FHIR Osiris Implementation Guide
2.1.0 - ci-build
FHIR Osiris Implementation Guide
2.1.0 - ci-build
FHIR Osiris Implementation Guide - Local Development build (v2.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions
| Official URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/molecular-sequence-3-prime | Version: 2.1.0 | |||
| Draft as of 2024-03-21 | Computable Name: MolecularSequence3Prime | |||
3 prime molecular sequence is for referencing the 3’ edge of a Fusion Observation.
Usage:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from MolecularSequence
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  MolecularSequence | MolecularSequence | |||
  type | 0..1 | code | aa | dna | rna Binding: Genome entity type Value Set (required) | |
| coordinateSystem | 1..1 | integer | Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end) Required Pattern: 0 | |
 patient | 0..1 | Reference(Oncology Patient) | Who and/or what this is about | |
 referenceSeq | 1..1 | BackboneElement | A sequence used as reference | |
 chromosome | 0..1 | CodeableConcept | Fusion chromosome 3 prime Binding: GeneticMaterial (extensible) | |
| strand | 0..1 | code | watson | crick Required Pattern: watson | |
 windowStart | 0..1 | integer | Fusion 3 prime position | |
| Documentation for this format | ||||
| Path | Conformance | ValueSet | URI |
| MolecularSequence.type | required | GenomeEntityTypehttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/GenomeEntityTypefrom this IG | |
| MolecularSequence.referenceSeq.chromosome | extensible | GeneticMaterialhttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/GeneticMaterialfrom this IG |
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| MolecularSequence | C | 0..* | MolecularSequence | Information about a biological sequence msq-3: Only 0 and 1 are valid for coordinateSystem |
 implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
 modifierExtension | ?!N | 0..* | Extension | Extensions that cannot be ignored Slice: Unordered, Open by value:url |
| type | Σ | 0..1 | code | aa | dna | rna Binding: Genome entity type Value Set (required) |
| coordinateSystem | Σ | 1..1 | integer | Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end) Required Pattern: 0 |
| patient | ΣC | 0..1 | Reference(Oncology Patient) | Who and/or what this is about ref-1: SHALL have a contained resource if a local reference is provided |
 referenceSeq | ΣC | 1..1 | BackboneElement | A sequence used as reference msq-6: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString; msq-5: GenomeBuild and chromosome must be both contained if either one of them is contained |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| chromosome | Σ | 0..1 | CodeableConcept | Fusion chromosome 3 prime Binding: GeneticMaterial (extensible) |
| strand | Σ | 0..1 | code | watson | crick Binding: strandType (required): Type for strand. Required Pattern: watson |
| windowStart | Σ | 0..1 | integer | Fusion 3 prime position |
| Documentation for this format | ||||
| Path | Conformance | ValueSet / Code | URI |
| MolecularSequence.type | required | GenomeEntityTypehttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/GenomeEntityTypefrom this IG | |
| MolecularSequence.referenceSeq.chromosome | extensible | GeneticMaterialhttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/GeneticMaterialfrom this IG | |
| MolecularSequence.referenceSeq.strand | required | Pattern: watsonhttp://hl7.org/fhir/ValueSet/strand-type|4.0.1from the FHIR Standard |
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| MolecularSequence | C | 0..* | MolecularSequence | Information about a biological sequence msq-3: Only 0 and 1 are valid for coordinateSystem | ||||
| id | Σ | 0..1 | id | Logical id of this artifact | ||||
| meta | Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
| contained | 0..* | Resource | Contained, inline Resources | |||||
 extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!N | 0..* | Extension | Extensions that cannot be ignored Slice: Unordered, Open by value:url | ||||
| identifier | Σ | 0..* | Identifier | Unique ID for this particular sequence. This is a FHIR-defined id | ||||
| type | Σ | 0..1 | code | aa | dna | rna Binding: Genome entity type Value Set (required) | ||||
| coordinateSystem | Σ | 1..1 | integer | Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end) Required Pattern: 0 | ||||
