Class: Annotation

A general note about clinical data. If an annotation has both a comment and flags, the flags should be related to the comment.

URI: odm:Annotation

erDiagram
Annotation {
    positiveInteger seqNum  
    TransactionType transactionType  
    oid ID  
}
Flag {

}
FlagType {
    nameType content  
}
FlagValue {
    nameType content  
}
Coding {
    text code  
    uriorcurie system  
    text systemName  
    text systemVersion  
    text label  
    uriorcurie href  
    uriorcurie ref  
    text commentOID  
}
Comment {
    CommentType sponsorOrSite  
}
TranslatedText {
    languageType language  
    text type  
    contentType content  
}

Annotation ||--|o Comment : "comment"
Annotation ||--}o Coding : "coding"
Annotation ||--}o Flag : "flag"
Flag ||--|o FlagValue : "flagValue"
Flag ||--|o FlagType : "flagType"
FlagType ||--|| CodeList : "codeListOID"
FlagValue ||--|| CodeList : "codeListOID"
Comment ||--}o TranslatedText : "translatedText"

Slots

Name Cardinality* and Range Description Inheritance
seqNum 1..1
positiveInteger		 When more than 1 Value element exists this attribute uniquely identifies each... direct
transactionType 0..1
TransactionType		 Identifies the transaction type when /ODM/@FileType is Transactional and ther... direct
ID 1..1
oid		 Unique identifier for the leaf that is referenced. direct
comment 0..1
Comment		 Comment reference: A free-text (uninterpreted) comment about clinical data. T... direct
coding 0..*
Coding		 Coding reference: Coding references a symbol from a defined code system. It u... direct
flag 0..*
Flag		 Flag reference: A machine-processable annotation. direct

* See LinkML documentation for cardinality definitions.

Usages

used by used in type used
ReferenceData annotation range Annotation
ClinicalData annotation range Annotation
SubjectData annotation range Annotation
StudyEventData annotation range Annotation
ItemGroupData annotation range Annotation
ItemData annotation range Annotation
Association annotation range Annotation

See Also

Identifier and Mapping Information

Schema Source

  • from schema: http://www.cdisc.org/ns/odm/v2.0

Mappings

Mapping Type Mapped Value
self odm:Annotation
native odm:Annotation

LinkML Source

Direct

name: Annotation
description: A general note about clinical data. If an annotation has both a comment
  and flags, the flags should be related to the comment.
from_schema: http://www.cdisc.org/ns/odm/v2.0
see_also:
- https://wiki.cdisc.org/display/PUB/Annotation
rank: 1000
slots:
- seqNum
- transactionType
- ID
- comment
- coding
- flag
slot_usage:
  seqNum:
    name: seqNum
    comments:
    - 'Required

      range: positiveInteger'
    domain_of:
    - Annotation
    - Value
    range: positiveInteger
    required: true
  transactionType:
    name: transactionType
    comments:
    - 'Optional

      enum values: (Insert | Update | Remove | Upsert | Context)

      An empty Annotation (one with no annotation value, no comment and no flags)
      is not allowed unless the TransactionType is Remove. On Update, the entire value
      of the annotation is replaced.'
    domain_of:
    - SubjectData
    - StudyEventData
    - ItemGroupData
    - ItemData
    - Annotation
    range: TransactionType
  ID:
    name: ID
    identifier: true
    domain_of:
    - Leaf
    - Signature
    - Annotation
    range: oid
  comment:
    name: comment
    domain_of:
    - Annotation
    range: Comment
    maximum_cardinality: 1
  coding:
    name: coding
    multivalued: true
    domain_of:
    - StudyEventGroupDef
    - StudyEventDef
    - ItemGroupDef
    - Origin
    - SourceItems
    - SourceItem
    - ItemDef
    - CodeList
    - CodeListItem
    - StudyIndication
    - StudyIntervention
    - StudyTargetPopulation
    - StudyParameter
    - ParameterValue
    - Criterion
    - Annotation
    range: Coding
    inlined: true
    inlined_as_list: true
  flag:
    name: flag
    multivalued: true
    domain_of:
    - Annotation
    range: Flag
    inlined: true
    inlined_as_list: true
class_uri: odm:Annotation

Induced

name: Annotation
description: A general note about clinical data. If an annotation has both a comment
  and flags, the flags should be related to the comment.
from_schema: http://www.cdisc.org/ns/odm/v2.0
see_also:
- https://wiki.cdisc.org/display/PUB/Annotation
rank: 1000
slot_usage:
  seqNum:
    name: seqNum
    comments:
    - 'Required

      range: positiveInteger'
    domain_of:
    - Annotation
    - Value
    range: positiveInteger
    required: true
  transactionType:
    name: transactionType
    comments:
    - 'Optional

      enum values: (Insert | Update | Remove | Upsert | Context)

