copyright © 2012 quintiles define.xml a case study describing how to produce define.xml from within...

Define.XMLA CASE study describing how to produce

Define.XML from within SAS

Dianne WeatherallSep 2012

Topics for Discussion

Why do we create the Define?

Requirements to create the Define?

What is Define.XML?

How do we create the Define in SAS?

Summary

• Examples and code are based on the Draft Define V2

• Slides are based on SDTM Define, but similar principles can be applied to the ADaM Define> Key differences are explained in the Define Draft V2

Why? Requirements? What? How? Summary

• To describe what is included in the electronic data transfer (datasets, variables, codelists, etc) -> METADATA-> an elaborate “PROC CONTENTS” and more

• To provide a user-friendly document with links to navigate easily, and to access information easily

• To easily access the annotated CRF and datasets

• To have a standard format to describe the electronic data transfer

• Why XML?> Machine readable format for use by software applications> Browser-based report (through the use of an XSL stylesheet)> Vendor neutral, platform independent

REQUIREMENTS

Requirements?

• Metadata in a usable format, easy to capture and ability to import into SAS (recommended format = Excel)> Dataset metadata:

list of domains -> name, description, class, structure, purpose, keys, location> Variable metadata:

list of variables: -> name, label, type, controlled terms / format, origin, role, comment> Controlled terms:

coded value, decode> Value-level metadata:

variable, where, type, controlled terms or format, origin, computation method> Computational algorithms:

reference name, name, computation method

• Data in XPT format

• Annotated CRF in PDF format

• Supporting documentation: > Reviewers guide / complex algorithms in PDF format

Requirements?

• Example: dataset metadata

Requirements?

• Example: variable metadata

Requirements?

• Example: controlled terms> Usually includes all possibilities on the CRF, not only those in the data> Needs to be set up from the CRF, not the data

Requirements?

• Example: value-level metadata> 2 types: SUPPQUAL (QVAL) and FINDINGS (ORRES)> Can be generated from the data, especially electronic labs

Requirements?

• Example: computational algorithms> Used for standard algorithms that can be applied across variables> Very long derivations should rather be specified in a PDF file, and linked from the variable

comment

Requirements?

• Specification vs Metadata

> Specification- Instructions to a programmer to get to the final SDTM / ADaM dataset- Contains derivations that often refer to raw variable names (for programming)- May contain SAS code in some cases- May refer to other documents (e.g. SAP etc)

> Metadata

- Describes the contents of the final SDTM/ADaM dataset - Contains derivations that describe in words how the data was derived (for traceability and

reviewer information)- Does not contain SAS code and does not refer to raw variables- Contains links to other documents

Requirements?

• Specification vs Metadata

> To combine or not to combine?- It makes sense to create one document that serves both purposes

» Prevents rework» Consistency» Less work» BUT… make sure you separate programmer notes from reviewer comments

> Example:

• Define.XML with and without stylesheet

• Define-XML Version 2.0.0 can be used for SDTM and ADaM

• Terminology:> Def: declaration of an object> Ref: reference to an object> OID: identify a metadata object

• Validation of the Define.XML:> It must properly reference versions of the CDISC standards> Conform to schemas> Meet all requirements of the Define-XML Specification> Can be checked using OpenCDISC according to defined rules

• Structure of the XML file> XML header, the ODM root element, Study and MetaDataVersion> Linked supporting PDF documents (e.g. aCRF)> Value List definitions (e.g. for Supplemental Qualifiers / Findings Tests)> Where Clause definitions (referenced in Value List definitions)> Dataset definitions (ItemGroup)> Variable definitions (ItemDef)> Code List definitions (Codelist)> Methods definitions (MethodDef)> Comments definitions (CommentDef)> Leafs definitions

PREPARATION BEFORE WRITING TO XML FILE

> Create XPT files of the SDTM datasets

> Import the specifications into SAS and create a dataset containing the Dataset and Variable metadata

> Import the methods into SAS and merge onto the metadata by the method name

> XML does not like special characters – convert characters to text

> Create a value-level metadata dataset by choosing “TESTCD”, “PARMCD” and “QNAM” variables and obtaining the values in those variables from the data

> Create a codelist dataset by running through variables and value-level variables with codelists attached to them and obtaining the values for those variables

> Codelists -> set up in specs vs create from data

• Create XML file within SAS using:> DATA steps> FILE and PUT statements

XML Header + ODM root element

> Example code:

XML Header + ODM root element

> Example code:

Study-specific derivations:- Creation date/time

XML Header + ODM root element> Example code:

Simple FILE and PUT statementsStudy-specific parameters can be read in using macro parameters or derived- e.g. creation date/time

Study + MetaDataVersion

> Example code:

Simple FILE and PUT statements – use the MOD option on the FILE statement to append to the text fileStudy-specific parameters can be read in using macro parameters or derived- e.g. study name and description

Linked supporting PDF documents (e.g. aCRF) + Leafs definition> Example code:

Linked supporting PDF documents (e.g. aCRF) + Leafs definition

> Example code:

Simple FILE and PUT statements with a MOD option

> Example code:

Simple FILE and PUT statements with a MOD option

Value List definitions (e.g. Findings Tests) and Where Clause definitions> Example code:

Value List definitions (e.g. Findings Tests) and Where Clause definitions

Example: VSORRESCreate a dataset in SAS of value-level variables and their values.Output an ITEMREF statement for each value of VSORRES (e.g. DIABP) and reference a WHERECLAUSE.

