The CDISC ODM Study Designer User Manual
Contents
1. i Similarly for the base type xsd duration Choose a duration 2 Positive period gt Negative period Years Months Days bode E Hours Minutes Seconds 34 23 3 88 The list of intelligent widgets for base XML Schema types is being extended continously In the following table with base XML Schema types a green background color is set for those types for which an intelligent widget has already been developed base64Binary hexBinary anyURI QName NOTATION Please note that for the datatypes involving time the timezone has not been implemented yet For extended datatypes in the Vendor Extension XML Schema derived from these base datatypes automatic generation of an intelligent widget will not always be possible However local validation using the Validate button and overall validation using the Validate Validate All menu will create an error message if the value is incorrect with respect to the datatype as defined in the XML Schema For example suppose the Vendor XML Schema defines a datatype scoreType which needs to be a xs decimal with a value between 2 0 and 5 0 inclusive The XML Schema definition 1s lt xs simpleType name scoreType gt lt xs restriction base xs decimal gt lt xs minInclusive value 1 gt lt xs maxInclusive value 5 gt lt xs restriction gt lt xs simpleType gt If we now have an attrib2. So using the combination of the table cells and the Add Information icons we can add all information necessary to set up and define and a clinical study in CDISC ODM format But how can we now see whether the information added is in agreement with the CDISC ODM standard We need some way of validation In the ODM Study Designer conformity checking is done on two levels A first very local and rather simple checking is done using the Validate button which appears in allmost every panel and dialog Let us look at a typical panel where all the individual items that can be used in the CRFs are defined ODM ItemDef ODM Study Designer by XML4Pharma File Validate Options Help Global Study Variables Basic Study Definitions Study Metadata tem Group Definitions Codelists _ imputation Methods Presentations Includes Protocols Study Event Definitions Form Defininitions E OlD Name DataType Length significantDl SASFieldNa SOSYarName Origin Comment Ee MA SITE Site Number integer SITEID SITEID EYALSUBJECTID SubjectID tet 1 HAIL SUBJECT Subject Initi text HAST date EYAILBRTHDT Date of Birth date D EYALSEX DM Sex text USUBJID USUBJID EYAILRACE DM Race text gt PACE RACE a Se SUBJINT VISITDAT RFSTOTG AAILSMOKING Smoking text BYAILDRINKING Drinking text BAILSYSBP Systolic BP__ integer EYAILDIABP Diastolic BP integer EYALHEIGHT Height __finteger__ HAI WEIGHT Weight
3. Subject IDjtext 4 BQ sua Sunject Ey QLvsit visit date date TR RAI BRTH Date of integer HAI SEx Dm Sex broat DAI RACE DM Ra liat BAI SMOK Smoking ter BRIORIN Drinking tatetime BQ SY5BP systolic AAJ DABP Diastoli ext Add Ro So it is impossible to add anything other than the values defined by the ODM standard For Vendor Extensions this is also the case as long as the enumerations have been defined as such in the Vendor Extension XML Schema Also for Vendor Extensions much effort has been done to cover as many possible situations and datatypes as possible and to provide a palette of inteligent widgets For example if a company has designed an extension for study event scheduling and defined an attribute Visit Date of type date then when the user of the ODM Designer needs to enter a date a Calendar widget shows up allowing to pick a date and so that it is correctly formatted in the ODM study design Extra information for Protocol StudyEventolD Orderumber Mandatory VisitDate SE 001 1 Yes a ee A E El November aO a A Sun Mon Tue Wed Thu Fri Sat Coo ooo E Add Row Delete Selected Row Sort by Order Humber Validate Save to Library Load from Library Similarly user friendly widgets have been developed for entering time and date time information Annotating CRFs with SDTM information More and more it becomes good custom to provide SDTM information right from the
4. BPo Cs Sy Stalic BP oo LDIABP O O O o o Diastolic BP oo HEIGHT Sight IAWEIGHT SiN ight LOAY Diary Day LOATE SCSCSCsCDiaary Date LDIARY Sale LAE OCCURRED O Adverse Event Experienced LAELEVENT Alverse Event Number LAETERM ARderse Event Term LAE_START sere Event Start Date LAESTOP CCCs Aer Event Stop Date LAE CONTINUES Adverse Event Continues LAE_SERIOUS Adverse Event Serious LAE_SEVERITY Ader Event Severity LAE RELATED ster Event Related LAE ACTION ss Adverse Event Action Taken LAE OUTCOME Adverse Event Subject Outcome LCM TAKEN ss Nor study Medications taken ILCM_NUMBER Medication Number LCM_NAME Medication Name LCM_DOSE si Medication Dose ByAIG_AE BAIG EM BAJI CEM HAIG LB oaded file C Similarly if the user needs to enter a reference to a codelist then the wizard takes care of finding all codelists that have been defined before and to list them into a non editable table so that the user can select a codelist without the danger of adding an reference to a non existing codelist This also means that if an OID 1s changed all references to that OID need to be updated This is also being taken care of by the software if the user changes an OID the application will ask whether all references to that OID need to be updated If the user tries to delete an OID either by deleting cell contents or by deleting a whole row the application checks whether there are reference
