confidential - property of navitas - 2015 accelerate define.xml using defineready - saravanan june...

Confidential - Property of Navitas - 2015

Accelerate define.xml

using

defineReady

- Saravanan June 17, 2015


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AgendaIntroduction – define.xmlCurrent situationWhy defineReady?defineReady StagesProcess Flow Key featuresdefineReady - ReportsdefineReady – Mile stonesQuestions 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 MetadataVariable Level MetadataValue Level MetadataControlled 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 SponsorRun OpenCDISC for xpt filesConvert XPT to SAS datasetsSplit Dataset if XPT size > 1 GBCreate destination in CRFInput sheet preparationGenerate Define XMLReview Define XMLRun OpenCDISC for define XML packageSign-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 Reporting

Verification / Review Step

Build Generate


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Process Flow


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Project and Study setup configurations

Process Flow (contd..)

Study related files

Submission Configurations

Submission Type(SDTM/ADaM)

Metadata Version Define XML version External Dictionaries

Datasets (XPTs/Dataset) Annotated Blank CRF*

Data Guide & Supplemental document*

Derivation Document*

Codelist files*

Study setup

Setup and Configuration


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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 domainIdentifies a column where the expected datatype inferred from the description file does not match the actual datatype in the datasetIdentifies a column listed in the domain description as Required ('Req') but not included in the SAS dataset for that domainIdentifies 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 descriptionIdentifies 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 standardIdentifies a domain for which metadata has not been provided



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Build

Build

Study Metadata

Domain Metadata

Variable Level

Metadata

Configure Value Level

Metadata

Configure

Codelists

Configure

Computation

methods

Configure External

Dictionary

DomainDomain

Label Purpose RepeatingIs Reference

Data StructureDomain

Keys ClassIs Custom Domain

Domain Variable LabelOrder

NumberData Type Length

Significant Digits

Display Format Origin Comment Mandatory Role

--TESTCD

-- PARAMCD

--CAT

QNAM

<< USER

>>

<< USER

>>

Dataset Where Element Derivation Origin

Pre-loaded Codelist

•Code List Name•Coded Value•Decoded Value

Sponsor-Defined


ExtendedCodelist


Computation

• Dataset• Variable Name• Computation Name• Computation

Method

External Codelist

• Variable Name• External Codelist

Name• Dictionary • Version



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• Study Specific Derivations

• Codelists• Computation

• Origin

• Code list & Decoded values

• Role• Origin• Comments

GMD CT

DDCRF

Build Process Flow (contd..)


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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

Microsoft Excel 97-2003 Worksheet



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The XML generation engine will read the information from Input sheet and generate the define.xml and exception report (Level 2 Report)

GenerateProcess Flow (contd..)

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

Also it will generate the Validation report to ensure that the generated XML matches with the standards, in terms of structure and content.



System will generate the define.xml based on the updated/provided inputs


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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

Process Flow (contd..)Reporting


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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.

Key features


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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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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

defineReady - Reports

Configure

Level 1 Reports

Build

User Friendly Reports (Domain Level, Variable Level, Value Level and Codelist )

Generate

1. Metadata INPUT EXCELS (Versioned)2. Level 2 Reports

Report

PrintablePDF


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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

defineReady – Reports (contd..)

Project-wise

Study-wise

Stage-wise

User-Wise


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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

defineReady – Mile Stones

CRF Auto Annotator

Reviewer Guide GeneratorValidation

Checks


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Thank You

confidential - property of navitas - 2015 accelerate define.xml using defineready - saravanan june...

Documents

confidential property

study data

study setupsetup

defined data

submission data

automated process

content of clinical

derivation document