| patient | ΣC | 0..1 | Reference(Oncology Patient) | Who and/or what this is about ref-1: SHALL have a contained resource if a local reference is provided | ||||
| specimen | ΣC | 0..1 | Reference(Specimen) | Specimen used for sequencing ref-1: SHALL have a contained resource if a local reference is provided | ||||
| device | ΣC | 0..1 | Reference(Device) | The method for sequencing ref-1: SHALL have a contained resource if a local reference is provided | ||||
| performer | ΣC | 0..1 | Reference(Organization) | Who should be responsible for test result ref-1: SHALL have a contained resource if a local reference is provided | ||||
| quantity | ΣC | 0..1 | Quantity | The number of copies of the sequence of interest. (RNASeq) qty-3: If a code for the unit is present, the system SHALL also be present | ||||
 referenceSeq | ΣC | 1..1 | BackboneElement | A sequence used as reference msq-6: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString; msq-5: GenomeBuild and chromosome must be both contained if either one of them is contained | ||||
 id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| chromosome | Σ | 0..1 | CodeableConcept | Fusion chromosome 3 prime Binding: GeneticMaterial (extensible) | ||||
| genomeBuild | Σ | 0..1 | string | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' | ||||
| orientation | Σ | 0..1 | code | sense | antisense Binding: orientationType (required): Type for orientation. | ||||
| referenceSeqId | Σ | 0..1 | CodeableConcept | Reference identifier Binding: ENSEMBL (example): Reference identifier. | ||||
| referenceSeqPointer | ΣC | 0..1 | Reference(MolecularSequence) | A pointer to another MolecularSequence entity as reference sequence ref-1: SHALL have a contained resource if a local reference is provided | ||||
| referenceSeqString | Σ | 0..1 | string | A string to represent reference sequence | ||||
| strand | Σ | 0..1 | code | watson | crick Binding: strandType (required): Type for strand. Required Pattern: watson | ||||
| windowStart | Σ | 0..1 | integer | Fusion 3 prime position | ||||
| windowEnd | Σ | 0..1 | integer | End position of the window on the reference sequence | ||||
| variant | Σ | 0..* | BackboneElement | Variant in sequence | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| start | Σ | 0..1 | integer | Start position of the variant on the reference sequence | ||||
| end | Σ | 0..1 | integer | End position of the variant on the reference sequence | ||||
| observedAllele | Σ | 0..1 | string | Allele that was observed | ||||
| referenceAllele | Σ | 0..1 | string | Allele in the reference sequence | ||||
| cigar | Σ | 0..1 | string | Extended CIGAR string for aligning the sequence with reference bases | ||||
| variantPointer | ΣC | 0..1 | Reference(Observation) | Pointer to observed variant information ref-1: SHALL have a contained resource if a local reference is provided | ||||
| observedSeq | Σ | 0..1 | string | Sequence that was observed | ||||
| quality | Σ | 0..* | BackboneElement | An set of value as quality of sequence | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| type | Σ | 1..1 | code | indel | snp | unknown Binding: qualityType (required): Type for quality report. | ||||
| standardSequence | Σ | 0..1 | CodeableConcept | Standard sequence for comparison Binding: FDA-StandardSequence (example): Reference identifier of the sequence that used to mark the quality of tested samples. | ||||
| start | Σ | 0..1 | integer | Start position of the sequence | ||||
| end | Σ | 0..1 | integer | End position of the sequence | ||||
| score | ΣC | 0..1 | Quantity | Quality score for the comparison qty-3: If a code for the unit is present, the system SHALL also be present | ||||
| method | Σ | 0..1 | CodeableConcept | Method to get quality Binding: FDA-Method (example): The method used to evaluate the numerical quality of the observed sequence. | ||||
| truthTP | Σ | 0..1 | decimal | True positives from the perspective of the truth data | ||||
| queryTP | Σ | 0..1 | decimal | True positives from the perspective of the query data | ||||
| truthFN | Σ | 0..1 | decimal | False negatives | ||||
| queryFP | Σ | 0..1 | decimal | False positives | ||||
| gtFP | Σ | 0..1 | decimal | False positives where the non-REF alleles in the Truth and Query Call Sets match | ||||