5. L SUBJECTID SubjectID text USUBJIO YSUBJID J GAI SUBJECT SubjectIniti tet Bo UBNT PP GAILST date oo MISITDAT OO RFSTDOTC EVALERTHDT Date of Birth date DOB BRTHDTE J EYAILSEX DM Sex text GENDER SEXP BYALRACE DM Race tet 20 RACE RACE AQILSMOKING Smoking tet 20 SMOKES SUDOSE SAILDRINKING Drinking text fo DRINKS fsuDosE J JAISYSBP Systolic BP__ integer B J SYSTL WSORRES JAJI DIABP_ Diastolic BP integer 3 DaSysTL WSORRES Jo o YAI HEIGHT Height integer 3 EIGHT WSORRES JAIWEIGHT Weight oat Booo WEIGHT WSORRES J JAIL DAY Diay Day integer OY YAI DATE DiayDate ldate l o o d fs d Add Row Delete Selected Row Suggest OIDs N Validate If one holds the mouse pointer over such a cell more information is provided about what kind of violation against the standard has occurred e g SIU EVENT VeATINTIONS F Length SignificantDi SASFieldNa SDSVarName SITEID SITEID ma be UsuBJD UsUBJID When DataType integer Length is required ME Ooo PANDAI DOE BRTIHDTC The standard says that when an Item is being defined as of type integer one also needs to provide information about its maximum value as defined by 10 where n in the integer number to be provided in the cell Length note that this is not the case anymore in the ODM 1 3 Remark that with the ODM Study Designer it is pretty difficult to enter nonsense information idiot p
6. Study Variables Basic Study Definitions Study Metadata tem Group Definitions tem Definitions i Codelists Imputation Methods Presentations meues Preteens Study Evert Detntions Form Defininitions Mame DataType SASF ormatMarme yA CL_SEX Sex text SEX GACLRACE Race oteto BRACE GACLSMOKING Smoking test 5MOKE GACLDRINKING Drinking tet DRINK BYAICLDIARY Diary integer O DIARY GACL DIARY DAY DiaryDay integer DIARYDAY GACL NOYES Noves integer NOES BYAICLLAE SEVERITY Adverse Event Severity integer JAESEV o o o GACLAE ACTION Adverse Event Action Ta integer _ AEACTION BYACLAE_OUTCOME Adverse Event Action Ta integer 0 JAEOUT GACL CM_FREQUENCY Medications Frequency integer JAEFREQ GACLNOTDONE Not Dona tat Add Row Delete Selected Row Suggest OIDs Validate Save to Libra ai Load from Library Save the contents ofthis panel oaded file CACDISC ODM_1 2 TFrocanweracara care A filechooser dialog shows up asking where for a filename and location where the library with codelists need to be stored Files containing libraries are formatted in CDISC ODM XML format so that they can easily be read or edited using any XML editor or e g being stored in an XML enabled database e g Oracle or native XML database lt xml version 1 0 encoding IS0 8859 1 7 gt root xmins http www cdisc org ns odm v1 2 xmins ds http www wd org 2000 09 xmildsig xmins xs https 7 wyn w3 org 2001 XMLSch
7. Text Let us give names to the units of measurement we will work with For example we need to define units for blood pressure for weight and length The table now looks like ODM Study Designer by XML4Pharma File Validate Options Help Global Study Variables Basic Study Definitions study Metadata Mame A L004 rrr mio ao kooo BAmuos CS BA muo em DAmuoos im ooo o BAwoe CO SMR e a a Amun O O OoOo o o OS OOOO y Add Row Delete Selected Row Suggest OIDs Validate Save to Library Load from Library So we have defined the following units mm Mercury for blood pressure kilograms pounds centimeters and inches As one has probably already remarked there are two clickable icons at the start of each row 1 e The Add Information icon and the Inspect icon B N Add Information icon Inspect 1con The Add Information icon does exactly what it means It allows to add extra information to an instance of a section element of the ODM The Inspect icon allows to see all the information that has been added to an instance in a tabular way Technically spoken the information that is added in the cells of the table e g OID Name are added to the XML ODM file as attributes Clicking the Add Information icon allows to add information that is stored as subelements or child elements of the current ODM element If we click the Add Information ic
8. The CDISC ODM Study Designer by Jozef Aerts XML4Pharma User Manual Introduction The CDISC ODM Study Designer is a software application to design and develop clinical studies in CDISC ODM format in a very user friendly way The application fully supports the ODM 1 2 and ODM 1 3 standards as well as any vendor extension based on the ODM1 2 1 or ODM1 3 0 XML Schema mechanism Starting the software The application is delivered as a Java application This means a Java installation at least version 1 5 needs to be installed on the computer of the user For details about installation of Java and of the application itself see the Installation Guide For Windows users a file ODMDesigner bat is delivered as part of the distribution Double clicking it the corresponding icon in Windows Explorer starts the software If the software does not start up please refer to the Installation Guide For Linux users a shell script 1s provided When the application has started a dialog giving you details about the owner and expiration date if any of the license shows up Secondly another dialog shows up asking you whether you want to develop a study design based on the ODM 1 2 on the ODM 1 3 or on a ODM Vendor Extension As the define xml has been designed as an ODM Extension you can also use the ODM Study Designer to create and assemble define xml files SLE want to work on a Study Design based on ODM 1 2 O ODM 1 3 m Vendor Exten
