FHIR Osiris Implementation Guide
1.1.0 - trial-implementation

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## Resource Profile: 5 Prime Molecular Sequence

Official URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/molecular-sequence-5-prime | Version: 1.1.0
Draft as of 2025-04-03 | Computable Name: MolecularSequence5Prime

5 prime molecular sequence is for referencing the 5' edge of a Fusion Observation.

Usage:

- Refer to this Resource Profile: Gene Fusion and Variant Annotation

### Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

- Key Elements Table
- Differential Table
- Snapshot Table
- Statistics/References
- All

Nom | Drapeaux | Card. | Type | Description et contraintes
--- | --- | --- | --- | ---
MolecularSequence | C | 0..* | MolecularSequence | Information about a biological sequence dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources dom-3: If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated dom-5: If a resource is contained in another resource, it SHALL NOT have a security label dom-6: A resource should have narrative for robust management 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 ele-1: All FHIR elements must have a @value or children
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
type | Σ | 0..1 | code | aa | dna | rna Binding: Genome entity type Value Set (required) ele-1: All FHIR elements must have a @value or children
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) ele-1: All FHIR elements must have a @value or children Required Pattern: 0
patient | Σ | 0..1 | Reference(Oncology Patient) | Who and/or what this is about ele-1: All FHIR elements must have a @value or children
referenceSeq | Σ C | 1..1 | BackboneElement | A sequence used as reference ele-1: All FHIR elements must have a @value or children msq-5: GenomeBuild and chromosome must be both contained if either one of them is contained msq-6: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
chromosome | Σ | 0..1 | CodeableConcept | Fusion chromosome 5 prime Binding: GeneticMaterial (extensible) ele-1: All FHIR elements must have a @value or children
strand | Σ | 0..1 | code | watson | crick Binding: strandType (required): Type for strand. ele-1: All FHIR elements must have a @value or children Required Pattern: crick
windowStart | Σ | 0..1 | integer | Fusion 5 prime position ele-1: All FHIR elements must have a @value or children
Documentation for this format

#### Terminology Bindings

Path | Conformité | ValueSet / Code | URI
MolecularSequence.type | required | GenomeEntityType `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GenomeEntityType` from this IG
MolecularSequence.referenceSeq.chromosome | extensible | GeneticMaterial `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GeneticMaterial` from this IG
MolecularSequence.referenceSeq.strand | required | Pattern: crick `http://hl7.org/fhir/ValueSet/strand-type|4.0.1` from the FHIR Standard

This structure is derived from MolecularSequence

Nom | Drapeaux | Card. | Type | Description et contraintes
--- | --- | --- | --- | ---
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 5 prime Binding: GeneticMaterial (extensible)
strand |  | 0..1 | code | watson | crick Required Pattern: crick
windowStart |  | 0..1 | integer | Fusion 5 prime position
Documentation for this format

#### Terminology Bindings (Differential)

Path | Conformité | ValueSet | URI
MolecularSequence.type | required | GenomeEntityType `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GenomeEntityType` from this IG
MolecularSequence.referenceSeq.chromosome | extensible | GeneticMaterial `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GeneticMaterial` from this IG

Nom | Drapeaux | Card. | Type | Description et contraintes
--- | --- | --- | --- | ---
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.
Bindings Additionnels | But
AllLanguages | Binding Max
text |  | 0..1 | Narrative | Text summary of the resource, for human interpretation
contained |  | 0..* | Resource | Contained, inline Resources
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored
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 | Σ | 0..1 | Reference(Oncology Patient) | Who and/or what this is about
specimen | Σ | 0..1 | Reference(Specimen) | Specimen used for sequencing
device | Σ | 0..1 | Reference(Device) | The method for sequencing
performer | Σ | 0..1 | Reference(Organization) | Who should be responsible for test result
quantity | Σ | 0..1 | Quantity | The number of copies of the sequence of interest. (RNASeq)
referenceSeq | Σ C | 1..1 | BackboneElement | A sequence used as reference msq-5: GenomeBuild and chromosome must be both contained if either one of them is contained msq-6: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
chromosome | Σ | 0..1 | CodeableConcept | Fusion chromosome 5 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 | Σ | 0..1 | Reference(MolecularSequence) | A pointer to another MolecularSequence entity as reference sequence
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: crick
windowStart | Σ | 0..1 | integer | Fusion 5 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 |  | 0..* | Extension | Additional content defined by implementations
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 | Σ | 0..1 | Reference(Observation) | Pointer to observed variant information
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 |  | 0..* | Extension | Additional content defined by implementations
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 | Σ | 0..1 | Quantity | Quality score for the comparison
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 |  | 0..* | Extension | Additional content defined by implementations
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 |  | 0..* | Extension | Additional content defined by implementations
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 | Σ | 0..* | Reference(MolecularSequence) | Pointer to next atomic sequence
structureVariant | Σ | 0..* | BackboneElement | Structural variant
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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 |  | 0..* | Extension | Additional content defined by implementations
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 |  | 0..* | Extension | Additional content defined by implementations
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

