计算机使用智能体分类English
R09.05.01.03 · 任务小类

CDISC SDTM映射

CDISC SDTM mapping

Map raw trial data to SDTM and pass validation.

20 条本项目编写的提案 · 分类 v1.1 · 新增基准运行 0 次。下方验证方式与部分得分规则是设计,不是执行结果。

典型应用
Pinnacle 21 · SAS · R
小类 GUI 需求标签
CL · CLI 足够

任务提案 · 20

展开查看完整原文与建议检查方式;两种界面均保留提案英文原文。

R09.05.01.03-T01 Map raw demographics to an SDTM DM dataset in R

原始指令

fixtures/raw/dm_raw.csv (synthetic study ABC-301, 48 subjects) and fixtures/rand.csv hold demographics and arm assignment. Write an R script that produces sdtm/dm.xpt (SAS v5 transport) with STUDYID, DOMAIN, USUBJID, SUBJID, RFSTDTC, RFENDTC, SITEID, AGE, AGEU, SEX, RACE, ETHNIC, ARMCD, ARM, ACTARMCD, ACTARM, COUNTRY per SDTMIG 3.4 and fixtures/ct_package.xlsx.

平台
mac · macOS lin · Linux
应用
R · haven
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
未声明
提案难度
2 / 5

建议验证方式

Hidden gold dm.xpt compared keyed by USUBJID (values, labels, types, lengths <= 200); CDISC CORE engine run on the output with 0 Error-level DM findings. Script re-run from a clean checkout must reproduce the file byte-identically.

建议部分得分

50% values match gold; 25% labels/types/lengths; 25% zero DM validator errors.

R09.05.01.03-T02 Reshape wide vital signs into a long VS domain with baseline flags

原始指令

fixtures/raw/vitals_wide.csv has one row per visit with SYSBP, DIABP, PULSE, TEMP, WEIGHT, HEIGHT columns and a dosing time. Produce sdtm/vs.xpt with VSTESTCD/VSTEST, VSORRES/VSORRESU, VSSTRESC/VSSTRESN/VSSTRESU, VISITNUM, VISIT, VSDTC, VSDY and VSBLFL (last non-missing value on or before first dose per test). Use R or SAS.

平台
lin · Linux win · Windows
应用
R · SAS
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
未声明
提案难度
3 / 5

建议验证方式

Row count and key-based diff vs gold vs.xpt (USUBJID, VSTESTCD, VISITNUM, VSDTC); VSBLFL set exactly on gold rows; VSDY has no day 0; CORE engine 0 Error-level VS findings.

建议部分得分

40% reshape and values; 30% VSBLFL exact; 15% VSDY; 15% validator clean.

R09.05.01.03-T03 Map adverse events with MedDRA coding to AE and SUPPAE

原始指令

fixtures/raw/ae_raw.csv (EDC export) and fixtures/ae_coded.csv (MedDRA coding output) for study ABC-301. Produce sdtm/ae.xpt (AETERM, AEDECOD, AEBODSYS, AESOC, AESEV, AESER and the SAE criteria flags, AEREL, AEACN, AEOUT, AESTDTC, AEENDTC, AESTDY, AEENDY, AESEQ) and sdtm/suppae.xpt for the two sponsor-defined fields listed in fixtures/spec_ae.xlsx.

平台
mac · macOS lin · Linux
应用
R
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
未声明
提案难度
3 / 5

建议验证方式

Gold diff on AE keyed by USUBJID+AESPID and on SUPPAE keyed by USUBJID+IDVARVAL+QNAM; QNAM <= 8 chars, QLABEL <= 40, IDVAR=AESEQ links resolve; CORE engine 0 Error-level AE/SUPPAE findings.

建议部分得分

45% AE values; 25% SUPPAE structure and linkage; 15% study days; 15% validator clean.

R09.05.01.03-T04 Map concomitant medications with partial ISO 8601 dates and WHODrug fields

原始指令

fixtures/raw/cm_raw.csv contains 612 medication rows with free-text partial dates ('UNK-MAR-2025', '2025', 'ONGOING') and fixtures/whodrug_coded.csv. Produce sdtm/cm.xpt with CMTRT, CMDECOD, CMCLAS/CMCLASCD (ATC level 4), CMDOSE/CMDOSU, CMROUTE, CMSTDTC/CMENDTC as truncated ISO 8601, CMENRTPT/CMENTPT for ongoing meds, and CMSTDY only when the date is complete.

