SDTM-ETL 3.1 User Manual and Tutorial Adding
Contents
1. Cu rrent CodeList _ New CodeList Current Origin Edit Origin Comment External document for comment another dialog is displayed STUDYID STUDYID 40 CLVSTESTCD Vital Signs TestCodetiex NONE DEFINED YET NO CODELIST ASSIGNED CLVSTESICD Vital Signs Test odote When then using the checkbox Edit Origin and then using the button Edit NONE DEFINED YET ll Es a aes 7 e feet Try 4 Carre Designing Updating Origin for Item STUDYID r l L New 5 Origin type Current O Assigned Edit Protocol Comme O paat is defined as cesta Trial Design preparation ae glAn example could be Vital Signs Position when prescribed by the protocol Extel Ext aa CRF Current Document leat ID C Ne Descrip O No page details current J O Page list physical reference Hew gt Named destinations _ Ne s Page list List of named destinations def Co gt Page range first page last page aaa i First page Last page C News cane when selecting Protocol when the STUDYID has been prescribed by the protocol In case the origin is CRF we usually want to provide additional information such as the location of the annotated CRF and the page numbers named destinations or page range For example for the SDTM var2. Sticky Note on SOTM Variable Remove Sticky Note from SOTM Variable This will display the following dialog Edit Manage links to external documents _ leaf ID Parent Element Parent OID link A CRF einer e eC po C Nempiost pdf Erama a _ bupotemertsl Document C E CMtempttestpdf LEAF A CRF ItemDef VS VSORRES aCRF _ Ctempitest pdf LEAF A CRF ltemDef IT HEIGHT aCRF _ Ctempitest pdf LEAF A CRF ItemDef IT WEIGHT aCRF _ Ctempitest pdf In this case we have an Annotated CRF two Supplemental Documents six generated data sets in this case in Dataset XML format and we have a few Origin s with a link to a specific page of the annotated CRF for three SDTM variables parent element is temDef Using the buttons Edit selected Delete selected and Add new we can now manage all this links to external documents and datasets For example one can edit the title and link location to the annotated CRF EET Wo Edit Link to external document ia leaf ID LEAF A CRF Parent Element Annotated CRF Parent OID title la CRF link d MystudiesiMystu dyXYZIMYZ_aCRF pdf Note that when changing information about the annotated CRF all links to this CRF will be updated e g Edit Manage links to external documents Ls 2 leaf ID Parent Element ParentoID title mk LEAF SUPPDOC1 _ SupplementalIDoc_ Supplemental Document 1 C temp suppdoc1 bt LEAF SUPPDO
3. additional documents using the menu Edit Links to external documents Somewhat later we will see how we can edit the information and or add additional supplemental document links to the define xml def leaf elements within def SupplementalDoc Adding Origin information to individual SDTM SEND variables If the SDTM datasets will be submitted to a regulatory authority it is mandatory to provide an Origin for each variable Whereas this was free text in define xml 1 0 it has been enumerated in define xml to and in the case of ADaM also Predecessor For further details and examples see the define xml 2 0 specificaton section 5 3 11 3 def Origin element For each SDTM SEND variable this information can easily be added by selecting the specific SDTM SEND information in the table on the right and then using the menu Edit SDTM Assigned Protocol Derived eDT electronic data transfer CRF individual judgement by an evaluator protocol enforced calculated using an algorithm obtained via data stream data from case report form Variable Properties This leads to the dialog Edit Properties for SDTM Variable STUDYID gt i OID Name Data type Current Length _ New Length Current Significant Digits C New Significant Digits Current Role New Role Current Role CodeList New Role CodeList Current Origin Edit Origin
