Adding Information to the Define.xml File :: SAS(R) Clinical Data Integration 2.6: User's Guide

Overview: Adding Information to the Define.xml File

You can save the data from the CDISC-Define Creation transformation so that you can edit the tables to add information to the define.xml file that is not represented in the SAS Clinical Data Integration metadata. The process involves the following tasks:

save the data from a CDISC-Define Creation transformation

For information, see Save the Work Tables from a CDISC-Define Creation Transformation.
include computational algorithm and codelist metadata in the define.xml file
add annotated CRF and value-level metadata to the define.xml file

For information, see Adding Annotated CRF and Value-Level Metadata to the Define.xml File.

Save the Work Tables from a CDISC-Define Creation Transformation

To save the work tables from a CDISC-Define Creation transformation, perform the following steps:

Create an empty job.

For detailed information about creating an empty job, see the SAS Data Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
In the Transformations tree, expand Clinical, and then drag and drop CDISC-Define Creation onto the diagram.

For information about adding a CDISC-Define Creation transformation, see Transforming SDTM Domains or ADaM Data Sets into a Define.xml File.
In the diagram, double-click CDISC-Define Creation.

The CDISC-Define Creation Properties dialog box appears.

For detailed information about the Properties dialog box, see the SAS Data Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
Click the Generation tab.
Select the Save work tables to permanent location check box, and then click Browse adjacent to the Location field.

The Select Path dialog box appears.

Tip
You might need to enlarge the dialog box to see these controls.

Note: The file type is Folder. You can select entries that are folders.
Select a folder, and then click OK twice.

Note: The folder must be accessible by the SAS Workspace Server where the code executes. This means that the folder that appears is not on your local computer, but is on the SAS Workspace Server. You must have Write access permission to this folder. If there are tables from a previous CDISC-Define Creation transformation in this folder, they will be overwritten without any prompting.

When creating a define.xml file, select a location into which tables that are created by the CDISC-Define Creation transformation can be copied.
Save and run the job.

SAS Data Integration Studio generates the SAS code for creating the define.xml file, and then submits the code to SAS. The define.xml file is created. Several tables are created in the folder that you selected. Depending on the metadata found for the domain and study, many of these tables will be empty. For more information about the tables that are created, see the SAS Clinical Standards Toolkit: User's Guide.

Adding Annotated CRF and Value-Level Metadata to the Define.xml File

Overview: Adding Annotated CRF and Value-Level Metadata to the Define.xml File

You can include the annotated Case Report Form (CRF) metadata and value-level metadata about the domains that you collected during a study. To do this, you edit the SAS data sets that were generated by the CDISC-Define Creation transformation to include the metadata. Then, you run the %CRTDDS_WRITE macro to generate the define.xml file.

Here is example code that includes annotated CRF metadata:

*Lookup OID for the SDTM 3.1.2 standard in MetaDataVersion;
proc sql noprint;
select OID into :mdv from _svWork.MetaDataVersion
where name="CDISC-SDTM 3.1.2";
quit;
*Add records for Annotated CRF;
proc sql;
insert into _svWork.AnnotatedCRFs
set DocumentRef = "BlankCRF",
leafID= "AnnotatedCRF",
FK_MetaDataVersion = "&mdv";
insert into _svWork.MDVLeaf
set ID= "AnnotatedCRF",
href = "./blankcrf.pdf",
FK_MetaDataVersion = "&mdv";
insert into _svWork.MDVLeafTitles
set title= "Blank Annotated CRF",
FK_MDVLeaf = "AnnotatedCRF";
quit;
*reassign srcdata to location of _svWork data sets;
data _null_; path=pathname('_svwork'); rc=libname('srcdata');
rc=libname('srcdata',path);
run;
*create new define.xml file using updated SAS CRT-DDS data sets;
%crtdds_write(_cstCreateDisplayStyleSheet=1);

Here is example code that includes the value-level metadata in the SC domain. The code includes two values: height without shoes and

weight
                        without shoes

.

