Demographics
Birthdate
This data element is meant to define patient date of birth. The module describes the one of the common data elements group. These elements, defined by the JRC, can be found on the EU RD Platform at this link.
Data visualization
The full date on which the patient was born, recorded in ISO 8601 formatted date.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Output_{{Output_}}:::usedInstance
Attribute_{{Attribute_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C142470["obo:NCIT_C142470<br/>(Data Capture)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
NCIT_C70856["obo:NCIT_C70856<br/>(Observation Result)"]:::classNode
NCIT_C68615["obo:NCIT_C68615<br/>(Birth Date)"]:::classNode
SIO_000614["sio:SIO_000614<br/>(attribute)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
ISO8601["ISO 8601 formatted date"]:::dataValue
%% Real edges (indices 0-20)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C142470
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"sio:SIO_000300 (has value)"| ISO8601
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"rdf:type"| NCIT_C70856
Output_ -->|"sio:SIO_000628 (refers to)"| Attribute_
Attribute_ -->|"rdf:type"| NCIT_C68615
Attribute_ -->|"rdf:type"| SIO_000614
%% Invisible layout-only chains (indices 21-29, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C142470 ~~~ Comments
OBI_0000272 ~~~ SIO_000090
ISO8601 ~~~ SIO_000015 ~~~ NCIT_C70856
NCIT_C68615 ~~~ SIO_000614
URIProtocol ~~~ Output_
%% rdf:type edges (indices 1,3,5,6,8,9,13,14,16,17,19,20) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,13,14,16,17,19,20 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 21,22,23,24,25,26,27,28,29 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Birthyear
Data visualization
The four-digit year representing the patient’s year of birth. Used when full birthdate is unavailable due to privacy concerns or data minimization policies.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Output_{{Output_}}:::usedInstance
Attribute_{{Attribute_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C142470["obo:NCIT_C142470<br/>(Data Capture)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
NCIT_C70856["obo:NCIT_C70856<br/>(Observation Result)"]:::classNode
NCIT_C83164["obo:NCIT_C83164<br/>(Birth Year)"]:::classNode
SIO_000614["sio:SIO_000614<br/>(attribute)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
BirthYearValue["The year in which a person was born, defined as YYYY."]:::dataValue
%% Real edges (indices 0-20)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C142470
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"rdf:type"| NCIT_C70856
Output_ -->|"sio:SIO_000300 (has value)"| BirthYearValue
Output_ -->|"sio:SIO_000628 (refers to)"| Attribute_
Attribute_ -->|"rdf:type"| NCIT_C83164
Attribute_ -->|"rdf:type"| SIO_000614
%% Invisible layout-only chains (indices 21-29, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C142470 ~~~ Comments
OBI_0000272 ~~~ SIO_000090
SIO_000015 ~~~ NCIT_C70856 ~~~ BirthYearValue
NCIT_C83164 ~~~ SIO_000614
URIProtocol ~~~ Output_
%% rdf:type edges (indices 1,3,5,6,8,9,13,14,15,16,19,20) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,13,14,15,16,19,20 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 21,22,23,24,25,26,27,28,29 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Birthplace
The country in which the patient was born.
Data visualization
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Output_{{Output_}}:::usedInstance
Attribute_{{Attribute_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Identifier_{{Identifier_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C142470["obo:NCIT_C142470<br/>(Data Capture)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
NCIT_C25464["obo:NCIT_C25464<br/>(Country)"]:::classNode
NCIT_C20108["obo:NCIT_C20108<br/>(Country Code)"]:::classNode
SIO_000614["sio:SIO_000614<br/>(attribute)"]:::classNode
NCIT_C176764["obo:NCIT_C176764<br/>(Birthplace)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
CountryName["Country name"]:::dataValue
CountryCodeValue["Country code, as a string"]:::dataValue
%% Real edges (indices 0-24)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C142470
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"sio:SIO_000671 (has identifier)"| Identifier_
Output_ -->|"rdf:type"| NCIT_C25464
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"sio:SIO_000628 (refers to)"| Attribute_
Identifier_ -->|"rdf:type"| SIO_000115
Identifier_ -->|"rdf:type"| NCIT_C20108
Identifier_ -->|"sio:SIO_000300 (has value)"| CountryCodeValue
Identifier_ -->|"rdfs:label"| CountryName
Attribute_ -->|"rdf:type"| SIO_000614
Attribute_ -->|"rdf:type"| NCIT_C176764
%% Invisible layout-only chains (indices 25-36, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C142470 ~~~ Comments
OBI_0000272 ~~~ SIO_000090
NCIT_C25464 ~~~ SIO_000015
SIO_000115 ~~~ NCIT_C20108 ~~~ CountryCodeValue ~~~ CountryName
SIO_000614 ~~~ NCIT_C176764
URIProtocol ~~~ Output_
Identifier_ ~~~ Attribute_
%% rdf:type edges (indices 1,3,5,6,8,9,13,14,16,17,19,20,23,24) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,13,14,16,17,19,20,23,24 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 25,26,27,28,29,30,31,32,33,34,35,36 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Deathdate
This module describes the data element in the Common Data Elemments group. These elements, defined by the JRC, can be found on the EU RD Platform at this link.
Data visualization
The full date on which the patient’s death, recorded in ISO 8601 formatted date. Also the underlying medical condition that directly led to the patient’s death.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Output_{{Output_}}:::usedInstance
Attribute_{{Attribute_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Causality_{{Causality_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C142470["obo:NCIT_C142470<br/>(Data Capture)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
NCIT_C70856["obo:NCIT_C70856<br/>(Observation Result)"]:::classNode
NCIT_C81239["obo:NCIT_C81239<br/>(Cause of Death)"]:::classNode
SIO_000614["sio:SIO_000614<br/>(attribute)"]:::classNode
NCIT_C70810["obo:NCIT_C70810<br/>(Date of Death)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
ISO8601["ISO 8601 formatted date"]:::dataValue
%% Real edges (indices 0-23)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C142470
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"rdf:type"| NCIT_C70856
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"sio:SIO_000300 (has value)"| ISO8601
Output_ -->|"sio:SIO_00243 (is causally related with)"| Causality_
Output_ -->|"sio:SIO_000628 (refers to)"| Attribute_
Causality_ -->|"rdf:type"| SIO_000015
Causality_ -->|"rdf:type"| NCIT_C81239
Attribute_ -->|"rdf:type"| SIO_000614
Attribute_ -->|"rdf:type"| NCIT_C70810
%% Invisible layout-only chains (indices 24-34, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C142470 ~~~ Comments
OBI_0000272 ~~~ SIO_000090
NCIT_C70856 ~~~ SIO_000015 ~~~ ISO8601
SIO_000015 ~~~ NCIT_C81239
SIO_000614 ~~~ NCIT_C70810
URIProtocol ~~~ Output_
Causality_ ~~~ Attribute_
%% rdf:type edges (indices 1,3,5,6,8,9,13,14,15,16,20,21,22,23) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,13,14,15,16,20,21,22,23 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 24,25,26,27,28,29,30,31,32,33,34 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Sex
This module describes the data element in the Common Data Elemments group. These elements, defined by the JRC, can be found on the EU RD Platform at this link.
