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1. CTChicago MV 1 3 0 ClinicalData xml It also contains the third version of the metadata v1 2 0 including the second one which includes the first one but also a fourth version of the metadata defining a new visit with a new form and adding the new visit to the protocol CDISC ODM Checker v 1 3 User Manual p 10 lt MetaDataVersion OID 1 2 0 Name Version 1 2 0 gt Include StudyOI0 123 456 789 MetaDataversionGID v1 1 0 gt lt Protocol gt lt StudyEventRef StudyEventOIO SE ISITO OrderNumber 1 Mandatory Yes gt lt StudyEventRef StudyEventOIO SE VISITL OrderNumber 2 Mandatory Yes gt lt Protocal gt lt l and we do REDEFINE some ItemPef from the earliest MetaDataVersion were Datatype text lt ItemDef OID IT AEENDT Mame Derived Stop Date AS DATE DataType date gt lt ItemDef OID IT STRT_DT Name Derived Start Date DataType date S45FieldName STRT_DT gt lt ItemDef OID IT STOP_DT Name Derived Stop Date DataType date SASFieldName STOP_DT gt lt DELIBERATE ERROR DataType datetest does not exist AND IT STOP DT already defined gt lt ItemDef CIO IT STOP_DT Name Derived Stop Date DataType datetest S4SFieldName STOP_DT gt lt MetaDataVersion gt l gt lt MetaDataVersion OID MER Name Version 1 3 0 gt lt Include StudyOI0 123 456 789 MetaDataversionGID v1 2 0 gt Clee If we add a new Visit we must also relist the o2. 3 0 by XML4Pharma Ernel Fue Options Help Eh ob ODM Sch Main File CACBISC ODM1 2 0 final CTChicago XSchema xml Included ODM Files CTChicago _X Schema xml Validation is started The course of the validation can easily be followed in the console which is located near the bottom of the application window CDISC ODM Checker v 1 3 0 by XML4Pharma SE Project File Options Help ODM Schema version 4 24 24 1 3 C CDISC ODM1 2 0 finahCTChicago Schema xml Included ODM Files TChicago XSchema xml Currently validating file CNCDISC_ODM1 2 0_finahCTChicago_ Schema xml eae validating Number fatal errors 0 F Number errors Number warnings Humber infos CDISC ODM Checker Made available to CDISC members by XML4Pharma 10 13 24 INFO Checking clinical data for Subject O02 10 13 25 INFO Checking clinical data for Subject OOS 10 15 35 INFO Checking clinical data for Subject oo4 lt Hi During validation the number of errors and warnings found sofar is constantly updated on the right side of the screen When the validation is ready a new window the report window is presented CDISC ODM Checker v 1 3 User Manual p 3 Results from checking the CDISC ODM Document ODM file C CDISC_ODM1 2 0_final CTChicago_xSchema xml Severity warning when reaching line 90 and column 169 The Role attibute in element ItemGroupDef is deprecated since ODM Y ersion 1 2
3. You are advised to use Purpose rather than Role Reference ODM Standard 3 1 1 3 5 ItemGroupDef Severity warning when reaching line 130 and column 210 The Role attibute in element ItemGroupDef is deprecated since ODM Yersion 1 2 You are advised to use Purpose rather than Role Reference ODM Standard 3 1 1 3 5 IbtemGroupDef Severity warning when reaching line 174 and column 203 The Role attibute in element ItemGroupDef is deprecated since ODM ersion 1 2 You are advised to use Purpose rather than Role Reference ODM Standard 3 1 1 3 5 ItemGroupDef Severity warning when reaching line 199 and column 235 The Role attibute in element ItemGroupDef is deprecated since ODM ersion 1 2 You are advised to use Purpose rather than Role Reference ODM Standard 3 1 1 3 5 IbtemGroupDef Severity warning when reaching line 213 and column 201 The Role attibute in element ItemGroupDef is deprecated since ODM Y ersion 1 2 You are advised to use Purpose rather than Role Reference ODM Standard 3 1 1 3 5 IbemGroupDef For each warning or error the line number in the ODM file is given as well as a description of the error or warning and a reference to the section of the ODM standard that is applicable Scrolling down to the bottom of the report window shows a short summary Summary Results Sumber of infos 3 Sumber of warnings 6 Sumber of errors 31 Sumber of fatal errors 0 Printing and Saving the validation report to fil
