Leveraging XML Transformations to Get Data into …...Leveraging XML Transformations to Get Data into SAS, R, CSV, and Other Formats Linas Silva Centre for Biostatistics and Clinical

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Leveraging XML Transformations to Get

Data into SAS, R, CSV, and Other FormatsLinas Silva

Centre for Biostatistics and Clinical Trials

Peter MacCallum Cancer Centre

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Goals

Demonstrate XML transformations are a viable way to

export OpenClinica data to any system

Encourage further development

Support for other formats/systems (e.g. SPSS, STATA, MS

SQL)

More seamless integration

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Agenda

Background on how the XML transformations were

developed

Describe how OpenClinica data is structured

3 powerful XML transformation commands

4 main transformation steps common to the 3 export

formats

Results for CSV, R and SAS

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Background

Peter MacCallum Cancer Centre, Australia’s only public

hospital solely dedicated to cancer treatment, research

and education

Centre for Biostatistics and Clinical Trials

Paper based clinical trials and MS Access

May 2010 - began implementing OpenClinica

XML transformations to MS Access

XML transformations to SAS, R and CSV

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Reference - Wikibooks

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Reference – Issue Tracker

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Transform what?

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Format to transform

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Sample CDISC ODM XML file

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Sample CRF – how many data tables?

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Sample CRF – 3 data tables

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Target lesion

data table

Non target lesion

data table

Response

data table

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CDISC ODM XML

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StudyEventDef FormRef

FormRef


Study MetaDataVersion FormDef ItemGroupRef

ItemGroupRef

FormDef ItemGroupRef

ODM FormDef ItemGroupRef

ItemGroupDef ItemRef

ItemRef


ItemDef

ItemDef

ClinicalData SubjectData StudyEventData FormData ItemGroupData ItemData

ItemData

ItemGroupData ItemData

FormData ItemGroupData ItemData

StudyEventData FormData ItemGroupData ItemData

SubjectData StudyEventData FormData ItemGroupData ItemData

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Study Events (Screen)

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4 Study Events: Baseline, Cycle 1, Cycle 2 and Off Study

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Study Events and Forms (XML)

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4 Study

Events

3 Forms

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Study Event Forms (Screen)

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Cycle 1 Study Event uses

Haematology and Tumour

Response Forms only

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Study Event Forms (XML)

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Cycle 1 Study Event uses

Haematology and Tumour

Response Forms only

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ItemGroups (Screen)

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Target lesion

ItemGroup

Non target lesion

ItemGroup

Response

ItemGroup

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ItemGroups (XML)

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5 ItemGroups

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Form ItemGroups (XML)

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Tumour Response Form

contains 3 ItemGroups

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ItemGroup items (Screen)

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Target Lesions ItemGroup

contains 2 items “site/organ”

and “LongestDiameter”

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ItemGroup fields (XML)

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Target Lesions

ItemGroup

contains 2 items

“site/organ” and

“LongestDiameter”

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Item Data (Screen)

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Values for “Site/Organ”

and “Longest Diameter”

items

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Item Data XML

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Values for “Site/Organ”

and “Longest Diameter”

items

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CDISC ODM XML – data tables?

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FormRef



ItemGroupRef




ItemRef


ItemDef

ItemDef


ItemData





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CDISC ODM XML – data tables

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FormRef



ItemGroupRef




ItemRef


ItemDef

ItemDef


ItemData





Tables Table columns

Records Data Values

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3 Transformation commands

VALUE OF

<xsl:value-of select=……>

Statement: <xsl:value-of

select=“/odm:ODM/odm:Study/odm:MetaDataVersion/odm:Stu

dyEventDef/@Name">

Data: Baseline, Cycle 1, Cycle 2, Off Study

Result: Baseline (first item found is selected)

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FOR EACH

<xsl:for-each select=……>

Statement: <xsl:for-each

select=“/odm:ODM/odm:Study/odm:MetaDataVersion/odm:Stu

dyEventDef">

Data: Baseline, Cycle 1, Cycle 2, Off Study

Result: Baseline, Cycle 1, Cycle 2, Off Study

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FILTER

<xsl:….. select=…[element=specific value]…>

Statement: <xsl:for-each

select=“/odm:ODM/odm:Study/odm:MetaDataVersion/odm:StudyEven

tDef[@name=“Cycle 1”]/odm:FormRef">

Data:

Baseline:Haematology, Cycle 1:Haematology,

Cycle 1:Tumour Response, Cycle 2:Haematology,

Cycle 2:Tumour Response, Off Study:Off Study

Result:

Cycle 1:Haematology, Cycle 1:Tumour Response

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4 Transformation Steps

For each ItemGroup definition

For each record for the current ItemGroup

For each column for the current ItemGroup

Find the data value for the current record and column

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4 Transformation steps

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FormRef



ItemGroupRef




ItemRef


ItemDef

ItemDef


ItemData





Tables Table

columns

Records Data Values

1. For each

ItemGroup

3. For each

column

2. For each

Record

4. Get the

value

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CSV transformation

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R Transformation

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SAS (map) Transformation

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SAS (data) Transformation

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CSV Results

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R Results

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SAS (map) results

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SAS (data) results

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SAS results

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Code Lists (SAS)

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Goals - Review

Demonstrate XML transformations are a viable way to

export OpenClinica data to any system

Encourage further development in the following

Support for other formats/systems (e.g. SPSS, STATA, MS

SQL)

More seamless integration

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Documents

Leveraging XML Transformations to Get Data into …...Leveraging XML Transformations to Get Data into SAS, R, CSV, and Other Formats Linas Silva Centre for Biostatistics and Clinical