Data visualization
The biological sex of the patient.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Output_{{Output_}}:::usedInstance
Attribute_{{Attribute_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C142470["obo:NCIT_C142470<br/>(Data Capture)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
NCIT_C160908["obo:NCIT_C160908<br/>(Sex Code)"]:::classNode
SIO_000614["sio:SIO_000614<br/>(attribute)"]:::classNode
SexOptions["One of the following:<br/>obo:NCIT_C16576 (Female)<br/>obo:NCIT_C20197 (Male)<br/>obo:NCIT_C124294 (Undetermined)<br/>obo:NCIT_C17998 (Unknown)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
SexName["Sex name"]:::dataValue
%% Real edges (indices 0-20)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C142470
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"rdf:type"| NCIT_C160908
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"sio:SIO_000300 (has value)"| SexName
Output_ -->|"sio:SIO_000628 (refers to)"| Attribute_
Attribute_ -->|"rdf:type"| SIO_000614
Attribute_ -->|"rdf:type"| SexOptions
%% Invisible layout-only chains (indices 21-29, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C142470 ~~~ Comments
OBI_0000272 ~~~ SIO_000090
NCIT_C160908 ~~~ SIO_000015 ~~~ SexName
SIO_000614 ~~~ SexOptions
URIProtocol ~~~ Output_
%% rdf:type edges (indices 1,3,5,6,8,9,13,14,15,16,19,20) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,13,14,15,16,19,20 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 21,22,23,24,25,26,27,28,29 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Participation and timeline
First confirmed visit
This module describes the data element in the Common Data Elemments group. These elements, defined by the JRC, can be found on the EU RD Platform at this link.
Data visualization
The date of the patient’s first verified interaction with the healthcare system or enrollment in a study.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Output_{{Output_}}:::usedInstance
Attribute_{{Attribute_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C142470["obo:NCIT_C142470<br/>(Data Capture)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
NCIT_C70856["obo:NCIT_C70856<br/>(Observation Result)"]:::classNode
NCIT_C159705["obo:NCIT_C159705<br/>(First Confirmed Visit)"]:::classNode
SIO_000614["sio:SIO_000614<br/>(attribute)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
ISO8601["ISO 8601 formatted date"]:::dataValue
%% Real edges (indices 0-20)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C142470
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000229 (has output)"| Output_
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"sio:SIO_000628 (refers to)"| Attribute_
Output_ -->|"rdf:type"| NCIT_C70856
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"sio:SIO_000300 (has value)"| ISO8601
Attribute_ -->|"rdf:type"| NCIT_C159705
Attribute_ -->|"rdf:type"| SIO_000614
%% Invisible layout-only chains (indices 21-29, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C142470 ~~~ Comments
OBI_0000272 ~~~ SIO_000090
NCIT_C70856 ~~~ SIO_000015 ~~~ ISO8601
NCIT_C159705 ~~~ SIO_000614
URIProtocol ~~~ Output_
%% rdf:type edges (indices 1,3,5,6,9,10,13,14,16,17,19,20) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,9,10,13,14,16,17,19,20 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 21,22,23,24,25,26,27,28,29 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Participation status
This module describes the data element in the Common Data Elemments group. These elements, defined by the JRC, can be found on the EU RD Platform at this link.
Data visualization
Indicates the current engagement of the patient in a healthcare program, study, or registry.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Output_{{Output_}}:::usedInstance
Attribute_{{Attribute_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C142470["obo:NCIT_C142470<br/>(Data Capture)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
OPMI_0000326["obo:OPMI_0000326<br/>(Status)"]:::classNode
SIO_000614["sio:SIO_000614<br/>(attribute)"]:::classNode
PersonStatusChildIRI["child IRI of obo:NCIT_C171086 (Person Status), e.g.:<br/>obo:NCIT_C37987 (Alive)<br/>obo:NCIT_C90387 (Found Dead)<br/>obo:NCIT_C48227 (Lost To Follow-Up)<br/>obo:NCIT_C124784 (Refusal to Participate)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
StatusName["Status name"]:::dataValue
%% Real edges (indices 0-20)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C142470
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000229 (has output)"| Output_
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"sio:SIO_000628 (refers to)"| Attribute_
Output_ -->|"sio:SIO_000300 (has value)"| StatusName
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"rdf:type"| OPMI_0000326
Attribute_ -->|"rdf:type"| SIO_000614
Attribute_ -->|"rdf:type"| PersonStatusChildIRI
%% Invisible layout-only chains (indices 21-29, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C142470 ~~~ Comments
OBI_0000272 ~~~ SIO_000090
StatusName ~~~ SIO_000015 ~~~ OPMI_0000326
SIO_000614 ~~~ PersonStatusChildIRI
URIProtocol ~~~ Output_
%% rdf:type edges (indices 1,3,5,6,9,10,13,14,17,18,19,20) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,9,10,13,14,17,18,19,20 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 21,22,23,24,25,26,27,28,29 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Symptoms onset
This module describes the data element in the Common Data Elemments group. These elements, defined by the JRC, can be found on the EU RD Platform at this link.
Data visualization
The date (recorded in ISO 8601 formatted date) when the patient first noticed or reported symptoms related to the condition of interest, also described.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Output_{{Output_}}:::usedInstance
Attribute_{{Attribute_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Target_{{Target_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C142470["obo:NCIT_C142470<br/>(Data Capture)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
NCIT_C4876["obo:NCIT_C4876<br/>(Symptom)"]:::classNode
NCIT_C70856["obo:NCIT_C70856<br/>(Observation Result)"]:::classNode
NCIT_C124353["obo:NCIT_C124353<br/>(Symptom Onset)"]:::classNode
SIO_000614["sio:SIO_000614<br/>(attribute)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
ISO8601OrAgeOnset["ISO 8601 formatted date OR<br/>Age of onset"]:::dataValue
%% Real edges (indices 0-23)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"sio:SIO_000291 (has target)"| Target_
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C142470
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000229 (has output)"| Output_
Target_ -->|"rdf:type"| NCIT_C4876
Target_ -->|"rdf:type"| SIO_000015
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"sio:SIO_000628 (refers to)"| Attribute_
Output_ -->|"rdf:type"| NCIT_C70856
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"sio:SIO_000300 (has value)"| ISO8601OrAgeOnset
Attribute_ -->|"rdf:type"| NCIT_C124353
Attribute_ -->|"rdf:type"| SIO_000614
%% Invisible layout-only chains (indices 24-34, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C142470 ~~~ Comments
NCIT_C4876 ~~~ SIO_000015
OBI_0000272 ~~~ SIO_000090
NCIT_C70856 ~~~ SIO_000015 ~~~ ISO8601OrAgeOnset
NCIT_C124353 ~~~ SIO_000614
Target_ ~~~ URIProtocol ~~~ Output_
%% rdf:type edges (indices 1,3,5,6,10,11,14,15,16,17,19,20,22,23) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,10,11,14,15,16,17,19,20,22,23 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 24,25,26,27,28,29,30,31,32,33,34 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Conditions and findings
Phenotype
This module describes the data element in the Common Data Elemments group. These elements, defined by the JRC, can be found on the EU RD Platform at this link.
