SDTM-ETL 3.0 User Manual and Tutorial
Contents
1. MLIETESTCD TTV VISITNUM TS TSSEQ TD TDMINPAI CO IDVAR CO IDVARVAL SE ELEMENT BE SESTDTC SV VISITDY SV SVSTDTC X EXSEQ EX EXGRPID EX EXREFID PR PRSEQ PR PRGRPID PR PRSPID ISU SUSEQ SU SUGRPID SU SUSPID AE AESEQ E CESEQ AE AEGRPID E CEGRPID AE AEREFID E CEREFID DV DVREFID DV DVSPID jO HOGRPID O HOREFID DS DSGRPID DS DSREFID B TranslatedText Prior or Concomitant Medications a TranslatedText M dications pr c dentes B TranslatedT ext Vorherige Medikationen TranslatedText cf ltemGroupDef Common o m Description o ci ite site Nu The division line between the two sides of the screen can be dragged in order to see more or less of each side of the screen It probably has already been noticed that some of the SDTM variables are colored red some blue and other ones green The red ones are the ones that are designated as being required in the SDTM IG the blue ones those that are designated as being expected and the green ones those that are permissible In order to obtain more information about a specific variable just hover the mouse over a cell e g A A MO Y A steel i E AELL TCD G EGTEST Length 80 One also sees that currently the maximal length for this variable has been set to 80 Later it will be demons2. So when calculating xxDY we must always add logic in our script to avoid that a value 0 is given as the result In this case it is pretty simple we can even reuse variables that were defined before For DMDY we write the mapping The Transformation Script amp DM DMDY dateditt DM DMDIC DM RFSIDIC DM DMDTC and DM RFSTDTC have been defined before i e more to the left so we can reuse them in read only mode The datediff function delivers the difference in days In case the first parameter value is later than the second a positive or better said non negative result is obtained One immediately sees that this can lead to a DMDY 0 result when DMDTC and RFSTDTC are identical as is the case So we adapt the mapping to Mapping Description SDOTM ETL mapping for DM DMDY The Transformation Script STEMP datediff DM DMDIC DM RFSIDIC STEMPNUMBER number STEMP if STEMPNUMBER gt 0 f SDM DMDY STEMPNUMBER 1 else SDM DMDY STEMPNUMBER There is one pecularity in this script the datediff function essentially returns a string which need to be transformed into a number kind of casting in order to do mathematical calculations with it The result for our two subjects is 17 That was meant sceptically 18 Essentially DMDY should never appear in SDTM as SDTM is about collected data not about derived data The tools of the FDA should do these kind of
3. RFSTDTC DM RFENDTC _ DM RFXST E BasicDefinitions SV sv brovo Doman us uasio sven vvn fvmsmoY SV SVSTD MetaDataVersion CDISC Example Stud EJ Protocol J StudyEventDef Baseline Visit C Description J FormDef Baseline Visit For o C Description gt E ltemGroupDef Common Ei ltemGroupDef Demogra c Description Generating a study specific domain instance The mapping can begin As we do not want to edit the template domains themselves well it 1s not possible within the tool we heed to create a study specific instance We will start with the DM domain There are two ways to do so 1 drag an drop the DM row to the last row which in our case is the S V using the mouse with the left mouse button down release the left mouse button to drop 2 select one of the cells of the DM row and use the menu Edit Copy Domain Dataset or use CTRL B Then select the last row of the table and use the menu Edit Past Domain Dataset or use CTRL U In both cases the following dialog is displayed Copy Domain DM lr Copy STUDYID from loaded ODM Copy DOMAIN from originator Automatically add USUBJID C Auto The three first checkboxes are already checked in advance The first means that the value for S LUDYID in the SDTM will automatically be set to the value of the Study OID in the ODM which is usually a wise decision The second will fix the value of the SDTM variab
4. a supplemental qualifier to provide the information on the other race If we change the mapping script to The Transformation Script Mapping using ODM element ItemData with ItemOID I RACE Using SDIM CodeList CL C74457 RACE Using a CodeList mapping between ODM CodeList CL RACE and SDIM CodeLisat CL C7 4457 RACE SCODEDVALUE xpath StudyEventData StudyEventOID BASELINE FormData FormOID F BASELINE ItemGrouphi SNEWCODEDVALUE if CODEDVALUE CAUCASIAN SNEWCODEDVALUE WHITE elsif CODEDVALUE BLACK SNEWCODEDVALUE BLACK OR AFRICAN AMERICAN elsif CODEDVALUE ASIAN SNEWCODEDVALUE ASIAN elsif CODEDVALUE OTHER SNEWCODEDVALUE OTHER else SNEWCODEDVALUE DM RACE NEWCODEDVALUE and test the mapping for the whole domain the following result is obtained partial view DM BRTHDTC DM AGE DM AGEU DM SEX DM RACE 1957 05 07 52 YEARS F WHITE 1961 09 08 48 YEARS Mo WHE W RFPENDTC It s not a bad idea to save all the work done sofar This is accomplished by using the menu File Save define xml or using CTRL S S a fe SDTM ETL Edit View Navigate Insert Transform Validate Options Load ODM file Stng O Create define xml Strg M Load Study define xml Sing D Load Template define xml Sirg S i 2 Example Study Metadata Exit and selecting a location and name for
5. described in a special document SDTM ETL Scripting Language In the current case the mapping script is very simply STUDYID CES stating the the variable STUDYID is a string remark the quotes with a fixed value of CES Also notice the semicolon at the end marking the end of the statement The lower panel Scripting Language Functions contain a series of buttons for generating snippets of coding involving build in functions To get more explanation about a specific function just hover the mouse over a button e g Scripting Language Functions usupa investigator se substring before substring after Substring Takes the substring from the first argument starting at position given by the second argument with length given by the third argument optional We will later treat the use of functions in detail For very complicated mappings which I hope is the minority but that depends on your study design one can blow up the central panel using the button Full Screen Transformation Script Panel which generates a full screen script editor panel When done editing the mapping script click the OK button or use the Cancel button to cancel all editing For the DM variables DOMAIN a similar mapping has already been generated automatically The Transformation Script DOMAIN DH Double clicking the cell USUBJID provides the mapping for the variable USUBJI
6. the SDS VarName in the ODM the CDASH name and or the SDTM Alias After clicking Find and if there is a hot candidate in the ODM the tree will automatically ex and and the hot candidate item is displayed and selected ee SDTM ETL version 3 0 File Edit View Navigate Insert Transform Validate Options About i ODM ie study o E GlobalVariables E BasicDefinitions gt E MetaDataVersion CDISC Example Study Metadata G Protocol gt Ei StudyEventDef Baseline Visit o E Description FormDef Baseline Visit Form E Description gt J ItemGroupDef Common o E3 Description temDef Visit Time Alias Common ltemGroup Alias o E ItemGroupDef Demographics But are there already any clinical data for this data point One can test using the menu View ODM Clinical Data This shows the window File with ODM Clinical Data C SDTM ETL_demo ODM_1 3 CES_Clinicalbata_single_subjectxml L Generalize for all Items _ Generalize for all ttemGroups _ Generalize for all Forms C Generalize for all StudyEvents _ Limit Results to first Results _ Also display RepeatKeys ODM uses non typed ltemData ODM uses TYPED ItemData View ODM Clinical Data As a file with clinical data has already been used for testing the field File with ODM Clinical Data is already prefilled So one only need to click the button View ODM Clinical Data which r