9. UTE ROUTE Route ofAd Char Qualifier Route ofad 20 intervention LOT LOT LotNumber Char Qualifier Lotnumber M 21 intervention LO LOC Location of Char Qualifier Specifies a 22 intervention TRTV TRTV Treatment Chat Qualifier Example R 23 intervention AD ADJ Reason for Chat Qualifier Mehiclefor 1 Events Ge TERM____ TERM___ Repored T Char Topice Topic aria 2 Events Ge MODIFY __ MODIFY Modified R Char Qualifier ifthevalue fJ J 3 Events Ge DECOD DECOD Dictionary Chat Qualifier Dictionary 4 Events Ge CAT CAT Category Chat Qualifier Usedtoder C an la The SDSVarName table is fully searchable so that one easily can find the appropriate SDS Variable Name if one has at least a slight idea about what the variable is about For fields that contain more extended information a text information dialog pops up when the user selects that field This makes it very easy to select the correct SDS Variable Name Optionally see Options one can choose also to directly fill the Role field of ItemDef with the corresponding value from the SDTM table References to OIDs The study design section of the CDISC ODM standard uses a referening method to add Items to an ItemGroup to add ItemGroups to a Form Forms to a StudyEvent etc First of all the user needs to define which Items ItemGroups Forms StudyEvents but also CodeList
10. e existing OIDs the new OIDs are only assigned to rows for which no OID has been assigned yet After clicking the OK button the table updates to ODM Study Designer by XML4Pharma File Validate Options Help j Global Study Variables Basic Study Definitions Study Metadata OID Mame HAMU Me BM BA muo o BM Dee Me IEA e Add Row Delete Selected Row Suggest OIDs Validate Save to Library Load from Library OIDs are very important in the ODM They define identifiers for all kinds of definitions of study events forms itemgroups codelists etc If a reference to such a definition is performed e g a reference to a codelist this 1s always done through the OID One can always change the contents of a cell in the table by just clicking in it An editor or a wizard or dialog then becomes available In order to delete the contents of a cell just right click in the cell A dialog pops up asking for confirmation E E E Now that we have defined OIDs for the Units of Measurement that we want to use in the Study Design we also need to give a meaningfull name to each of them Usually the Name is a very short description mostly in English or in the language that is usually used when designing a study Please note that the Name is not meant to be what appears on the paper or eCRF later For this and for the different languages the CRFs will be produced we will later use the section Translated
11. ema gt lt CodeList DataType text Name Sex OID CL_SEX SASFormatName SEX gt lt CodeListItem Coded alue M gt lt Decode gt lt TranslatedText xml lang en gt Male lt TranslatedText gt lt TranslatedText xml lang fr gt Masculin lt TranslatedText gt lt TranslatedText xml lang de gt Mannlich lt TranslatedText lt Decode gt lt CodeListItem gt lt CodeListItem Coded alue F gt lt Decode gt H lt TranslatedText xml lang en gt Female TranslatedText gt lt TranslatedText xml lang fe gt F minin lt TranslatedText gt lt TranslatedText xml lang de gt Weiblich lt TranslatedText gt lt Decode gt lt CodeListItem gt lt CodeList gt lt CodeList DataType text Name Race OID CL_RACE S45FormatName RACE gt lt CodeListItem Coded alue CAUCASIAN gt lt Decode gt lt TranslatedText xml lang en gt Caucasian lt TranslatedText gt lt TranslatedText xml lang fr gt Caucasien lt TranslatedText gt lt TranslatedText xml lang de gt Kaukasisch lt TranslatedText gt In order to load an existing library just use the Load from Library button A filechooser dialog shows up allowing to choose an XML file and then the dialog asks whether the loaded information must be appended to the existing one or whether the existing information must be overwritten OID Mame DataType SASF armatae Ay ACL_SEX Sex text SEX HAJCLRACE Race O o oteto RACE EYAICL_SMOKING Smoking t
12. erface Initially a table with 10 rows shows up s AST Global Study Variables Basic Study Definitions Study Metadata Clicking in a cell in the column OID allows you to add an ID for your unit of measurement Accordingly clicking in the cell in the Name column allows you to add a name for the unit of measurement Remark that the ODM standard requires that within a section e g Units of Measurement each OID must be unique this can be checked by the software Also in order to have a meaningfull and well organized set of OIDs in an ODM file it is good practice to use a prefix for OIDs e g MU for MeasurementUnit or IT for ItemDefs see later The application allows you to define a prefix it even suggests one in many cases and automatically fill the rows with OIDs for the section that is treated For example in one wishes to define 10 Units of Measurement click the Suggest OIDs button in the lower part of the interface The following dialog shows up ODM Study Designer by XML4Pharma Se File Validate Options Help j Global Study Variables Basic Study Definitions Study Metadata Ge a prefix for the OID it willbe extended by a number MU 001 Overwrite all existing OIDs O_O The application suggest to use the prefix MU and to add a number starting from 001 to form the OID name If some OIDs have already been defined one can overwrite them If one chooses not to overwrit
