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Path to Automation
In sdtm.oak: SDTM Data Transformation Engine
```{css, echo = FALSE}
pkgdown-sidebar{
display:none;
}
.wide .table{
font-size: 8px;
overflow: visible
}
```r
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
options(rmarkdown.html_vignette.check_title = FALSE)
The initial release of {sdtm.oak} provides a framework for modular programming of SDTM in R and sets the stage for potential automation of SDTM creation following the standardized SDTM specification. In the future, the automation workflow could involve preparing specifications and then making automated function calls to generate SDTM domains.
The future workflow for automation could look like:
- Prepare SDTM specification: Users can define the raw data source, target SDTM domain, target SDTM variables, and algorithms used for automation. A template is still under development; details are also provided in this article.
- Prepare SDTM-controlled Terminology: Users can define the SDTM-controlled terms applicable to the study. A template is still under development.
- An automated process to read the specification and make {sdtm.oak} function calls can create the code required to generate SDTM datasets or the datasets themselves.
This article provides an overview of metadata and a draft version of the standard SDTM specification. We plan to demonstrate the creation of standard SDTM specs from the CDISC library in collaboration with CDISC COSA. Sponsors may need to establish the necessary tools to generate this SDTM specification from their MDR to utilize the automation features of {sdtm.oak}. It's worth mentioning that this concept draws inspiration from Roche's existing implementation of the SDTM automation process using OAK. I would like to inform you that further development is required for this concept.
Throughout this article, the term "metadata"
is used several times. In this context, "metadata" refers to the specific
metadata used by {sdtm.oak}. This article aims to provide users with a more
detailed understanding of the {sdtm.oak} metadata.
In general, metadata can be defined as "data about data." It does not include
any patient-level data. Instead, the metadata provides a blueprint of the data
that needs to be collected during a study.
Standards Metadata
The standards metadata used in {sdtm.oak} is sourced from the CDISC Library or
sponsor MDR or any other form of documentation where standards are maintained.
This metadata provides information on the following:
- The relationship between Data Collection Standards (eCRF & eDT), SDTM mapping,
and Controlled Terminology
- Machine-readable standard SDTM mappings
- Algorithms and associated metadata required for the SDTM automation of
standards in the study.
In the upcoming releases of {sdtm.oak}, we will effectively utilize the
standards metadata and customize it to meet the study requirements.
Study Definition Metadata
Study Definition Metadata is also referred to as Study Metadata. Study Definition
Metadata provides information about the eCRF and eDT data collected in the study.
eCRF Metadata
The eCRF Design Metadata is fetched from the EDC system. This Metadata includes
-
Forms Metadata: Identifier, eCRF label, Repeating format and other properties of the eCRF.
-
Fields Metadata: Identifier, question label, datatype, and other
properties of data collection fields in the study.
-
Data Dictionaries: Identifier and the controlled terms collected at the
source.
-
Visits: Name of the visits as defined in the EDC.
eDT Metadata
eDT Metadata is the blueprint metadata that describes the data collected as part of that external data transfer (from clinical sites to the sponsor). This includes
-
Dataset name, label, repeating properties, etc.
-
Variable name, datatype, label and associated codelist, etc.
Study SDTM Mappings Metadata (specifications)
Study SDTM mappings metadata is the study SDTM specification. To develop the SDTM domains, {sdtm.oak} requires the user to prepare the Study SDTM mappings metadata. Unlike the conventional SDTM specification, which includes one tab per domain defining the target (SDTM domain, Variables) to source (raw dataset, raw variables) and SDTM mappings, the SDTM spec for {sdtm.oak} defines the source-to-target relationship. For each source, the SDTM mapping, algorithms, and associated metadata are defined. The table below presents the columns in the SDTM mapping specification and its explanation.
wzxhzdk:1
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sdtm.oak documentation built on April 3, 2025, 9:37 p.m.
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```{css, echo = FALSE}
pkgdown-sidebar{
display:none; } .wide .table{ font-size: 8px; overflow: visible }
```r knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) options(rmarkdown.html_vignette.check_title = FALSE)
The initial release of {sdtm.oak} provides a framework for modular programming of SDTM in R and sets the stage for potential automation of SDTM creation following the standardized SDTM specification. In the future, the automation workflow could involve preparing specifications and then making automated function calls to generate SDTM domains.
The future workflow for automation could look like:
- Prepare SDTM specification: Users can define the raw data source, target SDTM domain, target SDTM variables, and algorithms used for automation. A template is still under development; details are also provided in this article.
- Prepare SDTM-controlled Terminology: Users can define the SDTM-controlled terms applicable to the study. A template is still under development.
- An automated process to read the specification and make {sdtm.oak} function calls can create the code required to generate SDTM datasets or the datasets themselves.
This article provides an overview of metadata and a draft version of the standard SDTM specification. We plan to demonstrate the creation of standard SDTM specs from the CDISC library in collaboration with CDISC COSA. Sponsors may need to establish the necessary tools to generate this SDTM specification from their MDR to utilize the automation features of {sdtm.oak}. It's worth mentioning that this concept draws inspiration from Roche's existing implementation of the SDTM automation process using OAK. I would like to inform you that further development is required for this concept.
Throughout this article, the term "metadata" is used several times. In this context, "metadata" refers to the specific metadata used by {sdtm.oak}. This article aims to provide users with a more detailed understanding of the {sdtm.oak} metadata.
In general, metadata can be defined as "data about data." It does not include any patient-level data. Instead, the metadata provides a blueprint of the data that needs to be collected during a study.
Standards Metadata
The standards metadata used in {sdtm.oak} is sourced from the CDISC Library or sponsor MDR or any other form of documentation where standards are maintained. This metadata provides information on the following:
- The relationship between Data Collection Standards (eCRF & eDT), SDTM mapping, and Controlled Terminology
- Machine-readable standard SDTM mappings
- Algorithms and associated metadata required for the SDTM automation of standards in the study.
In the upcoming releases of {sdtm.oak}, we will effectively utilize the standards metadata and customize it to meet the study requirements.
Study Definition Metadata
Study Definition Metadata is also referred to as Study Metadata. Study Definition Metadata provides information about the eCRF and eDT data collected in the study.
eCRF Metadata The eCRF Design Metadata is fetched from the EDC system. This Metadata includes
-
Forms Metadata: Identifier, eCRF label, Repeating format and other properties of the eCRF.
-
Fields Metadata: Identifier, question label, datatype, and other properties of data collection fields in the study.
-
Data Dictionaries: Identifier and the controlled terms collected at the source.
-
Visits: Name of the visits as defined in the EDC.
eDT Metadata
eDT Metadata is the blueprint metadata that describes the data collected as part of that external data transfer (from clinical sites to the sponsor). This includes
-
Dataset name, label, repeating properties, etc.
-
Variable name, datatype, label and associated codelist, etc.
Study SDTM Mappings Metadata (specifications)
Study SDTM mappings metadata is the study SDTM specification. To develop the SDTM domains, {sdtm.oak} requires the user to prepare the Study SDTM mappings metadata. Unlike the conventional SDTM specification, which includes one tab per domain defining the target (SDTM domain, Variables) to source (raw dataset, raw variables) and SDTM mappings, the SDTM spec for {sdtm.oak} defines the source-to-target relationship. For each source, the SDTM mapping, algorithms, and associated metadata are defined. The table below presents the columns in the SDTM mapping specification and its explanation.
wzxhzdk:1
sdtm.oak documentation built on April 3, 2025, 9:37 p.m.
Try the sdtm.oak package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.