7. the main window drag and drop one of the items Visit date from the tree with the study design it doesn t matter which one and drop it in the cell RFENDTC The following dialog is displayed S Import ItemDef Visit Date for SDTM Variable DM RFENDTC ax Import XPath expression for ltemData Value attribute from Clinical Data C Import XPath expression for another ltemData attribute subelement from Clinical Data O Import ltemDef attribute value static value from Study Definition beneralize for all StudyEvents Except for No Exceptions No Inclusions Generalize for all Forms Except for No Exceptions No Inclusions _ Generalize for all temGroups Except for No Exceptions Only for No Inclusions _ Generalize for all Items Except for No Exceptions Only for No Inclusions _ View Edit XPath expression advanced Check the checkboxes Generalize for all StudyEvents and Generalize for all Forms stating that we want to have the item independent of the form or visit This leads to the mapping Mapping Description SDOTM ETL mapping for DM RFENDTC The Transformation Script Mapping using ODM element ItemData with ItemOID I VISIT Generalized for all StudyEvents Generalized for all Forms within the StudyEvent SDM RFENDIC xpath StudyEventData FormData ItemGroupData ItemGroupOIDE IG COMMON ItemData ItemOID But we only want the last one so we do a little rew
8. was not collected directly so we need to calculate it from the birth date and the reference start date Just double click the cell AGE to start the mapping process Mapping Description SDOTM ETL mapping for DWLAGE The Transformation Script As the birth date DM BRTHDTC and the reference start date DM RFSTDTC were already mapped before we can reuse them but in only in read mode Now look into the lower part of the mapping screen where the Scripting Language Functions are displayed If we scroll down we find Tienie aon aoe between two dates as an integer number of days A positive number is obtained when the first date is later than the second date n Transformation Script Panel m _ r So we can use the function datediff to calculate the difference in number of days between reference start date and the birth date If the result is then divided by 365 2 the average number of days in a year then the age in years is obtained So the mapping script becomes Mapping Description SDOTM ETL mapping for DM AGE The Transformation Script SDM AGE datediff DM RFSIDIC SDM BRIHDIC 365 2 and executing the mapping for the whole domain results in DM RFICDTC DM RFPENDTC DM BRTIHDTC 2010 02 27 1100 27 2010 03 13 957 05 07 52 861 6341 7305568 gt 2010 02 26714 33 2010 03 16 1961 09 06 48 485761226729508 which is not entirely w
9. within the software itself so click Execute Transformation XSLT Code This results in a new dialog cite Tansfomatn SUN Code We me o ODM file with clinical data a _ MetaData in separate ODM file _ Administrative data in separate ODM file A l t o Split records gt 200 characters to SUPP records _ Move non standard SDTM Variables to SUPP Move Comment Variables to Comments CO Domain Move Relrec Variables to Related Records RELREC domain _ Try to generate 1 N RELREC Relationships View Result SDTM tables Save Result SDTM tables as SAS XPORT files SAS XPORT files directory L Add location of SAS XPORT files to define xml C Store link as relative path 10 This can be useful to execute the transformations off line The upper field allows to add the location of the ODM file with clinical data One can use the Browse button to locate this file At the moment we do not need to generate any SAS XPT files so we leave the checkbox Save Result SDTM tables as SAS XPORT files unchecked The checkbox View Result SDTM files remains checked this will open an own viewer for the results that we have sofar One of the advantages of the SDTM ETL software is that one can start developing the mappings even before the first subject has enrolled But in order to test the mappings we need some clinical data even if it are mock data Consider the case that we alre
10. Close Project Stg W Def Demographics i Exit Stg pion The reason it speaks about a define xml is that all our mappings and any other metadata about our 1 This is a study design originally developed by Dave Iberson Hurst for demo purposes and later extended by others SDTM or SEND will be stored in a define xml structure which is kept in sync with everything that we do so that at the end we will be able to generate a define xml file for our study with just a few mouse clicks A dialog is then presented SDTM Version rE Which version of the CDISC SDTM SEND Standard would you like to work with 2 SDTM 1 2 SDTM G 3 1 2 2 SDTM 1 3 SDTM G 3 1 3 SDTM 1 4 SDTMAG 3 2 SEND 3 0 Define xml version C define xml 1 0 define xml 2 0 The user can choose between SDTM versions 1 2 1 3 or 1 4 the latter has been published early 2014 or SEND 3 0 Also one can choose between using define xml 1 0 and 2 0 for keeping the metadata As these are the latest versions we select SDTM 1 4 SDTM IG 3 2 and define xml 2 0 One can also come to this dialog using the keyboard combination CTRL N After clicking OK the system now starts loading the template which can take a few minutes When finished the following dialog is displayed SOTM define xml tables created SDTM Version is 1 4 define xml version is 2 0 Validate define xml structure now The reason that this dialog is displayed is that some user
11. D Mapping Description USUBJID from ODM ClinicalData The Transformation Script The field Mapping Description has been prefilled but you can edit that stating that the value will be taken from the ODM ClinicalData The transformation script itself uses a function usubjid which simply takes the value of the SubjectKey attribute of the SubjectData element in the ODM file with clinical data Let us now test this mapping on a real set of clinical data For this click the button Test Transform to XSLT This will generate a mapping script in XSLT language which you do not need to learn to transform XML files or to extract information from XML files such as CDISC ODM files with clinical data The result of clicking the button Test Transform to XSLT is a new window Select whether the ODM file with clinical data works with non typed or with typed ItemData wi it uses non typed ltemData It uses TYPED ItemData as in ODM 1 2 new as of ODM 1 3 _ Never ask again in current session It asks you whether your ODM clinical data is znon typed or typed If you don t know ask your EDC vendor or the source of your clinicalm data or just try one of both possibilities you will immediately find out which one applies You can also have a quick look at a file with clinical data In case you find a lot of ItemData elements with a Value attribute this means that your data i