平台
lin · Linux
应用
R · SAS
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
未声明
提案难度
4 / 5

建议验证方式

Key-based diff vs gold cm.xpt; all --DTC values match ISO 8601 regex with no imputation; ongoing rows use CMENRTPT='ONGOING' with CMENTPT; CORE engine 0 Error-level CM findings.

建议部分得分

35% treatment/coding fields; 35% partial dates exact; 15% ongoing handling; 15% validator clean.

R09.05.01.03-T05 Fix all Error-level Pinnacle 21 findings on a staged SDTM package

原始指令

sdtm_staged/ holds 9 XPT datasets and define.xml for study ABC-301. Open Pinnacle 21 Community, validate against SDTMIG 3.4 with the define.xml and the provided CT package, then correct the data or metadata behind every Error-level issue (do not delete records to silence them). Re-validate and save the final report as output/p21_final.xlsx.

平台
win · Windows mac · macOS
应用
Pinnacle 21 Community · R
交互表面
desk · 桌面 GUI term · 终端
GUI 需求 · 任务设定
HY · 混合
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
click · 指向与点击 code · 代码与命令 nav · 平移 / 缩放 / 滚动
工作产物
WP02 · 记录 / 表格
条件
multiapp · 多应用
提案难度
3 / 5

建议验证方式

Grader re-runs the P21 validator (CLI) on the edited package: Error count 0, Warning count not higher than baseline; record counts per dataset unchanged; output/p21_final.xlsx exists with the matching configuration (standard, CT version) read from its summary sheet.

建议部分得分

50% Error count to 0; 25% no record deletion or new warnings; 25% final report with correct configuration.

R09.05.01.03-T06 Build a complete SDTM package with define.xml 2.1 for a small study

原始指令

Study XYZ-102 (synthetic, 30 subjects) has raw EDC exports in fixtures/raw/ (11 CSVs), the protocol synopsis input/protocol.pdf and the annotated CRF input/acrf.pdf. Produce DM, AE, CM, VS, LB, EX, DS, SV, MH and trial design domains TA, TE, TV, TI, TS as XPT files plus define.xml 2.1 with value-level metadata for VS and LB, all in sdtm/.

平台
mac · macOS lin · Linux
应用
R · Pinnacle 21 Community
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
long · 长流程
提案难度
5 / 5

建议验证方式

Per-domain key-based diff vs gold (pass >= 98% cell agreement per domain); CORE engine and P21 CLI: 0 Errors; define.xml validates against the Define-XML 2.1 schema and its ItemDefs match dataset variables 1:1.

建议部分得分

40% subject-level domains match gold; 20% trial design domains; 20% define.xml schema-valid and consistent; 20% zero validator errors.

R09.05.01.03-T07 Derive study day variables for a lab dataset

原始指令

sdtm_staged/lb.xpt is missing LBDY and dm.xpt has RFSTDTC. Add LBDY to lb.xpt using the SDTM convention (no day 0; days before reference start are negative; leave blank when either date is partial) and keep every other variable and attribute unchanged. Save as sdtm/lb.xpt.

平台
lin · Linux
应用
R
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
未声明
提案难度
1 / 5

建议验证方式

LBDY equals gold for all 4,212 rows (blank where gold is blank); all other columns byte-equal to input; variable label 'Study Day of Specimen Collection' and numeric type.

建议部分得分

70% LBDY exact; 15% partial-date blanks; 15% other columns untouched.

R09.05.01.03-T08 Standardize lab units to SI and derive reference-range indicators in LB

原始指令

fixtures/raw/lab_raw.csv mixes conventional and SI units from two central labs; fixtures/unit_conversions.xlsx gives factors and fixtures/ref_ranges.csv gives ranges by lab, sex and age band. Produce sdtm/lb.xpt with original results/units in LBORRES/LBORRESU, standardized LBSTRESN/LBSTRESU in SI, LBSTNRLO/LBSTNRHI and LBNRIND (LOW/NORMAL/HIGH).

平台
lin · Linux win · Windows
应用
SAS · R
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
未声明
提案难度
3 / 5

建议验证方式

LBSTRESN within 0.1% relative of gold for all numeric rows; LBSTRESU exact; LBNRIND exact on 100% of rows with ranges; character results ('<0.5') kept in LBSTRESC with LBSTRESN null; CORE engine clean for LB.