4. supplemental documentation lt TranslatedText gt lt _ Description det DocumentReft leaf ID LEAF SUPPDOC2 gt def PDFPageReft PageRefs 335 Type PhaysicalRet gt lt def Documenther gt lt r det CommentDerl gt When information about comments in an external document has been added or is already present the button External document for comment is colored so that one knows that information is already present Edit properties for SDTM Domain MyStudy VS OID IMyStu dy YS Name Vital Signs Purpose Tabulation i Comment description of VSTESTCD comment for details see supplemental documentation IsReferenceData No Subject re A link to an external documentis already present Click the button to edit or remove the link l Repeating Yes more than 1 record per subject No 1 record per subject In order to add a comment with or without a reference to an external document for an individual SDTM variable the procedure is extremely similar just select an SDTM variable in the table on the right then use the menu Edit SDTM Variable Properties One can then add a short comment in the Comment field e g STESTCD comment Comment External document for comment and if additional information is in an external document use the bu
5. 5 No external document EA OT E TtTLAL A W S a A E a ir mba Phe LEAF SUPPDOC2 O Page list physical reference O Named destinations Page list List of named destinations _ Page range first page last page First page Last page allowing to define a document which already need to have been defined in Supplemental Documents and one or more pages or named destinations For example if the additional comments are defined in file C temp suppdoc2 pdf on page 33 one can fill the fields with Sisun oaae EN A te n _ No external document LEAF SUPPDOC LEAF SUPPDOC i ClMempisuppdoc tt Page list physical reference O Named destinations Page list List of named destinations 33 _ Page range first page last page First page Last page In the define xml this will later show as lt ItemGroupDeft ITsRefterenceData Wo Name Yital Signs OID Mystudy VS Furpose Tabulation Repeating Yes deft ArchiveLocationIDP Location NyStudy va def Class Findings left Comment0ID COM 3 def Sstructure O0ne record per V YS VSTESTCD per USUBJID gt lt Dbescription gt lt TranslatedText xml lang en gt ital Signs lt TranslatedText gt lt Description gt and the corresponding CommentDef def CommentDet UID COM VST Description lt TranslatedText xml lang en gt description af YSTESTCD comment Lor details see
6. C2 __ SupplementalDoc Supplemental Document 2 C Wtemp suppdoc2 t LEAFA CRF _ _ itemDef _______ VSVSORRES_ __ a CRF LEAF A CRF_ __ itemDef IT HEIGHT a CRF LEAF ACRE _ IitemDef __________ IT WEIGHT_____ a CRF One can also add new supplemental documents e g using Add New PRAY ae aa Add link to external document i C Add link to dataset for SOTM domain Add link to document for Supplemental Document O Add link to annotated CRF for SOTM Variable C Add AnnotatedCRF element O Add SupplementalDocElement Please make your choice followed by Oo Add new defDocumentRet te gt existing defiSupplementalDoc ladle iani idk _ Store link as relative path Title Supplemental document 3 Leaf ID LEAF SUPPD oca Cancel Resulting in a new entry to the table EaiManage iniiae documents U LEAF A CRF pease a CRF wane nena enn a LL ALE a TENE SUPPDOG ae OO O bt LEAFACRF iitemDef_ ss VS VSORRES la CRF_ MyStuddies MyStudyXYZ XYZ_a LEAFACRF itemDef_ ITHEIGHT fa CRF_ MyStuddies MyStudyXYZ XYZ_a LEAFACRF embe WECH CRF EM Studies WyStudyY ZZ a LEAF SUPPDOC3 SupplementalDoc Supplemental document D MyStudies MyStudyXYZ Supple Also notice that one cannot add a second annotated CRF If you try you will see that the corresponding radiobutton is disabled Add link to external document C Add link to dataset for SDTM domain O A
7. Questionnaires lt TranslatedText gt lt Description gt lt ItemReft ItemOIM STUDYID Mandatory Yes Method0OID IMP MyStody 05 25 5STUD YID OrderNumber 1 gt lt ItemRef ItemOID DOMAIN Mandatory Yes MethodOID IMP MysStudy 05 25 D0MAIN OrderNumber 23 gt lt ItemReft ItemOIM USUBJID Mandatory Yes Method0OID IMP MyStuody 05 25 05S0BJID OrderNumber 3 gt lt ItemReft ItemOID OS 05SE0 Mandatory Yes MethodOID IMP MyStudy 05 259 05 Q55E0 OrderNumber 4 gt lt ItemRef ItemOID O5 QOSTESTCD Mandatory Yes MethodOlID IMP MyStudy 03 259 08 Q0STESTCD OrderNumber 7 gt lt ItemRef ItemOID OS QOSTEST Mandatory Yes MethodOID IMP MyStudy 05 29 05 Q8TEST OrderNumber 8 gt lt ItemRef ItemOID O5 OS0RRES Mandatory Yes MethodOID IMP MyStudy 05 29 05 Q0S0ORRES OrderNumber 11 gt lt ItemReft ItemOID O5 050RRES0 Mandatory No Method0OID IMP MyStoudy 05 2595 05 Q50RRES0 OrderNumber 13 gt lt ItemRef ItemOID QOS VISIT Mandatory No MethodOID IMP MyStudy 05 29 03 VISIT OrderNumber 20 gt lt ItemRef ItemOID OS VISITNUM Mandatory Yes MethodOolID IMP MyStudy 05 25 05 VISITNUM OrderNumber 21 gt lt ItemRef ItemOID QOS 0SDTC Mandatory Yes MethodOlID IMP MyStudy 05 29 035 Q8DTcC OrderNumber 23 gt lt def leaf xmlns xlink httop wew w3 org 1999 xlink ID Location MyStudy 05 xlink href D temp 05 _ml gt lt def title gt Dataset Q5