      An empty Annotation (one with no annotation value, no comment and no flags)
      is not allowed unless the TransactionType is Remove. On Update, the entire value
      of the annotation is replaced.'
    domain_of:
    - SubjectData
    - StudyEventData
    - ItemGroupData
    - ItemData
    - Annotation
    range: TransactionType
  ID:
    name: ID
    identifier: true
    domain_of:
    - Leaf
    - Signature
    - Annotation
    range: oid
  comment:
    name: comment
    domain_of:
    - Annotation
    range: Comment
    maximum_cardinality: 1
  coding:
    name: coding
    multivalued: true
    domain_of:
    - StudyEventGroupDef
    - StudyEventDef
    - ItemGroupDef
    - Origin
    - SourceItems
    - SourceItem
    - ItemDef
    - CodeList
    - CodeListItem
    - StudyIndication
    - StudyIntervention
    - StudyTargetPopulation
    - StudyParameter
    - ParameterValue
    - Criterion
    - Annotation
    range: Coding
    inlined: true
    inlined_as_list: true
  flag:
    name: flag
    multivalued: true
    domain_of:
    - Annotation
    range: Flag
    inlined: true
    inlined_as_list: true
attributes:
  seqNum:
    name: seqNum
    description: When more than 1 Value element exists this attribute uniquely identifies
      each Value and defines the order of a Value in a list of Values.
    comments:
    - 'Required

      range: positiveInteger'
    from_schema: http://www.cdisc.org/ns/odm/v2.0
    rank: 1000
    alias: seqNum
    owner: Annotation
    domain_of:
    - Annotation
    - Value
    range: positiveInteger
    required: true
  transactionType:
    name: transactionType
    description: Identifies the transaction type when /ODM/@FileType is Transactional
      and there is no child element.
    comments:
    - 'Optional

      enum values: (Insert | Update | Remove | Upsert | Context)

      An empty Annotation (one with no annotation value, no comment and no flags)
      is not allowed unless the TransactionType is Remove. On Update, the entire value
      of the annotation is replaced.'
    from_schema: http://www.cdisc.org/ns/odm/v2.0
    rank: 1000
    alias: transactionType
    owner: Annotation
    domain_of:
    - SubjectData
    - StudyEventData
    - ItemGroupData
    - ItemData
    - Annotation
    range: TransactionType
  ID:
    name: ID
    description: Unique identifier for the leaf that is referenced.
    from_schema: http://www.cdisc.org/ns/odm/v2.0
    rank: 1000
    identifier: true
    alias: ID
    owner: Annotation
    domain_of:
    - Leaf
    - Signature
    - Annotation
    range: oid
    required: true
  comment:
    name: comment
    description: 'Comment reference: A free-text (uninterpreted) comment about clinical
      data. The comment may have come from the sponsor or the clinical site.'
    from_schema: http://www.cdisc.org/ns/odm/v2.0
    rank: 1000
    alias: comment
    owner: Annotation
    domain_of:
    - Annotation
    range: Comment
    maximum_cardinality: 1
  coding:
    name: coding
    description: 'Coding reference: Coding references a symbol from a defined code
      system. It uses a code defined in a terminology system to associate semantics
      with a given term, codelist, variable, or group of variables. The presence of
      a Coding element associates a meaning to its parent element. Including multiple
      Coding elements for a given parent indicates synonymous meanings provided by
      different code systems or code system versions.'
    from_schema: http://www.cdisc.org/ns/odm/v2.0
    rank: 1000
    multivalued: true
    alias: coding
    owner: Annotation
    domain_of:
    - StudyEventGroupDef
    - StudyEventDef
    - ItemGroupDef
    - Origin
    - SourceItems
    - SourceItem
    - ItemDef
    - CodeList
    - CodeListItem
    - StudyIndication
    - StudyIntervention
    - StudyTargetPopulation
    - StudyParameter
    - ParameterValue
    - Criterion
    - Annotation
    range: Coding
    inlined: true
    inlined_as_list: true
  flag:
    name: flag
    description: 'Flag reference: A machine-processable annotation.'
    from_schema: http://www.cdisc.org/ns/odm/v2.0
    rank: 1000
    multivalued: true
    alias: flag
    owner: Annotation
    domain_of:
    - Annotation
    range: Flag
    inlined: true
    inlined_as_list: true
class_uri: odm:Annotation