Data visualization
Describes qualitative observable characteristics, signs, or traits expressed by the patient.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Output_{{Output_}}:::usedInstance
Duration_{{Duration_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Target_{{Target_}}:::usedInstance
Startdate_{{Startdate_}}:::usedInstance
Enddate_{{Enddate_}}:::usedInstance
Attribute_{{Attribute_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C18020["obo:NCIT_C18020<br/>(Diagnostic Procedure)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
PhenotypeCode["IRI for the phenotype being tested, e.g.:<br/>obo:HP_0001638 (Cardiomyopathy)"]:::classNode
SIO_000614["sio:SIO_000614<br/>(attribute)"]:::classNode
NCIT_C217011["obo:NCIT_C217011<br/>(Duration Quantity Value)"]:::classNode
SIO_000417["sio:SIO_000417<br/>(time interval)"]:::classNode
SIO_000031["sio:SIO_000031<br/>(start date)"]:::classNode
SIO_000032["sio:SIO_000032<br/>(end date)"]:::classNode
NCIT_C16977["obo:NCIT_C16977<br/>(Phenotype)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
PhenotypeName["Phenotype name"]:::dataValue
PhenotypePresent["true / false"]:::dataValue
ISO8601Start["ISO 8601 formatted date"]:::dataValue
ISO8601End["ISO 8601 formatted date"]:::dataValue
%% Real edges (indices 0-33)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"sio:SIO_000291 (has target)"| Target_
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C18020
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000229 (has output)"| Output_
Target_ -->|"rdf:type"| SIO_000015
Target_ -->|"rdf:type"| PhenotypeCode
Target_ -->|"rdfs:label"| PhenotypeName
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"sio:SIO_000687 (exists at)"| Duration_
Output_ -->|"sio:SIO_000300 (has value)"| PhenotypePresent
Output_ -->|"sio:SIO_000628 (refers to)"| Attribute_
Output_ -->|"rdf:type"| NCIT_C16977
Output_ -->|"rdf:type"| SIO_000015
Attribute_ -->|"rdf:type"| SIO_000614
Attribute_ -->|"rdf:type"| PhenotypeCode
Duration_ -->|"rdf:type"| NCIT_C217011
Duration_ -->|"rdf:type"| SIO_000417
Duration_ -->|"sio:SIO_000680 (has start time)"| Startdate_
Duration_ -->|"sio:SIO_000681 (has end time)"| Enddate_
Startdate_ -->|"rdf:type"| SIO_000031
Startdate_ -->|"sio:SIO_000300 (has value)"| ISO8601Start
Enddate_ -->|"sio:SIO_000300 (has value)"| ISO8601End
Enddate_ -->|"rdf:type"| SIO_000032
%% Invisible layout-only chains (indices 34-50, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C18020 ~~~ Comments
SIO_000015 ~~~ PhenotypeCode ~~~ PhenotypeName
OBI_0000272 ~~~ SIO_000090
NCIT_C16977 ~~~ SIO_000015 ~~~ PhenotypePresent
SIO_000614 ~~~ PhenotypeCode
NCIT_C217011 ~~~ SIO_000417
SIO_000031 ~~~ ISO8601Start
ISO8601End ~~~ SIO_000032
Duration_ ~~~ Attribute_
Startdate_ ~~~ Enddate_
Target_ ~~~ URIProtocol ~~~ Output_
%% rdf:type edges (indices 1,3,5,6,10,11,14,15,17,18,22,23,24,25,26,27,30,33) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,10,11,14,15,17,18,22,23,24,25,26,27,30,33 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Diagnosis
This module describes the data element in the Common Data Elemments group. These elements, defined by the JRC, can be found on the EU RD Platform at this link.
Data visualization
A clinically established identification of a disease or condition affecting the patient.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Target_{{Target_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Output_{{Output_}}:::usedInstance
Attribute_{{Attribute_}}:::usedInstance
Input_{{Input_}}:::usedInstance
Duration_{{Duration_}}:::usedInstance
Startdate_{{Startdate_}}:::usedInstance
Enddate_{{Enddate_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C18020["obo:NCIT_C18020<br/>(Diagnostic Procedure)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
DiagnosisCode["IRI for the diagnosis being tested, e.g.:<br/>obo:ORDO_Orphanet_93552 (Marfan syndrome)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
SIO_000614["sio:SIO_000614<br/>(attribute)"]:::classNode
OGMS_0000073["obo:OGMS_0000073<br/>(Diagnosis)"]:::classNode
NCIT_C217011["obo:NCIT_C217011<br/>(Duration Quantity Value)"]:::classNode
SIO_000417["sio:SIO_000417<br/>(time interval)"]:::classNode
SIO_000031["sio:SIO_000031<br/>(start date)"]:::classNode
SIO_000032["sio:SIO_000032<br/>(end date)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
DiagnosisName["Diagnosis name"]:::dataValue
DiagnosisPresent["true / false"]:::dataValue
ISO8601Start["ISO 8601 formatted date"]:::dataValue
ISO8601End["ISO 8601 formatted date"]:::dataValue
%% Real edges (indices 0-35)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C18020
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000291 (has target)"| Target_
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
Process_ -->|"sio:SIO_000230 (has input)"| Input_
Target_ -->|"rdf:type"| SIO_000015
Target_ -->|"rdf:type"| DiagnosisCode
Target_ -->|"rdfs:label"| DiagnosisName
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"sio:SIO_000628 (refers to)"| Attribute_
Output_ -->|"sio:SIO_000687 (exists at)"| Duration_
Output_ -->|"sio:SIO_000300 (has value)"| DiagnosisPresent
Output_ -->|"rdf:type"| OGMS_0000073
Output_ -->|"rdf:type"| SIO_000015
Attribute_ -->|"rdf:type"| SIO_000614
Attribute_ -->|"rdf:type"| DiagnosisCode
%% Input_ is a deliberate empty-bnode placeholder -- see the note above the diagram
Input_ -->|"rdf:type"| SIO_000015
Duration_ -->|"rdf:type"| NCIT_C217011
Duration_ -->|"rdf:type"| SIO_000417
Duration_ -->|"sio:SIO_000680 (has start time)"| Startdate_
Duration_ -->|"sio:SIO_000681 (has end time)"| Enddate_
Startdate_ -->|"rdf:type"| SIO_000031
Startdate_ -->|"sio:SIO_000300 (has value)"| ISO8601Start
Enddate_ -->|"rdf:type"| SIO_000032
Enddate_ -->|"sio:SIO_000300 (has value)"| ISO8601End
%% Invisible layout-only chains (indices 36-53, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C18020 ~~~ Comments
SIO_000015 ~~~ DiagnosisCode ~~~ DiagnosisName
OBI_0000272 ~~~ SIO_000090
OGMS_0000073 ~~~ SIO_000015 ~~~ DiagnosisPresent
SIO_000614 ~~~ DiagnosisCode
Target_ ~~~ URIProtocol ~~~ Output_ ~~~ Input_
Attribute_ ~~~ Duration_
NCIT_C217011 ~~~ SIO_000417
SIO_000031 ~~~ ISO8601Start
SIO_000032 ~~~ ISO8601End
Startdate_ ~~~ Enddate_
%% rdf:type edges (indices 1,3,5,6,8,9,15,16,18,19,23,24,25,26,27,28,29,32,34) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,15,16,18,19,23,24,25,26,27,28,29,32,34 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Clinical and molecular measurements
Examination
Data visualization
Clinical findings obtained from structured evaluations such as quantitative physical exams, body measurements or medical imaging.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Specific_method_{{Specific_method_}}:::usedInstance
Target_{{Target_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Output_{{Output_}}:::usedInstance
Attribute_{{Attribute_}}:::usedInstance
Unit_{{Unit_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
MAXO_0000487["obo:MAXO_0000487<br/>(clinical assessment)"]:::classNode
NCIT_C16536["IRI for the specific<br/>measurement method, e.g.:<br/>obo:NCIT_C16536 (Electrophoresis)"]:::classNode
AnatomicStructureIRI["IRI for the anatomic structure<br/>measured, e.g.:<br/>obo:NCIT_C12419 (Head)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
AnnotationCodeIRI["IRI for the annotation code of the<br/>examination, e.g.:<br/>obo:NCIT_C25208 (Weight)<br/>obo:NCIT_C25347 (Height)<br/>obo:NCIT_C99524 (Left Ventricular<br/>Ejection Fraction)<br/>obo:NCIT_C16358 (Body Mass Index)"]:::classNode
SIO_000614["sio:SIO_000614<br/>(attribute)"]:::classNode
NCIT_C70856["obo:NCIT_C70856<br/>(Observation Result)"]:::classNode
UnitMeasurementIRI["IRI for unit of measurement"]:::classNode
SIO_000074["sio:SIO_000074<br/>(unit of measurement)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
ExamMeasurementValue["Examination<br/>measurement value"]:::dataValue
%% Real edges (indices 0-29)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| MAXO_0000487
