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2024 harmonization effort - convert schema to use lucidchart representation #11

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merged 4 commits into from
Dec 11, 2024
Merged

2024 harmonization effort - convert schema to use lucidchart representation #11

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c9df620
Pending work from bdc include working group
amc-corey-cox Aug 5, 2024
926f282
clean up failing tests according to last class and slot and conventio…
sierra-moxon Aug 6, 2024
966a954
stash changes
sierra-moxon Dec 11, 2024
1ea56f2
take lucid chart and convert to linkml
sierra-moxon Dec 11, 2024
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102 changes: 61 additions & 41 deletions project/plantuml/cmdr.puml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,39 +2,12 @@
skinparam nodesep 10
hide circle
hide empty members
class "Container" [[{None}]] {

}
class "Subject" [[{Demographic and clinical information about the subject}]] {
{field} id : uriorcurie
{field} name : string
}
class "MaterialEntity" [[{Physical entity that is an input our output of a process from a Subject}]] {
{field} id : uriorcurie
class "MaterialEntity" [[{Physical entity that is an input our output of a process from a Participant}]] {
{field} name : string
{field} internal_id(i) : uriorcurie
{field} global_id(i) : uriorcurie
{field} description(i) : string
}
class "Participation" [[{Subject/Study participation information}]] {
{field} id : uriorcurie
{field} name : string
}
class "SpecimenCollectionProcess" [[{A planned process with the objective of collecting a specimen}]] {
{field} has_input : string
{field} has_output : string
{field} id(i) : uriorcurie
{field} name(i) : string
}
"Container" *--> "0..*" "Subject" : "subjects"
"MaterialEntity" --> "0..1" "Subject" : "source"
"Participation" --> "0..1" "Subject" : "includes"
"SpecimenCollectionProcess" --> "0..*" "Subject" : "has_input"(i)
abstract "Process" [[{A planned process resulting in a material or data}]] {
{field} id : uriorcurie
{field} name : string
{field} has_input : string [0..*]
{field} has_output : string [0..*]
}
"Container" *--> "0..*" "SpecimenCollectionProcess" : "specimen_collection_processes"
"Process" ^-- "SpecimenCollectionProcess"
class "Quantity" [[{None}]] {
{field} has_raw_value : string
{field} has_numeric_value : float
Expand All @@ -43,26 +16,73 @@ class "Quantity" [[{None}]] {
}
"MaterialEntity" *--> "0..1" "Quantity" : "concentration"
"MaterialEntity" *--> "0..1" "Quantity" : "volume"
class "MaterialProcessing" [[{A planned process which results in physical changes in a specified input material}]] {
abstract "Process" [[{A planned process resulting in a material or data}]] {
{field} name : string
{field} has_input : string [0..*]
{field} has_output : string [0..*]
{field} id : uriorcurie
}
class "SpecimenCollectionProcess" [[{A planned process with the objective of collecting a specimen}]] {
{field} has_input : string
{field} has_output : string
{field} name(i) : string
{field} id(i) : uriorcurie
}
class "MaterialProcessing" [[{A planned process which results in physical changes in a specified input material}]] {
{field} name(i) : string
{field} id(i) : uriorcurie
}
"Process" ^-- "SpecimenCollectionProcess"
"Process" ^-- "MaterialProcessing"
class "Investigation" [[{General information about the Investigation}]] {
{field} id : uriorcurie
{field} name : string
class "Container" [[{None}]] {

}
"Participation" --> "0..*" "Investigation" : "involved_in"
"Container" *--> "0..*" "Participation" : "participations"
"Container" *--> "0..*" "SpecimenCollectionProcess" : "specimen_collection_processes"
"MaterialProcessing" --> "0..*" "MaterialEntity" : "has_output"
"MaterialProcessing" --> "0..*" "MaterialEntity" : "has_input"
"Container" *--> "0..*" "MaterialProcessing" : "material_processings"
"MaterialEntity" --> "0..*" "Investigation" : "used_in"
class "Participant" [[{Demographic and clinical information about the participant}]] {
{field} name : string
{field} internal_id(i) : uriorcurie
{field} global_id(i) : uriorcurie
{field} description(i) : string
}
class "Study" [[{General information about a Study}]] {
{field} url : string
{field} internal_id(i) : uriorcurie
{field} global_id(i) : uriorcurie
{field} name(i) : string
{field} description(i) : string
}
abstract "Entity" [[{The Entity class is the abstract parent class for all classes in the CMDR schema}]] {
{field} internal_id : uriorcurie
{field} global_id : uriorcurie
{field} name : string
{field} description : string
}
"MaterialEntity" --> "0..1" "Participant" : "source"
"MaterialEntity" --> "0..*" "Study" : "used_in"
"Container" *--> "0..*" "MaterialEntity" : "materials"
"SpecimenCollectionProcess" --> "0..*" "MaterialEntity" : "has_output"(i)
"Investigation" --> "0..1" "Investigation" : "part_of"
"Container" *--> "0..*" "Investigation" : "investigations"
class "DataObject" [[{A DataFile Associated with a Subject or Investigation or MaterialEntity}]] {
"Entity" ^-- "MaterialEntity"
class "Participation" [[{Study participation information}]] {
{field} name : string
{field} internal_id(i) : uriorcurie
{field} global_id(i) : uriorcurie
{field} description(i) : string
}
"Study" --> "0..1" "Study" : "part_of"
"Container" *--> "0..*" "Study" : "studies"
"Participation" --> "0..*" "Study" : "involved_in"
"Entity" ^-- "Study"
"Participation" --> "0..1" "Participant" : "includes"
"Container" *--> "0..*" "Participation" : "participations"
"Entity" ^-- "Participation"
"Container" *--> "0..*" "Participant" : "participants"(i)
"SpecimenCollectionProcess" --> "0..*" "Participant" : "has_input"(i)
"Container" --> "0..*" "Participant" : "participants"
"Entity" ^-- "Participant"
class "DataObject" [[{A DataFile Associated with a Participant or Study or MaterialEntity}]] {

}
@enduml
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