A Data-Driven Approach for Generating Define.xml v2.0 using ADaM Specifications and ADaM Datasets

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1 SESUG Paper A Data-Driven Apprach fr Generating Define.xml v2.0 using ADaM Specificatins and ADaM Datasets Jaskaran Sing Gill, Hima Bhatia, ICON Plc. ABSTRACT Case Reprt Tabulatin Data Definitin Specificatins (CRT-DDS) cmmnly knwn as Define.xml is an integral part f FDA s electrnic submissins. Define.xml facilitates the review prcess by prviding infrmatin abut the structure and cntent f standard clinical data (SDTM and ADaM) in a machine readable frmat. There are tw versins f define.xml v1.0 and v2.0 available. In March 2016, FDA annunced t end supprt fr Versin 1.0 f define.xml and mandate the use f versin 2.0 fr all the electrnic submissins. This paper presents a data-driven apprach fr generating define.xml v2.0 using ADaM ADS specificatins and ADaM datasets. A Define ready ADaM ADS specificatin plus ADaM datasets are passed int a macr that autmatically generates define.xml v2.0. This macr als prvides an errr reprt fr any incnsistencies identified between ADaM datasets and ADaM specificatins. This autmatin prcess cnsiderably reduces the time and effrt in generating a CDISC cmpliant define.xml fr FDA submissins. INTRODUCTION Spnsr generate ADaM ADS specificatins which serves as a prgramming guidance dcument fr generating ADaM datasets. These ADaM ADS specificatins are als submitted t FDA in the Case Reprt Tabulatin Data Definitin Specificatins frmat r Define.xml prepared by CDISC define.xml team. Define.xml prvide the structure and cntent f ADaM datasets in a machine readable frmat. The prcess f generating a define.xml can be very time cnsuming if dne manually. This paper depicts a prcess f generating define.xml v2.0 using ADaM ADS specificatins and ADaM datasets with least manual input. A Define.xml prvides infrmatin abut the fllwing metadata s: Dataset Metadata: Variable Metadata: Name, Descriptin, Class, Structure, Purpse, Key Variables, Lcatin, Dcumentatin Name, Label, Type, Length/Display Frmat, Cntrlled Terminlgy, Surce/Derivatin/Cmment Parameter Value Level Metadata Describes methd used t derive a particular variable fr different PARAMCDs in an BDS ADaM dataset Cntrlled Terminlgy Analysis Derivatin Cmments External Dcumentatin (ADRG, SAS cdes) PRE-REQUIRMENTS Find enclsed the list f the items that are required t generate define.xml using this apprach: Define Stylesheet(define2-0-0.xls) ADaM Datasets 1

2 Trimmed ADaM Datasets where character variable lengths are adjusted t the maximum length f the variable used acrss all the datasets in the study. SAS Transprt file using Trimmed ADaM Datasets ADaM ADS specificatins External Dcumentatin ADRG SAS Cdes ADS SPECIFICATIONS Other external dcumentatin that is being referred in ADaM ADS specificatins A standard ADaM ADS specificatin template is created t generate define.xml. A separate wrksheet is created fr each metadata that is being presented in define.xml. Study Infrmatin In this sectin, we ppulate Prtcl Number, Study Descriptin, Prtcl Name, ADaM IG versin and language used fr writing ADaM specificatins and generating ADaM datasets. Parameter StudyName Descriptin 111-P-222 StudyDescriptin Define fr Study XYZ PrtclName StandardName Define fr Study XYZ ADaM-IG StandardVersin 1.0 Language En Figure 1. Study Infrmatin Dataset Metadata Dataset metadata serves as a TOC that lists ut all the ADaM datasets. The fllwing infrmatin is cllected in dataset metadata: Dataset Name Dataset Descriptin r Dataset label Dataset Structure Dataset Purpse Analysis fr ADaM Datasets Dataset Class (ADSL, BDS, OCCD and ADaM OTHER) Key Variables Repeating Yes: Fr ADS that have mre than ne recrd fr each USUBJID 2

