If the name of the parent domain variable has a length of 8 then the sequential number replaces the last character of the name. In addition, some variables require the specification of a controlled terminology or format.
In such cases, the implementation guide specifies whether the controlled terminology is provided by an external source e. MedDRA or by the investigator. It is generally recommended that the text used in defining controlled terminology be placed in all uppercase.
Exceptions to this rule are controlled terminology from external sources or designations such as units, which employ a generally accepted use of mixed case text. When defining controlled terminology, it is important to prevent ambiguity. As with planning any journey, the first step is to specify your current location and the location of your destination.
By comparing alternate routes before starting the actual trip, you can avoid getting lost or needing to back track. The first step in the mapping process involves the comparison of the study metadata with the SDTM domain metadata. Note that the SDTM standards do not specify variable length. They do provide the standard variable label, so it is important to make sure you are keeping the SDTM label rather than your CDM data label. Automatic mapping can potentially results in a significant reduction in cost, however it is important to check the validity of the mappings.
This process only serves as a first pass of metadata mapping, in most cases some manual mapping will be necessary. The next step involves manually mapping the study data sets to the domain data sets and then mapping each individual variable to the appropriate domain. Depending on how the CDM data sets are structured, you may map each CDM file to a single domain, split its variables among multiple domains, or combine variables from multiple CDM files into a single domain.
There are several possible types of variable mappings. In some cases it may be necessary to use more that one method in order to create the desired SDTM variable from the existing data. A list of basic variable mappings is given below.
Effective manual mapping requires a method of managing and accessing the metadata for both your existing data and the SDTM domains. If your study data resides in SAS data sets, and you define a SAS library for their location, SAS will automatically provide a view to an internal table that contains the structure information for all data sets in any defined library.
This file contains the library name, data set name, variable name, type, length, label, format and more for every variable in every data set in every currently defined library. The amount of information in this view can be overwhelming and it is usually necessary to use a where clause to obtain only the specific information needed. The fact that it contains metadata for all currently accessible data sets facilitates easy metadata comparisons across data sets or across studies, such as determining which variables have identical or similar names.
Therefore, if multiple sites are used and subject numbers overlap between sites, then USUBJID must combine the initial site and subject numbers. An additional required key variable is —SEQ, where the two hyphens represent the domain name. When a subject has more than one record in a domain, then —SEQ is used to form a unique key. An additional, sponsor-defined key is —SPID. This variable is typically used for external identifiers, such as a sample number assigned by a lab.
The SDTM design provides several ways to relate records within and between domains. Each record also contains the key variables necessary to point to a record or group of records in a domain. The process of mapping study data to the SDTM domains can be complex. When decisions are made regarding process steps, it is important that the process be documented for consistency and repeatability.
Direct electronic access to metadata for both the study data and the SDTM domains facilitates an efficient mapping process. Automation of basic processes can save significant amounts of time. Metadata about the mapping process can be used to generate documentation of the process and to generate the SAS source code to perform the derivation of domain data sets.
Once the domain data sets have been produced, software tools documenting the metadata mapping can improve the efficiency of validating the domain data sets and producing the define. A typical ADaM data set is created by merging data from two or more SDTM data sets, restructuring the data to a form convenient for analysis and creating derived variables.
Including metadata on both transformations in one system will provide complete documentation of the creation of the analysis data sets. The process by which each variable was created can be traced back to the original source. The visual interface allows you to define data transformation and mapping steps using icons that represent predefined process steps. The system is extensible, allowing you to add new capabilities and the sequence of steps used in your process is stored in metadata.
Leveraging the power of SAS and Microsoft Excel together allows you to create a practical metadata mapping tool with relatively little programming. The combination of SAS and Excel allows you to combine a user interface with the familiarity of an Excel workbook with the power of SAS to access and manipulate data in a variety of forms.
The SDTM metadata mapping tool allows users to manage and document the mapping of study data to SDTM domains and it can produce text files containing SAS source code to be used as a starting point for programs to generate SDTM domain data sets from the study data sets.
An advantage of using Excel is that there is a great deal of functionality available without any programming. One example of this is the Excel auto filter. When an auto filter is set for a column, a selection button appears in the label cell. Clicking on it displays a pick list containing all of the unique items in that column.
If an item is selected, the sheet will then only display rows that contain that value in that column. This feature makes it easy to view subsets of the metadata. For example, you can view all of the variables in a particular data set or domain, or you can view all of the occurrences of a given variable name across all domains.
The sheet containing the SDTM metadata dictionary is shown in Figure 2, the study metadata sheet is shown in Figure 3. The functionality behind these menu options is provided by a series of Visual Basic modules containing subroutines and functions stored within the workbook. The SAS code is included the SAS program text files that are generated by the mapping tool and it also provides documentation on how the variable was created.
If only basic instructions or pseudo code are available, they can be entered as a SAS comment statement. A valuable addition to this sheet would be a column to containing the derivation or imputation description or algorithm. This would ensure that the method used to create a variable can be easily understood by those who do not program and the contents could serve as a source for ComputationMethod items in the define.
The mapping sheet with the variable selection user form is shown in Figures 4 and 5. Figure 4. Metadata mapping sheet showing the study variable pick list Figure 5. While the text file is not meant to be a read-to-run program, it helps increase efficiency and consistency by eliminating most of the tedious tasks associated with developing conversion programs and allows the programmer to focus on the challenging issues of data mapping and derivation.
A simple application like this can be useful in situations where timelines are tight and do not afford the opportunity to develop a full-scale application. In addition to filling immediate project needs, such an application can serve as a prototype for testing new ideas and as a focal point while defining and refining the user requirements for a more robust, enterprise-level application.
