OpenCDISC Validator 1.4

Whats New?

David Borbas

Sr Director, Data Management

Jazz Pharmaceuticals, Inc.

Bay Area CDISC Implementation Network

23 May 2013

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Disclaimers

The opinions expressed in this presentation

are not the official views or policies of Jazz

Pharmaceuticals, Inc.

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Topics

What is Open CDISC? Why is it important?

View of the FDA use of OpenCDISC Validator

Using the application

Understanding the Validation Reports

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Open CDISC

Open Source application Java and xml

Can check/validate SDTM, ADaM, SEND and

Define.xml files

Generate Define.xml limited

Based on published standards e.g. Draft Janus

validation rules and user suggested rules

Currently used in the FDA submission checking

process

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FDA Review Past, Present & FutureFDA Review Environment

Sponsor ReviewValidation

WebSDM

Open CDISC

Validator

Past

Present

Future 2013?

Data Fit

JANUS

Open CDISC

Validator

FDA

Electronic

Document

Room

Servers

FDA Review

Tools

WebSDM/

Empirica,

jReview,

SAS/JMP

Future Additional

Data Visualization

Tools - Evaluation

of JMP Clinical,

iReview, Spotfire

Sponsor Data

in eCTD format

for NDA or

sNDA

Dat

a Vie

ws

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Open CDISC Application

Website location http://www.opencdisc.org/

PC specs

Minimum RAM 1 GB

Any Java capable PC

Java version required >= ver 1.5

run check-java.bat file to confirm version

Command line option available

http://www.opencdisc.org/projects/validator/using-

opencdisc-validator

http://www.opencdisc.org/projects/validator/using-opencdisc-validatorhttp://www.opencdisc.org/projects/validator/using-opencdisc-validatorhttp://www.opencdisc.org/projects/validator/using-opencdisc-validatorhttp://www.opencdisc.org/projects/validator/using-opencdisc-validatorhttp://www.opencdisc.org/projects/validator/using-opencdisc-validator

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What is New in Version 1.4 - 1

Support for SDTM v1.3 and SDTMIG v3.1.3

SDTMIG 3.1.2 amend 1 removed upgraded to

SDTMIG 3.1.3

Controlled Terminology

Added ability to specify CDISC Controlled

Terminology versions

ADaM and SEND validation

Added ability to specify SEND or ADaM validation

types

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What is New in Version 1.4 - 2

New SDTM Validation Rules

Validator 1.3 Rule Count = 227

Validator 1.4 Rule Count = 360

Updates to SDTM, SEND and ADaM rules

Better support for split datasets

Specify MedDRA/CDISC Controlled Terminology

versions

Specify SEND/ADaM validation types

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GUI Screen View - 1

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Directories config

Note: Version 1.4 on the right panel in this and all following slides

Directories - data

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Directories cdisc

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New directory

Not present in ver 1.3

Directories cdisc/sdtm

Terminology Directories

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Directories 2012-12-21

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Terminology Files

Updating Terminology files

Create a new directory

Name with terminology version date

2013-04-12 newly added after the OpenCDISC validator ver

1.4 was downloaded

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Updated Terminology File added!

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MedDRA -1

Same process as Terminology versions

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MedDRA - 2

Add the MedDRA ascii files for each version to a

directory

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MedDRA versions in the GUI

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Using MedDRA with Define.xml

OpenCDISC Validator is programmed to use the

MedDRA Version that is specified in the define.xml file.

So running validation with a define.xml file will support

checking against that MedDRA version. NOTE: You

cannot override the MedDRA version specified in the

define.xml file by selecting a different version of

MedDRA from the Options menu of the GUI.

If you do not use a define.xml file OR the define file does

not specify the MedDRA version you can use a drop

down list choice during the Options selection phase of

the MedDRA GUI.

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Running OpenCDISC Validator - GUI

Start in the main Validator directory where you

unzipped the files and find the file client.bat.

This is the file that will start the GUI and for most

users will be the easiest way to run validation

checking of CDISC Standards files.

Select client.bat to start the program.

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Client Application - Options

Validate (data) or Generate Define.xml

Standard Choices SDTM AdaM

Define.xml SEND

Custom (Tabular)

Source / Input files: select location SAS V5 Transport

Delimited (CSV, Tab etc)

Configuration Depends on Standard choice

Define.xml optional

Reports Report settings link: use to customize report filename etc

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Viewing the Validation Report - 1

Once the validation is complete you will see a brief

summary of the validation statistics

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Viewing the Validation Report - 2

Once the validation is complete you have three

options

View the validation report - click the View Report

button OR

Start another validation or define generation activity -

click the New Session button OR

Exit the GUI application by clicking the File - > Exit or

the close window red x and confirm the exit.