13. et SMOKE HAC DRN HACE DARY X AAJCL_NOYES y Do you want to Overwrite existing rows or Append to existing rows 7 ACL AE SEVE RM ACL_AE OUT Append FA B ACL_NOTDONE NotDone tet Add Row Delete Selected Row Suggest OIDs Validate Save to Library Load from Library As such it is very easy to build up reusable libraries over time and to reuse them in new studies if appropriate Saving ODM study designs to file ii 4 To save the results of your work to an ODM file remark that no propriety format is used only the open CDISC format use the File Save menu or the corresponding icon A dialog shows up asking you for some information that needs to be added at the top level of the ODM a file OID this is not the filename a Study OID and information about the version of the study metadata OID Name and Description Some of this information is mandatory indicated by the green fields if the user does not provide the required information the dialog will keep asking for it until the information is provided If an ODM file was loaded from disc the old information will already be filled in in the forms Add MetaData Wizard i CDISC ODM File OID ODM File Descrit The cDISC ODM File OID this is notthe file name Description Clinical study created using the xML4Pharma OOM Study Designer Study ID required ODM_Exarnple_001 Metadata Version OID required version 1 1 Metadata Ver
14. float d3 WEIGHT _ _ VSORRES GALDA DiaryDay integer ft HALDATE Diay Date date Pfs O Add Row Delete Selected Row CC n Suggest OIDs a Validate gt Save to Library Load from Library Near the bottom at the right one observes the Validate button When clicking it the contents of the cells in the table are validated against the CDISC ODM standard for Vendor Extensions they are validated against the Vendor Extension XML Schema and the ODM standard Note that subinformation as added using the Add Information icons is only partially validated In order to fully validate the subinformation one needs to click the Add Information button and then use the Validate button in the dialog that shows up Later we will see that one can also validate the complete information i e the complete study setup in one go For the above example when the Validate button is clicked one observes that some of the cells are colored red This means that information is missing or that invalid information has been provided ODM Study Designer by XML4Pharma File Validate Options Help Global Study Variables Basic Study Definitions Study Metadata tem Group Definitions f Imputation Methods Presentations Includes Protocols Study Event Definitions Form Defininitions O DID Name DataType Length SignificantDi SASFieldNa SDSVarNamel Origin Comment AAI SITE Site Number jinteger SITEID SITEID ao o A HAI
15. iables Basic Study Definitions element BasicDefinitions and Study Metadata element MetaDataVersion Accordingly the application shows 3 buttons allowing to switch between these 3 sections When e g the button Global Study Variables is selected a tabbed panel shows up allowing to add information about the Study Name the Study Description and the Protocol Name Clicking on one of these tabs allows you to switch between these 3 items The tabs can be colored The currently selected tab is always colored yellow the other tabs can have a gray or green color When a tab is colored green this means that according to the ODM standard information within that section MUST be provided in order to have a valid CDISC ODM file If the tab is colored gray adding information to that section is optional Please be aware however that even when a Section is optional according to the ODM standard it can contain essential information about your clinical study setup When you select a tab a table with one or more rows is shown If there is only row in the table this means that you can only have one instance of the piece of information in the ODM file according to the rules of the ODM standard For example if you have selected the Study Name tab you can only add 1 name for the study If however you have clicked the Basic Study Definitions button and use the Units of Measurement tab initially 10 rows show up i
