This page is part of the OSIRIS FHIR Implementation Guide (v1.1.0: Release) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version. For a full list of available versions, see the Directory of published versions

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Resource Profile: Annotation Reference

The annotation reference profile indicates the reference genome / pfam domain / database used to generate the Annotation instance linked.

Usage:

• Refer to this Resource Profile: Variant Annotation
• Examples for this Resource Profile: MolecularSequence/fhir-osiris-annotation-reference-1

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
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	SΣ	0..1	Reference(Oncology Patient)	Who and/or what this is about ele-1: All FHIR elements must have a @value or children
referenceSeq	ΣC	0..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
orientation	SΣ	0..1	code	DNA strand orientation Binding: orientationType (required): Type for orientation. ele-1: All FHIR elements must have a @value or children
referenceSeqId	SΣ	1..1	CodeableConcept	Type of the referenced annotation Binding: Reference Type Value Set (extensible) ele-1: All FHIR elements must have a @value or children
Slices pour repository	Σ	1..*	BackboneElement	External repository which contains detailed report related with observedSeq in this resource Slice: Unordered, Open by pattern:type ele-1: All FHIR elements must have a @value or children
repository:All Slices				Content/Rules for all slices
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
type	Σ	1..1	code	directlink | openapi | login | oauth | other Binding: repositoryType (required): Type for access of external URI. ele-1: All FHIR elements must have a @value or children
repository:reference-db	Σ	1..1	BackboneElement	External repository which contains detailed report related with observedSeq in this resource ele-1: All FHIR elements must have a @value or children
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
type	Σ	1..1	code	directlink | openapi | login | oauth | other Binding: repositoryType (required): Type for access of external URI. ele-1: All FHIR elements must have a @value or children Required Pattern: other
name	SΣ	1..1	string	Reference database name ele-1: All FHIR elements must have a @value or children
datasetId	SΣ	1..1	string	Identifier of the annotation in the database ele-1: All FHIR elements must have a @value or children
repository:pfam-domain	SΣ	0..1	BackboneElement	External repository which contains detailed report related with observedSeq in this resource ele-1: All FHIR elements must have a @value or children
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
type	Σ	1..1	code	directlink | openapi | login | oauth | other Binding: repositoryType (required): Type for access of external URI. ele-1: All FHIR elements must have a @value or children Required Pattern: directlink
url	Σ	0..1	uri	URI of the repository ele-1: All FHIR elements must have a @value or children Required Pattern: http://pfam.xfam.org/
name	Σ	0..1	string	Repository's name ele-1: All FHIR elements must have a @value or children Required Pattern: pfam
datasetId	SΣ	0..1	string	Pfam ID ele-1: All FHIR elements must have a @value or children
readsetId	SΣ	0..1	string	Pfam domain name ele-1: All FHIR elements must have a @value or children
Documentation for this format

Terminology Bindings

Path	Conformité	ValueSet / Code	URI
MolecularSequence.referenceSeq.orientation	required	orientationType http://hl7.org/fhir/ValueSet/orientation-type|4.0.1 from the FHIR Standard
MolecularSequence.referenceSeq.referenceSeqId	extensible	ReferenceType https://ig-osiris.cancer.fr/ig/osiris/ValueSet/ReferenceType from this IG
MolecularSequence.repository.type	required	repositoryType http://hl7.org/fhir/ValueSet/repository-type|4.0.1 from the FHIR Standard
MolecularSequence.repository:reference-db.type	required	Pattern: other http://hl7.org/fhir/ValueSet/repository-type|4.0.1 from the FHIR Standard
MolecularSequence.repository:pfam-domain.type	required	Pattern: directlink http://hl7.org/fhir/ValueSet/repository-type|4.0.1 from the FHIR Standard

This structure is derived from MolecularSequence

Nom	Drapeaux	Card.	Type	Description et contraintes
MolecularSequence		0..*	MolecularSequence	Information about a biological sequence
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	S	0..1	Reference(Oncology Patient)	Who and/or what this is about
referenceSeq
orientation	S	0..1	code	DNA strand orientation
referenceSeqId	S	1..1	CodeableConcept	Type of the referenced annotation Binding: Reference Type Value Set (extensible)
Slices pour repository		1..*	BackboneElement	External repository which contains detailed report related with observedSeq in this resource Slice: Unordered, Open by pattern:type
repository:reference-db		1..1	BackboneElement	External repository which contains detailed report related with observedSeq in this resource
type		1..1	code	directlink | openapi | login | oauth | other Required Pattern: other
name	S	1..1	string	Reference database name
datasetId	S	1..1	string	Identifier of the annotation in the database
repository:pfam-domain	S	0..1	BackboneElement	External repository which contains detailed report related with observedSeq in this resource
type		1..1	code	directlink | openapi | login | oauth | other Required Pattern: directlink
url		0..1	uri	URI of the repository Required Pattern: http://pfam.xfam.org/
name		0..1	string	Repository's name Required Pattern: pfam
datasetId	S	0..1	string	Pfam ID
readsetId	S	0..1	string	Pfam domain name
Documentation for this format

Terminology Bindings (Differential)