3 Dcumentatin Dcument N: Fr ADS that have ne recrd fr each USUBJID A unique shrt name given t each external dcument. Each shrt name has t start with a prefix LF. Dataset Descriptin Structure Purpse Class ADSL Subject Level One recrd per screened subject Analysis SUBJECT LEVEL ANALYSIS Analysis DATASET ADVS Vital Signs One recrd per subject per parameter per visit Analysis BASIC DATA STRUCTURE Key Variables Repeating Dcumentatin Dcument USUBJID N SAP, Prtcl LF.ADRG; LF.ADSL.PGM; USUBJID,PARAMCD,AVISITN Yes SAP, Prtcl LF.ADVS.PGM; Figure 2. Dataset Metadata Variable Metadata All the variables that are included in each ADaM dataset are described in variable metadata. Dataset Name Variable Name Variable Label Variable Type as per data types give in CDISC ODM Variable length text, integer, flat, date, time, datetime, partialdate, partialtime, partialdatetime, incmpletedatetime Sigdigit: Significant digits. Only ppulated where variable type is flat Key: Integer value assigned t all the key variables Frmat: date and time frmats assciated with date/time numeric variables Cdelist: A unique name assigned t standard r spnsr defined valid values and decdes Origin: Derived, Assigned and Predecessr Surce/Derivatin: Describes the derivatin f a variable. If the derivatin is mre than 1000 characters, the derivatin will be saved in an external dcument. A shrt name fr this dcument will be listed in Dcument clumn Valuelist Ppulated nly fr BDS type f ADaM datasets 3

4 Mandatry Dcument Ppulated with a value f Y fr thse variables whse derivatin changes fr each parameter Value Level Metadata will be ppulated fr the variable fr whm valuelist is marked as Y Ppulated with values f Yes/N depending upn whether a variable is required r nt. A unique shrt name given t each external dcument. Each shrt name has t start with a prefix LF. Dataset Variable Label Type Length Sigdigit Key Frmat ADSL STUDYID Study Identifier text 15 ADSL SITEID Study Site Identifier text 25 ADSL INVID Investigatr Identifier text 25 ADSL INVNAM Investigatr Name text 200 ADSL USUBJID Unique Subject Identifier text 25 1 ADSL SUBJID Subject Identifier fr the Study text 25 CdeList Origin Surce ValueList Mandatry Dcument Predecessr DM.STUDYID Yes Predecessr DM.SITEID Yes Predecessr DM.INVID Yes Predecessr DM.INVNAM N Predecessr DM.USUBJID Yes Predecessr DM.SUBJID N Figure 3. Variable Metadata Value Level Metadata Value level metadata will be ppulated fr all the variables fr whm ValueList clumn is marked as Y in the variable metadata. Dataset Name Variable attributes fr which value level metadata is generated Variable Name Variable Label Variable Type Variable Length Sigdigit: Significant digits. Only ppulated when variable type is flat Origin: Derived/Assigned PARAMCD: List f PARAMCD that are being generated in a particular ADaM dataset Surce: Describes the derivatin f a variable fr each PARAMCD. If the derivatin is mre than 1000 characters, the derivatin will be saved in an external dcument. A shrt name fr this dcument will be listed in Dcument clumn 4

5 Dcument A unique shrt name given t each external dcument. Each shrt name has t start with a prefix LF. Dataset Variable Label Type Length Sigdigit Origin PARAMCD Surce Dcument Derived VSALL PARAM= trim(left(vs.vstest)) Derived BMI PARAM= trim(left(vs.vstest)) Derived DIABP PARAM= trim(left(vs.vstest)) " (" trim(left(vs.vsstresu)) ")" Derived HEIGHT PARAM= trim(left(vs.vstest)) " (" trim(left(vs.vsstresu)) ")" Derived PULSE PARAM= trim(left(vs.vstest)) " (" trim(left(vs.vsstresu)) ")" Derived SYSBP PARAM= trim(left(vs.vstest)) " (" trim(left(vs.vsstresu)) ")" Derived WEIGHT PARAM= trim(left(vs.vstest)) " (" trim(left(vs.vsstresu)) ")" Figure 4. Value Level Metadata Cntrlled Terminlgy Cntrlled terminlgy cllects standard r spnsr defined valid values and decdes. Cdelist Name: A unique shrt name assigned t a cdelist Cdelist Label: A shrt descriptin f cdelist Cdelist Type: text/integer/flat Cde: Standard r spnsr defined valid values Decde: Cded value fr each standard r spnsr defined value Rank: Ppulated nly fr cdelists that have a numeric significance. Rank shuld nt be used t define a display rder OrderNumber: OrderNumber is used t define a display rder fr the items in a particular cdelist CdeListNum: C-cdes prvided in Natinal Cancer Institute s Enterprise Vcabulary System if unique shrt name f a cdelist matches with standard cdelist names prvided in Natinal Cancer Institute s Enterprise Vcabulary System. CdeNum: C-cdes prvided in Natinal Cancer Institute s Enterprise Vcabulary System if any f standard r spnsr defined valid values matches with standard names prvided in Natinal Cancer Institute s Enterprise Vcabulary System. 5