4. the file with only metadata has been loaded followed by a file with only clinical data The first file that was loaded is automatically set to be the Main File This means that the metadata will be taken from that file and that for all other files the clinical data will be validated against the metadata from the Main File Removing files from the list Files can always be removed from the list by selecting the file in the list and using the menu File Remove or by clicking the cissor icon on the menu bar If there are still files in the list after the Remove operation then the first file in the list is automatically being set to be the Main File Setting a specific file as the Main File One can set a specific file in the list to be the Main File CDISC ODM Checker v 1 3 User Manual p 5 To do so select the file in the list and click the Set as Main ODM File icon on the toolbar or use the menu File Define Main File CDISC ODM Checker v 1 3 0 by XML4Pharma Esoiert File oplos Help BOYS ODM Schema versiol Main File CACBISC ODM1 2 0 final CTChicago XSchema_ClinicalData_only xml Included ODM Files CTChicago_XSchema_ClinicalData_only xml CT Chicago_ASchema_metadataonly xml The selected file is moved to the top of the list and is then listed as the Main File CDISC ODM Checker v 1 3 0 by XML4Pharma Project File Options Hel
5. the toolbar CDISC ODM Checker v 1 3 0 by XML4Pha Project File Options Help JOD Stop Validation OL CACDISC ODM1 2 0 finalCTChicago Schema_ Clinic Included ODM Files CTChicago_XSchema_ClinicalData_only xml The validator then halts the validation and starts creating the report with all the errors and warnings obtained sofar Generating report Metadata files using the MetaDataVersion Include mechanism In many cases there are several versions of a study design often using an earlier version as a base for the new version In ODM this 1s accomplished through the Include mechanism The directory testfiles Include that comes with the distribution contains a number of sample files file CTChicago MV 1 0 0 xml contains the first metadata version only containing ItemDef s and CodeList s It can be regarded as a base library file CTChicago MV 1 1 0 xml contains definitions for the StudyEvents Forms and ItemGroups It does not have definitions for the Items but these are referenced by an Include element using _ lt MetaDataVersion OID v1 1 0 Name Version 1 1 0 gt lt Include StudyOID 123 456 789 MetaDataVersianOID SMInO gt CDISC ODM Checker v 1 3 User Manual p 8 referencing the first metadata version to be included file CTChicago MV 1 2 0 ClinicalData xml is the third version of the metadata for the study It contains the Protocol element referencin
6. 20011019710 45 57 05 00 of attribute EffectiveDate on element MetaData ersionRetl is not valid with respect to its type date Severity error when reaching line 76 and column 116 The value 270011019710 45 57 05 00 of attribute EffectiveDate on element MetaData ersionRel is not valid with respect to its type date Severity error when reaching line 79 and column 116 The value 20011019710 45 57 05 00 of attribute EffectiveDate on element MetaData ersionRet is not valid with respect to its type date Severity error when reaching line 110 and column 46 StudyEventData error StudyEventData with StudyEventOID SE ISITO has no StudyEventRepeatKey but the corresponding StudyEventDef has been defined as being Repeating Reference ODM Standard 3 1 4 1 1 StudyEventData _ Severity error when reaching line 434 and column 55 alue of ItemData with ItemOID IT AEENDT is not valid with respect to its type date alue 19990614 is not a valid value of type date Reference ODM Standard 7 13 Data Formats Originally in the first version of the metadata the Item with OID IT AEENDT was defined as being of type text but in the third version it was redefined to be of type date So when in the clinical data a value 19990614 is found an error is generated as the latter value is not a valid XML date Different metadata versions do not have to be in the same file This can be seen in the sample file