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Validation Report - 1

At the end of a validation run you can choose to view the

report. When you select this option the spreadsheet file

will open.

You can review the report, save the file in another location, or

attach to an email.

Since version 1.3 the Excel report has been revised to

improve readability.

The issues summary tab is now grouped by domain

The terminology issues are collapsed into instances of distinct

terms. This reduces the size of the details tab.

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Validation Report - 2

Formats CSV file unlimited rows

4 tabbed Excel worksheets1. Dataset Summary with Error counts

Errors (High) Warnings (Med) Infos (Low)

2. Issue Summary by Rule ID with error counts

3. Details dataset, variables, values, rules, messages

Contains the complete list of the validation findings sorted by domain name.

4. Rules Rule ID with message, description and type

Report file name and headers can be input with Protocol, date, time, other text etc

Useful to communicate with vendors and internal team

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Validation Report - 3

The Details worksheet can be filtered and sorted

to identify the individual data items you want to

investigate by dataset or by rule or by type of

check.

There are a two characteristics of this list to

highlight that will aid the interpretation of your

results.

Validation Report - 4

Unique Row Findings

If the finding is related to a specific row in the data

then a record number will be present. And the specific

variable(s) and value(s) will be identified.

If character values are placed into numeric fields OR

numeric values placed into text fields these will be

treated as unique records in the finding list.

Global Findings

Controlled Terminology findings for a variable that are

present across multiple records will be counted for

each specific term.

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Interpreting the Validation Results - 1

What Open CDISC can automate for you

dataset structure var names / labels

data integrity checks reference to DM subjects

presence of baseline flags

dates after disposition

Results units consistency

Terminology checks

referential integrity Start date before End date

Disposition references - sometimes

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Interpreting the Validation Results - 2

What you still have to do dataset structure

do you have the right vars per spec?

custom domains

data integrity baseline flags does not see 2 per subject

Review Terminology flags, If a codelist is expandable is it correct?

data validation more content focused right subjects

right dates

right codelists

right testcodes

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Interpreting the Validation Results - 3

False positive results may occur

Lab tests without units will generate error SD0026

and SD0029 e.g. Urine Ph = 5, specific gravity 1.012

Terminology

Extensible codelists with non matches in the terminology file

where the sponsor has added codes / values not present

E.g. Oxygen Saturation as O2SAT VSTESTCD

Some program bugs may generate false error

messages

Post to Open CDISC forum

Interpreting the Validation Results - 4

View of Validation Report

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OpenCDISC Forum Feedback on this New Rule! - 1

SD1082 -- variable length is too long for actual data

graded as an ERROR in the AE domain

Remember All Errors should be addressed and fixed if

possible prior to eSubmission.

.Note, that variable length issue is not SDTM compliance. Its very

specific to SAS format used for regulatory submission.

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OpenCDISC reply - 2

Defining requirements for variable lengths is a very interesting and

controversial topic. This week we have productive discussion on

FDA/PhUSE Data Validation workgroup meeting. There are several

basic and mutually exclusive needs or risks.

1. Datasets should be re-sized (not compressed!) to minimal size

because (very long list of reasons, e.g., data transfer, archiving

storage, analysis tools limitations, hardware limitations, etc.)

2. Variables in SAS XPORT datasets should have consistent/pre-

defined length to avoid data truncation during data integration. There

are many un-perfect and un-complete recommendations how to achieve

this. E.g., --TESTCD variables lengths should be always 8 Chars.

3. Variable length should be defined by data collection process. E.g., it

can be set to maximum length of value in your data collection or control

terminology codelist.

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Rule change 3 New Release v 1.4.1

Note, that variable length issue is not SDTM compliance.

Its very specific to SAS format used for regulatory

submission. OpenCDISC validator will remove all current

Variable Length related checks. Only one new Rule will

be introduced. Before sending data to FDA you need to

re-size you data by each variable to actual maximum

value.

Note, that its needed only for actual data transfer to

FDA. You can do whatever you want before this event.

Its very easy to do.

Profiles will be updated soon. Watch for v1.4.1

OpenCDISC Validator release in the next weeks.

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Suggested Process for OpenCDISC Validator

Review Setup / Parameters

Confirm SDTM Version

Confirm MedDRA version compared to Data Mgt Plan

Confirm Terminology version

Include the define.xml file if present

Set report parameters

Study Name / Number / Dates / other text / Excel message limit

Run validation

Review Error report

Update Issue Summary tab with Comments

Refer to details tab as needed

Identify / report any new bugs

Consider submitting an update to terminology team

If final dataset for submission to CBER then complete word doc with validation findings. CBER doc UCM209772

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Questions?

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Thank you!

David Borbas RN, MISSr. Director, Data ManagementJazz Pharmaceuticals, Inc

David.Borbas@jazzpharma.comP. 650-496-2637