16. icking in a cell Language a language chooser pops up It allows us to select a language either using the buttons or using the selection box remark that typing the first letter allows to jump quickly in the list If we select English the TranslatedText table updates and we find en in the cell of the first row The ODM uses the internationalized codes for languages IETF RFC 3066 Most of these all the two letter codes SO 639 have been implemented in the software So the two letter code for English is en for French is fr and for German is de Deutsch We can now do the same for French and for German Extra information for Symbol m z Language Sen Ber BAe BA Choose a language using a button or the selector fou can use the autocompletion facilities of the selector Somali Sotho Southern For each of these languages we now still need to add the translated text as we like it to appear on the CRF As usual we can add extra information by clicking the Add Information icon If we do this for the english row a text field appear where we can add the text Inches For the french row we add the text Pouces and for the german row we add the text Zoll ma Language Hen FA DAR HN Extra information for TranslatedText BA After we have done so we also see that the background color of the Add Information ico
17. ired attribute for element CodeList Attribute Mame is a required attribute for element CodeList Attribute DataType is a required attribute for element CodeList Options The Options menu allows you to set a number of options for working with the software The number of them is currently pretty low but with time we will add more and more options Options and Settings 2 _ Remember last used directoy _ Show Protocols Study Events Forms as a Matrix _ Get temData Origin attribute automatically from SDTM table The first option allows to indicate that the application should remember the directory that was last used for input or output The second option allows you to get a more extended view on the data when using the Inspect icon when working at the Protocol StudyEvent or Form level For example when working at the StudyEvent level and inspecting the information for the StudyEvent Week 1 a table matrix is shown which forms are used in this StudyEvent and which ItemGroups are used within which forms Using this feature one sees immediately whether all envisaged information has been added to the StudyEvent Contents of element StudyEventDef Ei eee ee eee Fie isweor ite study Event Overview Week 1 Visit Physical Ad Event Demographics Smoking Drinking ysic verse Events History History E Occurred F DIARY Diary Form Conc ormutarnt Medication
18. more information Search for Total daily Find Next Matchcase Whole words only Search within All Columns r Sequence for Order Observation Class r Domain Prefix r Variable Name without Prefix e Variable Name Variable Label Type Controlled Terms or Format Origin Role CDISC Notes Core References 1 Intervention TRY TRT Mame of Tr Char Topic The topic fo 2 intervention MODIFY MODIFY Modified Tr Char Qualifier Ifthe value E 3 intervention DECOD DECOD _ Standardiz Cha Qualifier Standardiz 4 intervention CAT CAT Category Charea Qualifier Usedtodef M 5 merention SCAT SCAT Subeategory Char Qualifier Usedtodef J M 6 intervention OCCUR _ _ pPOCCUR Occurrence Chat Qualifier Usedonly 8 Intervention REASND f US foualiier _ Reasonno 9 Intervention INDE Qualifier Denotesth 10 Intervention LAS Total daily dose of TRT Qualifier Class fora 1 imervention CLASCD f using the units in DOSU Qualifier Usedtosto 12 Intervention JOBE Qualifier Amountof Quali BE a Se 13 Intervention DO STAT 14 Intervention DOSU h Qualifier Unitsfor 16 Intervention _ DOSFRM Qualifier Doseform J M 16 Intervention DOSFRQ DOSFR posmgFre pha Qualifier Usuallyexp 18 intervention SS DOSRGM DOSRGM IntendedD Char Qualifier Textdescri 19 Intervention RO
19. n has changed to orange This means that information has been added and is stored Let us now click the OK button in the TranslatedText dialog so that we return to the Symbol dialog remark that when using the Cancel button none of the underlying information is stored In order to get an overview of all the translated texts for the measurement unit in click the Inspect icon this is the icon with the magnifying glass the second one from the left Extra information for Measu A new dialog pops up showing us all the texts as they will appear on the CRF for each of the languages that we defined Contents of element Symbol Contents of Symbol Content for TranslatedText We can now do the same for all other Units of Measurement in the study A typical result looks like Global Study Variables Basic Study Definitions Study Metadata Mame A MLIOO mm ee 5 0 007 ooo BA muo Oo i i e Hamad o O HAM S a O SMB Ee ti Me a ae eUT A Add Row Delete Selected Row l FL If one now clicks on the Inspect icon for the row with OID MU 003 one gets a tabular view of all the translations entered Contents of element MeasurementUnit Contents of NeasurementUnit wit OLD MU 005 and wit Name in Attributes Content for Symbol ranslatedText Language English Text inches Language French Text pouces Language Germar Text Zol Local validation