#### Terminology Bindings

Path | Conformité | ValueSet / Code | URI
MolecularSequence.language | preferred | CommonLanguages `http://hl7.org/fhir/ValueSet/languages` from the FHIR Standard
Bindings Additionnels | But
AllLanguages | Binding Max
MolecularSequence.type | required | GenomeEntityType `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GenomeEntityType` from this IG
MolecularSequence.referenceSeq.chromosome | extensible | GeneticMaterial `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GeneticMaterial` from this IG
MolecularSequence.referenceSeq.orientation | required | orientationType `http://hl7.org/fhir/ValueSet/orientation-type|4.0.1` from the FHIR Standard
MolecularSequence.referenceSeq.referenceSeqId | example | ENSEMBL `http://hl7.org/fhir/ValueSet/sequence-referenceSeq` from the FHIR Standard
MolecularSequence.referenceSeq.strand | required | Pattern: crick `http://hl7.org/fhir/ValueSet/strand-type|4.0.1` from the FHIR Standard
MolecularSequence.quality.type | required | qualityType `http://hl7.org/fhir/ValueSet/quality-type|4.0.1` from 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-standardSequence` from the FHIR Standard
MolecularSequence.quality.method | example | FDA-Method `http://hl7.org/fhir/ValueSet/sequence-quality-method` from the FHIR Standard
MolecularSequence.repository.type | required | repositoryType `http://hl7.org/fhir/ValueSet/repository-type|4.0.1` from the FHIR Standard
MolecularSequence.structureVariant.variantType | required | LOINC LL379-9|4.0.1 `http://loinc.org/vs/LL379-9|4.0.1`

This structure is derived from MolecularSequence

Résumé

Mandatory: 1 element

Structures

This structure refers to these other structures:

- Oncology Patient (https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/onco-patient)

Key Elements View

Nom | Drapeaux | Card. | Type | Description et contraintes
--- | --- | --- | --- | ---
MolecularSequence | C | 0..* | MolecularSequence | Information about a biological sequence dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources dom-3: If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated dom-5: If a resource is contained in another resource, it SHALL NOT have a security label dom-6: A resource should have narrative for robust management 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 ele-1: All FHIR elements must have a @value or children
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
type | Σ | 0..1 | code | aa | dna | rna Binding: Genome entity type Value Set (required) ele-1: All FHIR elements must have a @value or children
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) ele-1: All FHIR elements must have a @value or children Required Pattern: 0
patient | Σ | 0..1 | Reference(Oncology Patient) | Who and/or what this is about ele-1: All FHIR elements must have a @value or children
referenceSeq | Σ C | 1..1 | BackboneElement | A sequence used as reference ele-1: All FHIR elements must have a @value or children msq-5: GenomeBuild and chromosome must be both contained if either one of them is contained msq-6: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
chromosome | Σ | 0..1 | CodeableConcept | Fusion chromosome 5 prime Binding: GeneticMaterial (extensible) ele-1: All FHIR elements must have a @value or children
strand | Σ | 0..1 | code | watson | crick Binding: strandType (required): Type for strand. ele-1: All FHIR elements must have a @value or children Required Pattern: crick
windowStart | Σ | 0..1 | integer | Fusion 5 prime position ele-1: All FHIR elements must have a @value or children
Documentation for this format

#### Terminology Bindings

Path | Conformité | ValueSet / Code | URI
MolecularSequence.type | required | GenomeEntityType `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GenomeEntityType` from this IG
MolecularSequence.referenceSeq.chromosome | extensible | GeneticMaterial `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GeneticMaterial` from this IG
MolecularSequence.referenceSeq.strand | required | Pattern: crick `http://hl7.org/fhir/ValueSet/strand-type|4.0.1` from the FHIR Standard

