Here is the second part of ‘Dive into CDISC Express’, written by Jiangtang Hu. You can read the first part here.
Step 1 of 6: Create a new study (create_new_study.sas)
Open create_new_study.sas in C:\Program Files\CDISC Express\programs\, you can see only one line of a macro call:
%addnewstudy(studyname=my new study);
Just assign a study name to the macro variable, &studyname, e.g, “CLINCAP”:
Submit the codes, you can find a folder named “CLINCAP” with the same structure as the two demo studies imbedded in this application(example1 and example2) in C:\Program Files\CDISC Express\studies\, see(the left and right panels are folders and files before and after the execution of create_new_study.sas. The following the same):
Folder ‘doc’ is used to hold the mapping files;
Folder ‘log’ used to hold log files generated by following macro calls, such as generate SDTM domains;
Folder ‘results’ and its subfolder will hold all the outputs, such as define.xml, SAS transport file, validation reports and SDTM datasets;
Folder ‘source’ holds all the clinical raw data used as inputs for SDTM domains;
Folder ‘tempdata’ holds all the temporary datasets generated by following macro calls.
Also, a configuration file named CLINCAP_configuration.sas put in C:\Program Files\CDISC Express\programs\study configuration\. This file is used to set some study level parameters, such as lab and toxicity specifications (details in C:\Program Files\CDISC Express\specs\Lab specs\).
Two versions of SDTM implementation guides are supported by CDISC Express, CDISC SDTM Implementation Guide Version 3.1.1 and Version 3.1.2. You can find the corresponding specification files in C:\Program Files\CDISC Express\specs\SDTM specs\:
The choosing of SDTM implementation version is also coded in the configuration file, in Line 41:
Version 3.1.1 is used by default. You can also choose Version 3.1.2 if needed:
Assign a study name and choose a SDTM implementation version. That’s all needed in step 1. Let’s take few minutes to navigate the software. CDISC Express is a set of macros and Excel files. It is important to know the file structure.
C:\Program Files\CDISC Express\
├─documentation : FAQ, Quick Start, User Guide
│ ├─ClinMap : system level macros
│ └─function_library : study level macros
├─programs : “action taken” macros
│ ├─study configuration : study parameters configuration, e.g, choose SDTM version
├─SDTM Validation : For validation of SDTM domains
├─specs : specification files
│ ├─Excel engine : ExcelXP tagset file
│ ├─Lab specs : lab and toxicity
│ ├─Mapping validation : validation rules
│ ├─SDTM specs : hold two versions of SDTM implementation
│ └─SDTM Terminology : SDTM codelist(including NCI terminology)
└─temp : hold temporary data not specified to any studies
As we already got, all the “action taken” programs such as create_new_study.sas are located in C:\Program Files\CDISC Express\programs\. In create_new_study.sas, one macro is called, %addnewstudy, which is in C:\Program Files\CDISC Express\macros\ClinMap\.
Note that in C:\Program Files\CDISC Express\macros\, there are two sets of macros in different folders:
C:\Program Files\CDISC Express\macros\ClinMap\: this folder holds all “system” level macros used by the application only. No modification encouraged.
C:\Program Files\CDISC Express\macros\function_library\: macros used for mapping among studies. You can also create you own macro in this folder. The application imbedded macros also documented in user guide.
Next part on the mapping file next week!
CDISC Express Mapping contest comes to an end today!
The challenge was to create a mapping file to map the source data set provided on this page to the SDTM DM domain using CDISC Express. Learn more about CDISC Express.
The winner is Jiangtang Hu! He is a reader and a blogger, lives in Beijing, China. He is a statistical SAS programmer at Sanofi Pasteur and a new member of the “Elite Fathers’ Club” by life. He wins an iPad2!
Jiangtang is one of the eraly testers and adopters of CDISC Express. He wrote a paper to help users like him ‘Dive into CDISC Express’. We posted the first part of this paper on our blog last week. There are 4 parts focused on guiding the user in the different features on the application. Next part will be published next week.
Thank you to all the participants and congratulations to Jiangtang
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