3.8 CDISC Syntax File Specifications

The Operational Data Model (ODM) of Clinical Data Interchange Standards Consortium (CDISC) is a vendor neutral, platform independent format for interchange and archive of data collected in clinical trials. The model represents study metadata, data and administrative data associated with a clinical trial. The ODM has been designed to be compliant with guidance and regulations published by the FDA for computer systems used in clinical trials.

The ODM model categorize a clinical study's data into several kinds of entities including subjects, study events, forms, item groups, items, and annotations. The metadata of a study describes the types of study events, forms, item groups, and items that allowed in the study. The clinical data of a study will typically have many actual entities corresponding to their definitions described in the metadata.

Like any XML file, an ODM file consists of a tree of elements which correspond to entities. Each element consists of required attributes and optional attributes. An ODM file type must be either Snapshot or Transactional. A Snapshot file shows the current state of the included data. A Transactional file shows both latest state and (optionally) some prior states of an included entity. An ODM file has Granularity attribute which describes the coverage information of the ODM file.

For more details about ODM specification, see Specification For The Operational Data Model (ODM)

This document addresses, in the OpenClinica *_odm.xml file, what portions of the CDISC ODM standard has been implemented and how OpenClinica data schema has been mapped with CDISC ODM model.




OpenClinica 2.0.1 ( 2007 )

 

Changes have been made in this version:
  • OpenClinica Date (MM/DD/YYYY) datatype has been convert to CDSIC ODM Date (YYYY-MM-DD) datatype.
  • Add two more Metadata elements, i.e. Question and Comment
  • Change the mapping of ODM Metadata element ItemDef - Name, and ItemDef - SASFieldName has the same mapping as ItemDef - Name.
    In the previous version, this attribute has been mapped to OpenClinica ITEM_FORM_METADATA table's field left_item_text. In the current version, it has been mapped to ITEM table's field Name.
  • Change the criterion for ItemGroupRef - Mandatory.
    Before, it has been set as "No". Now, it has been set as "Yes" if there is at least one item in this group which has been marked as required. If there is no required item in this item group, Mandatory has been set as "No".
  • Change the mapping of element StudyDescription so that all of elements StudyName, StudyDescription and ProtocolName refer to the same active study.
  • When one item's data type is integer, it will be converted to CDSIC integer type only if this item's value can be used to do calculation. Its data type will be treated as "text" if its value is actually index of different selection buttons.
  • Generate unique SASDatasetName in the whole file.

 

List-1: Elements implemented (OpenClinica 2.0.1 - 2007).
  1. General Elements
    • ODM (Description, FileType, FileOID, CreationDateTime)
      FileType has been default set as Snapshot. CreationDataTime is set automatically when the file is created.
    • Study (OID)
    • GlobalVariables
    • StudyName
    • StudyDescription
    • ProtocolName
  2. Metadata Elements
    • MetaDataVersion (OID, Name)
      Both OID and Name could be inputted by users. Or, by default is OID = "v1.0.0"; Name = "Version 1.0.0"
    • Include (StudyOID, MetaDataVersionOID)
      Both StudyOID and MetaDataVersionOID are from users' input. In order to have "Include" elements, MetaDataVersionOID, i.e. OID of the previous MetaDataVersion, must be given. If only MetaDataVersionOID is available and StudyOID, i.e. OID of the previous Study, has not been provided, then StudyOID is as the same as the current Study OID.
    • Protocol
    • StudyEventRef (StudyEventOID, Mandatory)
      Mandatory has been set as "Yes".
    • StudyEventDef (OID, Name, Repeating, Type)
    • FormRef (FormOID, Mandatory)
    • FormDef (OID, Name, Repeating)
      Repeating has been set as "No"
    • ItemGroupRef (ItemGroupOID, Mandatory)
      Mandatory has been set as "Yes" if there is at least one item in this group which has been marked as required, otherwise it has been set as "No".
    • ItemGroupDef (OID, Name, Repeating, SASDatasetName)
      Repeating has been set as "No"
    • ItemRef (ItemOID, Mandatory)
    • ItemDef (OID, Name, DataType, SASFieldName, Comment)
    • Question
  3. Clinical Data Elements
    • ClinicalData (StudyOID, MetaDataVersionOID)
      StudyOID is same as OID of Study; MetaDataVersionOID is same as OID of MetaDataVersion.
    • SubjectData (SubjectKey)
    • StudyEventData (StudyEventOID)
    • FormData (FormOID)
    • ItemGroupData (ItemGroupOID, TransactionType)
      TransationType is set as "insert".
    • ItemData (ItemOID, Value)

 

Table-1: Mapping Among OpenClinica Data Schema, OpenClinica CRF Spreadsheet and CDISC ODM (OpenClinica 2.0.1 - 2007).
CDISC ODM         OpenClinica Data Schema OpenClinica CRF Spreadsheet
ODM - Description DATASET - description
ODM - FileOID DATASET - dataset_id
Study - OID DATASET - study_id
StudyName STUDY - name
StudyDescription STUDY - summary
ProtocalName STUDY - unique-identifier
StudyEventRef - StudyEventOID STUDY_EVENT_DEFINITION - study_event_definition_id
StudyEventDef - OID same as StudyEventRef - StudyEventOID
StudyEventDef - Name STUDY_EVENT_DEFINITION - name
StudyEventDef - Repeating STUDY_EVENT_DEFINITION - repeating
StudyEventDef - Type STUDY_EVENT_DEFINITION - type
FormRef - FormOID CRF - crf_id
FormRef - Mandatory EVENT_DEFINITION_CRF - required_crf
FormDef - OID same as FormRef - FormOID
FormDef - Name CRF - name CRF_NAME
ItemGroupRef - ItemGroupOID SECTION - section_id
ItemGroupDef - OID same as ItemGroupOID
ItemGroupDef - Name SECTION - label SECTION_LABEL
ItemGroupDef - SASDataSetName same as ItemGroupDef - Name SECTION_LABEL
ItemRef - ItemOID ITEM - name ITEM_NAME
ItemRef - Mandatory ITEM_FORM_METADATA - required REQUIRED
ItemDef - OID same as ItemRef - ItemOID
ItemDef - Name ITEM - name ITEM_NAME
ItemDef - DataType ITEM_DATA_TYPE - name DATA_TYPES
ItemDef - SASFieldName same as ItemDef - Name ITEM_NAME
ItemDef - Comment ITEM - description DESCRIPTION_LABEL
Question ITEM_FORM_METADATA -
header + left_item_text + right_item_text
SubjectData - SubjectKey STUDY_SUBJECT - label
StudyEventData - StudyEventOID same as StudyEventDef - OID
FormData - FormOID same as FormDef - OID
ItemGroupData - ItemGroupOID same as ItemGroupDef - OID
ItemData - ItemOID same as ItemDef - OID
ItemData - Value ITEM_DATA - value