建议部分得分

40% SI conversion; 25% reference ranges joined; 20% LBNRIND; 15% character results handled.

R09.05.01.03-T09 Generate define.xml 2.1 with value-level metadata from a spec in Pinnacle 21

原始指令

input/define_spec_draft.xlsx (Pinnacle 21 Community spec template) for study ABC-301 lacks codelists for VSTESTCD/LBTESTCD and value-level metadata for VSORRESU and LBORRESU by test. Complete the spec in Excel, generate define.xml in Pinnacle 21 Community with the CDISC stylesheet, and confirm the rendered HTML shows working links from VS variables to their value-level rows.

平台
win · Windows mac · macOS
应用
Pinnacle 21 Community · Excel
交互表面
desk · 桌面 GUI
GUI 需求 · 任务设定
HY · 混合
GUI 需求 · 普通权限
G2 · GUI 必要
交互原语
click · 指向与点击 type · 文字与表单 vis · 视觉判断
工作产物
WP02 · 记录 / 表格
条件
multiapp · 多应用
提案难度
4 / 5

建议验证方式

define.xml validates against the Define-XML 2.1 schema; codelists and ValueListDefs match gold (set equality on test codes and where-clauses); P21 define validation 0 Errors; grader renders it with the stylesheet in headless Chromium and checks every VLM hyperlink resolves.

建议部分得分

30% codelists; 40% value-level metadata and where-clauses; 30% schema-valid and links resolve.

R09.05.01.03-T10 Move non-standard demographics variables into SUPPDM

原始指令

fixtures/raw/dm_raw.csv includes three sponsor fields not in SDTMIG DM: handedness, years of education and a genetic-substudy consent flag. Build sdtm/suppdm.xpt with RDOMAIN, USUBJID, IDVAR (blank), QNAM, QLABEL, QVAL, QORIG and QEVAL per fixtures/spec_dm.xlsx, and make sure DM itself is unchanged.

平台
mac · macOS lin · Linux
应用
R
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
未声明
提案难度
3 / 5

建议验证方式

Key-based diff vs gold suppdm.xpt; QNAM values exact and <= 8 chars; QLABEL <= 40 chars; no blank QVAL rows; dm.xpt checksum unchanged; CORE engine 0 Error-level SUPPDM findings.

建议部分得分

50% SUPPDM rows; 25% QNAM/QLABEL/QORIG metadata; 25% DM untouched and validator clean.

R09.05.01.03-T11 Collapse a daily dosing log into EX records with interruptions

原始指令

fixtures/raw/dosing_log.csv has one row per subject per day with dose taken (mg), dose modifications and reasons. Produce sdtm/ex.xpt where consecutive days at the same dose and frequency collapse into one record (EXSTDTC/EXENDTC), interruptions start a new record, and EXDOSE, EXDOSU, EXDOSFRQ, EXROUTE, EXADJ are populated per fixtures/spec_ex.xlsx.

平台
lin · Linux
应用
R · SAS
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
未声明
提案难度
4 / 5

建议验证方式

Record-level diff vs gold ex.xpt keyed by USUBJID+EXSTDTC (pass: 100% intervals match); total dose per subject recomputed from EX equals the raw log total; EXADJ populated only where a modification occurred; CORE engine clean.

建议部分得分

45% interval collapsing; 25% dose totals reconcile; 15% EXADJ; 15% validator clean.

R09.05.01.03-T12 Build trial design domains for a three-period crossover from the protocol

原始指令

input/protocol_xover.pdf describes a 3-period, 3-sequence crossover with screening, 7-day washouts and follow-up, plus inclusion/exclusion criteria. Produce TA, TE, TV, TI and TS XPTs (TS must include the required parameters listed in fixtures/ts_required.csv) and write the same values into the define.xml in sdtm_staged/.

平台
mac · macOS lin · Linux
应用
R · Pinnacle 21 Community
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
未声明
提案难度
5 / 5

建议验证方式

TA arms/elements/epochs match gold exactly (order-sensitive on TAETORD); TE start/end rules and TV planned visits match gold; TI has every criterion with IETESTCD <= 8 chars; TS covers all required TSPARMCD; P21 CLI 0 Errors on trial design domains.