| precision | Σ | 0..1 | decimal | Precision of comparison | ||||
| recall | Σ | 0..1 | decimal | Recall of comparison | ||||
| fScore | Σ | 0..1 | decimal | F-score | ||||
| roc | Σ | 0..1 | BackboneElement | Receiver Operator Characteristic (ROC) Curve | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| score | Σ | 0..* | integer | Genotype quality score | ||||
| numTP | Σ | 0..* | integer | Roc score true positive numbers | ||||
| numFP | Σ | 0..* | integer | Roc score false positive numbers | ||||
| numFN | Σ | 0..* | integer | Roc score false negative numbers | ||||
| precision | Σ | 0..* | decimal | Precision of the GQ score | ||||
| sensitivity | Σ | 0..* | decimal | Sensitivity of the GQ score | ||||
| fMeasure | Σ | 0..* | decimal | FScore of the GQ score | ||||
| readCoverage | Σ | 0..1 | integer | Average number of reads representing a given nucleotide in the reconstructed sequence | ||||
| repository | Σ | 0..* | BackboneElement | External repository which contains detailed report related with observedSeq in this resource | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| type | Σ | 1..1 | code | directlink | openapi | login | oauth | other Binding: repositoryType (required): Type for access of external URI. | ||||
| url | Σ | 0..1 | uri | URI of the repository | ||||
| name | Σ | 0..1 | string | Repository's name | ||||
| datasetId | Σ | 0..1 | string | Id of the dataset that used to call for dataset in repository | ||||
| variantsetId | Σ | 0..1 | string | Id of the variantset that used to call for variantset in repository | ||||
| readsetId | Σ | 0..1 | string | Id of the read | ||||
| pointer | ΣC | 0..* | Reference(MolecularSequence) | Pointer to next atomic sequence ref-1: SHALL have a contained resource if a local reference is provided | ||||
| structureVariant | Σ | 0..* | BackboneElement | Structural variant | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| variantType | Σ | 0..1 | CodeableConcept | Structural variant change type Binding: LOINC Answer List LL379-9|4.0.1 (required): DNA change type. | ||||
| exact | Σ | 0..1 | boolean | Does the structural variant have base pair resolution breakpoints? | ||||
| length | Σ | 0..1 | integer | Structural variant length | ||||
| outer | Σ | 0..1 | BackboneElement | Structural variant outer | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| start | Σ | 0..1 | integer | Structural variant outer start | ||||
| end | Σ | 0..1 | integer | Structural variant outer end | ||||
| inner | Σ | 0..1 | BackboneElement | Structural variant inner | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| start | Σ | 0..1 | integer | Structural variant inner start | ||||
| end | Σ | 0..1 | integer | Structural variant inner end | ||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet / Code | URI | |||
| MolecularSequence.language | preferred | CommonLanguages
http://hl7.org/fhir/ValueSet/languagesfrom the FHIR Standard | ||||
| MolecularSequence.type | required | GenomeEntityTypehttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/GenomeEntityTypefrom this IG | ||||
| MolecularSequence.referenceSeq.chromosome | extensible | GeneticMaterialhttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/GeneticMaterialfrom this IG | ||||
| MolecularSequence.referenceSeq.orientation | required | orientationTypehttp://hl7.org/fhir/ValueSet/orientation-type|4.0.1from the FHIR Standard | ||||
| MolecularSequence.referenceSeq.referenceSeqId | example | ENSEMBLhttp://hl7.org/fhir/ValueSet/sequence-referenceSeqfrom the FHIR Standard | ||||
| MolecularSequence.referenceSeq.strand | required | Pattern: watsonhttp://hl7.org/fhir/ValueSet/strand-type|4.0.1from the FHIR Standard | ||||
| MolecularSequence.quality.type | required | qualityTypehttp://hl7.org/fhir/ValueSet/quality-type|4.0.1from the FHIR Standard | ||||
| MolecularSequence.quality.standardSequence | example | FDA-StandardSequence (a valid code from https://precision.fda.gov/files/)http://hl7.org/fhir/ValueSet/sequence-quality-standardSequencefrom the FHIR Standard | ||||
| MolecularSequence.quality.method | example | FDA-Methodhttp://hl7.org/fhir/ValueSet/sequence-quality-methodfrom the FHIR Standard | ||||
| MolecularSequence.repository.type | required | repositoryTypehttp://hl7.org/fhir/ValueSet/repository-type|4.0.1from the FHIR Standard | ||||
