sdtm-etltm - XML4Pharma
SDTM-ETLTM
The user-friendly ODM – SDTM Mapping software package
Transforming CDISC ODM datasets with clinical data into SDTM datasets is not an easy process.
Therefore, XML4Pharma has developed a visual, easy-to-use mapping software package for defining
and executing ODM to SDTM mappings, and to create and fill an SDTM database.
The SDTM-ETLTM software package is a real ETL software tool allowing to:
Extract: ODM metadata and clinical data from ODM files
Transform: describe (even complicated) mappings between ODM and SDTM and execute them
Load: create an SDTM database and load the SDTM data into the database.
Extract ODM data
The mapping process typically starts with loading ODM
metadata (study setup) and reference data. These are
validated against the XML-Schema and against the ODM
specification. The metadata and reference data are
transformed into a deep tree, which is visualized in the left
part of the graphical interface.
A good number of functions is then available to navigate
through the tree, and to find similar items in other groups,
forms and visits.
If requested, also data files with clinical data can be
validated against the standard and the currently loaded
metadata.
Load SDTM tables
The whole SDTM standard table is loaded from a template define.xml file, which is shown in the right
part of the graphical interface. The use of a define.xml file has the advantage that the template can
easily be extended when CDISC
publishes new SDTM domains.
This SDTM template is the source
for the development of studyspecific domains. These are created
by a simple copy-and-paste
procedure, during which mappings
for a number of basic SDTM
variables (USUBJID, DOMAIN, -SEQ) can already be generated
automatically.
“CDISC Notes” have been implemented for each
SDTM variable, so that it is not necessary to
search through the CDISC Implementation Guide
in order to find out what the meaning of an SDTM
variable is and what its use is.
Several options for viewing the ODM data as well
as the SDTM tables are provided. For example,
the SDTM table can be viewed as a set of HTML
tables, with easy navigation (hyperlinks provided).
Create mappings
When the user selects an SDTM variable, the suitability for mapping
of each of the items in the ODM tree is shown using “traffic lights”,
and “hot candidates” are highlighted1. When a tree ODM item is
selected (this can also be a StudyEvent, Form or ItemGroup), it can
simply be dragged into the SDTM cell for starting the mapping.
A set of wizards then guides the user through the “import” process,
allowing to make the right decisions about what exactly should be
used in the mapping.
The wizard then automatically creates the mapping script.
If a 1:1 mapping is needed, this is usually the
only action that needs to be taken.
1 Based on the value of the ODM SDSVarName attribute
In many cases however, several ODM data needs to be combined in order to create a mapping to an
SDTM variable. In those cases, the
building blocks can simply be
dragged into the SDTM cell and
then combined using a simple,
extremely easy-to-learn scripting
language.
For creating the combinations, a
large number of functions is
available, for which the script
snippets are generated by a simple
mouse click.
Mathematical functions are
available, as well as string
manipulation functions, as well as
date, time, and datetime
manipulation, extraction and
creation functions.
Once a script generated, it can be tested on real clinical data.
During drag-and-drop, the system checks whether codelist are involved either at the ODM side or at the
SDTM site, and generates wizards for setting up the necessary codelist mappings.
The wizard then automatically creates the
mapping script for transformation between the
codelists involved, or to categorize the data
according to the SDTM codelist2.
Also import of the ODM codelists and
measurement unit definitions into the SDTM
structure is possible using a menu function.
Many of the SDTM domains have a structure, e.g. “One record per subject per visit per time point per
measurement”. These structures are already implementated in the define.xml template, but can easily
be adapted for each study-specific domain. The mappings can be constructed so, that “generalizations”
can be defined, e.g. for the QS domain, where a record needs to be generated for each question
(ItemDef) that was ever asked to a patient. When later executing the mapping, the software
automatically creates the necessary iterations implementing the required SDTM domain structure.
All mapping and other information is always stored in a define.xml structure that can easily be
exported to a define.xml file. As such, at the end of the mapping process, the resulting define.xml is
ready for use for submission to the FDA3.
Note that also the locations for annotated CRFs (def:AnnotatedCRF) and supplemental documents
(def:SupplementalDoc) can be added in a visual way.
2 The latest CDISC codelists from the CDISC Controlled Terminology team are included in the template define.xml file
3 The define.xml structure can also be validated against the standard, and for internal consistency
Create SDTM datasets
Once a (partial) mapping has been developed, it can be executed on ODM clinical data files (i.e.
transformation of ODM data into SDTM records). The developed mapping scripts are transformed to a
set of XSLT scripts (which can be saved to file) and executed on the selected ODM file with clinical
data. The output are SDTM records in XML format, which is a precursor of the upcoming SDTMXML standard4. Also a tabular view of the SDTM records is generated.
All this is done in such a way that the user does not need to know anything about XSLT, so essentially,
XML knowledge is not required at all.
The SDTM records in XML format
4 As soon as the SDTM-XML standard is available, it will be implementated in the software.
Create an SDTM database and load SDTM records into the SDTM database
An SDTM database can be easily created as the software allows to generate all necessary SQL5 “Create
Table” statements from the define.xml structures. A number of options for renaming table names and
variable names is provided through another wizard.
Once the SDTM records have been generated, they can be loaded into the SDTM database, as the
software allows to create all necessary SQL “Insert” statements.
The SDTM-ETL process
5 ANSI SQL is generated
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