12. DTC DM RFXSTDTC DM RFXENDTC DM RFICDTC DM RFPENDTC 2010 03 13 2010 02 27710 27 2010 03 13 2010 02 27T 10 27 33 2010 03 13 2010 02 27T 10 27 Meanwhile we have received the data of a second subject so we can test our mapping again Execute Transformation XSLT Code l e EE ODM file with clinical data CASDOTM ETL_demo0DM_1 3CES5_ClinicalData_two_subjects xml _ MetaData in separate ODM file _ Administrative data in separate ODM file Brow s _ Split records gt 200 characters to SUPP records Resulting in COV a I O oa STUDYID DOMAIN USUBJID SUBJID DM RFSTDTC DM RFENDTC DM RFXSTDTC DM RFXENDTC DM RFICDTC DM RFPENC ICES DM 00 00 2010 02 27T10 27 33 2010 03 13 2010 02 27T10 27 33 2010 03 13 2010 02 27T 10 27 33 2010 03 13 0 0 y i 1 1 5 Ices Dm o2 ooz 2010 02 287T1433 12 2010 03 16 2010 02 28T14 33 12 2010 03 16 2010 02 28T14 33 12 2010 03 16 Let us now concentrate on two other important SDTM variables in the SDTM domain BRTHDTC and AGE Again we first try to find a hot candidate in our ODM tree Find hot candidate for SDTM BRTHDTC SDSVarName to find RTHDTC _ CDASH Names to find SDTM Alias to find BRTHDTC ry Start from top G Start from current position Find With the result EI Protocol o EI StudyEventDef Baseline Visit EI Description 4 EJ FormDef Baseline Visit Form EI Description o Ei ltemGroupDef Common gt E I
13. DTM CDISC Notes This displays the window SDTM CDISC Note for Variable DM RFSTDTC Reference Start Date time for the subject in 150 8601 character format Usually equivalent to date time when subject was first exposed to study treatment Required for all randomized subjects will be null for all subjects who did not meet the milestone the date requires such as screen failures or unassigned subjects Core Exp We can easily map this to the date of the first visit Maybe there is a hot candidate in the ODM for RFSTDTC i e the ODM has been annotated that the item is ideally suited to be used for RFSTDTC For finding out first select the RFSTDTC cell and then use the menu Navigate Find hot SDTM Candidate Navigate Insert Transform Validate Next node Unten Previous node Oben Collapse node Links Expand node Rechts Next Instance Strg Bild ab Previous Instance Strg Bild auf Select associated CodeList F2 Find tree node by OID Name F2 Find hot SOTM Candidate 4 The following dialog is displayed 11 Our very simple sample study does not have a data point for date of first study treatment If there is such a data point the corresponding date can or even is advised to be used i Find hot candidate for SDTM R i SDSVarName to find RFSTDTC _ CDASH Names to find SDTM Alias to find RFSTDTC Start from top O Start from current position L One can select to search using
14. SDTM ETL 3 0 User Manual and Tutorial Author Jozef Aerts XML4Pharma Last update 2014 02 15 Loading an SDTM template mappings for DM After having loaded and inspected a CDISC ODM file with the study design we can start working on the mapping with SDTM or SEND At the left side of the screen the tree view of the clinical study design is already shown in this case of the CES study oe bom ven 300 File Edit View Navigate Insert Transform Validate Options About MetaDataVersion CDISC Example Study Metadata E Protocol E8 StudyEventDef Baseline Visit o EI Description FormDet Baseline Visit Form CI Description o ltemGroupDef Common temGroupDef Demographics CI Description BN a N S ud N enr E Paa a E oe t Darn temDef DM Race Alias DM amp CI ltemGroupDef Smoking History the right side of the screen being still empty In order to start mapping to SDTM or SEND a template which is implementing the SDTM IG or SEND IG needs to be loaded In order to do so use the menu File Create define xml SDTM ETL version 3 File Edit View Navigate Insert Transform Validate Load ODM file Stg O Example Study Metadata ath fas aot oa Pa rh F z IK prip F YE IE a g i Load Study define xml Himi Create an SOTM or SEND define xml Load Template define xmm ste gt aline Visit Form Save define xml Sig S save cleaned define xml Def Common
15. ady have some but not all collected data of a first subject We can already use these data to test our mapping For example Execute Transformation XSLT Code S i ODM file with clinical data CASDTM ETL_demovDM_1 3 CES_ClinicalData_single_subjectxml MetaData in separate ODM file _ Administrative data in separate ODM file and we can now click the button Execute Transformation on Clinical Data _ Save Result SDTM tables as SAS XPORT files SAS XPORT files directory C Add location of SAS XPORT files to define xml L Store link as relative path Messages and error messages Execute Transformation on Clinical Data n eee After a few seconds the transformation has been executed and a new window with the results those that we have sofar is displayed aa F B SDTM yee Remark If you would liked to have a dash between the study ID and the subject ID for USUBJID you could have used USUBJID concat STUDYID STEMP In the remaining of the tutorial we will however use the default mapping which is SUSUBJID usubjid taking the value of the ODM SubjectKey attribute of the SubjectData element For the variable SUBJID we can also use the same mapping USUBJID usubjid but you can also decide otherwise The next variable is RFSTDTC Reference Start Date time In order to get more information on this item use CTRL H or the menu View S
16. aking a big risk A mapping already exists for SOTM Variable USUBJID Overwrite existing mapping O Append to existing mapping at top gt Append to existing mapping at bottom _ With other variable name than USUBJID New Variable name as a mapping already exists for USUBJID Select Overwrite existing mapping and click OK This displays a new dialog 4 Import ItemDef Subject ID for SDTM Variable USUBJID e Import XPath expression for ItemData Value attribute from Clinical Data O Import XPath expression for another ltemData attribute subelement from Clinical Data C Import ItemDef attribute value static value from Study Definition _ Generalize for all StudyEvents Except for No Exceptions Only for No Inclusions _ Generalize for all Forms Except for No Exceptions Only for No Inclusions _ Generalize for all temGroups Except for No Exceptions Only for No Inclusions _ Generalize for all Items Except for No Exceptions Only for No Inclusions ODM ItemDef Lenghth 11 SDTM Variable Length 60 _ Set SDTM Variable Length to ODM ItemDef Length _ View Edit XPath expression advanced The most important radiobutton is the button Import Xpath expression for ItemData Value attribute from Clinical Data meaning that we want to import a collected value this will be gt 90 of the cases We will come to the function of the other radiobuttons later The lower part of th