Differential View

This structure is derived from MolecularSequence

Nom | Drapeaux | Card. | Type | Description et contraintes
--- | --- | --- | --- | ---
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 5 prime Binding: GeneticMaterial (extensible)
strand |  | 0..1 | code | watson | crick Required Pattern: crick
windowStart |  | 0..1 | integer | Fusion 5 prime position
Documentation for this format

#### Terminology Bindings (Differential)

Path | Conformité | ValueSet | URI
MolecularSequence.type | required | GenomeEntityType `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GenomeEntityType` from this IG
MolecularSequence.referenceSeq.chromosome | extensible | GeneticMaterial `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GeneticMaterial` from this IG

Snapshot View

Nom | Drapeaux | Card. | Type | Description et contraintes
--- | --- | --- | --- | ---
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.
Bindings Additionnels | But
AllLanguages | Binding Max
text |  | 0..1 | Narrative | Text summary of the resource, for human interpretation
contained |  | 0..* | Resource | Contained, inline Resources
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored
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 | Σ | 0..1 | Reference(Oncology Patient) | Who and/or what this is about
specimen | Σ | 0..1 | Reference(Specimen) | Specimen used for sequencing
device | Σ | 0..1 | Reference(Device) | The method for sequencing
performer | Σ | 0..1 | Reference(Organization) | Who should be responsible for test result
quantity | Σ | 0..1 | Quantity | The number of copies of the sequence of interest. (RNASeq)
referenceSeq | Σ C | 1..1 | BackboneElement | A sequence used as reference msq-5: GenomeBuild and chromosome must be both contained if either one of them is contained msq-6: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
chromosome | Σ | 0..1 | CodeableConcept | Fusion chromosome 5 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 | Σ | 0..1 | Reference(MolecularSequence) | A pointer to another MolecularSequence entity as reference sequence
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: crick
windowStart | Σ | 0..1 | integer | Fusion 5 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 |  | 0..* | Extension | Additional content defined by implementations
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 | Σ | 0..1 | Reference(Observation) | Pointer to observed variant information
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 |  | 0..* | Extension | Additional content defined by implementations
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 | Σ | 0..1 | Quantity | Quality score for the comparison
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 |  | 0..* | Extension | Additional content defined by implementations
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 |  | 0..* | Extension | Additional content defined by implementations
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 | Σ | 0..* | Reference(MolecularSequence) | Pointer to next atomic sequence
structureVariant | Σ | 0..* | BackboneElement | Structural variant
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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 |  | 0..* | Extension | Additional content defined by implementations
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 |  | 0..* | Extension | Additional content defined by implementations
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

#### Terminology Bindings

Path | Conformité | ValueSet / Code | URI
MolecularSequence.language | preferred | CommonLanguages `http://hl7.org/fhir/ValueSet/languages` from the FHIR Standard
Bindings Additionnels | But
AllLanguages | Binding Max
MolecularSequence.type | required | GenomeEntityType `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GenomeEntityType` from this IG
MolecularSequence.referenceSeq.chromosome | extensible | GeneticMaterial `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/GeneticMaterial` from this IG
MolecularSequence.referenceSeq.orientation | required | orientationType `http://hl7.org/fhir/ValueSet/orientation-type|4.0.1` from the FHIR Standard
MolecularSequence.referenceSeq.referenceSeqId | example | ENSEMBL `http://hl7.org/fhir/ValueSet/sequence-referenceSeq` from the FHIR Standard
MolecularSequence.referenceSeq.strand | required | Pattern: crick `http://hl7.org/fhir/ValueSet/strand-type|4.0.1` from the FHIR Standard
MolecularSequence.quality.type | required | qualityType `http://hl7.org/fhir/ValueSet/quality-type|4.0.1` from 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-standardSequence` from the FHIR Standard
MolecularSequence.quality.method | example | FDA-Method `http://hl7.org/fhir/ValueSet/sequence-quality-method` from the FHIR Standard
MolecularSequence.repository.type | required | repositoryType `http://hl7.org/fhir/ValueSet/repository-type|4.0.1` from the FHIR Standard
MolecularSequence.structureVariant.variantType | required | LOINC LL379-9|4.0.1 `http://loinc.org/vs/LL379-9|4.0.1`

This structure is derived from MolecularSequence

Résumé

Mandatory: 1 element

Structures

This structure refers to these other structures:

- Oncology Patient (https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/onco-patient)

Other representations of profile: CSV, Excel, Schematron