE | AEDECOD | Dictionary-Derived Term | character | Take AEDECOD from the AE record matching on the shared output keys, where AE.AESER = 'Y', and no match yields blank. | Derived | ||
| ADAE | TRTA | Actual Treatment | character | Copy value from ADSL.TRT01A. | Predecessor | ||
| ADAE | CQ01NAM | Customized Query 01 Name | character | Take CQNAM from the CQTERM record matching on AEDECOD, and no match yields blank. | Derived | ||
| ADAE | SRCDOM | Source Data | character | Set constant value "AE". | Assigned |
| Template | Include when | STUDYID | USUBJID | AESEQ |
|---|---|---|---|---|
| serious | Copy STUDYID from the AE record matching on the shared output keys, where AE.AESER = 'Y', and no match yields blank | Copy USUBJID from the AE record matching on the shared output keys, where AE.AESER = 'Y', and no match yields blank | Copy AESEQ from the AE record matching on the shared output keys, where AE.AESER = 'Y', and no match yields blank |
| 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 |