17. ater we will learn how to edit the properties of the domain In the case of the DM domain there 1s currently no necessity to do so The mapping for a specific variable e g STUDYID can be edited by double clicking the cell This leads to a new window that opens and shows Lx Create XPath expression for new script variable Variable Name PO Clinical data Variable Comment PO C Reference data StudyEvent ama Rep Key temGroup a Item i STUDYID from ODM Study OID The Transformation Script SSTUDYID CES m i i 4 Scripting Language Functions 4 Test Transform to XSLT Hide Upper Panel Full screen Transformation Script Panel i OK Cancel This window is named the mapping editor which we will use a lot Let us first look at the basic features of this mapping editor The upper panel is for advanced usage when complicated selections for items must be made It can be hidden by using the button Hide Upper Panel The smaller panel Mapping Description has already been prefilled It contains a short description of the mapping Please feel free to edit its text The most important panel is the panel The Transformation Script This is where the script is generated and or edited The scripting is in a special easy to learn language Although most of the scripts are generated automatically it will be necessary to learn about this scripting language which is
18. bject 001 USUBJID 001 Notice that this testing mechanism only works for a single variable in a single domain Later we will learn how to do more sophisticated testing Let us now generate an alternative mapping for USUBJID For example we would like to have the value of USUBJID to be a concatenation of the STUDYID and of the subject ID from the Common section of each form For doing so first select the cell USUBJID and then expand the tree with the study design so that you see an item Subject ID in a group of items Common One can of course also do a search in the study design tree see the document Loading ODM For example File Edit View Navigate Insert Transform Validate Options About 9 EI StudyEventDef Baseline Visit Domains ltemGroups Ei FormDef Baseline Visit Form DM STUDYID DOMAIN USUBJID SUBJID gt 5 Description ysv STUDYID DOMAIN USUBJID __ISV VISITNUM ee cesDw_sTuDyiD__PowAIN__ JSUEWIDIENNNNN SUBJID o ma Bonai S Keera visitTime B Alias Common temGroup Alias ltemGroupDef Demographics o J ltemGroupDef Smoking History J ltemGroupDef Drinking History J ltemGroupDef Physical Exam o I ltemGroupDef XRay gt Ej ltemGroupDef Complaints due to smoking If one looks carefully two important observations can be made a the items that are visible have a green traffic light in fron of them b the item Subject ID has a traffic light that has a sq
19. calculations 19 The reason for this is that in XSLT a datediff returns a duration e g P1D meaning a period of 1 day IMLAGE DM AGEU DM SEX DM RACE DM DMDTC DM DMDY YEARS F WHITE 2010 02 27 1 YEARS M MHE 2010 02 28 E In the next chapter we will work on the SV subject visits domain and also introduce a new output format and an alternative better viewer for inspecting the resulting records
20. cance and the codelist mapping wizard SDTM CodeList Item AMERICAN INDIAN OR ALASKA NA 7 INDIAN OR ALASKA NA INDIAN OR ALASKA NA OTHER AMERICAN INDIAN OR ALASKA NA MISSING INVALID VALUE AMERICAN INDIAN OR ALASKA NA ODM CodeList item SDTM CodeList item CAUCASIAN WHITE Ba BLACK BLACK OR AFRICAN AMERICAN MISSINGINVALID VALUE C The two ODM entries mapped to NULL empty This leads to the automatically generated mapping script SDTM ETL mapping for ODM RACE The Transformation Script Mapping using ODM element ItemData with ItemOID I_RACE Using SDIM CodeList CL C74457 RACE Using a CodeList mapping between ODM CodeList CL RACE and SDIM CodeList CL C74457 RACE SCODEDVALUE xpath StudyEventData StudyEventOID BASELINE FormData FormOID F BASELINE ItemGroupDi SNEWCODEDVALUE if SCODEDVALUE CAUCASTAN SNEWCODEDVALUE WHITE elsif SCODEDVALUE BLACK SNEWCODEDVALUE BLACK OR AFRICAN AMERICAN elsif SCODEDVALUE ASIAN SNEWCODEDVALUE ASIAN elsif SCODEDVALUE OTHER SNEWCODEDVALUE else SNEWCODEDVALUE SDH RACE SNEWCODEDVALUE Other is not part of the official CDISC codelist but we could of course add it later we will see how and add it to the mapping script In that case depending on whether the study design had also a please specify field one should also add
21. d slvariable gt lt l day part if only one character add a 0 atthe beginning gt lt l do NOT try to correct invalid days gt lt xSi variable name DAYPART select substring before SMONTHDAYPART P lt xSi variable name DAY gt xslichoose gt xslwhen test string length SDAYPART 1 gt xslvalue of select concat l xslotherwise gt lt xslvalue of select DAYPART lt xslotherwise gt xshchoose gt sl variable gt l put everything together gt xSl variable name ISODATE xslichoose gt xslwhen test string length SVYEAR gt 0 and string length SMONTH gt 0 a xslvalue of Select concat SVEAR SMONTH SDAY hsltwhen xslwhen test string length VYEAR gt 0 and string length S MONTH at 07 gt xsl value of select concat VEAR SMONTH ksltwhen gt xslwhen test string length SVEAR gt 0 gt lt xsl value of select BYEAR gt hslwhen l empty value gt xsl when test string length SYEAR 0 and string length SMONTH 0 ang should never occur ifthe input date was correctly formatted gt xslothernwise ERROR xslothernwise gt kslchoose gt lt ieslvariable gt lt l output the end result gt lt xslvalue of select SISODATE lt ieslfunction HEY lt xslstlesheet GS Save Transformation XSLT Code Execute Transformation XSLT Code One can now save the transformation XSLT code to file but we will execute the code
22. d how the domain properties can be edited Viewing and hiding domains SDTM 1 4 has a lot of new domains and it is easy to loose overview Therefore individual domains in the table on the right can be hidden or be displayed so that one can concentrate on the ones that currently are of importance To do so use the menu View View Hide domains 3 One only need to set the path to the favorite PDF viewer in the properties dat file as explained in the SDTM ETL installation guide Navigate Insert Transform Validate Options About ODM tree with Names ODM tree with OIDs ODM tems with traffic lights ODM Items without traffic lights ODM tree nodes with graying out mapped nodes ODM tree nodes without graying out mapped Recalculate ODM tree nodes usage in mapping graying out A list of domains then is displayed and we can check the ones that we want to keep displayed in the table all others are hidden For the moment we just keep DM Demography and SV Subject visits as these can usually best be mapped first Please check the domains to be displayed All other domains will be hidden i DM C TE E TA LJ TI E Tv HTS E TD E co C SE e SV After clicking OK the table on the right reduces to 1S SOTM ETL version 30 me a aaa File Edit View Navigate Insert Transform Validate Options About opm Ef Globalvariables ID STUDYID Douu USUBJID SUBJID DM
23. e dialog states that we currently have set the maximal length for USUBJID to 60 being the default from the template but that the maximal length in the study was defined to be 11 Checking the box Set SDTM Variable Length to ODM ItemDef Length allows to reduce the SDTM variable length to the one given in the study design wich is 11 Don t check the checkbox for now as we still want to concatenate with the Study ID After clicking the OK button the mapping scripting shows up Mapping Description SDTM ETL mapping for USUBJID The Transformation Script Mapping using ODM element ItemData with ItemOID I_SUBJECTID SUSUBJID xpath StudyEventData StudyEventOID BASELINE FormData FormOID F BASELINE ItemGroupData 4 e Scripting Language Functions l xpath comment E Essentially what is does is to define a path to the item in the clinical data and store the result in the variable USUBJID As it is a path in XML this is called an XPath expression One can now test this script again on clincal data as before giving the same result as before Now we want to concatenate the value of STUDYID with the above result In order to do so we need to adapt the script slightly First the variable USUBJID is renamed into TEMP We then have Mapping Description SDOTM ETL mapping for USUBJID The Transformation Script Mapping using ODM element ItemData with ItemOID I SUBJI STEMP xpath S