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000028 (has part)"| Specific_method_
Process_ -->|"sio:SIO_000291 (has target)"| Target_
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
Specific_method_ -->|"rdf:type"| NCIT_C16536
Specific_method_ -->|"rdf:type"| SIO_000006
Target_ -->|"rdf:type"| AnatomicStructureIRI
Target_ -->|"rdf:type"| SIO_000015
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"sio:SIO_000628 (refers to)"| Attribute_
Output_ -->|"sio:SIO_000221 (has unit)"| Unit_
Output_ -->|"rdf:type"| NCIT_C70856
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"sio:SIO_000300 (has value)"| ExamMeasurementValue
Attribute_ -->|"rdf:type"| AnnotationCodeIRI
Attribute_ -->|"rdf:type"| SIO_000614
Unit_ -->|"rdf:type"| UnitMeasurementIRI
Unit_ -->|"rdf:type"| SIO_000074
%% Invisible layout-only chains (indices 30-44, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ MAXO_0000487 ~~~ Comments
NCIT_C16536 ~~~ SIO_000006
AnatomicStructureIRI ~~~ SIO_000015
OBI_0000272 ~~~ SIO_000090
NCIT_C70856 ~~~ SIO_000015 ~~~ ExamMeasurementValue
AnnotationCodeIRI ~~~ SIO_000614
UnitMeasurementIRI ~~~ SIO_000074
Specific_method_ ~~~ Target_ ~~~ URIProtocol ~~~ Output_
Attribute_ ~~~ Unit_
%% rdf:type edges (indices 1,3,5,6,8,9,15,16,17,18,19,20,23,24,26,27,28,29) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,15,16,17,18,19,20,23,24,26,27,28,29 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Laboratory
Data visualization
Quantitative or qualitative results from laboratory tests. Results can be represented including the measured value, units, anatomic structure and sample.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Specific_method_{{Specific_method_}}:::usedInstance
Input_{{Input_}}:::usedInstance
Target_{{Target_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Output_{{Output_}}:::usedInstance
Unit_{{Unit_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C25294["obo:NCIT_C25294<br/>(Laboratory procedure)"]:::classNode
NCIT_C147324["IRI for a specific method, e.g.:<br/>obo:NCIT_C147324<br/>(Creatinine Clearance Adjusted for BSA)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
NCIT_C17610["IRI for the input sample source, e.g.:<br/>obo:NCIT_C17610<br/>(Blood Sample)"]:::classNode
NCIT_C399["IRI for the chemical or<br/>Biomedical Material, e.g.:<br/>obo:NCIT_C399<br/>(Creatinine)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
NCIT_C70856["obo:NCIT_C70856<br/>(Observation Result)"]:::classNode
SIO_000074["sio:SIO_000074<br/>(unit of measurement)"]:::classNode
UO_0000022["IRI for unit of measurement, e.g.:<br/>obo:UO_0000022<br/>(milligram)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
LabMeasurementValue["Laboratory<br/>measurement value"]:::dataValue
%% Real edges (indices 0-29)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C25294
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000028 (has part)"| Specific_method_
Process_ -->|"sio:SIO_000230 (has input)"| Input_
Process_ -->|"sio:SIO_000291 (has target)"| Target_
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
Specific_method_ -->|"rdf:type"| SIO_000006
Specific_method_ -->|"rdf:type"| NCIT_C147324
Input_ -->|"rdf:type"| SIO_000015
Input_ -->|"rdf:type"| NCIT_C17610
Target_ -->|"rdf:type"| NCIT_C399
Target_ -->|"rdf:type"| SIO_000015
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"sio:SIO_000221 (has unit)"| Unit_
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"rdf:type"| NCIT_C70856
Output_ -->|"sio:SIO_000300 (has value)"| LabMeasurementValue
Unit_ -->|"rdf:type"| SIO_000074
Unit_ -->|"rdf:type"| UO_0000022
%% Invisible layout-only chains (indices 30-44, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C25294 ~~~ Comments
SIO_000006 ~~~ NCIT_C147324
SIO_000015 ~~~ NCIT_C17610
NCIT_C399 ~~~ SIO_000015
OBI_0000272 ~~~ SIO_000090
SIO_000015 ~~~ NCIT_C70856 ~~~ LabMeasurementValue
SIO_000074 ~~~ UO_0000022
Specific_method_ ~~~ Input_ ~~~ Target_ ~~~ URIProtocol ~~~ Output_
%% rdf:type edges (indices 1,3,5,6,8,9,16,17,18,19,20,21,22,23,25,26,28,29) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,16,17,18,19,20,21,22,23,25,26,28,29 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Genetic
This module describes the data element in the Common Data Elemments group. These elements, defined by the JRC, can be found on the EU RD Platform at this link.
Data visualization
Results from genomic analyses performed on the patient’s DNA or RNA. Findings may include details such as the specific genetic method, as well as the identified variants, the source of the biological sample, and zygosity information.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Specific_method_{{Specific_method_}}:::usedInstance
Input_{{Input_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Output_{{Output_}}:::usedInstance
Attribute_{{Attribute_}}:::usedInstance
Identifier_{{Identifier_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C15709["obo:NCIT_C15709<br/>Genetic Testing"]:::classNode
NCIT_C18477["IRI for a specific method, e.g.:<br/>obo:NCIT_C18477<br/>(Microarray Analysis)"]:::classNode
NCIT_C17610["IRI for the input sample<br/>source, e.g.:<br/>obo:NCIT_C17610<br/>(Blood Sample)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
SIO_000614["sio:SIO_000614<br/>(attribute)"]:::classNode
GENO_0000133["Child of obo:GENO_0000133<br/>(zygosity) e.g.:<br/>obo:GENO_0000134 (hemizygosity)<br/>obo:GENO_0000135 (heterozygosity)<br/>obo:GENO_0000136 (homozygosity)<br/>obo:GENO_0000978 (nullizygosity)<br/>obo:GENO_0000402 (compound heterozygosity)"]:::classNode
NCIT_C171178["obo:NCIT_C171178<br/>(Sequence Variant Report)"]:::classNode
NCIT_C164607["obo:NCIT_C164607<br/>(Sequence Identifier)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
LexicalSequenceVariant["Lexical sequence variant, e.g.:<br/>NC_000023.9:g.32317682G>A"]:::dataValue
%% Real edges (indices 0-29)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C15709
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000028 (has part)"| Specific_method_
Process_ -->|"sio:SIO_000230 (has input)"| Input_
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
Specific_method_ -->|"rdf:type"| SIO_000006
Specific_method_ -->|"rdf:type"| NCIT_C18477
Input_ -->|"rdf:type"| NCIT_C17610
Input_ -->|"rdf:type"| SIO_000015
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"sio:SIO_000628 (refers to)"| Attribute_
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"rdf:type"| NCIT_C171178
Attribute_ -->|"rdf:type"| SIO_000614
Attribute_ -->|"rdf:type"| GENO_0000133
Attribute_ -->|"sio:SIO_000671 (has identifier)"| Identifier_
Identifier_ -->|"rdf:type"| SIO_000115
Identifier_ -->|"sio:SIO_000300 (has value)"| LexicalSequenceVariant
Identifier_ -->|"rdf:type"| NCIT_C164607
%% Invisible layout-only chains (indices 30-43, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C15709 ~~~ Comments
SIO_000006 ~~~ NCIT_C18477
NCIT_C17610 ~~~ SIO_000015
OBI_0000272 ~~~ SIO_000090
SIO_000015 ~~~ NCIT_C171178
SIO_000614 ~~~ GENO_0000133
SIO_000115 ~~~ LexicalSequenceVariant ~~~ NCIT_C164607
Specific_method_ ~~~ Input_ ~~~ URIProtocol ~~~ Output_
%% rdf:type edges (indices 1,3,5,6,8,9,15,16,17,18,19,20,22,23,24,25,27,29) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,15,16,17,18,19,20,22,23,24,25,27,29 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 30,31,32,33,34,35,36,37,38,39,40,41,42,43 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Functional Assessment
Measures what a patient can or cannot do, using a named, structured instrument — anything from a single objective performance test (e.g. the 10-Metre Walk Test) to a multi-item battery or self-reported questionnaire (e.g. WHODAS 2.0). The specific instrument/metric being used is recorded separately from the exact protocol by which it was administered, since the same instrument can be delivered under different protocols (e.g. with or without a warm-up period).