OpenClinica 2.0 ( Nov. 11, 2006 )
  • This version uses CDISC ODM 1.2.1 Standard for creating OpenClinica data in ODM XML format.
  • The generated ODM file is Snapshot type.
  • The generated ODM file includes one study and required attributes of elements for Metadata and ClinicalData in this study.
  • Metadata describes the types of all study event definitions happened in a study and all items associated with clinical report forms belong to those study event definitions at the state when this ODM file is created.
  • ClinicalData includes all chosen StudyEventData, FormData, ItemGroupData and ItemData for all chosen subjects in the study.

 

List-1: Elements implemented (OpenClinica 2.0-Nov. 11, 2006).
  1. General Elements
    • ODM (Description, FileType, FileOID, CreationDateTime)
      FileType has been default set as Snapshot. CreationDataTime is set automatically when the file is created.
    • Study (OID)
    • GlobalVariables
    • StudyName
    • StudyDescription
    • ProtocolName
  2. Metadata Elements
    • MetaDataVersion (OID, Name)
      Both OID and Name could be inputted by users. Or, by default is OID = "v1.0.0"; Name = "Version 1.0.0"
    • Include (StudyOID, MetaDataVersionOID)
      Both StudyOID and MetaDataVersionOID are from users' input. In order to have "Include" elements, MetaDataVersionOID, i.e. OID of the previous MetaDataVersion, must be given. If only MetaDataVersionOID is available and StudyOID, i.e. OID of the previous Study, has not been provided, then StudyOID is as the same as the current Study OID.
    • Protocol
    • StudyEventRef (StudyEventOID, Mandatory)
      Mandatory has been set as "Yes".
    • StudyEventDef (OID, Name, Repeating, Type)
    • FormRef (FormOID, Mandatory)
    • FormDef (OID, Name, Repeating)
      Repeating has been set as "No"
    • ItemGroupRef (ItemGroupOID, Mandatory)
      Mandatory has been set as "No"
    • ItemGroupDef (OID, Name, Repeating, SASDatasetName)
      Repeating has been set as "No"
    • ItemRef (ItemOID, Mandatory)
    • ItemDef (OID, Name, DataType, SASFieldName)
  3. Clinical Data Elements
    • ClinicalData (StudyOID, MetaDataVersionOID)
      StudyOID is same as OID of Study; MetaDataVersionOID is same as OID of MetaDataVersion.
    • SubjectData (SubjectKey)
    • StudyEventData (StudyEventOID)
    • FormData (FormOID)
    • ItemGroupData (ItemGroupOID, TransactionType)
      TransationType is set as "insert".
    • ItemData (ItemOID, Value)

 

Table-1: Mapping OpenClinica Data Schema To CDISC ODM (For OpenClinica 2.0-Nov. 11, 2006).
CDISC ODM         OpenClinica Data Schema
ODM - Description DATASET - description
ODM - FileOID DATASET - dataset_id
Study - OID DATASET - study_id
StudyName STUDY - name
StudyDescription STUDY - summary
ProtocalName STUDY - unique-identifier
StudyEventRef - StudyEventOID STUDY_EVENT_DEFINITION - study_event_definition_id
StudyEventDef - OID same as StudyEventRef - StudyEventOID
StudyEventDef - Name STUDY_EVENT_DEFINITION - name
StudyEventDef - Repeating STUDY_EVENT_DEFINITION - repeating
StudyEventDef - Type STUDY_EVENT_DEFINITION - type
FormRef - FormOID CRF - crf_id
FormRef - Mandatory EVENT_DEFINITION_CRF - required_crf
FormDef - OID same as FormRef - FormOID
FormDef - Name CRF - name
ItemGroupRef - ItemGroupOID SECTION - section_id
ItemGroupDef - OID same as ItemGroupOID
ItemGroupDef - Name SECTION - label
ItemGroupDef - SASDataSetName same as ItemGroupDef - Name
ItemRef - ItemOID ITEM - name
ItemRef - Mandatory ITEM_FORM_METADATA - required
ItemDef - OID same as ItemRef - ItemOID
ItemDef - Name ITEM_FORM_METADATA - left_item_text
ItemDef - DataType ITEM_DATA_TYPE - name
ItemDef - SASFieldName same as ItemDef - Name
SubjectData - SubjectKey STUDY_SUBJECT - label
StudyEventData - StudyEventOID same as StudyEventDef - OID
FormData - FormOID same as FormDef - OID
ItemGroupData - ItemGroupOID same as ItemGroupDef - OID
ItemData - ItemOID same as ItemDef - OID
ItemData - Value ITEM_DATA - value

 

Exit Help