24. ee and the subsequent drag and drop leads to A Codelistisessocistedwith ODMRem DMaiiaee ames Gaus Lx The ODM ItemDef is ruled by a CodeList You can either keep using the associated ODM CodeList Variabh or take the current CodeList from the SDTM Variable CL C74457 RACE DM ETHNIC or select another CodeList from the define xml structure In the case a CodeList from the SDTM define xml is selected _ DM ETHNIC a CodeList mapping will be necessary In all applicable cases a new CodeList reference will be added to the corresponding ItemDef in the define xml structure Use Study CodeList from ODM Coded Values Use Study CodeList from ODM Decoded Values at deta el Use CodeList from the SDTM Variable Coded Value Use another CodeList from define xml pa MONN Bhd Sacto Le OOS Previous LACK OR AFRICAN AMERICAN PO CL C66767 ACN Action Taken with Study Treatment a halide a ede dais o d n WHITE O j CL C101365 ACSPCAT Acute Coronary Syndrome Presentation Category CL C66781 AGEU Age Unit CL C74456 LOC Anatomical Location CL C101842 CACRDSC Canadian Cardiovascular Society Classification CL C101866 CRYDFMAN Cardiac Rhythm Device Failure Manifestation CL C101853 CVLVRSEV Cardiac Valvular Regurgitation Severity CL C101854 CVLST SEV Cardiac Valvular Stenosis Severity CL C101847 CVEXAMCD Cardiovascular Test Code CL C101846 CVEXAM Cardiovascular Test Name ok
25. eneralize for all ttemGroups Generalize for all Forms Generalize for all StudyEvents _ Limit Results to first Results _ Also display RepeatKeys ODM uses non typed ItemData ODM uses TYPED ItemData View ODM Clinical Data This time check the checkboxes Generalize for all Forms and Generalize for all StudyEvents This means that we want to see each data point Visit Date independent from within which form and within which visit Clicking the View ODM Clinical Data button leads to View ODM Clinical Data Subject StudyE ltemGroup 001 001 BASELINE F_Cl S COMMON 001 BASELINE FL G_COMMON slala lalale e 001 WEEK 1 F_WEEK_1_2 IG_COMMON LVS 010 03 06 oou CWEEK 20 F_WEEK_1 2 IG NIS 2010 03 13 o WEEK 20 gow CARY G G oi AE FG SEARE OL ZS AAAA showing all the visit dates ever registered It looks as at least for this subject the last visit date was on March 13 2010 and the visit was either WEEK 2 or DIARY or AE which all happened on the same day However we cannot know whether this will apply to all subjects The ODM standard states that clinical data for subjects MUST come in chronological order with earliest data first and latest data last in the file So we can simply look for the last occurrence of Visit Date for each subject in the file with clinical data After having gone back to
26. ent CL C101865 ACSPCAT Acute Coronary Syndrome Presentation Category CL C66781 AGEU Age Unit CL C 4456 LOC Anatomical Location CL C101842 CACRDSC I Canadian Cardiovascular Society Classification CL C101866 CRYDFMAN Cardiac Rhythm Device Failure Manifestation CLC101853 CVLVRSEV Cardiac Valvular Regurgitation Severity CL C101854 CVLSTSEV Cardiac Valvular Stenosis Severity CL C101847 CVEXAMCD Cardiovascular Test Code CL C101846 CVEXAM Cardiovascular Test Name Show CodeList details a asking whether we want to use the ODM codelist coded or decoded values the currently to DM SEX asscociated codelist or another list from the SDTM define xml list We want to use the SDTM codelist so we select Use codelist from the SDTM Variable We can quickly inspect that codelist using the Show CodeList Details button CodeList details for CLC66 31L5Ex So Coded Value Decode F Female MO Mate M UNO Undifferentiated After clicking the OK button in the A CodeList is associated wizard a new wizard is displayed allowing us to map the ODM codelist with the SDTM codelist CodeList mapping between ODM Sex and SDTM Sex iin U U _ s ODM CodeList Item SDTM CodeList Item MISSINGANVALID VALUE In this case it is easy and even the wizard will have an easy task finding out so click the Attemp 1 1 mapping based on coded value button resulting in a proposal
27. esults in View ODM Clinical Data Subject StudyEvent Form ltemGroup item Value 001 BASELINE F_BASELINE IG_COMMON L_VISIT 2010 02 27 ODM uses non typed ltemData ODM uses TYPED ItemData The rightmost column showing the value and the other columns the subject ID the StudyEvent visit Form and ItemGroup as well as the current Item The same can be applied to check whether also the time of the first visit was collected using the Item Visit Time OID I VISIT TIME View ODM Clinical Data Subject StudyEvent Form ltemGroup Item Value 001 BASELINE F_BASELINE IG COMMON _VISITTIME 10 27 33 As as well a visit date as time is present they can both be used to populate RFSTDTC To do so drag the item Visit Date to the cell RFSTDTC leading to Mapping Description SDTM ETL mapping for DMLRFSTDTC The Transformation Script Mapping using ODM element ItemData with ItemOID I VISIT SDM RFSTDTC xpath StudyEventData StudyEventOID BASELINE FormData FormOID F BASELINE ItemGroupDi and rename DM RFSTDTC into VISITDATE Then drag and drop the item Visit Time to the same cell RFSTDTC The following wizard is displayed ji A mapping already exists for SOTM Variable DM RFSTDTC O Overwrite existing mapping Ju O Append to existing mapping at top Append to existing mapping at bottom _ With other variable name than DM RFSTDTC New variable name We
28. hat we want as we would like to obtain an integer number If we look again to the available functions we find Scripting Language Functions yea A A BA _ with the floor function delivering what we want So the mapping is adapted to The Transformation Script TEMP datediff DM RFSTDIC DM BRIHDIC 365 2 DM AGE floor TEMP Resulting in 14 Of course one can develop more precise and sophisticated mapping scripts for the age but this is out of the scope of the current tutorial 15 We can not do a local testing as the variables DM RFSTDTC and DM BRTHDTC are out of scope as they have been defined in previous mappings DM RFICDTC DM R FPENDTC DM BRTHDTC DM AGE which is exactly what we want This kind of calculations should be the exception in SDTM as SDTM is about collected data and not about derived data Unfortunately derivations have sneaked in in SDTM in the last years as the tools of the regulatory authorities are not able to calculate them on the fly from the already available data A typical example are all the DY variables The next SDTM variable is AGEU In our case it just is the string YEARS So the mapping is Mapping Description SDTM ETL mapping for DM AGEU The Transformation Script DM AGEU YEARS For SEX we once again first look for a hot candidate and find J ltemGroupDef Demographics E Descriptio