8. SDTM ETL 3 1 User Manual and Tutorial Author Jozef Aerts XML4Pharma Last update 2015 05 25 Adding editing and managing links to external documents in define xml Define xml contains the metadata of our SDTM SEND datasets If the define xml 1s intended to be submitted to the FDA there is a so called context of a regulatory submission this also includes references to external documments such as e the annotated CRF as a single PDF file e supplemental documents usually also as PDF files e references to single pages or named destinations within the annotated CRF SDTM ETL has all the necessary features to add this kind of information to the underlying define xml and to edit and manage these references to external files Adding a reference to the annotated CRF The FDA requires that a submission comes with an annotated CRF file which must be a PDF file In order to add the location of the annotated CRF file use the menu Insert Link to annotated CRF insert Transform Validate Options About MeasurementUnit definitions from ODM into define xml All CodeList definitions from ODM into define xml Selected CodeList definitions from ODM into define xml CodeList definitions from File into define xml Create new SOTM CodeList from existing CodeList Create new SOTM CodeList from MeasurementUnits Create new ValueList from existing CodeList Create mapping formula Ctrl M Sponsor defined SOTM Domain Ctrl P Do
9. dd link to document for Supplemental Document O Add link to annotated CRF for SDTM Variable C Add AnnotatedCRF element O Add SupplementalDocElement Please make your choice For the case of links to specific pages of the annotated CRF parent element ItemDef one can only edit the link and the title itself For editing e g the page numbers use the main menu Edit SDTM Variable Properties followed by Edit Origin and Edit
10. e list physical reference C Named destinations Page list List of named destinations W Page range first page last page First page and detailed information about where additional information can be found in the external document can be provided e g Edit FTT Valuelist Variabl aa Comment on valuelist variable WEIGHT _ No external document LEAF SUPPDOC1 AF SUPPDOC 2 No page details D Page list physical reference First page Last page When using define xml 2 0 it is usually expected that a WhereClause for each valuelevel variable is provided indicating under which conditions the valuelevel variable is used So when using the menu Edit SDTM ValueList and selecting a single valuelist the following table will appear here for example for the valuelist for VSORRES Oooo O External document for comment Number of RangeChecks 1H Comparator Item OID VS VSORRES CheckValue WEIGHT V3 VSORRESU VS VSSTRESC here indicating that the metadata from IT WEIGHT must be applied e g on VSORRES when VSTESTCD has the value WEIGHT At the top one also sees a Comment field allowing to add a short comment e g Designing Updating WhereCla OID WC T WEIGHT Comment luse metadata of WEIGHT when VSTESTCD WEIGHT External document for comment As soon as one adds something in the Comment field also the External document fo
11. iable VSORRES vital sign original result Designing Updating Ongin far iem VSORRES i Origin type O Assigned _ Protocol O Derived Electronic Data Transfer CRF Oocument eat HLF ama O No page details Page list physical reference Named destinations Page list List of named destinations 44 13 15 19 22 35 O Page range first page last page here stating that the field on the annotated CRF can be found on pages 11 13 15 19 22 and 35 of the document described by the identifier leaf ID LEAF A CRF which we have generated a few moments ago This dialog allows us to define the details for each kind of origin It is idiot proof for example in case of CRF the dialog will remain visible unless all necessary information is provided or the Cancel button is clicked Note again that an Origin must be provided for each individual SDTM SEND variable when the context is a regulatory submission This is however not checked by tools such as OpenCDISC as the latter can not know whether the define xml is meant for a regulatory submission or not In the case you prefer to provide a page range f CRF Document leaf ID LEAF A CRF a C No page details Page list physical reference O Named destinations Page list List of named destinations Page range first page last page Firstpage 11 0 l Last page 35 O 00 O i Adding a link
