Source | arkhn.fhir.uv.osiris#current:FHIR Osiris Implementation Guide (v4.0.1) |
resourceType | StructureDefinition |
id | variant-annotation |
canonical | https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/variant-annotation |
version | 2.1.0 |
status | draft |
publisher | Arkhn |
name | VariantAnnotation |
title | Variant Annotation |
date | 2023-08-28T10:50:04+00:00 |
description | The Annotation profile allows to add information about a SNP, a fusion, an expression or a copy number event. It is generally used to compare variant from a reference genome. There can be multiple instance of Variant Annotation Resource for one instance of SNP, CopyNumber, Expression or Fusion Resource. |
fhirVersion | 4.0.1 |
kind | resource |
abstract | false |
sdTtype | Observation |
derivation | constraint |
base | http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant |
Usages | (none) |
Name | Flags | Card. | Type |
Description & Constraints
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Variant | |||
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S | Reference (Oncology Patient) | ||
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S | 2..2 | Reference (Genome Entity | Annotation Reference) | |
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S | 1 .. 2 | Reference ( Single Nucleotide Polymorphism | Gene Fusion | Gene Expression | Variant Copy Number | 5 Prime Molecular Sequence | 3 Prime Molecular Sequence ) | Slice: Unordered, Open by pattern:reference |
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1.. | |||
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S | ..1 | ||
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Gene name | |||
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S | ..1 | Gene region | |
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Gene region | |||
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S | Incidence on the coding region of the gene | ||
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S | 1.. | Type of alteration | |
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Type of alteration Binding: Alteration Type Value Set ( required ) |
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S | 1..1 | ||
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S | Genomic incidence | ||
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S | Incidence on the protein | ||
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S | Nomenclature of changes at protein-level | ||
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Nomenclature of changes at protein-level | |||
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S | 0..1 | ||
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Required Pattern: At least the following | |||
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1..* | Coding |
Code defined by a terminology system Fixed Value: (complex) |
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1..1 | uri |
Identity of the terminology system Fixed Value: http://loinc.org |
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1..1 | code |
Symbol in syntax defined by the system Fixed Value: LP91038-7 |
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Required Pattern: Prediction software | |||
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CodeableConcept |
Prediction software Binding: Mutation prediction Value Set ( example ) |
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S | 0..1 | ||
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Required Pattern: At least the following | |||
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1..* | Coding |
Code defined by a terminology system Fixed Value: (complex) |
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1..1 | uri |
Identity of the terminology system Fixed Value: http://loinc.org |
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1..1 | code |
Symbol in syntax defined by the system Fixed Value: LP70194-3 |
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Required Pattern: Prediction of the variation effect over the protein | |||
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Quantity | Prediction of the variation effect over the protein | ||
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S | 0..1 | ||
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Required Pattern: At least the following | |||
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1..* | Coding |
Code defined by a terminology system Fixed Value: (complex) |
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1..1 | uri |
Identity of the terminology system Fixed Value: http://loinc.org |
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1..1 | code |
Symbol in syntax defined by the system Fixed Value: 93044-6 |
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Required Pattern: Confidence score | |||
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string | Confidence score | ||
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S | 0..1 | Incidence on the transcript | |
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Required Pattern: At least the following | |||
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1..* | Coding |
Code defined by a terminology system Fixed Value: (complex) |
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1..1 | uri |
Identity of the terminology system Fixed Value: http://loinc.org |
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1..1 | code |
Symbol in syntax defined by the system Fixed Value: LP232001-0 |
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Required Pattern: Incidence on the transcript | |||
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CodeableConcept | Binding: todo ( extensible ) | ||
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S | 0..1 | Splice site | |
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Required Pattern: At least the following | |||
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1..* | Coding |
Code defined by a terminology system Fixed Value: (complex) |
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1..1 | uri |
Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls |
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1..1 | code |
Symbol in syntax defined by the system Fixed Value: C0035687 |
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boolean | |||
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Produced 08 Sep 2023