7. Validating CDISC ODM files with the XML4Pharma ODM Checker v 1 3 Author Jozef Aerts XML4Pharma Last update October 20 2009 Introduction The CDISC ODM Checker v 1 3 is a validation tool made freely available to CDISC members to check ODM instance files against the ODM standard v 1 2 or v 1 3 Validation for ODM files version 1 1 or v 1 2 which use a DTD Document Type Definition is not supported anymore For these please use the old ODM Checker v 0 7 Installation The CDISC ODM Checker is a Java application For installation instructions please see the installation manual or follow the instructions as you obtained by e mail Starting the application If the software has been correctly installed a double click on the entry ODMChecker bat Windows or ODMChecker sh Linux Unix in your file explorer should start up the software If nothing happens please read the troubleshooting section in the installation manual first The following screen is presented CDISC ODM Checker v 1 3 0 by XML4Pharma Ef Project File Options Help ODM Schema version 1 24 24 43 Main File NONE ASSIGNED YET Included ODM Files Currently validating file stopped Number fatal errors Number errors Number warnings Number infos CDISC ODM Checker Made available to CDISC members by XML4Pharma CDISC ODM Checker v 1 3 User Manual p 1 Selecting an ODM file
8. e The contents of the validation report can either be printed or saved to file To print the contents use the File Print menu File SEVE NE LENI S l JID IT SEX has Save as RTF file was found wh Exit 1 In all cases the reference is to the ODM 1 3 standards document CDISC ODM Checker v 1 3 User Manual p 4 To save the contents of the report to a Windows RTF file choose File Save as RTF file One can also save the file as a simple text file using File Save as text file To close the window use the menu File Exit Loading several ODM files You can load several ODM files for validation The system however expects that there is a Main File containing at least the metadata for the study for which the other ODM files will be validated So for example if the metadata for a study are located in one file and the clinical data come as separate files one will usually first load the file with metadata and then add the other files To load several files use the menu File Add several times or use the Add ODM File icon on the toolbar until all necessary files are listed in the Included ODM files list For example CDISC ODM Checker v 1 3 0 by XML4Pharma Project File Options Help ODM Schema vers Main File CACDISC ODM1 2 0 final CTChicago XSchema_metadataonly xml Included ODM Files lChicago KSchema_ metadataonly xml rs First
9. e last file was loaded This can also be switched off The basic font site for all the labels in the graphical user interface GUI can be changed The default value is 11 Setting it to a larger value can especially be interesting for people with a visual handicap The colors used to make up the report with warnings and errors can be changed Options and Settings eT Errors and Warning Directories Basic Font Size Report Colors CDISC ODM Checker v 1 3 User Manual p 14 We can change the color for e g Error Color by clicking the radiobutton A colorchooser shows up If we e g select a blue color the background color in the dialog is changed Options and Settings Sbbrechen Clicking OK brings us back If we now do a validation we see that the red color for errors in the report has been changed into blue Severity error when reaching line 3 and column 36 Element AdminData has an unregistered value for the StudyOID attri StudyOID attribute value 123 456 739 has not been registered in a n Study elements can be found under the ODM element Reference ODM Standard 7 11 Element Identifiers and References Limitations Currently the validation does not cope very well with a situation where more than one Study is being defined in the main file with metadata only the first Study from that file is taken CDISC ODM Checker v 1 3 User Manual p 15
10. g the StudyEvents from the second metadata version using an Include statement lt MetaData Version OID 1 2 0 Name VYersion 1 2 0 gt lt Include StudyOID 123 456 789 MetaDataVersianOID v1 1 0 gt lt Protocal gt lt StudyEventRef StudyEventOID SE ISITO OrderNumber 1 Mandatory Yes gt lt StudyEventRef StudyEventOID SE VISITL OrderNumber 2 Mandatory Yes gt lt Protacal gt lt and we do REDEFINE some ItemPet from the earliest MetadataVersion were Datatype text lt lt lt ItemDef OID IT AEENDT Name Derived Stop Date AS DATE DataType date gt lt ItemDef OID IT STRT_DT Name Derived Start Date DataType date SASFieldName STRT_DT gt lt ItemDef OID IT STOP_DT Name Derived Stop Date DataType date SASFieldName STOP_DT gt lt MetaData version gt It also redefines a number of Items from the first metadata version for the data type As such the third metadata version v1 2 0 contains a full study description Additionally it contains a set of reference data and clinical data for the third version of the metadata Essentially all the metadata is distributed over 3 files with the file CTChicago MV_1 2 0 ClinicalData xml containing the latest version of the metadata So it is this file that we need to set as Main File We also need to add the two other files CTChicago MV 1 1 0 xml and CTChicago MV_1 0 0 xml to the list so that the system can exec