29. heck the checkbox Never ask again in current session and then this dialog will not show up again Clicking OK leads to a dialog lt xstwhen gt lt 1 empty value gt lt xskiwhen test stringlength YEAR 0 and string length MONTH lt _ should never occur if the input date was correctly formatted gt xslothenvise ERROR xslothenvise gt e xshchoose gt xskvanable gt lt __ output the end result gt xskvalue of select SISODATE gt xSifunction 4 3 lt xsiistylesheet _ File with ODM Clinical data contains the MetaData Validate XSLT Test XSLT on ODM Clinical Data _ File with ODM Clinical data contains the AdminData One can then validate the correctness of the generated XSLT or just inspect it specialists with very complicated scripts like to do so for debugging In 99 of the cases you will however just want to continue by clicking the Test XSLT in ODM Clinical Data This leads to a filechooser allowing to pick the ODM file with clinical data For example Open aBa a IE CES_ClinicalData_simple_subject xml CES_Metadata_i18n xml My Study ClinicalData_only xml MyStudy_ODM_1_3 xml 4 MyStudy_ ODM 1 3 typed ltemData xml File Name CES Clinicalbata simple _subjectxm Files of Type ODM files with clinical data Clicking Open then immediately executes the script As our file only contains the data for a single subject the output is su
30. le DOMAIN to the one from the template This is almost always the case later we will see in which cases one might want to make an exception The third tells the system that for the SDTM variable USUBJID it can take the value from the ODM i e from the SubjectKey attribute of the SubjectData element in the ODM file with clinical data The fourth checkbox allows to have the SEQ variable be calculated automatically by the system In the DM domain however there is not DMSEQ variable so this checkbox is disabled here Accepting the prespecified checkboxes and clicking the OK button leads to our first mappings Domains ItemGroups Domain Variable Variable Variable Variable Variable Variable DM_LRFENDTC E TUDYID C DOMAIN USUBJID SV VISITNUM VISIT VMISITDY s CES DM STUDYID USUBJID SUBJID DM RFSTDTC DM RFENDTC Dh One sees that a new row has been created with the name OID in the define xml CES DM for the our study specific DM domain The color of three cells STUDYID DOMAIN and USUBJID is changed to grey meaning that a mapping script for these variables now exists Hovering the mouse over the first cell CES DM shows Domain Variable Variable DOMAIN so grup IMA STUDYID DOMAIN OD CES DM Name DM Purpose Tabulation Repeating No Is Reference Data No Label Demographics Class Special Purpose Structure One record per USUBJID Archive Location ID Location DM 46 L
31. mapping CodeList mappi qt 3 ODM CodeList Item SDIM CodeListitem _ a i ie l EO fF 7 ISSING INVALID VALUE Poe which we only need to extend for missing invalid value ors T i l T Ge aa ae T a ist mapping between ODM Sex and SDTM Sex be SDIM Codelistitem where U stands for unknown as we found out before by using show codelist details After clicking OK the mapping script is completely automatically created Mapping Description SOTM ETL mapping for DM SEX The Transformation Script Mapping using ODM element ItemData with ItemO0ID I SEX Using SDIM CodeList CL C66731 5ExX Using a CodeList mapping between ODM CodeList CL SEX and SDIM CodeList CL C66731 5EXx SCODEDVALUE xpath StudyEventData StudyEventOID BASELINE FormData FormOID F BASELINE ItemGroupDi SNEWCODEDVALUE 4 if CODEDVALUE M SNEWCODEDVALUE M elsif CODEDVALUE F f SNEWCODEDVALUE F else SNEWCODEDVALUE U SDH SEX NEWCODEIWALUE the 1f elsif else construct being generated automatically In many cases wizards will create mapping scripts completely automatically but the user can always further enhance or change the mapping script manully A similar mapping needs to be done for RACE Using the menu Naviage Find hot SDTM Candidate the ODM item Race is quickly found in the study design tr
32. n Alias DM o Ei ltemGroupDef Smoking History o Eq ltemGroupDef Drinking History It is seen that the traffic light is blue meaning that the variable is under controlled terminology The information about the SDTM controlled terminology can be obtained using the menu View SDTM associated codelist which delivers CodeList CLC66731 SEX in standing for female male unknown and undifferentiated intersex Also on the ODM side there is an associated codelist Selecting the item Sex and using the menu View Item CodeList details provides a dialog Details for CodeList Sex OID CL_SEX i3 j Coded Value Language Decoded Text nI en Male fr Masculin de M nnlich k en Female fr F minin de Weiblich k Max Length for CodedValue 1 stating that in the ODM only the values M and F are foreseen Drag and drop from the item Sex in the study design tree to the SDTM cell DM SEX displays the wizard Import ItemDef DM Sex for SDTM Variable DM SEX Es Import XPath expression for ttemData Value attribute from Clinical Data O Import XPath expression for another ItemData attribute subelement from Clinical Data O Import ItemDef attribute value static value from Study Definition Generalize for all StudyEvents Except for No Exceptions Only for No I
33. nclusions _ Generalize for all Forms Except for No Exceptions Only for No Inclusions _ Generalize for all ltemGroups Except for No Exceptions Only for No Inclusions L Generalize for all tems Except for No Exceptions Only for No Inclusions ODM ItemDef Lenghth 1 SDTM Variable Length 2 C Set SDTM Variable Length to ODM ItemDef Length _ View Edit XPath expression advanced and then clicking OK leads to the following dialog 16 See the published CDISC controlled terminology lists published by NCI The ODM ItemDef is ruled by a CodeList You can either keep using the associated ODM CodeList or take the current CodeList from the SDTM Variable CL C66731 SEX or select another CodeList from the define xml structure In the case a CodeList from the SDTM define xml is selected a CodeList mapping will be necessary In all applicable cases a new CodeList reference will be added to the corresponding ItemDef in the define xml structure C Use Study CodeList from ODM Coded Values O Use Study CodeList from ODM Decoded Values Use CodeList from the SDTM Variable C Use another CodeList from define xml CL C66767 ACN Action Taken with Study Treatm
34. or our first 1f else statement Like for the concat function one can use the if elsif and else buttons from the Scripting Language Functions panel to insert snippets Scripting Language Functions a a FA Did Wk E F ile Da De substring before substring after concat test a contains Starts with ends with matches e g leading to The Transformation Script SVISITDATE xpath StudyEventData StudyEventOID BAS t Mapping using ODM element ItemData with ItemOID I VI SVISITTIME xpath StudyEventData 5tudyEventOID BASI iO else One can then fill in the individual parts The Transformation Script SVISITDATE xpath StudyEventData StudyEventOID BASELINE FormData Mapping using ODM element ItemData with ItemOID I VISITTIIME SVISITTIME xpath StudyEventData StudyEventOID BASELINE FormData LE SVISITIIME SDM RFSIDTC concat SVISIITDATE I SVISITIIME else SDM RFSIDTIC sVISITDATE ET The if statement saying that in case the VISITTIME variable is not empty symbol then the value of DM RFSTDTC is the concatenation of the visitdate with the characted T and the visit time In any other case else statement the value of DM RFSTDTC only consist of the date Testing on our single subject leads to 4 lt xststylesheet subject 001 DALRFSTOTC 2010 02 27 1100 27 33 The next SDTM variable that need