Example: VSORRESOutput a WHERECLAUSEDEF statement for each value of VSORRES (e.g. DIABP) and use the same WHERECLAUSE name referenced in the ITEMREF.

Value List definitions (e.g. for Supplemental Qualifiers) and Where Clause definitions> Example code:

Value List definitions (e.g. for Supplemental Qualifiers) and Where Clause definitions

Example: SUPPDM.QVALOutput an ITEMREF statement for each value of SUPPDM.QNAM (e.g. RACE1) and reference a WHERECLAUSE.

Example: SUPPDM.QVALOutput a WHERECLAUSEDEF statement for each value of SUPPDM.QVAL (e.g. RACE1) and use the same WHERECLAUSE name referenced in the ITEMREF.

Dataset definitions (ItemGroup)

• Dataset Definitions:> Dataset definitions:- ItemGroupDef element- Include references to variable definitions- Include references to actual data file

> Variable references:- ItemDef element

> Dataset definition:- def:leaf element

• Attributes:> Repeating:- No for datasets with one record per subject - Yes for datasets with more than one record per subject

> Mandatory:- Yes for required variables- No for Expected or Permissible variables

> Domain:- Name of the domain

> IsReferenceData:- Yes for reference datasets (no subjects)- No for subject-level datasets

> Example code:

Dataset definitions (ItemGroup)> Example code:

Example: DMOutput ITEMGROUP statement for each domain and include a ITEMREF statement for each variable. Include a link to the dataset.

Variable definitions (ItemDef)

• Variable Definitions:> Variable definitions:- ItemDef element

> Other elements:- Controlled terminology: CodeList- Value level metadata: def:ValueListDef- Computational method: MethodDef- Comments: def:CommentDef- Origin: def:Origin

• Data types:> text> integer> float> datetime> date> time> partialDate> partialTime> incompleteDatetime> durationDatetime

> Example code:

Example: DMOutput ITEMDEF statement for each variable. Include a link to the BLANKCRF for CRF Page origins and include the page number. This comes from the metadata in specs.

Code List definitions (Codelist)

> Example code:

Example: AE.AESEVOutput CODELISTREF in the ITEMDEF statement for each variable with a codelist.

> Example code:

Example: AE.AESEVOutput a CODELIST statement for each codelist and include each value as a CODEDVALUE. Use the same name for the codelist as referenced in the ITEMDEF statement.

Methods definitions (MethodDef)

> Example code:

Example: EG.EGDRVFLFor variables with method attached to them, include the METHODOID in the ITEMREF in the ITEMGROUP statement.

> Example code:

Example: EG.EGDRVFLOutput a METHODDEF statement for each method. Use the same name as referenced in the ITEMREF statement. Include a link to the Complex Algorithms document if required.

Comments definitions (CommentDef)> Example code:

Comments definitions (CommentDef)

> Example code:

Example: AE.AEENDYFor variables with comments attached to them, include the COMMENTOID in the ITEMDEF.Output a COMMENTDEF statement for each comment. Use the same name as referenced in the ITEMDEF statement.

SUMMARY

Summary

• Define.XML files help to describe what is in an electronic submission of data

• Define.XML is a user-friendly document when rendered using a stylesheet

• DATA steps and PUT statements can be used to create a Define.XML file in SAS using dataset, variable and value-level metadata and codelists/method information

copyright © 2012 quintiles define.xml a case study describing how to produce define.xml from within...

Documents

sanderson weatherall - i-bidder

dianne weatherall: 2013-04-11

ed weatherall

quintiles analyst day presentation 2014

monika kawohl statistical programming accovion gmbh...

keynote speech - david weatherall

best value contracting from collaboration? weatherall... ·...

the jilting of granny weatherall - mrs. garrett's...

weatherall windows - shepparton building supplies (sbs) ·...

sanderson weatherall carlton industrial estate 3 norman

quintiles new healthreport_2011

inflación quintiles ingresos: anual, mensual y acumulada

sanderson weatherall crimble mill, crimble lane,

beneficios estudiantiles. evaluación socioeconómica....

by chrissy hall analysis: the jilting of granny weatherall

creating define.xml v2 using sas® for fda...

what is the define.xml (crt-dds)?

quintiles second quarter 2014 earnings presentation

copyright © 2013 quintiles quintiles site management kim...

quintiles site management