12. is information into the define xml Adding a reference to a supplemental document For adding a reference to a supplemental document the procedure is very similar use the menu Insert Link to Supplemental Doc Transform Validate Options About MeasurementUnit definitions from ODM into define xml All CodeList definitions from ODM into define xml Selected CodeList definitions from ODM into define xml CodeList definitions from File into define xml Create new SOTM CodeList from existing CodeList Create new SOTM CodeList from MeasurementUnits Create new ValueList from existing CodeList Create mapping formula Ctrl M Sponsor defined SOTM Domain Ctrl P Domain specific SUPPQUAL Global Subject Variables Domain New SDTM Variable Ctrl l New non standard SDTM Variable for SUPPQUAL New SDTM Variable for COMMENT New SDTM Variable for RELREC Link to Annotated CRF which leads to a very similar dialog that can e g be filled like Add Supplemental Document link uN ma cas DTM ETLIMyStudyisuppdoct pdf Tithe supplemental Document 1 Leaf ID LEAF SUPPD oc This creates a def SupplementalDoc element in the define xml and adds an element def leaf with leafID LEAF SUPPDOC 1 to it After this if you try to create the Supplemental Document element again you will obtain a notification Warning A def SupplementalDoc element is already present You can edit its contents e g add
13. lt def ititle gt lt def leat gt lt ItemGroupDetf gt External documents with comments As of define xml 2 0 one can add comments to following elements e Domains datasets define xml ItemGroupDef e Variables define xml ItemDef e Where clauses define xml WhereClauseDef For the latter also see the document Where clauses for valuelists In each of these cases one can also make a reference to an external document such as the reviewers guide and even indicate on which page This is done especially for very long comments or explanations that one considers to be too long for the define xml Remark that in define xml there is no 200 character limitation for comments Let us start with comments on the level of domains datasets In order to add a comment and or comment reference to a domain select the row in the SDTM or SEND table on the right than use the menu Edit SDTM Domain Properties or double click the first cell with the dataset name In the field Comment one can now add a short comment For example for VS MyStudy VS IMyStu dvs Name Vital Signs Purpose Tabulation description of VSTESTCD comment for details see supplemental documentation Ed ieee External document for comment If you are working with define xml 2 0 you will also find a button External document for comment When clicked the following dialog appears omic a a E f
14. main specific SUPPQUAL Global Subject Variables Domain New SDTM Variable Ctrl I New non standard SDTM Variable for SUPPQUAL New SDTM Variable for COMMENT New SDTM Variable for RELREC Link to Annotated CRF Link to Supplemental Doc This opens the dialog 1 It would be much better if the FDA required the ODM file with the study design especially in the case of eCRFs Add Annotated CRF link ry j Cox Leaf ID O E _ i EE a You can then browse for your file with the annoted CRF using the Browse button If you do not want to have the link appear as an absolute file path check the box Store link as relative path When writing the define xml the software will then try to generated a path relative to where the define xml is written You can however also just type the name of the file e g aCRF pdf and leave the checkbox unchecked The system will then assume that you will later copy the file with the annotated CRFs to the same directory as where you have the define xml file as is usual You also need to provide a title and a leaf ID For example Add Annotated CRF link E Cox ICASDTW ETLIMyStu dyiaCRF pdt Title File with the annoated CRFs Leaf ID LEAF A CRA a Sw EEE You are free to choose an ID for the leaf ID as long as it is unique within your define xml For example in most CDISC examples one will find something like LF blankCRF for leaf ID Clicking OK then stores th