35. our file e g DM define 2 0 xml save i elez DM_define_ _0 xml File Name Files of Type CDISC Define xml files ha The Country is fixed in this study So one can just add DM COUNTRY xxx where xxx is the three character code in ISO 3166 notation Examples are USA United States of America CAN Canada GER Germany AUT Austria AUS Australia The next variable is DMTDC When using CTRL H more information is displayed SDTM CDISC Note for Variable DM DMDTC aS Date time of demographic data collection Core Perm We can just take it as the Visit Date for the form where also the demographics data was collected o EI FormDef Baseline Visit Form Description gt 1 ItemGroupDef Common E Description o o k temDef Visit Time Alias Common ltemGroup Alias temGroupDef Demographics In this case a simple drag and drop from the item Visit date is all is needed The next one is DMDY SDTM CDISC Note for Variable DM DMDY i ES Study day of collection measured as integer days Core Perm There is something very special see the SDTM IG In SDTM the day the study starts for a specific subject has xxDY 1 and not 0 as one might think The day before the study starts however is then not day 0 as one might think but day 1 So in SDTM there is no day 0 and xxDY can never have the value 0 Logical isn t it
36. rite into The Transformation Script Mapping using ODM element ItemData with ItemOID I VISIT Generalized for all StudyEventa Generalized for all Forms within the StudyEvent STEMP xpath StudyEventData FormData ItemGroupData ItemGrour SDM RFENDTC STEMP last i e By generating a temporary variable and then adding a condition last to the expression Executing the script then results in 12 Later we will see how to work with the buttons Except for and Only for 13 take the first one available is written as 1 CES DM oTUDYID DOMAIN USUBIID SUBIID DM RFSTDTC DM RFENDTC CES DM 004 001 2010 02 277T 10 2 7 2070 03 13 In a good number of cases earlier defined mappings i e for variables more to the left in the same domain can be easily reused For example for the next variable RFXSTDTC in the DM domain we can write Mapping Description SDOTM ETL mapping for DM RFXSTDTC The Transformation Script copied from RFSTDIC SDM RFXSTDTC SDM RFSTDIC Similarly we can set for the next DM variables DM RFXENDTC DM RFENDTC DM RFICDTC DM RFSTDTC DM RFPENDTC DM RFENDTC but of course only in the case dates were really indentical to the first and last visit date correspondingly This leads to the following result ie E a eal a ll 7 ener SDTM Tables cscs ee L Ze gt USUBJID SUBJID DM RFSTDTC DM RFEN
37. s untyped For example lt FormData FormdiD F BASELINE I Itembroupbata ItemGroupOID IG COMMONS lt ItemPata Item0ID I SITE Value 25 gt ItemPata Item0ID I SUBJECTID VYalue 001 gt lt I Itempata ItemUID I YISIT Value 2010 Q2 27 gt lt ItemPata ItemOID I VISITTINE Value LOie27i 33a gt lt I tenmGrouplata gt Itembroupbata ItemGroupOID IG_DM gt lt Itempata ItemUID I BETHET VYalue 1957 05 07 gt ItemPata Item0ID I SEX Value F gt lt ItemPata Item0ID I RACE Value CAUCASTAN gt lt temGbroupDbata gt If your data however contain elements like temDataString or temDataDate and there is no Value attribute this means that your data is typed For example 4 XSLT is an international standard from the W3C for transforming XML documents lt SubjectData SubjectKey O002 gt lt StudyEventData StudyEventd0ID StudyEvent0Olb StudyEventRepeatkey 1 gt lt Formbata Form0ID Form0ID FormRepeatKey 1 gt lt ItemGroupbata ItemGroupolD DATATYPE ItemGroupRepeatKey ALL ELEMENT TransactionType Ingsert gt lt ItemPataPartialDate ItemO0ID ID Pb gt 1959 lee TtembataPartialDate gt lt ItemPataPartialTime Item0ID ID PT les temDataPartialTine gt In our case we work with untyped data so we leave the radiobutton 1t uses non typed ItemData selected If it is sure that your clinical data will always come as untyped one can c
38. s like to work on the templates e g for adding newly published draft domains This is pretty easy as the template files are just XML files which can be edited by any kind of XML editor After clicking OK we are ready to work with SDTM 2 For any SDTM or SEND submission the FDA requires a define xml file to be submitted together with the actual data sets containing the metadata for the submission files One can now see that the right side of the screen is now filled with an SDTM table containing a row for each SDTM domain in the SDTM IG and a cell for each SDTM variable with the first cell containing the SDTM domain name DM TE SDTM ETL version 3 File Edit View Navigate Insert Transform Validate Options About Ef MetaDataVersion CDISC Example Study Metadata Ef Protocol CE StudyEventDef Baseline Visit c Description J FormDef Baseline Visit Form cJ Description o c ItemGroupDef Common J ltemGroupDef Demographics c Description G Alias DM o C ltemGroupDef Smoking History o Cf ltemGroupDef Drinking History C ltemGroupDef Physical Exam c ltemGroupDef XRay C ItemGroupDef Complaints due to smoking E FormDef Prior or Concomitant Medications ACRO Description Domains ItemGroups L Variable Variable Variable Variable Variable Variable Variable F STUDYID DOMAIN DM RFSTDTC DM RFENDTC DM RFXSTDTC
39. s to be mapped is RFENDTC Reference end date time Using CTRL H tells us SDTM CDISC Note for Variable DM RFENDTC eS Reference End Date time for the subject in 150 8601 character format Usually equivalent to the date time when subject was determined to have ended the trial and often equivalent to date time of last exposure to study treatment Required for all randomized subjects null for screen failures or unassigned subjects Core Exp But now the question arises what was the date the subject ended the trial Was it the Week 2 Visit or was it the Patient Diary Event or maybe even the Adverse Event visit This time the menu Navigate Find hot SDTM Candidate does not give any results so we need to find out ourselves We can easily find out what the last visit date is as it was always collected i e in each visit using the same item Visit date with OID I VISIT One can easily see this by selecting the item and then use Navigate Next Instance or use CTRL Page down One will then see that it was collected for each form for each visit But what was the last one Here again the menu View ODM Clinical Data is of great help So select an item Visit Date and then use the menu View ODM Clinical Data View Clinical Data lee i File with ODM Clinical Data CA SOTM ETL_demo ODM_1 3 CES_ClinicalData_single_subjectxml _ Generalize for all Items C G
40. temGroupDef Demographics EI Description E 4 Alias DM o Ei ItemGroupDef Smoking History A view in the clinical data for this item using View ODM Clinical Data results in ODM uses non typed ltemData ODM uses TYPED ItemData StudyEven l Value BASELINE F_BASELINE 1957 05 07 o2 BASELINE F_BASELINE BRTHDT 1961 09 06 Dragging and dropping the item from the tree into the cell DM BRTHDTC results in the mapping Mapping Description SDTM ETL mapping for DM BRTHDTC The Transformation Script Mapping using ODM element ItemData with Item0ID I _BETHDT DM BRTHDTC xpath StudyEventData StudyEventOID BASELINE FormData FormOID F BASELINE ItemGroupDi and doing a local quick test of this mapping results in Xs stylesheet Subject 001 DM BRTHDTC 1957 05 07 Subject 002 DM BRTHOTC 1961 09 06 Or executing the mapping for all SDTM variables in the DM that we mapped sofar in CES DM VID SUBJID DM RFSTDTC DM RFENDTC DM RFXSTDTC DM RFXENDTC DM RFICDTC DM RFPENDTC DM BRTHDTC 001 2010 02 27T 10 27 2010 03 13 2010 02 27T 10 27 2010 03 13 2010 02 27T10 27 2010 03 13 1957 05 07 a 002 2010 02 28T14 33 2010 03 16 2010 02 28T14 33 2010 03 16 2010 02 28T14 33 2010 03 16 4961 09 06 The next variable that needs to be mapped is AGE However it looks as the age of the subject
