Automatic Creation of Define.xml for ADaM
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1 Automatic Creation of Define.xml for ADaM Alessia Sacco, Statistical Programmer 1
2 Indice Define.xml Pinnacle 21 Community Valos ADaM Metadata 2
3 Define.xml Cos è: Case Report Tabulation Data Definition Specification (CRT-DDS, o define.xml). File formato XML (machinereadable) A cosa serve: Fornisce datasets, variabili, controlled terms e altri specifici metadata Perché: Standard richiesto da FDA (U.S) e PMDA (Japan) per la sottomissione di dati Define.xml 3
4 Pinnacle 21 Community Pinnacle 21 (prima OpenCDISC) viene largamente usato nell industria farmaceutica per validare i clinical trial data. 1. Validator (controlla conformità con SDTM, SEND, ADaM, e Define.xml) 2. Define.xml Generator (crea un conforme Define.xml 2.0 per SDTM, SEND, and ADaM datasets) 3. Converter (converte data tra SAS XPORT, Excel, CSV, and Dataset-XML) 4
5 Pinnacle 21 Community 5
6 Pinnacle 21 Community 6
7 Pinnacle 21 Community Define.xml Generator SAS XPORT DATASET Pinnacle 21 Create Spec EXCEL SPEC DEFINE.XML 7
8 Pinnacle 21 Community Excel Specification Study nome, descrizione, protocollo, standard Datasets lista dei datasets e corrispondenti metadata Variables lista delle variabili trovate durante la scansione ValueLevel, WhereClauses, Codelists, Dictionaries, Methods, Comments, Documents Excel Spec 8
9 Pinnacle 21 Community Completing Specifications Correzioni automatiche di Excel («ACN» «CAN») Paste Special per evitare caratteri speciali Define.xml è case sensitive Colonne ID e i riferimenti con le altre tab Trailing space characters (usare la funzione di Excel TRIM) Precisare il numero della pagina quando ORIGIN=CRF Inserire tutti i valori della Codelist, non solo quelli raccolti... 9
10 Valos ADaM Metadata Macro Valos EXCEL SPEC DEFINE.XML 10
11 Valos ADaM Metadata Dataset Name Parameter identifier ( Req, Perm, Cond ) Variable Name/Label/Type Display format Controlled Term Source/Derivation Comments Codelist Origin ADaM_Metadata 11
12 Valos ADaM Metadata Origin Predecessor, per variabili pre-esistenti in un SDTM o in un altro ADaM Assigned, per variabili che sono una classificazione di altre Derived, per variabili derivate da pre-esistenti variabili tramite uno specifico algoritmo Composite, per le quali si usa la number>@<origin>@<variable>@<comparator>@<condition> 12
13 Valos ADaM Metadata Origin Composite <order number>: numero provvisorio per identificare la condizione <origin>: tipo di origine per questa condizione <variable>: la variabile a cui viene applicata la condizione <comparator>: operatore di confronto (EQ, NE, GT, LT, IN,...) <condition>: condizione per la variabile 13
14 Valos ADaM Metadata condition description> <order number>: indice corrispondente all order number nella colonna Origin <full condition description>: testo con la source/derivation di ogni condizione 14
15 Valos ADaM Metadata Origin&Source/Derivation Example 15
16 Valos ADaM Metadata Macro Valos EXCEL SPEC Excel_Spec Completed 16
17 Dall ADaM Metadata all Excel Spec CODELISTS: Possibili Codelists: CDISC Controlled Terminology extensible codelist CDISC Controlled Terminology not extensible codelist Non-standard CDISC codelist Input: ADAM Terminology.xls SDTM Terminology.xls Terms e Decoded Values dai datasets 17
18 Pinnacle 21 Community Define.xml Generator 18
19 Pinnacle 21 Community Define.xml Validator 19
20 Conclusioni Creazione del Define.xml immediata Compilazione dell ADaM Metadata contemporanea alla costruzione dei datasets Documentazione dettagliata dal programmatore e validazione piu semplice e veloce Notevole risparmio di tempo 20
21 Grazie per l attenzione! Registered office: Savona Italy C.so Italia 15/6 zip code Head office: Genova Italy via Ceccardi 4/31 zip code Tel. and fax : info@valos.it 21
22 Bibliografia Usage of Pinnacle 21 Community Toolset for Clinical Programmers, Sergiy Sirichenko, Michael DiGiantomasso, Travis Collopy (Pinnacle 21, Plymouth Meeting, Pennsylvania) Automatic creation of define.xml for ADaM: a fast way approach starting from ADaM Metadata (Phuse 2017), Dmitri Petratchenko, Andrea Parodi, Anna Romanova (Valos srl) 22
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