20. n the table allowing to add information for a number of Units of Measurement up to the maximum number allowed in the XML Schema for Units of Measurement this number is infinite ODM Study Designer by XML4Pharma SEE File Validate Options Help Global Study Variables Basic Study Definitions Study Metadata Add Row Delete Selected Row Suggest OIDs Validate Save to Library Load from Library Schema read Using the Add Row and Delete Selected Row buttons in the lower part of the graphical interface one can always add extra rows or delete a selected row Adding rows will only work up to the moment that the maximum number of instances of that piece of information as defined in the XML Schema is not exceeded So if you try to add a second row to the panel with tab Study Name under Global Study Variables the application will refuse to add another row and nothing happens For the Units of Measurement tab the maximum number of instances defined in the XML Schema is infinite so that you can add as many rows as you want When saving the ODM file later however only those rows will be saved to file containing real information Empty rows will not be saved to file Let us now have a look at a single row The essentials of adding information can best be explained using the Units of Measurement tab which 1s shown when clicking the Basic Study Definitions button at the top of the graphical int
21. on of the fifth row with OID MU 005 in the following new dialog pops up Extra information for MeasurementUnit with OID MU 005 Add Row Delete Selected Row Suggest OIDs Validate Save to Library Load from Library The title of the new dialog says Extra information for MeasurementUnit with OID MU 003 When one clicks in the only cell of the table that is available remark that it doesn t have a header nothing happens This means that no information can be added that goes into an XML attribute for the Symbol element There is however an Add Information icon If that is clicked a new dialog appears Extra information for Symbol Fs Language EEEEEEEEE B Ey Add Row Delete Selected Row Suggest Obs Validate Save to Library Load from Library A new table shows up that allows us to add the translated text for the symbol for up to 10 languages and even more when we add the Add Row button The information we will add here is typically the one that will later appear on the paper or eCRF So one of the benefits of the CDISC ODM 1s that one can provide all necessary information to create automatically or not all CRFs for each language and country needed In this example we will add the translations for our unit inches in three languages english french and german As such this will allow to have the unit written as Zoll on a german CRF and as Pouces on a french CRF By cl
22. roofness For example if one tries to enter a non numeric character into the field Length the application just refuses it so that it is really impossible to e g enter aa into the Length field link In some of the dialogs when using the Validate button one will remark that also the Add Information icon gets a red background color This means that the subinformation is lacking although required by the ODM standard or that it is invalid Global Study Variables Basic Study Definitio OID AAMU MMHG ay SMU POUNDS Pounds BQwUINCHES inches n AOOO invalid content ra In this example the subinformation in Symbol subelement of MeasurementUnit is missing but required by the ODM standard Click the Add Information icon and then add the necessary information User friendly widgets As already mentioned the graphical interface has been concipated so that it is pretty difficult to add invalid information non conform with respect to the standard For example if only an integer is allowed the corresponding cell in the table or textfield will only accept integer values Similarly if only a floating point is allowed it will be impossible to enter anything else When the standard only allows certain values 1 e enumerations the widget that shows up in a table or dialog is a list of choices combobox e g LAILI MAE Odl E LETIO ZITI AISTE Site Mu integer BYAILSUBJ
23. s CACKO F LABS Laboratory 4 The third option Get ItemData Origin Attribute automatically from SDTM table means that when you select an SDS Variable Name from the SDTM table used at the ItemData level also the information from the Origin field in the SDTM is copied to the table with attributes for ItemData Vendor Extensions The ODM Study Designer has full support for ODM Vendor Extensions based on the ODM 1 2 1 or ODM 1 3 Vendor Extension mechanism This means that any Vendor Extension XML Schema can be read upon startup of the program and that all necessary table fields wizards and widgets will be created automatically by the software Also upon validation of the created input the latter will be validated against the Vendor Extension XML Schema For example if the extension defines an attribute month which is defined as an integer between 1 and 12 then upon validation an error will be generated if the input value is not in the range given by the XML Schema Moreover the software generates intelligent widgets for most of the XML Schema base types see e g http www w3 org TR 2001 REC xmlschema 2 20010502 This means e g that if an vendor extension attribute has been defined as an xsd time a TimeChooser widget shows up when trying to add a time for that attribute mto OrderNumber Wandatory O CC ee Choose a time 2 220 sofa 30 a ESE H k LF en VisitDate VisitTime i x