6 Cdelist Name CdeList Label CdeList Type Cde Decde Rank OrderNumber CdeListNum Cdenum AGEU Age Unit text YEARS 1 C66781 C29848 SEX Sex text M 1 C66731 C20197 SEX Sex text F 2 C66731 C16576 AVISITN AVISITN integer 1 Screening 1 1 AVISITN AVISITN integer 2 Day -2 t AVISITN AVISITN integer 3 Day 1 t AVISITN AVISITN integer 4 Day RACE Race text WHITE 5 C74457 C41261 Figure 5. Cntrlled Terminlgy Dcuments This sectin cllects the fllwing infrmatin abut each external dcumentatin that is being referred in ADaM ADS specificatins: Dcument ID: A unique shrt name with a prefix f LF., given t each external dcument. Title: Text that will be displayed in define.xml HRef: Physical lcatin f the file with the actual file name and file extensin. If define.xml and external dcumentatin is lcated in the same flder, ppulate actual file name and file extensin nly. Dcument ID Title HRef LF.ADRG Analysis Data Reviewer's Guide analysis-data-reviewers-guide.pdf LF.ADSL.PGM adsl.sas d0_adsl.sas LF.ADVS.PGM advs.sas d1_advs.sas Figure 6. Dcuments 6

PROCESS FLOW OF GENREATING DEFINE.XML Trimmed ADaM Datasets ADaM ADS Specificatins External Dcumentatin External Dcumentatin Define.sas Define.xml v2.0 Figure 7. Prcess Flw f Generating Define.

7 PROCESS FLOW OF GENREATING DEFINE.XML Trimmed ADaM Datasets ADaM ADS Specificatins External Dcumentatin External Dcumentatin Define.sas Define.xml v2.0 Figure 7. Prcess Flw f Generating Define.xml The lcatin f trimmed ADaM datasets and final ADaM ADS specificatins are passed int define.sas macr which generates define.xml v2.0. Define.sas macr refers t trimmed ADaM datasets fr variable attributes (Name, label, type, length), rder f the variables in a particular ADaM dataset and cntrlled terminlgy fr derived variables. Figure 8. Define.xml v2.0 viewed via Micrsft Internet Explrer CONCLUSION 7

8 This data driven apprach f generating define.xml using ADaM datasets and ADaM ADS specificatins is a time-saving, straightfrward and easy way f generating define.xml v2.0. Prgrammers desn t need t have XML knwledge fr generating define.xml via this methd. REFERENCES CDISC Define-XML Specificatin, Versin 2.0, March 5, Jansen, Lex Creating Define-XML versin 2 including Analysis Results Metadata with the SAS Clinical Standards Tlkit. Pharma SUG RECOMMENDED READING CDISC Define-XML Specificatin, Versin 2.0 Study Data Technical Cnfrmance Guide, March 2016 CONTACT INFORMATION Yur cmments and questins are valued and encuraged. Cntact the authr at: Jaskaran Singh Gill ICON Plc Jaskaran.Gill@icnplc.cm Hima Bhaita ICON Plc Hima.Bhatia@icnplc.cm 8

Generating Define.xml v2.0 and Analysis Result Metadata using ADaM Specifications, ADaM Datasets and TFL Annotation

PhUSE US Cnnect 2018 Paper DS10 Generating Define.xml v2.0 and Analysis Result Metadata using ADaM Specificatins, ADaM Datasets and TFL Anntatin Mark Crangle, ICON Clinical Research, Marlw, UK Hima Bhatia,