| MolecularSequence.structureVariant.variantType | required | LOINC LL379-9|4.0.1http://loinc.org/vs/LL379-9|4.0.1 |
This structure is derived from MolecularSequence
Differential View
This structure is derived from MolecularSequence
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| MolecularSequence | MolecularSequence | |||
| type | 0..1 | code | aa | dna | rna Binding: Genome entity type Value Set (required) | |
| coordinateSystem | 1..1 | integer | Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end) Required Pattern: 0 | |
| patient | 0..1 | Reference(Oncology Patient) | Who and/or what this is about | |
| referenceSeq | 1..1 | BackboneElement | A sequence used as reference | |
| chromosome | 0..1 | CodeableConcept | Fusion chromosome 3 prime Binding: GeneticMaterial (extensible) | |
| strand | 0..1 | code | watson | crick Required Pattern: watson | |
| windowStart | 0..1 | integer | Fusion 3 prime position | |
| Documentation for this format | ||||
| Path | Conformance | ValueSet | URI |
| MolecularSequence.type | required | GenomeEntityTypehttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/GenomeEntityTypefrom this IG | |
| MolecularSequence.referenceSeq.chromosome | extensible | GeneticMaterialhttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/GeneticMaterialfrom this IG |
Key Elements View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| MolecularSequence | C | 0..* | MolecularSequence | Information about a biological sequence msq-3: Only 0 and 1 are valid for coordinateSystem |
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| modifierExtension | ?!N | 0..* | Extension | Extensions that cannot be ignored Slice: Unordered, Open by value:url |
| type | Σ | 0..1 | code | aa | dna | rna Binding: Genome entity type Value Set (required) |
| coordinateSystem | Σ | 1..1 | integer | Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end) Required Pattern: 0 |
| patient | ΣC | 0..1 | Reference(Oncology Patient) | Who and/or what this is about ref-1: SHALL have a contained resource if a local reference is provided |
| referenceSeq | ΣC | 1..1 | BackboneElement | A sequence used as reference msq-6: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString; msq-5: GenomeBuild and chromosome must be both contained if either one of them is contained |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| chromosome | Σ | 0..1 | CodeableConcept | Fusion chromosome 3 prime Binding: GeneticMaterial (extensible) |
| strand | Σ | 0..1 | code | watson | crick Binding: strandType (required): Type for strand. Required Pattern: watson |
| windowStart | Σ | 0..1 | integer | Fusion 3 prime position |
| Documentation for this format | ||||
| Path | Conformance | ValueSet / Code | URI |
| MolecularSequence.type | required | GenomeEntityTypehttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/GenomeEntityTypefrom this IG | |
| MolecularSequence.referenceSeq.chromosome | extensible | GeneticMaterialhttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/GeneticMaterialfrom this IG | |
| MolecularSequence.referenceSeq.strand | required | Pattern: watsonhttp://hl7.org/fhir/ValueSet/strand-type|4.0.1from the FHIR Standard |
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| MolecularSequence | C | 0..* | MolecularSequence | Information about a biological sequence msq-3: Only 0 and 1 are valid for coordinateSystem | ||||
| id | Σ | 0..1 | id | Logical id of this artifact | ||||
| meta | Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
| contained | 0..* | Resource | Contained, inline Resources | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!N | 0..* | Extension | Extensions that cannot be ignored Slice: Unordered, Open by value:url | ||||
| identifier | Σ | 0..* | Identifier | Unique ID for this particular sequence. This is a FHIR-defined id | ||||
| type | Σ | 0..1 | code | aa | dna | rna Binding: Genome entity type Value Set (required) | ||||
| coordinateSystem | Σ | 1..1 | integer | Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end) Required Pattern: 0 | ||||
| patient | ΣC | 0..1 | Reference(Oncology Patient) | Who and/or what this is about ref-1: SHALL have a contained resource if a local reference is provided | ||||
| specimen | ΣC | 0..1 | Reference(Specimen) | Specimen used for sequencing ref-1: SHALL have a contained resource if a local reference is provided | ||||