建议部分得分

35% TA/TE structure; 20% TV visits; 20% TI criteria; 25% TS parameters and validator clean.

R09.05.01.03-T13 Map medical history with MedDRA coding in SAS

原始指令

fixtures/raw/mh_raw.sas7bdat and fixtures/mh_coded.csv hold medical history for study ABC-301. In SAS write mh_map.sas that creates sdtm/mh.xpt with MHTERM, MHDECOD, MHBODSYS, MHCAT, MHPRESP/MHOCCUR for pre-specified conditions, MHSTDTC, and MHENRTPT='ONGOING' with MHENTPT = screening date for ongoing conditions.

平台
win · Windows lin · Linux
应用
SAS
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
未声明
提案难度
3 / 5

建议验证方式

mh_map.sas runs in batch SAS without errors in the log; key-based diff vs gold mh.xpt; pre-specified rows carry MHPRESP='Y' and correct MHOCCUR; CORE engine 0 Error-level MH findings.

建议部分得分

45% values; 25% pre-specified handling; 15% ongoing variables; 15% clean SAS log and validator.

R09.05.01.03-T14 Convert raw date strings to ISO 8601 across three domains

原始指令

sdtm_staged/ae.xpt, cm.xpt and ds.xpt store --DTC values in raw EDC formats ('12MAR2025 14:30', 'UN-JAN-2025', '2025/02/--'). Rewrite every --DTC variable to ISO 8601 (keeping the original precision, never imputing) and save to sdtm/ without changing any other variable.

平台
lin · Linux
应用
R · Python
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
未声明
提案难度
2 / 5

建议验证方式

All --DTC values match gold strings exactly and the ISO 8601 regex; non-DTC columns byte-equal to inputs; row counts unchanged.

建议部分得分

70% DTC values exact; 30% no other changes.

R09.05.01.03-T15 Triage a 40-issue Pinnacle 21 report: fix true errors, explain the rest in the cSDRG

原始指令

input/p21_report.xlsx lists 40 issues on sdtm_staged/. Fix every issue caused by a mapping error (in the data or define.xml) after reviewing it in Pinnacle 21 Community, then add an entry to output/csdrg_issues.xlsx (columns: Rule ID, Dataset, Count, Explanation) for each issue that is justified by study design and remains.

平台
win · Windows mac · macOS
应用
Pinnacle 21 Community · Excel · R
交互表面
desk · 桌面 GUI term · 终端
GUI 需求 · 任务设定
HY · 混合
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
click · 指向与点击 code · 代码与命令 type · 文字与表单
工作产物
WP01 · 文档
条件
multiapp · 多应用
提案难度
4 / 5

建议验证方式

P21 CLI re-run: all 11 seeded mapping errors gone, no new issues; the set of rule/dataset pairs in csdrg_issues.xlsx equals the remaining-issue set exactly; Explanation quality scored by an LLM rubric (only that part, 15%).

建议部分得分

50% seeded mapping errors fixed; 35% remaining issues listed exactly; 15% explanation quality (LLM rubric).

R09.05.01.03-T16 Map 12-lead ECG results to the EG domain

原始指令

fixtures/raw/ecg_central.csv is a central-reader export with PR, QRS, QT, RR, QTcF intervals in ms and an overall interpretation, one row per triplicate tracing. Produce sdtm/eg.xpt with EGTESTCD/EGTEST from the CT package, EGORRES/EGSTRESN in msec, EGTPT/EGTPTNUM for the triplicates, EGEVAL='INDEPENDENT ASSESSOR' and EGBLFL.

平台
mac · macOS lin · Linux
应用
R
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
未声明
提案难度
3 / 5

建议验证方式

Key-based diff vs gold eg.xpt (USUBJID, EGTESTCD, VISITNUM, EGTPTNUM); interpretation stored as EGTESTCD='INTP' with character result; EGBLFL exact; CORE engine 0 Error-level EG findings.

建议部分得分

45% interval values; 20% interpretation rows; 20% timepoints and baseline flag; 15% validator clean.

R09.05.01.03-T17 Annotate a blank CRF with SDTM mappings in Acrobat Pro

原始指令

input/blankcrf.pdf (42 pages, study ABC-301) and the mapping spec fixtures/spec_all.xlsx. In Adobe Acrobat Pro add SDTM annotations per the CDISC Metadata Submission Guidelines: a domain box per form, a variable text box next to each collected field, 'NOT SUBMITTED' for unmapped fields, consistent fonts/colors per domain, and bookmarks by visit and by form. Save as output/acrf.pdf.