11. hing line 1 and column 1 Namespace problem the file does not seem to be an ODM file of version 1 2 The reason is that the elements of the ODM file live in a namespace which is different for each of the ODM versions and that the namespace of the instance file must always match that of the XML Schema file A similar error may be obtained when the file is not an ODM file at all or when the ODM file 1s still an ODM 1 0 or 1 1 file or when it is an old ODM file that still references a DTD Document Type Definition The latter do not have a namespace assigned One of the main features of v 1 3 of the standard is that it allows the use of typed ItemData e g CDISC ODM Checker v 1 3 User Manual p 12 lt SubjectData Subjectkey 002 gt lt StudyEventData StudyEventOID StudyEventOID StudyEventRepeatKkey 1 gt lt FormData FormOIo FormOID FormRepeatKey 1 gt lt ItemGroupData ItemGroupOID DATATYPE ItemGroupRepeatKey 4ALL ELEMENT TransactionT ype Insert gt lt ItemDataPartialbate ItemOID ID PDB gt 1959 12 ItemDataPartialbate gt lt ItemDataPartialTime ItemOID ID PT gt 12 lt ItemDataPartialTime gt lt ItemDataPartialbatetine ItemOID IB PDT gt 1959 12 117T12 ItemDataPartialbatetine gt lt ItemDataDurationDatetine ItemCID IB BDDT PO3 11M07DT16H ItemDataDurationDatetime gt lt ItemDatalntervalDatetime ItemOID ID IDT 19591211 700311077T1624 lt lItemDatalntervalbatetine gt lt ItemDataInco
12. ime Severity error when reaching line 692 and column 73 The value 4 of the element ItemDataFloat is not valid with respect to its type float For example one sees an error message for line 285 because the standard does not allow mixing CDISC ODM Checker v 1 3 User Manual p 13 classic ItemData elements usually having a Value attribute with typed ItemData elements such as ItemDataAny The error for line 190 may seem strange first but we must recognize that there hasn t been a February 29 in 2009 Because the standard uses a native XML datatype here it immediately recognizes non existing dates This is one of the major advantages of using typed ItemData Options and Settings A number of options and settings can be changed using the menu Options Settings The following dialog appears Options and Settings D Errors and Warning Directories Basic Font Size Report Colors Sort Errors and Warnings by linenumber For erran nr Vann F earn orri we Lil 7 itn re ima tiake LENF Li Bei Le i r Do not sort adviced when large number of errors warnings First of all one can choose whether the errors and warnings are sorted by linenumber default yes One can disable sorting in case one expects a large number of errors and warnings as the sorting process can be a time consuming one in the case of a large amount of errors Normally the system remembers the directory from where th
13. ld visits otherwise it is meant that the old visits MUST be removed 2 lt Protocoal gt lt StudyEventRef StudyEventOQIO SE VISITO OrderNumber 1 Mandatory Yes gt lt StudyEventRef StudyEventOQIO SE VISITL OrderNumber 2 Mandatory Yes gt lt l new visit gt lt StudyEventRef StudyEventOID SE NEWY ISIT OrderNumber 3 Mandatory Yes j gt lt l DELIBERATE ERROR StudyEvent SE NOTEXIST does not exist gt lt StudyEventRef StudyEventOIO SE NOTEXIST OrderNumber 3 Mandatory Yes gt lt Protocal gt lt l DELIBERATE ERROR should have Repeating attribute AND a Type attribute gt lt StudyEventDeft O1ID SE NEWYVISIT Name Follow Up gt lt FormRef FormOlo FORM FOLLOWUP Mandatory Yes gt lt StudyEventDet gt FormDef O10 FORM FOLLOWUP Name Follow Up Repeating Na gt It also contains a set of reference data and clinical data for the second version of the metadata and a small set of clinical data for the third version of the metadata We can now validate the file but need to add the files CTChicago MV_1_1 0 xml and CTChicago MV 1 0 0 xml to the list as metadata from them are being referenced CDISC ODM Checker v 1 3 0 by XML4Pharma Project File Options Help BEL EA D ODM Schema version O 1 27 Main File C 00MChecker 2008testiilesinclude CTChicago MV 1 3 0 ClinicalData xml Included ODM Files CTChicago MV 1 3 0 ClinicalData xml Curr TChicago MV 1 1 0 xmi