Data visualization
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Target_{{Target_}}:::usedInstance
Output_{{Output_}}:::usedInstance
Duration_{{Duration_}}:::usedInstance
Unit_{{Unit_}}:::usedInstance
Startdate_{{Startdate_}}:::usedInstance
Enddate_{{Enddate_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
OMIT_0005448["obo:OMIT_0005448<br/>(Disability Evaluation)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
FunctionalMetric["IRI for the specific functional assessment<br/>instrument/metric used, e.g.:<br/>WHODAS 2.0, 10-Metre Walk Test"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
NCIT_C49149["obo:NCIT_C49149<br/>(Answer)"]:::classNode
SIO_000074["sio:SIO_000074<br/>(unit of measurement)"]:::classNode
IRIUnitMeasurement["IRI for<br/>unit of measurement"]:::classNode
NCIT_C217011["obo:NCIT_C217011<br/>(Duration Quantity Value)"]:::classNode
SIO_000417["sio:SIO_000417<br/>(time interval)"]:::classNode
SIO_000031["sio:SIO_000031<br/>(start date)"]:::classNode
SIO_000032["sio:SIO_000032<br/>(end date)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
ScaleScoreValue["Scale/Score/Value"]:::dataValue
OutputLabel["Human-readable label describing the output,<br/>e.g. 'output from WHODAS 2.0'"]:::dataValue
ISO8601Start["ISO 8601 formatted date"]:::dataValue
ISO8601End["ISO 8601 formatted date"]:::dataValue
%% Real edges (indices 0-33)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| OMIT_0005448
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000291 (has target)"| Target_
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
Target_ -->|"rdf:type"| SIO_000015
Target_ -->|"rdf:type"| FunctionalMetric
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"sio:SIO_000687 (exists at)"| Duration_
Output_ -->|"sio:SIO_000221 (has unit)"| Unit_
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"rdf:type"| NCIT_C49149
Output_ -->|"sio:SIO_000300 (has value)"| ScaleScoreValue
Output_ -->|"rdfs:label"| OutputLabel
Unit_ -->|"rdf:type"| SIO_000074
Unit_ -->|"rdf:type"| IRIUnitMeasurement
Duration_ -->|"rdf:type"| NCIT_C217011
Duration_ -->|"rdf:type"| SIO_000417
Duration_ -->|"sio:SIO_000680 (has start time)"| Startdate_
Duration_ -->|"sio:SIO_000681 (has end time)"| Enddate_
Startdate_ -->|"rdf:type"| SIO_000031
Startdate_ -->|"sio:SIO_000300 (has value)"| ISO8601Start
Enddate_ -->|"rdf:type"| SIO_000032
Enddate_ -->|"sio:SIO_000300 (has value)"| ISO8601End
%% Invisible layout-only chains (indices 34-50, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ OMIT_0005448 ~~~ Comments
SIO_000015 ~~~ FunctionalMetric
OBI_0000272 ~~~ SIO_000090
SIO_000015 ~~~ NCIT_C49149 ~~~ ScaleScoreValue ~~~ OutputLabel
SIO_000074 ~~~ IRIUnitMeasurement
NCIT_C217011 ~~~ SIO_000417
SIO_000031 ~~~ ISO8601Start
SIO_000032 ~~~ ISO8601End
Target_ ~~~ URIProtocol ~~~ Output_
Duration_ ~~~ Unit_
Startdate_ ~~~ Enddate_
%% rdf:type edges (indices 1,3,5,6,8,9,14,15,16,17,20,21,24,25,26,27,30,32) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,14,15,16,17,20,21,24,25,26,27,30,32 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary. (Glossary and CSV/Toolkit tag still say “Disability” — renaming those is pending propagation work; see note below the diagram.)
Patient-reported outcomes
Questionnaire
Data visualization
Structured responses provided by the patient through standardized forms or surveys and standarized by Patient Reported Outcomes (PRO) or similar assessment questions.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Output_{{Output_}}:::usedInstance
Input_{{Input_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C20993["obo:NCIT_C20993<br/>(Research or Clinical Assessment Tool)"]:::classNode
NCIT_C91102["obo:NCIT_C91102<br/>(Clinical or Research Assessment Question)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
NCIT_C177377["obo:NCIT_C177377<br/>(Patient Reported Outcome Measures)"]:::classNode
NCIT_C49149["obo:NCIT_C49149<br/>(Answer)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
LexicalOutcome["Lexical reported outcome value/score"]:::dataValue
%% Real edges (indices 0-20)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C20993
Process_ -->|"sio:SIO_000230 (has input)"| Input_
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
Input_ -->|"rdf:type"| NCIT_C91102
Input_ -->|"rdf:type"| SIO_000015
URIProtocol -->|"rdf:type"| SIO_000090
URIProtocol -->|"rdf:type"| NCIT_C177377
Output_ -->|"rdf:type"| NCIT_C49149
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"sio:SIO_000300 (has value)"| LexicalOutcome
%% Invisible layout-only chains (indices 21-29, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C20993 ~~~ Comments
NCIT_C91102 ~~~ SIO_000015
SIO_000090 ~~~ NCIT_C177377
NCIT_C49149 ~~~ LexicalOutcome
Input_ ~~~ URIProtocol ~~~ Output_
%% rdf:type edges (indices 1,3,5,6,8,9,14,15,16,17,18,19) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,14,15,16,17,18,19 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 21,22,23,24,25,26,27,28,29 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Treatments and interventions
Medication
Records of medications that have been prescribed or administered to the patient by a healthcare professional. Includes details such as drug name, dosage, frequency, route of administration, and medication duration.
