Advanced SDTM Programming Tips
Streamline Your SDTM Development with Expert Techniques
Tip 1: Automating SUPPQUAL Domain Creation
The SUPPQUAL (Supplemental Qualifiers) domain can be automated using SAS macros to handle additional variables in a systematic way. Refer to the macro example provided earlier to simplify your SUPPQUAL generation process.
Tip 2: Handling Date Imputation
Many SDTM domains require complete dates, but raw data often contains partial or missing dates. Use the following code snippet for date imputation:
data imputed_dates;
set raw_data;
/* Impute missing day to the first day of the month */
if length(strip(date)) = 7 then date = cats(date, '-01');
/* Impute missing month and day to January 1st */
else if length(strip(date)) = 4 then date = cats(date, '-01-01');
format date yymmdd10.;
run;
Tip: Always document the imputation logic and ensure it aligns with the study protocol.
Tip 3: Dynamic Variable Label Assignment
Avoid hardcoding labels when creating SDTM domains. Use metadata-driven programming for consistency:
data AE;
set raw_ae;
attrib
AESTDTC label="Start Date/Time of Adverse Event"
AEENDTC label="End Date/Time of Adverse Event";
run;
Tip: Store labels in a metadata file (e.g., Excel or CSV) and read them dynamically in your program.
Tip 4: Efficient Use of Pinnacle 21 Outputs
Pinnacle 21 validation reports can be overwhelming. Focus on the following key areas:
- Major Errors: Address structural and required variable issues first.
- Traceability: Ensure SUPPQUAL variables and parent records are linked correctly.
- Controlled Terminology: Verify values against the CDISC CT library to avoid deviations.
Tip: Use Excel formulas or conditional formatting to prioritize findings in Pinnacle 21 reports.
Tip 5: Debugging Complex Mapping Issues
When debugging mapping logic, use PUTLOG statements strategically:
data SDTM_AE;
set raw_ae;
if missing(AEDECOD) then putlog "WARNING: Missing AEDECOD for USUBJID=" USUBJID;
run;
Tip: Use PUTLOG with conditions to reduce unnecessary log clutter.
Tip 6: Mapping RELREC Domain
The RELREC domain is used to define relationships between datasets. Automate its creation using a data-driven approach:
data RELREC;
set parent_data;
RELID = "REL1";
RDOMAIN1 = "AE"; USUBJID1 = USUBJID; IDVAR1 = "AESEQ"; IDVARVAL1 = AESEQ;
RDOMAIN2 = "CM"; USUBJID2 = USUBJID; IDVAR2 = "CMSEQ"; IDVARVAL2 = CMSEQ;
output;
run;
Tip: Validate RELREC with Pinnacle 21 to ensure all relationships are correctly represented.
Tip 7: Using PROC DATASETS for Efficiency
Leverage PROC DATASETS for efficient dataset management:
proc datasets lib=work nolist;
modify AE;
label AESTDTC = "Start Date/Time of Adverse Event"
AEENDTC = "End Date/Time of Adverse Event";
run;
quit;
Tip: Use PROC DATASETS to modify attributes like labels, formats, and lengths without rewriting the dataset.
Tip 8: Deriving Epoch Variables
EPOCH is a critical variable in SDTM domains, representing the study period during which an event occurred. Automate its derivation as follows:
data AE;
set AE;
if AESTDTC >= TRTSDTC and AESTDTC <= TRTEDTC then EPOCH = "TREATMENT";
else if AESTDTC < TRTSDTC then EPOCH = "SCREENING";
else if AESTDTC > TRTEDTC then EPOCH = "FOLLOW-UP";
run;
Tip: Ensure EPOCH values are consistent with the study design and align with other SDTM domains like EX and SV.
Tip 9: Validating VISITNUM and VISIT Variables
VISITNUM and VISIT are critical for aligning events with planned visits. Use a reference table for consistency:
proc sql;
create table validated_data as
select a.*, b.VISIT
from raw_data a
left join visit_reference b
on a.VISITNUM = b.VISITNUM;
quit;
Tip: Cross-check derived VISITNUM and VISIT values against the Trial Design domains (e.g., TV and TA).
Tip 10: Generating Define.XML Annotations
Define.XML is a crucial deliverable for SDTM datasets. Use metadata to dynamically create annotations:
data define_annotations;
set metadata;
xml_annotation = cats("<ItemDef OID='IT.", name, "' Name='", name,
"' Label='", label, "' DataType='", type, "'/>");
run;
proc print data=define_annotations noobs; run;
Tip: Validate the Define.XML file using tools like Pinnacle 21 or XML validators to ensure compliance.