平台
win · Windows mac · macOS
应用
Adobe Acrobat Pro
交互表面
desk · 桌面 GUI
GUI 需求 · 任务设定
G2 · GUI 必要
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
click · 指向与点击 type · 文字与表单 geom · 精确几何 drag · 拖放
工作产物
WP10 · 标注
条件
licensed · 授权专业软件 long · 长流程
提案难度
5 / 5

建议验证方式

Grader parses FreeText annotations: each of 318 CRF fields has an annotation with the gold variable text within 40 pt of the field bbox (IoU-free proximity); domain boxes per page match gold; colors consistent per domain; both bookmark trees present. Acrobat's JavaScript console is disabled and no PDF libraries are installed on the VM; annotations without Acrobat /RC rich-text streams (scripted insertion) are rejected.

建议部分得分

45% variable annotations correct and placed; 20% domain boxes and colors; 15% NOT SUBMITTED; 20% bookmarks.

R09.05.01.03-T18 Map subject disposition and protocol milestones to DS

原始指令

fixtures/raw/ds_raw.csv holds consent, randomization, end-of-treatment and end-of-study pages, with free-text reasons for discontinuation. Produce sdtm/ds.xpt with DSCAT ('PROTOCOL MILESTONE' vs 'DISPOSITION EVENT'), DSSCAT for epoch-level disposition, DSDECOD from the NCOMPLT codelist in the CT package, DSTERM verbatim, DSSTDTC and EPOCH.

平台
lin · Linux
应用
R · SAS
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
未声明
提案难度
4 / 5

建议验证方式

Key-based diff vs gold ds.xpt; every DSDECOD is in the codelist or an 'OTHER' row with verbatim DSTERM; each randomized subject has exactly one end-of-treatment and one end-of-study disposition; CORE engine clean for DS.

建议部分得分

35% milestone rows; 35% disposition events and DSDECOD; 15% one-per-epoch rule; 15% validator clean.

R09.05.01.03-T19 Upgrade controlled terminology to a newer CDISC CT package

原始指令

sdtm_staged/ (8 domains) and define.xml use an older CDISC CT package; fixtures/ct_new.xlsx is the newer package and fixtures/ct_changes.csv its change log. Recode every affected value, add sponsor extensions only for extensible codelists, update codelist versions and terms in define.xml, and list unresolved non-extensible conflicts in output/ct_conflicts.csv.

平台
mac · macOS lin · Linux
应用
R · Python
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
未声明
提案难度
3 / 5

建议验证方式

Value-level diff vs gold datasets; define.xml codelists equal gold (including ExtendedValue flags); ct_conflicts.csv equals the 4 seeded conflicts; P21 CLI with the new CT: 0 terminology Errors except the listed conflicts.

建议部分得分

40% recoded values; 25% define.xml codelists; 20% conflicts listed exactly; 15% validator result.

R09.05.01.03-T20 Produce a dataset-level change log between two SDTM deliveries

原始指令

delivery_v1/ and delivery_v2/ hold two transfers of the same 10 SDTM domains for study ABC-301. Produce output/sdtm_changes.csv with one row per change (DOMAIN, USUBJID, key, VARIABLE, OLD, NEW, CHANGE_TYPE in {added, deleted, modified}) using natural keys from define.xml, plus a per-domain summary in output/summary.csv.

平台
mac · macOS lin · Linux
应用
R · Python
交互表面
term · 终端
GUI 需求 · 任务设定
CL · CLI 足够
GUI 需求 · 普通权限
CL · CLI 足够
交互原语
code · 代码与命令
工作产物
WP02 · 记录 / 表格
条件
未声明
提案难度
3 / 5

建议验证方式

sdtm_changes.csv compared as a set with the gold change log (F1 >= 0.99 on DOMAIN+key+VARIABLE+CHANGE_TYPE, values exact); summary counts equal gold; --SEQ renumbering alone must not be reported as modifications.

建议部分得分

60% change-log F1; 20% summary counts; 20% no false changes from --SEQ renumbering.

已有研究映射

以下沿用研究目录中的基准与小类映射,不是逐题标注、执行记录或产品背书。

同工作流族的小类