24. s Presentations and ImputationMethods can occur or will be used The details of these need not be defined right from the start Once the user has defined the OIDs and Names from most of the Items ItemGroups Forms etc or loaded them from a library see further the user can start adding Items to ItemGroups Forms to Visits etc Wizards are provided to help the user doing so If for example the user want to add Items to an ItemGroup click the Add Information icon in the row in the Item Group Definitions panel under Study MetaData One comes into the ItemRef dialog This dialog allows to add all necessary items to the current ItemGroup by entering theoir OID referencing mechanism Now the wizard has been set up so that upon clicking the field ItemOID a new dialog shows up with a non editable table listing all currently defined Items and their respective names The user can then easily select one of the Items and add it to the ItemGroup by clicking the OK button As such it becomes impossible to add Items to an ItemGroup with an OID that is invalid or that has not been defined yet 2 ee ee Select a n Item teml temNare Site Mumber LSUBJECTID SC Subject ID Alias LYSBJECTINTIALS Subject initials ItemolD Ord LMIBIT sit Date LBRTHDT DateofBimh LSEX T EE Lvisit B LRACE O Z O o o MRa e LSMOKING 0s Stnoking E i LDRINKING Drinking Tr OC YSC SY LSys
25. s however when a Vendor Extension element or attribute has the same name as a regular ODM element some confusion may still arise leading to problem We are currently working on removing this limitattion It remains however good practice NOT to give Vendor Extension elements and attributes identical names as existing ODM elements and attributes Vendor Extension elements that are child elements of the ODM Study element currently of each of such Vendor Extension child elements only one instance is created by the software Please note that this is NOT applicable to other Vendor Extension elements or subelements For example if you have the following extension schema lt xs group name StudyElementExtension gt lt xs sequence gt lt xs group ref StudyElementExtension gt lt xs element ref my StudyChild minOccurs 0 maxOccurs unbounded gt lt xs sequence gt lt xs group gt then only one instance of my StudyChild will be created But if this element itself can have more than one child as in lt xs element name StudyChild gt lt xs complexType gt lt xs sequence gt lt xs element ref my subsub minOccurs 1 maxOccurs unbounded gt lt xs sequence gt lt xs attribute name lt xs complex Type gt lt xs element gt subattribute use optional gt then the software will allow to create an unlimited number of instances of the my subsub element So the limitation only applies to elements tha
26. s to this OID and if so will refuse to delete the cell contents or the row This guarantees that there are no dangling references i e references to non existing OIDs TPL PLUL E a om All SUBJECKD ARI SUBJECTINITI 2 The Value of the OID has changed aA VISIT O Update all references to it 7 HAJILBRTHOT BA ires No AALRACE AAI SMOKING smoking text 20 In case you want to automatically update all references to OIDs in all cases and automatically you can set so in the Options see further In case the user wants to clear the cell contents of a cell containing an OID the application will give a warning that all references to that OID may be lost and give the user another chance not to clear the contents of that cell Creating libraries In many cases it will be very useful to maintain a set of libraries for items groups of items forms codelists etc and to be able to reuse them later or in other studies The ODM Study Designer allows to save sets of items forms codelists etc to a set of files and to load these files later when working on another study Suppose we have defined a good number of codelists with all their decodes translated texts etc and we want to reuse this set of codelists later e g in another study To save the set of codelists just click the Save to Library button at the bottom left ODM Study Designer by XML4Pharma File Validate Options Help Global
27. sion based on ODM 1 2 1 or 1 3 O Define xml The appropriate XML Schema is then loaded and used to automatically create all the menus panels and wizards Only in case the user choose for working with a Vendor Extension a filechooser pops up allowing you to select the appropriate Vendor Extension XML Schema Open Ed Lookin C CDISC_ODM_1_3 Vendor Extensions cal lea ca z A ny simple extension xsd e xmldsig core schema xsd a my simple ns xsd Dryss OOO i ODM 1 3 0 foundation draft xsd ODM1 3 0 xsd a xlink xsd A xmLxsd File Name my simple xsd Files of Type CDISC Vendor Extension ODM Schema files ha The Graphical User Interface adding information When you have choosen with wich version of the CDISC ODM standard you want to work or a Vendor Extension the application reads the XML Schema and builds up the graphical user interface from the information in the XML Schema This ensures that in the case of a vendor extension also panels dialogs and wizards for the extension elements and attributes are created ODM Study Designer by XML4Pharma File Validate Options Help GCL Global Study Variables Basic Study Definitions Study Metadata 2 Add Row Delete Selected Row Suggest OIDs Validate Save to Library Load from Library The Study Design part XML element Study of the CDISC ODM standard has 3 main sections Global Study Variables element Global Var