| device | ΣC | 0..1 | Reference(Device) | The method for sequencing ref-1: SHALL have a contained resource if a local reference is provided | ||||
| performer | ΣC | 0..1 | Reference(Organization) | Who should be responsible for test result ref-1: SHALL have a contained resource if a local reference is provided | ||||
| quantity | ΣC | 0..1 | Quantity | The number of copies of the sequence of interest. (RNASeq) qty-3: If a code for the unit is present, the system SHALL also be present | ||||
| referenceSeq | ΣC | 1..1 | BackboneElement | A sequence used as reference msq-6: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString; msq-5: GenomeBuild and chromosome must be both contained if either one of them is contained | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| chromosome | Σ | 0..1 | CodeableConcept | Fusion chromosome 3 prime Binding: GeneticMaterial (extensible) | ||||
| genomeBuild | Σ | 0..1 | string | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' | ||||
| orientation | Σ | 0..1 | code | sense | antisense Binding: orientationType (required): Type for orientation. | ||||
| referenceSeqId | Σ | 0..1 | CodeableConcept | Reference identifier Binding: ENSEMBL (example): Reference identifier. | ||||
| referenceSeqPointer | ΣC | 0..1 | Reference(MolecularSequence) | A pointer to another MolecularSequence entity as reference sequence ref-1: SHALL have a contained resource if a local reference is provided | ||||
| referenceSeqString | Σ | 0..1 | string | A string to represent reference sequence | ||||
| strand | Σ | 0..1 | code | watson | crick Binding: strandType (required): Type for strand. Required Pattern: watson | ||||
| windowStart | Σ | 0..1 | integer | Fusion 3 prime position | ||||
| windowEnd | Σ | 0..1 | integer | End position of the window on the reference sequence | ||||
| variant | Σ | 0..* | BackboneElement | Variant in sequence | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| start | Σ | 0..1 | integer | Start position of the variant on the reference sequence | ||||
| end | Σ | 0..1 | integer | End position of the variant on the reference sequence | ||||
| observedAllele | Σ | 0..1 | string | Allele that was observed | ||||
| referenceAllele | Σ | 0..1 | string | Allele in the reference sequence | ||||
| cigar | Σ | 0..1 | string | Extended CIGAR string for aligning the sequence with reference bases | ||||
| variantPointer | ΣC | 0..1 | Reference(Observation) | Pointer to observed variant information ref-1: SHALL have a contained resource if a local reference is provided | ||||
| observedSeq | Σ | 0..1 | string | Sequence that was observed | ||||
| quality | Σ | 0..* | BackboneElement | An set of value as quality of sequence | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| type | Σ | 1..1 | code | indel | snp | unknown Binding: qualityType (required): Type for quality report. | ||||
| standardSequence | Σ | 0..1 | CodeableConcept | Standard sequence for comparison Binding: FDA-StandardSequence (example): Reference identifier of the sequence that used to mark the quality of tested samples. | ||||
| start | Σ | 0..1 | integer | Start position of the sequence | ||||
| end | Σ | 0..1 | integer | End position of the sequence | ||||
| score | ΣC | 0..1 | Quantity | Quality score for the comparison qty-3: If a code for the unit is present, the system SHALL also be present | ||||
| method | Σ | 0..1 | CodeableConcept | Method to get quality Binding: FDA-Method (example): The method used to evaluate the numerical quality of the observed sequence. | ||||
| truthTP | Σ | 0..1 | decimal | True positives from the perspective of the truth data | ||||
| queryTP | Σ | 0..1 | decimal | True positives from the perspective of the query data | ||||
| truthFN | Σ | 0..1 | decimal | False negatives | ||||
| queryFP | Σ | 0..1 | decimal | False positives | ||||
| gtFP | Σ | 0..1 | decimal | False positives where the non-REF alleles in the Truth and Query Call Sets match | ||||
| precision | Σ | 0..1 | decimal | Precision of comparison | ||||
| recall | Σ | 0..1 | decimal | Recall of comparison | ||||
| fScore | Σ | 0..1 | decimal | F-score | ||||
| roc | Σ | 0..1 | BackboneElement | Receiver Operator Characteristic (ROC) Curve | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| score | Σ | 0..* | integer | Genotype quality score | ||||