When using an Excel application of this type, it is important to limit the extent to which users and modify the functionality. The most critical safeguard is to password protect the Visual Basic source code modules so that only those with sufficient skill and adequate knowledge of the application can modify them. With SAS version 9. Future version will provide additional functionality. The same process is done with the comments data set if the COMM parameter is not missing.
This standard expresses dates and times with character strings in a format that can readily be understood by humans and interpreted by software. Years are represented using four digits, the remaining date and time components are all two digits with leading zeros if necessary.
The date components are separated by a hyphen and the time components are separated by a colon. There are no spaces between components and delimiters. The ISO standard allows for the use of either the basic format, without delimiters, or the extended format described above. In the original standard, the representation would start with the largest scale component e. The representation would end at that point, resulting in a reduced precision representation. For example, if a date was recorded with a year and day, but missing month, it would only be stored in ISO format as a year.
With the new standard, hyphens could be inserted for the two missing month digits, resulting in a missing component representation. The SDTM 3. The examples below show the full representation of AM on March 3, , and the partial representations if the day was missing. This might be necessary if the ISO formats were used in creating the source data sets and you need to perform computations or comparisons of dates to create your SDTM domains.
Partial dates or times will result in a missing value for the SAS date or time variable. The applicable SAS informats are listed below. The individual date and time components can be extracted, formatted and combined with the appropriate delimiter characters to form the equivalent ISO representation. XML FDA guidance for electronic submissions specifies that all electronic submissions include a Data Definition Document that describes the structure and content of the data included in the submission.
PDF files for metadata. XML files. By transitioning from the use of define. Placing both study data and metadata in a standard XML schema will facilitate validation and transfer into a data warehouse. The schema for the SDTM define.
Details on define. CDISC also provides standard style sheets that can be used to render the define. The creation of the define. The XML specification does not define a single file structure definition as is common with proprietary file formats such as SAS data sets or Excel spreadsheets.
Within the XML specification, matching tags are used to delimit items. In XML however, it is possible to define new tags to meet specific needs. The define. The file also contains SDTM study-level metadata. The table of contents section contains domain-level metadata including the data set name for each domain, a description, structure description e. Validation of the define.
Developing an adequate understanding of the SDTM standard is an important first step. Proper planning and the use of metadata mapping tools can increase both the efficiency of the process and the quality of the resulting data sets. The use of standard processes and tools will increase the return on your development investment if they are flexible enough to be used on future conversion projects.
If you are allowed to submit SDTM domain data sets in lieu of study report listings, patient profiles or monitoring board report listings, the cost of creating the STDM domain data sets can be offset. I think people underestimate how little clean data there is out there, and how hard it is to clean and link the data.
The promise of AI will remain out of reach until organizations find a sustainable and repeatable means to manage and harmonize data from disparate sources. A critical component will be data managers applying the practice of data science to master the idiosyncrasies of biologic and real-world data. Clean data allows greater confidence in patterns and ability to predict outcomes.
Once achieved, organizations can affordably and productively apply AI to produce the much-anticipated benefits. In most organizations, the EDC is the sole system designed to manage clinical data. Organizations ready to invest in their clinical data infrastructure should consider three main technologies:. Data managers will work more efficiently with a purpose-built platform to aggregate, clean, and normalize data. While a dedicated platform for managing all data sources was historically a luxury, they could now be considered core.
Two of the most important steps for data management are selecting the appropriate data aggregation platform and learning to use the query and reporting capabilities provided. Visualization tools help you look at data and extract meaning from what the data is showing. Usability is key to enabling data managers to move quickly and explore different aspects of a problem. Visualizations help you explore different ideas and formulate the right questions to ask.
Augmented intelligence applications such as ML, natural language processing, and robotic process automation are valuable tools for a data scientist and should be considered in partnership with the data management team, not as a replacement of the team.
Data scientists play an important role in training the learning algorithms and are the natural partners enabling these systems to deliver value. Pragmatically, what does this mean for data managers today? Challenges with data quality were the third most-cited barrier to completing clinical trials in 3 and data management is becoming even more difficult with each new source.
And yet, innovation in the tools and training to support data managers has been stagnant. To truly capitalize on AI and RWD, biopharmaceutical companies must invest in the data science skills and resources of their data management teams. March 13, Richard Young Applied Clinical Trials. Good data science Quality issues that slip through data management impact downstream users such as medical monitors, potentially the most expensive resource in our organizations.
Identifying compliant patients and decreasing loss-to-follow-up reduces the number of patients needed and speeds database lock. Enrollment dashboards showing site performance help surface what is or is not working earlier so other sites can course correct. Data visualizations of patient data such as blood pressure readings can surface outliers or potential adverse events. Organizations ready to invest in their clinical data infrastructure should consider three main technologies: 1 A clinical data platform.
Skills development for data science Pragmatically, what does this mean for data managers today? Researching the specific ALCOA attributable, legible, contemporaneous, original, accurate risks and limitations associated with each real-world data RWD source. For example, patient registries provide extensive observational data on patients that is of good quality and relatively inexpensive.
However, confounding i. Familiarizing oneself with FDA guidance on using electronic health record EHR data in clinical investigations, which includes recommended practices for common situations such as handling data modifications. Data managers should advise the organization on integration decisions that help preserve data lineage, protect personal identifiable data, and preserve identity masking.
Advising study teams on data source selections.
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It is helpful but not required to have known how to map (transform, integrate, standardize) data before reading this paper. It will be helpful. This paper discusses the database-only approach to implementation of. SDTM version and SDTMIG (Implementation Guide) version and explores the pros and. The basic component of the planning phase involves metadata mapping – determining how each Map variables in source data sets to SDTM domain variables 6.