14. mpleteDatetime ItemOID ID NDT gt 1959 11712 34 56 05 00 lt ItemDatalIncompleteDatetime gt lt ItemGroupData gt lt FormData gt lt StudyEventData gt lt SubjectData gt Performance The CDISC ODM has a large number of rules so validating large files especially when containing lots of clinical data can take a considerable amount of time Showing sample data for some of the new data types of ODM 1 3 The rules concerning typed ItemData have also been implemented in the ODM Checker and the distribution contains a sample test file containing a good amount of deliberate errors in directory testfiles ODM_ 1 3 odm130data xml File Severity error when reaching line 190 and column 64 Yalue of ItemData with ItemOID ID D is not valid with respect to its type date Yalue 2009 02 29 is not a valid value of type date Reference ODM Standard 27 13 Data Formats Severity error when reaching line 265 and column 48 Invalid content was found starting with element ItemDataAny One of ItemData is expected Severity error when reaching line 669 and column 68 The value 4 of the element temDataDate is not valid with respect to its type date Severity error when reaching line 690 and column 68 The value A of the element ItemDataTime is not valid with respect to its type time Severity error when reaching line 691 and column 73 The value a of the element temDataDatetime is not valid with respect to its type datet
15. p ODM Schema vers Main File CACDISC ODM1 2 0_finahCTChicago 5chema_metadataonly xml Included ODM Files CTChicago Schema_metadataonly xml CTChicago Schema_ClinicalData_only xml One can now starting validating as the file containing the metadata is now correctly assigned The validator will first validate the metadata in the first file the Main File and then will validate all other information from all including the first file against the metadata The resulting report looks like 2 Essentially the system will build a so called DOM document of metadata in memory and validate all data against that DOM document with metadata CDISC ODM Checker v 1 3 User Manual p 6 Results from checking the CDISC ODM Document ODM file C CDISC_ODM1 2 0_final CTChicago_xSchema_metadataonly xml Severity warning when reaching line 39 and column 169 The Role attibute in element ItemGroupDet is deprecated since ODM ersion 1 2 You are advised to use Purpose rather than Role Reference ODM Standard 3 1 1 3 5 ItemGroupDet Severity warning when reaching line 129 and column 710 The Role attibute in element ItemGroupDet is deprecated since ODM ersion 1 2 You are advised to use Purpose rather than Role Reference ODM Standard 3 1 1 3 5 ItemGroupDet giving the results for the first file followed by the results for the second file using the metadata fro the first file Number of infos 0 Sumber of warning
16. s 6 Number of errors 0 Number of Fatal errors 0 Results from checking the CDISC ODM Document ODM file C CDISC_ODM1 2 0_final CTChicago_ Schema_ClinicalData_only xml Severity error when reaching line 17 and column 49 ItemData error Item with DID IT R_DRUG cannot belong to the ItemGroup with OID IG DEMOG A previously registered temGroupDef with OID I1G DEMOG or does not contain a ItemRef element with ItemOID IT R_DRUG Severity error when reaching line 50 and column 46 ItemData with ItemOID IT SEX has a Yalue which could not be found in the CodeList with OID null TtemData Yalue MM was found whereas only one of the following values from the Code List is allowed F M Of course one can add more files with clinical data If the files that have not been designated as the main file contain study metadata these metadata will undergo a basic check against the standard so not a complete check and they will not be used to serve as a base for validation of any clinical data CDISC ODM Checker v 1 3 User Manual p 7 So if one would like complete validation of the metadata in these files one is enouraged to do so separately by setting each of them once as the Main File Interrupting the validation If one observes that very many errors are generated one can decide to interrupt the validation In order to do so either use the menu Project Stop Validation or click the icon Stop Validation on