Data visualization
The module shows how the individual, defined as a patient, participates in a drug administration procedure. At this process, the agent of this medication is defined, being the drug prescribed and its route of administration. Also this procedure has as output the medication as a prescription and its value, measured among its unit of measurement and frequency.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Specific_method_{{Specific_method_}}:::usedInstance
Input_{{Input_}}:::usedInstance
Frequency_{{Frequency_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Output_{{Output_}}:::usedInstance
Unit_{{Unit_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C70962["obo:NCIT_C70962<br/>(Agent Administration)"]:::classNode
NCIT_C28161["IRI for route of administration, e.g.:<br/>obo:NCIT_C28161<br/>(Intramuscular Route of Administration)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
NCIT_C177929["obo:NCIT_C177929<br/>(Drug Product Component)"]:::classNode
SIO_001367["sio:SIO_001367<br/>(frequency)"]:::classNode
NCIT_C66968["IRI for frequency, e.g.:<br/>obo:NCIT_C66968<br/>(Per Day)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
IAO_0000104["obo:IAO_0000104<br/>(plan specification)"]:::classNode
DoseClasses["One of the following:<br/>obo:NCIT_C167190<br/>(Dose Administered)<br/>obo:NCIT_C198143<br/>(Prescribed Dose)"]:::classNode
UO_0000022["IRI for unit of measurement, e.g.:<br/>obo:UO_0000022<br/>(milligram)"]:::classNode
SIO_000074["sio:SIO_000074<br/>(unit of measurement)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
FrequencyValue["Frequency value:<br/>e.g. 2"]:::dataValue
DoseValue["Dose value:<br/>e.g. 10.5"]:::dataValue
%% Real edges (indices 0-30)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C70962
Process_ -->|"sio:SIO_000028 (has part)"| Specific_method_
Process_ -->|"sio:SIO_000230 (has input)"| Input_
Process_ -->|"sio:SIO_000900 (has frequency)"| Frequency_
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000229 (has output)"| Output_
Specific_method_ -->|"rdf:type"| NCIT_C28161
Specific_method_ -->|"rdf:type"| SIO_000006
Input_ -->|"rdf:type"| SIO_000015
Input_ -->|"rdf:type"| NCIT_C177929
Frequency_ -->|"rdf:type"| SIO_001367
Frequency_ -->|"rdf:type"| NCIT_C66968
Frequency_ -->|"sio:SIO_000300 (has value)"| FrequencyValue
URIProtocol -->|"rdf:type"| SIO_000090
URIProtocol -->|"rdf:type"| IAO_0000104
Output_ -->|"sio:SIO_000221 (has unit)"| Unit_
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"rdf:type"| DoseClasses
Output_ -->|"sio:SIO_000300 (has value)"| DoseValue
Unit_ -->|"rdf:type"| UO_0000022
Unit_ -->|"rdf:type"| SIO_000074
%% Invisible layout-only chains (indices 31-44, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C70962 ~~~ Comments
SIO_000015 ~~~ NCIT_C177929
SIO_001367 ~~~ NCIT_C66968 ~~~ FrequencyValue
SIO_000090 ~~~ IAO_0000104
DoseClasses ~~~ DoseValue
UO_0000022 ~~~ SIO_000074
Specific_method_ ~~~ Input_ ~~~ Frequency_ ~~~ URIProtocol ~~~ Output_
%% rdf:type edges (indices 1,3,5,6,8,9,16,17,18,19,20,21,23,24,26,27,29,30) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,16,17,18,19,20,21,23,24,26,27,29,30 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 31,32,33,34,35,36,37,38,39,40,41,42,43,44 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Hospitalization
Data visualization
Records of inpatient stays, including dates of admission and discharge and the reason for hospitalization.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Specific_method_{{Specific_method_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Output_{{Output_}}:::usedInstance
Duration_{{Duration_}}:::usedInstance
Startdate_{{Startdate_}}:::usedInstance
Enddate_{{Enddate_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C25179["obo:NCIT_C25179<br/>(Hospitalization)"]:::classNode
NCIT_C164212["IRI for the specific cause of<br/>intervention and procedure, e.g.:<br/>obo:NCIT_C164212<br/>(Tumor Resection)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
NCIT_C217011["obo:NCIT_C217011<br/>(Duration Quantity Value)"]:::classNode
SIO_000417["sio:SIO_000417<br/>(time interval)"]:::classNode
SIO_000031["sio:SIO_000031<br/>(start date)"]:::classNode
SIO_000032["sio:SIO_000032<br/>(end date)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
OutputValue["Output value (optional, free-form --<br/>no output type has been defined for this<br/>model yet; add one here if/when needed)"]:::dataValue
ISO8601Start["ISO 8601 formatted date"]:::dataValue
ISO8601End["ISO 8601 formatted date"]:::dataValue
%% Real edges (indices 0-28)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C25179
Process_ -->|"sio:SIO_000028 (has part)"| Specific_method_
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
Specific_method_ -->|"rdf:type"| SIO_000006
Specific_method_ -->|"rdf:type"| NCIT_C164212
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"sio:SIO_000687 (exists at)"| Duration_
Output_ -->|"sio:SIO_000300 (has value)"| OutputValue
Duration_ -->|"rdf:type"| NCIT_C217011
Duration_ -->|"rdf:type"| SIO_000417
Duration_ -->|"sio:SIO_000680 (has start time)"| Startdate_
Duration_ -->|"sio:SIO_000681 (has end time)"| Enddate_
Startdate_ -->|"rdf:type"| SIO_000031
Startdate_ -->|"sio:SIO_000300 (has value)"| ISO8601Start
Enddate_ -->|"rdf:type"| SIO_000032
Enddate_ -->|"sio:SIO_000300 (has value)"| ISO8601End
%% Invisible layout-only chains (indices 29-40, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C25179 ~~~ Comments
OBI_0000272 ~~~ SIO_000090
SIO_000015 ~~~ OutputValue
NCIT_C217011 ~~~ SIO_000417
SIO_000031 ~~~ ISO8601Start
SIO_000032 ~~~ ISO8601End
Specific_method_ ~~~ URIProtocol ~~~ Output_
Startdate_ ~~~ Enddate_
%% rdf:type edges (indices 1,3,5,6,8,9,14,15,16,17,18,21,22,25,27) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,14,15,16,17,18,21,22,25,27 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 29,30,31,32,33,34,35,36,37,38,39,40 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Surgical intervention
Data visualization
Documentation of surgical procedures performed on the patient. Includes the type of surgery, date and description of the anatomical site.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Specific_method_{{Specific_method_}}:::usedInstance
Target_{{Target_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Output_{{Output_}}:::usedInstance
Duration_{{Duration_}}:::usedInstance
Startdate_{{Startdate_}}:::usedInstance
Enddate_{{Enddate_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C15329["obo:NCIT_C15329<br/>(Surgical Procedure)"]:::classNode
NCIT_C164212["IRI for the specific cause of intervention and procedure, e.g.:<br/>obo:NCIT_C164212<br/>(Tumor Resection)"]:::classNode
NCIT_C33024["IRI for the anatomic structure, e.g.:<br/>obo:NCIT_C33024<br/>(Lung Tissue)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
NCIT_C217011["obo:NCIT_C217011<br/>(Duration Quantity Value)"]:::classNode
SIO_000417["sio:SIO_000417<br/>(time interval)"]:::classNode
SIO_000031["sio:SIO_000031<br/>(start date)"]:::classNode
SIO_000032["sio:SIO_000032<br/>(end date)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
OutputValue["Output value (optional, free-form --<br/>no output type has been defined for this<br/>model yet; add one here if/when needed)"]:::dataValue
ISO8601Start["ISO 8601 formatted date"]:::dataValue
ISO8601End["ISO 8601 formatted date"]:::dataValue
%% Real edges (indices 0-31)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C15329
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000028 (has part)"| Specific_method_
Process_ -->|"sio:SIO_000291 (has target)"| Target_
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
Specific_method_ -->|"rdf:type"| NCIT_C164212
Specific_method_ -->|"rdf:type"| SIO_000006
Target_ -->|"rdf:type"| NCIT_C33024
Target_ -->|"rdf:type"| SIO_000015
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"sio:SIO_000687 (exists at)"| Duration_
Output_ -->|"sio:SIO_000300 (has value)"| OutputValue
Duration_ -->|"rdf:type"| NCIT_C217011
Duration_ -->|"rdf:type"| SIO_000417
Duration_ -->|"sio:SIO_000680 (has start time)"| Startdate_
Duration_ -->|"sio:SIO_000681 (has end time)"| Enddate_
Startdate_ -->|"rdf:type"| SIO_000031
Startdate_ -->|"sio:SIO_000300 (has value)"| ISO8601Start