15. r comment becomes available allowing to add a reference and page details to an external document Clicking the button brings up the now well know dialog tone cnet i hs tee i S la No external document LEAF SUPPDOC2 O No page details O Page list physical reference Named destinations Page list List of named destinations Page range first page last page First page fis Last page in which we can provide the information where the reviewer can find additional information about the where clause 1 e additional information about when the metadata of IT WEIGHT should be applied For example ama document OE No external document LEAF SUPPDOC O No page details O Page list physical reference Named destinations Page list List of named destinations WEIGHT_WHERECLAUSE Page range first page last page First page Last page indicating that there is a named destination in the supplemental document Adding Editing links to external documents management Links to external documents can also be generated or altered or removed using the menu Edit Links to external documents View Navigate Insert Transform Validate Copy Domain Dataset Ctrl B Paste Domain Dataset Ctrl U Remove Domain Dataset Ctrl Delete Transpose Domain Dataset Ctrl T SDTM Variable Properties SDTM Domain Properties SDTM CodeList SDTM ValueList
16. to the location of each dataset For each dataset that is generated being it either in SAS XPORT format or in the new Dataset XML format the location and name of the dataset must be provided in the define xml When executing your mappings and generating dataset you can already provide this information Le ODM file with clinical data CASDTM ETLiTestFilesiODM1 2 MyStudy_ClinicalData_only xml _ MetaData in separate ODM file _ Administrative data in separate ODM file Dataset AML Output Files Directory SDTM SEND Results _ Try to generate 1 N RELREC Relationships _ View Results in Smart Dataset XML Viewer Add location of Dataset XML files to define xml When the checkbox Add location of Dataset XML files to define xml is checked the system will add the information where the datasets have been generated to the define xml The same applies but with a slightly different checkbox label for SAS XPT files Essentially this means that for each dataset that is created a def AcrchiveLocationID attribute and corresponding def leaf element within the corresponding I temGroupDef are generated lt ItemGroupDetft IsReferenceData No Name 085 OTM MyStudy 05 Purpose Tabulation Repeating Yes deft ArchiveLocationlD Location MyStudy 0s def Class Findings def Structure One record per 05 Q0STESTCD per Q2 VISIT per USUBJID gt lt Description gt lt TranslatedText xml lang en gt
17. tton External document for comment leading to External document A mem _ No external document LEAF SUPPDOC1 LEAF SUPPDOC Cltemp suppdoct tt D No page details O Page list physical reference O Named destinations Page list List of named destinations Page range first page last page First page 33 Last page 55 where you state that additional comments can be found in the external document at C temp suppdoc1 txt from pages 33 to 55 For valuelevel metadata one can do exactly the same thing using the menu Edit SOTM ValueList e g i a eS E Edit it SDTM ValueLis meer me ee ee ig eeh im Dials tan Comment gommen Description IT WEIGHT WEIGHT a a lt a S IT BMI BM Moat s __ E EE When selecting the Comment field and when using define xml 2 0 a similar dialog is displayed ae a Edit Comment for ValueList V No external document LEAF SUPPDOC 3 No page details Page list physical reference 2 Named destinations Page lis list List of named destinations l O Page range first page last page First page Last page As soon as some text is entered into the Comment field also the fields about a reference to an external document becomes available Edit owes for ValueList Variable Comment on valuelist variable WEIGHT _ No external document LEAF SUPPDOC1 Ww No page details Pag
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