*Lookup OID for the SDTM 3.1.2 standard in MetaDataVersion;
proc sql noprint;
select OID into :mdv from _svWork.MetaDataVersion
where name="CDISC-SDTM 3.1.2";
quit;
*Lookup OID for the SCTEST column in ItemDefs;
proc sql noprint;
select OID into :srccol from _svWork.ItemDefs
where name='SCTEST';
quit;
*add record for a new valuelist SCTESTVALS;
proc sql ;
insert into _svWork.ValueLists
set OID= "SCTESTVALS",
FK_MetaDataVersion = "&mdv";
*add record associating the value list SCTESTVALS to the OID for SCTEST ItemDefs record;
insert into _svWork.ItemValueListRefs
set ValueListOID= "SCTESTVALS",
FK_ItemDefs = "&srccol";
*add records to the ItemDefs data set for each value in the SCTESTVAL value list;
insert into _svWork.ItemDefs
set OID= "VAL001",
Name = "SCTEST",
DataType = "text",
Length = 3,
SASFieldName = "SCTEST",
comment = "Height taken barefoot",
label="Height in inches",
FK_MetaDataVersion = "&mdv"
set OID= "VAL002",
Name = "SCTEST",
DataType = "text",
Length = 4,
SASFieldName = "SCTEST",
comment = "Weight without shoes",
label="Weight in pounds",
FK_MetaDataVersion = "&mdv";
*add records associating the value list SCTESTVALS to rows in the ItemDefs data set;
insert into _svWork.ValueListItemRefs
set ItemOID= "VAL001",
OrderNumber=1,
Mandatory="Yes",
KeySequence=1,
FK_ValueLists = "SCTESTVALS"
set ItemOID= "VAL002",
OrderNumber=2,
Mandatory="Yes",
KeySequence=2,
FK_ValueLists = "SCTESTVALS";
quit;
*reassign srcdata to location of _svWork data sets;
data _null_; path=pathname('_svwork'); rc=libname('srcdata');
rc=libname('srcdata',path);
run;
*create new define.xml file using updated SAS CRT-DDS data sets;
%crtdds_write(_cstCreateDisplayStyleSheet=1);

For the example code, the define.xml file created contains the value-level metadata for Height and Weight for the SCTEST column in the SC domain.

Note: If you are viewing an electronic version of this document, you can cut and paste the example code.

Add Annotated CRF Metadata or Value-Level Metadata to the Define.xml File

To add annotated CRF metadata or value-level metadata to the define.xml file, perform the following steps:

Create an empty job.

For detailed information about creating an empty job, see the SAS Data Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
In the Transformations tree, expand Clinical, and then drag and drop CDISC-Define Creation onto the diagram.

For detailed information about adding a CDISC-Define Creation transformation, see Transforming SDTM Domains or ADaM Data Sets into a Define.xml File.
In the diagram, double-click CDISC-Define Creation.

The CDISC-Define Creation Properties dialog box appears.

For detailed information about the Properties dialog box, see the SAS Data Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
Click the Generation tab.
Select the Save work tables to permanent location check box, click Browse adjacent to the Location field, and then select a location.

Tip
You might need to enlarge the dialog box to see these controls.

For more information about saving tables, see Save the Work Tables from a CDISC-Define Creation Transformation.
Click OK twice.
Click Run.

The define.xml file is generated, and the SAS data sets used to generate the file are included.
To add records to the annotatedcrfs, mdvleaf, and mdvleaftitles data sets (for CRF metadata), or valuelists, itemvaluelistrefs, valuelistitemrefs, and itemdefs data sets (for value-level metadata), perform the following steps:
1. In the Transformations tree, expand Data, and then drag and drop User Written Code onto the diagram.
2. In the diagram, double-click User Written.
  
  The User Written Properties dialog box appears.
  
  For more information about the properties dialog box, see the SAS Data Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
3. (Optional) Click the General tab, and then rename the transformation.
4. Click the Code tab.
5. From the Code generation mode drop-down list, select All user written.
6. In the code editor, enter the code to include annotated CRF metadata or the value-level metadata.
  
  For example code, see Overview: Adding Annotated CRF and Value-Level Metadata to the Define.xml File.
7. Click OK.
Click Run, and then review the define.xml file to ensure that the annotated CRF metadata or the value-level metadata is included.