Enddate_ -->|"rdf:type"| SIO_000032
Enddate_ -->|"sio:SIO_000300 (has value)"| ISO8601End
%% Invisible layout-only chains (indices 32-45, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C15329 ~~~ Comments
NCIT_C33024 ~~~ SIO_000015
OBI_0000272 ~~~ SIO_000090
SIO_000015 ~~~ OutputValue
NCIT_C217011 ~~~ SIO_000417
SIO_000031 ~~~ ISO8601Start
SIO_000032 ~~~ ISO8601End
Specific_method_ ~~~ Target_ ~~~ URIProtocol ~~~ Output_
Startdate_ ~~~ Enddate_
%% rdf:type edges (indices 1,3,5,6,8,9,15,16,17,18,19,20,21,24,25,28,30) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,15,16,17,18,19,20,21,24,25,28,30 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 32,33,34,35,36,37,38,39,40,41,42,43,44,45 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Research
Biobank
This module describes the data element in the Common Data Elemments group. These elements, defined by the JRC, can be found on the EU RD Platform at this link.
Data visualization
A record indicating whether the patient has donated biological samples for long-term storage in a biobank. This entry includes information on the type of samples collected, the date of collection, the sample accession number, and details about the biobank.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Input_{{Input_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Output_{{Output_}}:::usedInstance
Output_identifier_{{Output_identifier_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
OBIB_0000668["obo:OBIB_0000668<br/>(sampling specimens for biobank)"]:::classNode
NCIT_C12692["IRI for anatomic structure or substance sampled, e.g.:<br/>obo:NCIT_C12692<br/>(Cerebrospinal Fluid)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
NCIT_C19697["obo:NCIT_C19697<br/>(Tissue Sample)"]:::classNode
NCIT_C25402["obo:NCIT_C25402<br/>(Accession Number)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
SampleAccessionIdentifier["Sample accession identfier"]:::dataValue
%% Real edges (indices 0-23)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| OBIB_0000668
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000230 (has input)"| Input_
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
Input_ -->|"rdf:type"| NCIT_C12692
Input_ -->|"rdf:type"| SIO_000015
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"rdf:type"| NCIT_C19697
Output_ -->|"sio:SIO_000671 (has identifier)"| Output_identifier_
Output_identifier_ -->|"rdf:type"| SIO_000115
Output_identifier_ -->|"rdf:type"| NCIT_C25402
Output_identifier_ -->|"sio:SIO_000300 (has value)"| SampleAccessionIdentifier
%% Invisible layout-only chains (indices 24-32, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ OBIB_0000668 ~~~ Comments
NCIT_C12692 ~~~ SIO_000015
OBI_0000272 ~~~ SIO_000090
NCIT_C25402 ~~~ SampleAccessionIdentifier
Input_ ~~~ URIProtocol ~~~ Output_
%% rdf:type edges (indices 1,3,5,6,8,9,14,15,16,17,18,19,21,22) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,14,15,16,17,18,19,21,22 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 24,25,26,27,28,29,30,31,32 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Consent
This module describes the data element in the Common Data Elemments group. These elements, defined by the JRC, can be found on the EU RD Platform at this link.
Data visualization
The module shows how the individual, defined as a patient, participates in an informed consent process that has as output the permission to be contacted or reusing his/her data. This output refers to the consent given by the individual.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Output_{{Output_}}:::usedInstance
Attribute_{{Attribute_}}:::usedInstance
Input_{{Input_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000093["obo:OBI_0000093<br/>(patient role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
OBI_0000810["obo:OBI_0000810<br/>(Informed consent process)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
DUO_0000001["IRI that describes the consent statement, e.g.:<br/>obo:DUO_0000001 (Data Use Permission)<br/>obo:OBIB_0000488 (willingness to be contacted)"]:::classNode
NCIT_C25460["obo:NCIT_C25460<br/>(Consent)"]:::classNode
SIO_000614["sio:SIO_000614<br/>(attribute)"]:::classNode
NCIT_C16468["obo:NCIT_C16468<br/>(Consent Form)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
LexicalConsentStatement["Lexical consent statement"]:::dataValue
ConsentFormFilename["Consent form filename + version,<br/>e.g. 'consent_form_v2.1.pdf'<br/>(not a URL)"]:::dataValue
%% Real edges (indices 0-24)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000093
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| OBI_0000810
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
Process_ -->|"sio:SIO_000230 (has input)"| Input_
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"sio:SIO_000628 (refers to)"| Attribute_
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"rdf:type"| DUO_0000001
Output_ -->|"sio:SIO_000300 (has value)"| LexicalConsentStatement
Attribute_ -->|"rdf:type"| NCIT_C25460
Attribute_ -->|"rdf:type"| SIO_000614
Input_ -->|"rdf:type"| SIO_000015
Input_ -->|"rdf:type"| NCIT_C16468
Input_ -->|"sio:SIO_000300 (has value)"| ConsentFormFilename
%% Invisible layout-only chains (indices 25-36, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000093 ~~~ SIO_000016
SIO_000006 ~~~ OBI_0000810 ~~~ Comments
OBI_0000272 ~~~ SIO_000090
SIO_000015 ~~~ DUO_0000001 ~~~ LexicalConsentStatement
NCIT_C25460 ~~~ SIO_000614
SIO_000015 ~~~ NCIT_C16468 ~~~ ConsentFormFilename
URIProtocol ~~~ Output_ ~~~ Input_
%% rdf:type edges (indices 1,3,5,6,8,9,14,15,17,18,20,21,22,23) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,14,15,17,18,20,21,22,23 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 25,26,27,28,29,30,31,32,33,34,35,36 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Clinical trial
Data visualization
Information about the patient’s enrollment in a clinical trials, including the associated diasease and condition and participant healthcare institute.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Target_{{Target_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Output_{{Output_}}:::usedInstance
Output_identifier_{{Output_identifier_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000097["obo:OBI_0000097<br/>(participant under investigation role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C71104["obo:NCIT_C71104<br/>(Clinical trial)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
NCIT_C7057["obo:NCIT_C7057<br/>(Disease or Disorder)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
NCIT_C142439["obo:NCIT_C142439<br/>(Clinical Study Report)"]:::classNode
NCIT_C83082["obo:NCIT_C83082<br/>(Study Identifier)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
ReportStudyIdentifier["Report study identifier"]:::dataValue
%% Real edges (indices 0-23)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000097
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C71104
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000291 (has target)"| Target_
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
Target_ -->|"rdf:type"| SIO_000015
Target_ -->|"rdf:type"| NCIT_C7057
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"rdf:type"| NCIT_C142439
Output_ -->|"sio:SIO_000671 (has identifier)"| Output_identifier_
Output_identifier_ -->|"rdf:type"| SIO_000115
Output_identifier_ -->|"rdf:type"| NCIT_C83082
Output_identifier_ -->|"sio:SIO_000300 (has value)"| ReportStudyIdentifier
%% Invisible layout-only chains (indices 24-32, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000097 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C71104 ~~~ Comments
SIO_000015 ~~~ NCIT_C7057
OBI_0000272 ~~~ SIO_000090
NCIT_C83082 ~~~ ReportStudyIdentifier
Target_ ~~~ URIProtocol ~~~ Output_
%% rdf:type edges (indices 1,3,5,6,8,9,14,15,16,17,18,19,21,22) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,14,15,16,17,18,19,21,22 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 24,25,26,27,28,29,30,31,32 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
Cohort
Data visualization
Information about the patient’s enrollment in a cohort, including the associated diasease and condition and participant healthcare institute.