41. tion SOTM ETL mapping for USUBJID The Transformation Script Mapping using ODM element ItemData with ItemOID I SUBJECTI STEMP xpath StudyEventData StudyEventOID BASELINE For SSIUD YID CES SUSUBJID concat SS5SITUDYID sTEMP Do not forget the semicolon at the end You might already have noticed the coloring in the script comments starting with a are colored blue Functions are colored green and strings that are between quotes are colored red Reexecuting the mapping script on real clinical data results in Se ee ed Daa Subject 001 USUBJID CESO01 One can also execute all the available mappings together After clicking OK for the mapping script editor we come into the main window again Now use the menu Transform Generate Transformation XSLT Code for CDISC SDS XML or use Transform Generate Transformation XSLT Code for SAS XPT The former will generate data files in the new CDISC SDS XML format the latter in the classic SAS XPT format Let us first try the classic way The following 7 Ifthe semicolon is forgotten a warning message will be displayed when trying to execute the mapping 8 As in every programming effort it is advised to add as many comments as possible for a later good understanding what the intention of the statement or snippet was 9 Later it will explain how to do the same generating results in the new SDS XML format dialog is presente
42. trated how this value can be adapted to a more suitable value in agreement with what is in the collected data In order to get real in depth information about a specific SDTM variable select the cell and then use View SDTM CDISC Notes or use CTRL H A new window is then displayed e g for AEMODIFY SDTM CDISC Note for Variable AEAEMODIFY 9 n E lf AETERM is modified to facilitate coding then AEMODIFY will contain the modified text Core Perm View PDF Document for SOTM Spec v 1 4 SDTM G v 3 2 One can then open the corresponding section of either the standard specification or implementation guide SDTM IG by either clicking the button SDTM Spec v 1 4 or SDTM IG v 3 2 as the latter documents come with the distribution Later we will also learn how to add additional standard variables and how to add non standard variables that later typically go into SUPPQUAL Now have a look at the first cell in a row Also here hovering the mouse displays some more information e g MO STUDYID DOMAIN USUBJID PC STUDYID TUDYID DOMAIN USUBJID OID MO 1 Name MO Purpose Tabulation Repeating Yes ls Reference Data No ss Label Morphology One record per MO MOTESTCD per USUBJID aia Location ID Location MO 30 The label for this domain is Morphology and it belongs to the Findings class The other information will be explained later when it is explaine
43. tudyEventData StudyEventOID BASELINE Do not change anything in the XPath expression Now we do already have a mapping for the SDTM variable STUDYID We can just copy paste from the previous mapping which results in Mapping Description SOTM ETL mapping for USUBJID The Transformation Script t Mapping using ODM element ItemData with ItemOID I SUBJECTID STEMP xpath StudyEventData StudyEventOID BASELINE FormData Fc SSIUDYID CES Now have a look at the functions in the lower panel the Scripting Language Functions panel You will find a concat function with the following explanation aE Concatenates the contents ofthe arguments into a single string 6 It will be very seldom that one needs to change something in the XPath expression We will give some examples later though The concat function has at least two arguments but there can be more It is used to concatenate a set of strings into a new string Now in the mapping script editor just type USUBJID and then click the concat button The string is extended with the function with empty parameters Mapping Description SOTM ETL mapping for USUBJID The Transformation Script Mapping using ODM element ItemData with ItemO0ID I SUBJECTID STEMP xpath StudyEventData StudyEventOID BASELINE FormDi SSlUDYID CES SUSUBJID concat which can now easily be extended as Mapping Descrip
44. uare around it The green traffic light means that the item is of a suitable data type for mapping to the SDTM variable For example if one expects a datetime for an SDTM variable the traffic light on the item Subject ID in the study design tree will be read The square around the green traffic light means that the item is a hot candidate 1 e has been annotated in the ODM as being ideally suited for mapping with the given SDTM variable This can also be seen by hovering the mouse over the item Subject ID in the study design tree J ltemGroupDef Common o FF aana amita OID SUBJECTID Name Subject ID SOTM Variable Name USUBJID Alias cory Alias USUBJID J ltemGroupier Non stum ramona Technically this was done by adding the attribute SDSVarName USUBJID in the ODM To use the item Subject ID in the mapping for the SDTM variable USUBJID select the item Subject ID in the tree with the mouse then drag it keep the left mouse button down to the cell USUBJID in the table on the right then drop it by releasing the left mouse button During the dragging you will see a yellow copy symbol replacing your mouse cursor meaning that you are in the copy mode After having dropped in the USUBJID cell the following dialog is displayed 5 Which does not mean that it cannot be used in that mapping people drive through red traffic lights but that is t
45. want to append to the existing mapping but as we still need to combine both items we choose to rename the current one e g to VISITTIME A mapping already exists for SOTM Variable DM RFSTDTC O Overwrite existing mapping O Append to existing mapping at top Append to existing mapping at bottom With other variable name than DM RFSTDTC New Variable name visirTime You do not need to add a in front of the new variable name the system will take care of it This results in a mapping Mapping Description SDTM ETL mapping for DM RFSTDTC The Transformation Script Mapping using ODM element ItemData with ItemOID I VISIT SVISITDATE xpath StudyEventData StudyEventOIDe BASELINE FormData FormOID F BASELINE ItemGroupDa Mapping using ODM element ItemData with ItemOID I VISITTIME SVISITTIME xpath StudyEventData StudyEventOID BASELINE FormData FormOID F BASELINE ItemGroupDa Remark that the two comment lines have been generated automatically The SDTM Implementation Guide explains the usage of ISO 8601 dates times and datetimes In case of a complete datetime the format is Y Y YY MM DDThh mm ss The central T separating the date part from the time part So for our mapping we can use DM RFSTDTC concat VISITDATE T VISITTIME Hey wait a minute What in the case that the visit time was not collected Then the central T should not be present So time f
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