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

Copyright © 2012 Quintiles

Define.XMLA CASE study describing how to produce

Define.XML from within SAS

Dianne WeatherallSep 2012

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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

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Note

• 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

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WHY

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Why?

Why? Requirements? What? How? Summary

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Why?

• 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


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REQUIREMENTS

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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


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Requirements?

• Example: dataset metadata


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Requirements?

• Example: variable metadata


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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


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Requirements?

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


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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


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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


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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:


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WHAT

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What?

• Define.XML with and without stylesheet

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What?


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What?


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What?


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What?


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What?


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What?

• 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


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What?

• 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


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HOW

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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


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How?

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


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XML Header + ODM root element

> Example code:


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XML Header + ODM root element

> Example code:

Study-specific derivations:- Creation date/time


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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

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Study + MetaDataVersion

> Example code:


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> 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


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


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


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> Example code:

Simple FILE and PUT statements with a MOD option


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> Example code:

Simple FILE and PUT statements with a MOD option


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


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


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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.

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

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


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


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

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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.

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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


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• 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


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> Example code:


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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.

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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


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


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> Example code:


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> 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.

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Code List definitions (Codelist)

> Example code:


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> Example code:


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> Example code:


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

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> 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.

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Methods definitions (MethodDef)

> Example code:


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> Example code:


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> Example code:


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

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> 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.

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Comments definitions (CommentDef)> Example code:


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Comments definitions (CommentDef)

> Example code:


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> 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.

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SUMMARY

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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


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Q&A

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