%%{init: {"themeVariables": {"lineColor": "#888888"}}}%%
flowchart TD
classDef usedInstance fill:#ffffff,stroke:#d79b00,stroke-width:7px,color:#333,font-size:20px
classDef classNode fill:transparent,stroke:#b9c9b4,stroke-width:1.5px,color:#888,font-size:14px
classDef dataValue fill:#ffffff,stroke:#6c8ebf,stroke-width:7px,color:#333,font-size:18px
linkStyle default stroke:#888888,stroke-width:3px
%% Instances
ID_{{ID_}}:::usedInstance
Individual_{{Individual_}}:::usedInstance
Role_{{Role_}}:::usedInstance
Process_{{Process_}}:::usedInstance
Target_{{Target_}}:::usedInstance
URIProtocol{{"URI for the protocol"}}:::usedInstance
Output_{{Output_}}:::usedInstance
Output_identifier_{{Output_identifier_}}:::usedInstance
%% Classes
SIO_000115["sio:SIO_000115<br/>(identifier)"]:::classNode
SIO_000498["sio:SIO_000498<br/>(person)"]:::classNode
OBI_0000097["obo:OBI_0000097<br/>(participant under investigation role)"]:::classNode
SIO_000016["sio:SIO_000016<br/>(role)"]:::classNode
SIO_000006["sio:SIO_000006<br/>(process)"]:::classNode
NCIT_C15208["obo:NCIT_C15208<br/>(Cohort Study)"]:::classNode
SIO_000614["sio:SIO_000614<br/>(attribute)"]:::classNode
NCIT_C7057["obo:NCIT_C7057<br/>(Disease or Disorder)"]:::classNode
OBI_0000272["obo:OBI_0000272<br/>(protocol)"]:::classNode
SIO_000090["sio:SIO_000090<br/>(specification)"]:::classNode
SIO_000015["sio:SIO_000015<br/>(information content entity)"]:::classNode
NCIT_C142439["obo:NCIT_C142439<br/>(Clinical Study Report)"]:::classNode
NCIT_C83082["obo:NCIT_C83082<br/>(Study Identifier)"]:::classNode
%% Data values
IndividualID["individual ID"]:::dataValue
Comments["comments"]:::dataValue
ReportStudyIdentifier["Report study identifier"]:::dataValue
%% Real edges (indices 0-23)
ID_ -->|"sio:SIO_000300 (has value)"| IndividualID
ID_ -->|"rdf:type"| SIO_000115
ID_ -->|"sio:SIO_000020 (denotes)"| Role_
Individual_ -->|"rdf:type"| SIO_000498
Individual_ -->|"sio:SIO_000228 (has role)"| Role_
Role_ -->|"rdf:type"| OBI_0000097
Role_ -->|"rdf:type"| SIO_000016
Role_ -->|"sio:SIO_000356 (is realized in)"| Process_
Process_ -->|"rdf:type"| SIO_000006
Process_ -->|"rdf:type"| NCIT_C15208
Process_ -->|"rdfs:comment"| Comments
Process_ -->|"sio:SIO_000291 (has target)"| Target_
Process_ -->|"sio:SIO_000339 (is specified by)"| URIProtocol
Process_ -->|"sio:SIO_000229 (has output)"| Output_
Target_ -->|"rdf:type"| SIO_000614
Target_ -->|"rdf:type"| NCIT_C7057
URIProtocol -->|"rdf:type"| OBI_0000272
URIProtocol -->|"rdf:type"| SIO_000090
Output_ -->|"rdf:type"| SIO_000015
Output_ -->|"rdf:type"| NCIT_C142439
Output_ -->|"sio:SIO_000671 (has identifier)"| Output_identifier_
Output_identifier_ -->|"rdf:type"| SIO_000115
Output_identifier_ -->|"rdf:type"| NCIT_C83082
Output_identifier_ -->|"sio:SIO_000300 (has value)"| ReportStudyIdentifier
%% Invisible layout-only chains (indices 24-32, hidden below) force siblings into one column
IndividualID ~~~ SIO_000115
OBI_0000097 ~~~ SIO_000016
SIO_000006 ~~~ NCIT_C15208 ~~~ Comments
SIO_000614 ~~~ NCIT_C7057
OBI_0000272 ~~~ SIO_000090
NCIT_C83082 ~~~ ReportStudyIdentifier
Target_ ~~~ URIProtocol ~~~ Output_
%% rdf:type edges (indices 1,3,5,6,8,9,14,15,16,17,18,19,21,22) de-emphasized so the structural backbone stands out
linkStyle 1,3,5,6,8,9,14,15,16,17,18,19,21,22 stroke:#bbb,stroke-width:2px,stroke-dasharray:4 3
linkStyle 24,25,26,27,28,29,30,31,32 stroke:none
How to populate this data using CARE-SM: A CSV glossary for this data element is described in our Implementation Guide. Check our CSV Glossary.
List of ontogies used
Prefix |
Ontology Name or Namespace |
Prefix IRI |
|---|---|---|
obi |
Ontology for Biomedical Investigations |
http://purl.obolibrary.org/obo/OBI_ |
ncit |
NCI Thesaurus |
http://purl.obolibrary.org/obo/NCIT_ |
geno |
Genotype Ontology |
http://purl.obolibrary.org/obo/GENO_ |
sio |
Semanticscience Integrated Ontology |
http://semanticscience.org/resource/SIO_ |
obib |
Ontology for Biobanking |
http://purl.obolibrary.org/obo/OBIB_ |
duo |
Data Use Ontology |
http://purl.obolibrary.org/obo/DUO_ |
uo |
Units of Measurement Ontology |
http://purl.obolibrary.org/obo/UO_ |
maxo |
Medical Action Ontology |
http://purl.obolibrary.org/obo/MAXO_ |
opmi |
Ontology of Precision Medicine and Investigation |
http://purl.obolibrary.org/obo/OPMI_ |
ogms |
Ontology for General Medical Science |
http://purl.obolibrary.org/obo/OGMS_ |
iao |
Information Artifact Ontology |
http://purl.obolibrary.org/obo/IAO_ |
omit |
Ontology for MIRNA Target |
http://purl.obolibrary.org/obo/OMIT_ |