| numTP | Σ | 0..* | integer | Roc score true positive numbers | ||||
| numFP | Σ | 0..* | integer | Roc score false positive numbers | ||||
| numFN | Σ | 0..* | integer | Roc score false negative numbers | ||||
| precision | Σ | 0..* | decimal | Precision of the GQ score | ||||
| sensitivity | Σ | 0..* | decimal | Sensitivity of the GQ score | ||||
| fMeasure | Σ | 0..* | decimal | FScore of the GQ score | ||||
| readCoverage | Σ | 0..1 | integer | Average number of reads representing a given nucleotide in the reconstructed sequence | ||||
| repository | Σ | 0..* | BackboneElement | External repository which contains detailed report related with observedSeq in this resource | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| type | Σ | 1..1 | code | directlink | openapi | login | oauth | other Binding: repositoryType (required): Type for access of external URI. | ||||
| url | Σ | 0..1 | uri | URI of the repository | ||||
| name | Σ | 0..1 | string | Repository's name | ||||
| datasetId | Σ | 0..1 | string | Id of the dataset that used to call for dataset in repository | ||||
| variantsetId | Σ | 0..1 | string | Id of the variantset that used to call for variantset in repository | ||||
| readsetId | Σ | 0..1 | string | Id of the read | ||||
| pointer | ΣC | 0..* | Reference(MolecularSequence) | Pointer to next atomic sequence ref-1: SHALL have a contained resource if a local reference is provided | ||||
| structureVariant | Σ | 0..* | BackboneElement | Structural variant | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| variantType | Σ | 0..1 | CodeableConcept | Structural variant change type Binding: LOINC Answer List LL379-9|4.0.1 (required): DNA change type. | ||||
| exact | Σ | 0..1 | boolean | Does the structural variant have base pair resolution breakpoints? | ||||
| length | Σ | 0..1 | integer | Structural variant length | ||||
| outer | Σ | 0..1 | BackboneElement | Structural variant outer | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| start | Σ | 0..1 | integer | Structural variant outer start | ||||
| end | Σ | 0..1 | integer | Structural variant outer end | ||||
| inner | Σ | 0..1 | BackboneElement | Structural variant inner | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| start | Σ | 0..1 | integer | Structural variant inner start | ||||
| end | Σ | 0..1 | integer | Structural variant inner end | ||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet / Code | URI | |||
| MolecularSequence.language | preferred | CommonLanguages
http://hl7.org/fhir/ValueSet/languagesfrom the FHIR Standard | ||||
| MolecularSequence.type | required | GenomeEntityTypehttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/GenomeEntityTypefrom this IG | ||||
| MolecularSequence.referenceSeq.chromosome | extensible | GeneticMaterialhttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/GeneticMaterialfrom this IG | ||||
| MolecularSequence.referenceSeq.orientation | required | orientationTypehttp://hl7.org/fhir/ValueSet/orientation-type|4.0.1from the FHIR Standard | ||||
| MolecularSequence.referenceSeq.referenceSeqId | example | ENSEMBLhttp://hl7.org/fhir/ValueSet/sequence-referenceSeqfrom the FHIR Standard | ||||
| MolecularSequence.referenceSeq.strand | required | Pattern: watsonhttp://hl7.org/fhir/ValueSet/strand-type|4.0.1from the FHIR Standard | ||||
| MolecularSequence.quality.type | required | qualityTypehttp://hl7.org/fhir/ValueSet/quality-type|4.0.1from the FHIR Standard | ||||
| MolecularSequence.quality.standardSequence | example | FDA-StandardSequence (a valid code from https://precision.fda.gov/files/)http://hl7.org/fhir/ValueSet/sequence-quality-standardSequencefrom the FHIR Standard | ||||
| MolecularSequence.quality.method | example | FDA-Methodhttp://hl7.org/fhir/ValueSet/sequence-quality-methodfrom the FHIR Standard | ||||
| MolecularSequence.repository.type | required | repositoryTypehttp://hl7.org/fhir/ValueSet/repository-type|4.0.1from the FHIR Standard | ||||
| MolecularSequence.structureVariant.variantType | required | LOINC LL379-9|4.0.1http://loinc.org/vs/LL379-9|4.0.1 |
This structure is derived from MolecularSequence
Other representations of profile: CSV, Excel, Schematron
IG © 2020+ Arkhn. Package arkhn.fhir.uv.osiris#2.1.0 based on FHIR 4.0.1. Generated 2024-03-21
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