28. sion Name required coisc Example Study Wetadata Metadata Version Description COSC Example Study Metadata Once all the necessary information is provided and OK is clicked a filechooser shows up allowing to save the ODM file to disc Remark that some information like the CreationDateTime attribute in the ODM element is automatically generated Before saving to file it is always good custom to do a full validation of the ODM contents Performing full validation Besides performing a local validation of each of the panels using the Validate button near the bottom of the panel it is also recommended to perform a full validation of all the work that has been done so far Using the Validate Validate All menu the full ODM is assembled and conformity checking 1s performed against the XML Schema but also against all other ODM rules that are mentioned in the specification but that could not be implemented in an XML Schema Validation Result The following violations against the standard were found Attribute Repeating is a required attribute for element StudyEventDef Attribute Type is a required attribute for element StudyEventDef Element StudyEventDet needs to have information in subelements Gne of the following elements is Element FormRef in namespace Athi cdisc orginstodiyd 2 Attribute Mame is a required attribute for element Formbet Attribute DataType is a requ
29. start of a clinical study 1 e at the study design stage In the ODM 1 2 the CRFs can be annotated with SDTM information using the attributes Domain in element ItemGroupDef 1 e definitions of groups of items for the CRFs and in the attributes SDSVarName Comment and Origin in the element TtemDef i e definitions of items that can occur in the CRF The possibility to add further SDTM information to the an ODM study design will be available in the ODM 1 3 and will be fully supported by our application Dialogs for adding SDTM annotation information have already been implemented when one clicks in a cell to add Domain information a dialog pops up with a list of all possible domains as has been defined in the SDS 3 1 SDTM 1 1 Similarly for the SDSVarName a dialog pops up showing a very large table over 600 entries with all possible information from the SDTM Implementation Guide Select a Domain Domain Code Domain Marne Catego a E TN TN Purpose Domains COU Comments Specia Fumes Domains _ Purpose Domains a i e sU Z o SubstameUse interventions W MBO iMicroBiology Findings O o PP Pharmacokinetics Paramet Findings Domain selection for the Domain attribute in ItemGroupDef if SUPP is chosen an extra dialog pops up for allowing to add an existing domain code so that e g SUPPAE is formed Select a SDTM Variable Role or Purpose Click a cell to see
30. t are direct children of the ODM Study element Also currently attributes for the my StudyChild element cannot yet be created This is a limitation that will be removed soon Vendor extensions declaration of namespace In order to find the binding between namespace URI and the prefix the software currently looks in the top schema file for the Vendor Extension only If e g the Vendor Extension is composed of the following schema files according to the ODM1 2 1 extension mechanism e Foo xsd e Foo ns xsd e Foo extension xsd Then the software scans the Foo xsd file to find the binding between the Vendor Extension namespace URI e g http www mycompany com Foo ODM XMLSchema and the prefix e g foo So the Foo xsd file MUST contain the statement lt xs schema targetNamespace http www cdisc org ns odm v1 2 xmins http www cdisc org ns odm v1 2 xmlns xs http www w3 org 2001 XMLSchema xmlns xlink http www w3 org 1999 xlink xmins foo http www mycompany com Foo ODM XMLSchema elementFormDefault qualified attributeFormDefault unqualified gt We realize this is not a rule implied by XML Schema if the statement does not appear in the Foo xsd file but does appear in the Foo ns xsd file then instance files will correctly validate against the XML Schema so we will remove this limitation soon
31. ute score in element subsub defined as lt xs element name subsub gt lt xs complexType gt lt xs attribute name score type lt xs complexType gt lt xs element gt my scoreType use required gt The widget created for this attribute will be accepting decimal values only but this including values outside the 1 0 to 5 0 range If a value outside this range is entered and the validate button is clicked the software will complain that the value is out of range for the defined schema type Similarly when the Validate All menu is used an error message will be generated ID Value is too large maximum inclusive is 5 0 Current Limitations Currently the following limitations apply There can be only one MetaDataVersion element child of Study element When upon loading an ODM file with more than one MetaDataVersion element then only the last MetaDataVersion element is taken Thus for the moment please keep different metadataversions of the same study in different files Naming of Vendor Extension elements and attributes although vendor extension elements live in separate namespaces it is good custom not to give them identical names as existing ODM elements and attributes In almost all cases the software checks whether an element or attributes lives in another namespace and consequently adds the necessary prefix to the element name or attribute In very special case
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