Accelerate define.xml
using
defineReady
- Saravanan
June 17, 2015
Confidential - Property of Navitas - 2015
Agenda
Introduction – define.xml
Current situation
Why defineReady?
defineReady Stages
Process Flow
Key features
defineReady - Reports
defineReady – Mile stones
Questions and Answers
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Introduction - Define.XML
The FDA reviewer requires a document which navigates through the study
data presented in individual dataset. CDISC define.xml is the one such
document which describes the structure and content of clinical data in a
machine readable format for electronic submissions of CDISC datasets,
such as SDTM and ADaM.
The define.xml describes metadata in 5 Levels:
Table Level Metadata
Variable Level Metadata
Value Level Metadata
Controlled Terminology
Computational Algorithm
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Current situation
Daunting and time consuming job in terms of collecting the CRF
pages, handling the Origin, codelists, valuelists and study specific
derivations.
Requires multiple eyes on each area like metadata repository building,
handling sponsor defined data along with standards
Also it requires a lot more in-depth understanding in terms of other
technologies like XML, Style Sheets, SAS®, interacting with PDF/RTF/XLS
and also important to adhere standards of CDISC/FDA.
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Current situation (contd…)
Receive files from Sponsor
Run OpenCDISC for xpt files
Convert XPT to SAS datasets
Split Dataset if XPT size > 1 GB
Create destination in CRF
Input sheet preparation
Generate Define XML
Review Define XML
Run OpenCDISC for define XML package
Sign-off
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Why defineReady?
– defineReady is an automated solution that will
help generate the define.xml to meet the FDA
requirement in a regulated environment with
greater accuracy and integrity.
– Predefined process with the minimal user
interaction.
– Ease of use.
– No need of technology experts to generate a
define.xml.
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defineReady Stages
The automated process involves three main stages
– Setup and Configuration
– Build and Generate
– Reporting
Setup and
Configuration
Build
Generate
Verification / Review Step
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Reporting
Process Flow
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Process Flow (contd..)
Setup and Configuration
Project and Study
setup configurations
 Study setup
 Datasets (XPTs/Dataset)
 Annotated Blank CRF*
 Data Guide & Supplemental
document*
 Derivation Document*
 Codelist files*
Study related files
 Submission
Type(SDTM/ADaM)
 Metadata Version
 Define XML version
 External Dictionaries
Submission
Configurations
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Process Flow (contd..)
Setup and Configuration
•
System will execute the pre-loaded confirmation rules (Level 1 – Metadata
Checks) to ensure the submission data meet the standards
• System will generate the exception report grouped by domain and severity
Identifies a column that was described in the domain description but not included in the SAS dataset for that
domain
Identifies a column where the expected datatype inferred from the description file does not match the actual
datatype in the dataset
Identifies a column listed in the domain description as Required ('Req') but not included in the SAS dataset for
that domain
Identifies a column listed in the domain description as Expected ('Exp') but not included in the SAS dataset for
that domain
Identifies a column that appears in the SAS dataset but is not listed in the domain description
Identifies a variable where datatype in (study specific) description is not consistent with datatype implicit in
SAS dataset
Identifies a variable present in SAS dataset but not present in (study specific) description file
Identifies a domain that is referenced in a description file but for which there is no source data
Identifies a variable whose description does not match the standard label
Identifies a variable that has been deprecated according to the CDISC SDTM standard
Identifies a domain for which metadata has not been provided
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Process Flow (contd..)
Build
Domain
Metadata
Computation
Variable
Level
Metadata
Study
Metadata
Configure
External
Dictionary
Pre-loaded
Codelist
Build
•Code List Name
Value
••Coded
Dataset
•Decoded Value
• Variable Name
Name
-- • Computation
-TESTCD
• Computation
PARAMCD
Sponsor-Defined
Method
Configure
Value
Level
Metadata
•Code List Name
-•Coded Value QNAM
CAT
•Decoded
Value
External
Codelist
<<
<<
Extended
USER
USER• Variable
Name
Codelist
>> • External>>Codelist
Domain
•Code
List Name
Name
Value
••Coded
Dictionary
Is Custom
•Decoded Value
Domain
Label
Domain Variable
Is Reference
Domain
Purpose Repeating
Data
Structure
Keys
•Class
Version Domain
Order
Data
Significant Display
Label
Type Length
Format Origin
DatasetNumberWhere
Element Digits
Derivation
OriginComment Mandatory Role
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Process Flow (contd..)
Build
• Role
• Origin
• Comments
• Code list &
Decoded values
GMD
CT
CRF
DD
• Origin
• Study Specific
Derivations
• Codelists
• Computation
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Process Flow (contd..)
Build
 System will generate the combined metadata information, which
user could be extracted in the form of Excel (Input sheet)
 Input sheet includes Domain Level Metadata, Variable Level Metadata,
Value Level Metadata, Control Terminology, Computational Algorithms and
External Codelists
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Process Flow (contd..)
Generate
 The XML generation engine will read the information from Input
sheet and generate the define.xml and exception report (Level 2
Report)
 The Level 2 exception report is reviewed by the Analyst and study
specific documents are updated. The system will then generate a
versioned Input sheet
 System will generate the define.xml based on the updated/provided inputs
 Also it will generate the Validation report to ensure that the generated XML
matches with the standards, in terms of structure and content.
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Process Flow (contd..)
Reporting
 Final submission package is ready along with the required supporting files
 Generating Define.PDF to get a printable version of define.xml
 Generate management reports
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Key features
 Pre-loaded Global Metadata repository to support all SDTM/ADaM
versions.
 Able to handle the multiple versions of define.xml (various
versions of style sheets for the respective submissions of ADaM and
SDTM).
 System will support the sponsor defined code lists along
with pre-loaded standard codelist provided by National Cancer
Institute.
 System will auto import the derivation documents and
annotated CRFs.
 System will support CUSTOM domains and SPLITTING of large
datasets.
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Key features (contd..)
 System can read the CRF origin from the annotated CRFs and cross
check against the origins provided.
 Provided standards to reference Data guide & Supplemental
document
 Handling pre-loaded standard codelists, Sponsor defined
codelists and Extended codelists
 System will automatically populate the Value level and codelist
level information
 Able to support multiple versions of Input excel and also multiple
versions of define xml.
 System will also help us to generate the printable version of define
XML where known as printable PDF
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defineReady - Reports
System will generate the reports at each stages to ensure or give the
flexibility to the user to make a decision
Overview of the reports generated by each stage
Configure
Level 1
Reports
Build
Generate
1. Metadata INPUT
EXCELS (Versioned)
User Friendly Reports
(Domain Level, Variable
Level, Value Level and
Codelist )
2. Level 2 Reports
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Report
Printable
PDF
defineReady – Reports (contd..)
System will also generate the reports which will be used for audit trial
purpose and help us to identify the project status
Overview of the generated Reports by System Level
Project-wise
Study-wise
Stage-wise
User-Wise
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defineReady – Mile Stones
List of features will be added to the defineReady in a near feature, where it
will help and support our submission package in an effective manner
Validation
Reviewer
Guide
Generator
Checks
CRF Auto
Annotator
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Confidential - Property of Navitas - 2015
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Thank You
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