RareLink Implementation Guide - Local Development build (v2.0.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions
Extension: Phenotype Causing Organism
| Official URL: https://rarelink.bih-charite.de/fhir/StructureDefinition/causing-agent | Version: 2.0.0 | |||
| Draft as of 2025-05-12 | Computable Name: CausingOrganism | |||
The organism that is causing the phenotypic feature (e.g., a virus, bacteria, etc.).
Context of Use
This extension may be used on the following element(s):
- Element ID Element
Usage info
Usage:
- Use this Extension: RareLink Observation Phenotypic Feature
Formal Views of Extension Content
Description of Profiles, Differentials, Snapshots, and how the XML and JSON presentations work.
This structure is derived from Extension
This structure is derived from Extension
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Extension |
0..* | Extension | Phenotype Causing Organism | |
  extension |
0..0 | |||
| url |
1..1 | uri | "https://rarelink.bih-charite.de/fhir/StructureDefinition/causing-agent" | |
  value[x] |
0..1 | CodeableConcept | Value of extension | |
 coding |
1..1 | Coding | Code defined by a terminology system | |
| system |
0..1 | uri | Identity of the terminology system Required Pattern: http://purl.obolibrary.org/obo/NCBITaxon.owl | |
 code |
S | 0..1 | code | Symbol in syntax defined by the system |
| Documentation for this format | ||||
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Extension |
0..* | Extension | Phenotype Causing Organism | |
 id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..0 | |||
| url |
1..1 | uri | "https://rarelink.bih-charite.de/fhir/StructureDefinition/causing-agent" | |
| value[x] |
0..1 | CodeableConcept | Value of extension | |
| id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |
 coding |
Σ | 1..1 | Coding | Code defined by a terminology system |
 id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |
| system |
Σ | 0..1 | uri | Identity of the terminology system Required Pattern: http://purl.obolibrary.org/obo/NCBITaxon.owl |
| version |
Σ | 0..1 | string | Version of the system - if relevant |
| code |
SΣ | 0..1 | code | Symbol in syntax defined by the system |
| display |
Σ | 0..1 | string | Representation defined by the system |
| userSelected |
Σ | 0..1 | boolean | If this coding was chosen directly by the user |
| text |
Σ | 0..1 | string | Plain text representation of the concept |
| Documentation for this format | ||||
This structure is derived from Extension
Differential View
This structure is derived from Extension
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Extension |
0..* | Extension | Phenotype Causing Organism | |
| extension |
0..0 | |||
| url |
1..1 | uri | "https://rarelink.bih-charite.de/fhir/StructureDefinition/causing-agent" | |
| value[x] |
0..1 | CodeableConcept | Value of extension | |
| coding |
1..1 | Coding | Code defined by a terminology system | |
| system |
0..1 | uri | Identity of the terminology system Required Pattern: http://purl.obolibrary.org/obo/NCBITaxon.owl | |
| code |
S | 0..1 | code | Symbol in syntax defined by the system |
| Documentation for this format | ||||
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Extension |
0..* | Extension | Phenotype Causing Organism | |
| id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..0 | |||
| url |
1..1 | uri | "https://rarelink.bih-charite.de/fhir/StructureDefinition/causing-agent" | |
| value[x] |
0..1 | CodeableConcept | Value of extension | |
| id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |
| coding |
Σ | 1..1 | Coding | Code defined by a terminology system |
| id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |
| system |
Σ | 0..1 | uri | Identity of the terminology system Required Pattern: http://purl.obolibrary.org/obo/NCBITaxon.owl |
| version |
Σ | 0..1 | string | Version of the system - if relevant |
| code |
SΣ | 0..1 | code | Symbol in syntax defined by the system |
| display |
Σ | 0..1 | string | Representation defined by the system |
| userSelected |
Σ | 0..1 | boolean | If this coding was chosen directly by the user |
| text |
Σ | 0..1 | string | Plain text representation of the concept |
| Documentation for this format | ||||
Other representations of profile: CSV, Excel, Schematron
Constraints
| Id | Grade | Path(s) | Details | Requirements |
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both : extension.exists() != value.exists() |