17. t CTChicago MV_1 0 0 xmi If we also add another file with clinical data 1 e file CTChicago MV 1 2 0 ClinicalData xml but not as the main file its clinical data will be checked against the third version of the metadata v1 2 0 but the metadata themselves will not be used to define the full set of metadata Saving a project CDISC ODM Checker v 1 3 User Manual p 11 It may be useful to save all the settings and the file list for future use e g for the case one regularly receives updates of the files with clinical data In order to save the project use the menu Project Save A filechooser is then displayed allowing the settings to be saved to a file The file suffix for project files is pry Similarly one can load previously saved project files using the menu Project Open One is then prompted to select a file having the suffix prj Working with CDISC ODM 1 3 files Until now we only worked with ODM 1 2 files The distribution contains a small set of ODM 1 3 files Validation of ODM 1 3 files exactly works the same way as for ODM 1 2 files one only needs to take care that the radiobutton 1 3 for Schema Version 1s selected If this 1s not done the schema validation cannot work correctly and a fatal error 1s thrown File Results from checking the CBDISC ODM Document ODM file C oODMChecker _2008 testfiles ODM_1_3 0odm120data xMIL Severity fatal error when reac
18. to validate One can select a single ODM file to be validate either by using the menu File Open or by using the Add ODM File icon on the toolbar CDISC ODM Checker v 1 3 0 by XML4 Project File Options Help eve A filechooser then pops up preselecting the files that have the xml suffix If your ODM files use another suffix please select All files under File type Selecting a file and clicking the OK button then loads the file For example CDISC ODM Checker v 1 3 0 by XML4Pharma Eee le See ee ODM Sch CACBISC ODM1 2 0 final CTChicago XSchema xml Included ODM Files CTChicago XSchema xml The filename of the selected file is added to the list of Included ODM Files and it is also listed under the heading Main File Performing a first validation If you know that your ODM file is an ODM file that has the ODM namespace assigned leave the radiobutton 1 2 for ODM Schema Version checked If you know your ODM file is a v 1 3 ODM file select 1 3 for the ODM Schema Version Please remark that old ODM files v 1 1 or v 1 2 with a DTD Document Type Definition cannot be validated anymore using the current version of the 0DMChecker To start validation either use the menu Project Start Validation or click the Start Validation icon on the toolbar CDISC ODM Checker v 1 3 User Manual p 2 CDISC ODM Checker v 1
19. ute the Include statements from the metadata in the main file The order of these two additional files in the list is unimportant So we may have CDISC ODM Checker v 1 3 0 by XML4Pharma ee eS eee ee KEL ETA D ODM Schema versi Main File C00MChecker_ 2008testfilesiInclude CT Chicago MV 1 27 0 Clinicall Included ODM Files CTChicago MV 4 2 0 ClinicalData xml CTChicago MV 1 1 0 xmi CTChicago MV_1_0 0 xml The system will first build a full set of the metadata by using executing the Include statements and searching in as well in the main file as in the other files for the to be included previous metadata versions Once the full metadata set build it starts again with the first file and validates the reference data and the clinical data against the full metadata set 3 This as there is an Include for the second metadata version which has an Include for the first metadata version CDISC ODM Checker v 1 3 User Manual p 9 It then performs a basic validation of the metadata in the other files and validates the reference data and the clinical data against the full metadata version set if reference data and or clinical data is present which 1s not the case here Some results are File Results from checking the CDISC ODM Document ODM file C ODMChecker_ 008 testfiles Include CTChicago_MV _1_ 0 ClinicalData xml Severity error when reaching line 73 and column 116 The value
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