Path	Conformité	ValueSet	URI
MolecularSequence.referenceSeq.referenceSeqId	extensible	ReferenceType https://ig-osiris.cancer.fr/ig/osiris/ValueSet/ReferenceType 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: sequenceType (required): Type if a sequence -- DNA, RNA, or amino acid sequence.
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	SΣ	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	ΣC	0..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	Chromosome containing genetic finding Binding: chromosome-human (example): Chromosome number for human.
genomeBuild	Σ	0..1	string	The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
orientation	SΣ	0..1	code	DNA strand orientation Binding: orientationType (required): Type for orientation.
referenceSeqId	SΣ	1..1	CodeableConcept	Type of the referenced annotation Binding: Reference Type Value Set (extensible)
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.
windowStart	Σ	0..1	integer	Start position of the window on the reference sequence
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
Slices pour repository	Σ	1..*	BackboneElement	External repository which contains detailed report related with observedSeq in this resource Slice: Unordered, Open by pattern:type
repository:All Slices				Content/Rules for all slices
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
repository:reference-db	Σ	1..1	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. Required Pattern: other
url	Σ	0..1	uri	URI of the repository
name	SΣ	1..1	string	Reference database name
datasetId	SΣ	1..1	string	Identifier of the annotation in the database
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
repository:pfam-domain	SΣ	0..1	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. Required Pattern: directlink
url	Σ	0..1	uri	URI of the repository Required Pattern: http://pfam.xfam.org/
name	Σ	0..1	string	Repository's name Required Pattern: pfam
datasetId	SΣ	0..1	string	Pfam ID
variantsetId	Σ	0..1	string	Id of the variantset that used to call for variantset in repository
readsetId	SΣ	0..1	string	Pfam domain name
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	sequenceType http://hl7.org/fhir/ValueSet/sequence-type|4.0.1 from the FHIR Standard
MolecularSequence.referenceSeq.chromosome	example	chromosome-human http://hl7.org/fhir/ValueSet/chromosome-human from the FHIR Standard
MolecularSequence.referenceSeq.orientation	required	orientationType http://hl7.org/fhir/ValueSet/orientation-type|4.0.1 from the FHIR Standard
MolecularSequence.referenceSeq.referenceSeqId	extensible	ReferenceType https://ig-osiris.cancer.fr/ig/osiris/ValueSet/ReferenceType from this IG
MolecularSequence.referenceSeq.strand	required	strandType 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.repository:reference-db.type	required	Pattern: other http://hl7.org/fhir/ValueSet/repository-type|4.0.1 from the FHIR Standard
MolecularSequence.repository:pfam-domain.type	required	Pattern: directlink 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: 4 elements(1 nested mandatory element)
Must-Support: 8 elements

Structures

This structure refers to these other structures:

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

Slices

This structure defines the following Slices:

• The element 1 is sliced based on the value of MolecularSequence.repository

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
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	SΣ	0..1	Reference(Oncology Patient)	Who and/or what this is about ele-1: All FHIR elements must have a @value or children
referenceSeq	ΣC	0..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
orientation	SΣ	0..1	code	DNA strand orientation Binding: orientationType (required): Type for orientation. ele-1: All FHIR elements must have a @value or children
referenceSeqId	SΣ	1..1	CodeableConcept	Type of the referenced annotation Binding: Reference Type Value Set (extensible) ele-1: All FHIR elements must have a @value or children
Slices pour repository	Σ	1..*	BackboneElement	External repository which contains detailed report related with observedSeq in this resource Slice: Unordered, Open by pattern:type ele-1: All FHIR elements must have a @value or children
repository:All Slices				Content/Rules for all slices
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
type	Σ	1..1	code	directlink | openapi | login | oauth | other Binding: repositoryType (required): Type for access of external URI. ele-1: All FHIR elements must have a @value or children
repository:reference-db	Σ	1..1	BackboneElement	External repository which contains detailed report related with observedSeq in this resource ele-1: All FHIR elements must have a @value or children
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
type	Σ	1..1	code	directlink | openapi | login | oauth | other Binding: repositoryType (required): Type for access of external URI. ele-1: All FHIR elements must have a @value or children Required Pattern: other
name	SΣ	1..1	string	Reference database name ele-1: All FHIR elements must have a @value or children
datasetId	SΣ	1..1	string	Identifier of the annotation in the database ele-1: All FHIR elements must have a @value or children
repository:pfam-domain	SΣ	0..1	BackboneElement	External repository which contains detailed report related with observedSeq in this resource ele-1: All FHIR elements must have a @value or children
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
type	Σ	1..1	code	directlink | openapi | login | oauth | other Binding: repositoryType (required): Type for access of external URI. ele-1: All FHIR elements must have a @value or children Required Pattern: directlink
url	Σ	0..1	uri	URI of the repository ele-1: All FHIR elements must have a @value or children Required Pattern: http://pfam.xfam.org/
name	Σ	0..1	string	Repository's name ele-1: All FHIR elements must have a @value or children Required Pattern: pfam
datasetId	SΣ	0..1	string	Pfam ID ele-1: All FHIR elements must have a @value or children
readsetId	SΣ	0..1	string	Pfam domain name ele-1: All FHIR elements must have a @value or children
Documentation for this format

Terminology Bindings

Path	Conformité	ValueSet / Code	URI
MolecularSequence.referenceSeq.orientation	required	orientationType http://hl7.org/fhir/ValueSet/orientation-type|4.0.1 from the FHIR Standard
MolecularSequence.referenceSeq.referenceSeqId	extensible	ReferenceType https://ig-osiris.cancer.fr/ig/osiris/ValueSet/ReferenceType from this IG
MolecularSequence.repository.type	required	repositoryType http://hl7.org/fhir/ValueSet/repository-type|4.0.1 from the FHIR Standard
MolecularSequence.repository:reference-db.type	required	Pattern: other http://hl7.org/fhir/ValueSet/repository-type|4.0.1 from the FHIR Standard
MolecularSequence.repository:pfam-domain.type	required	Pattern: directlink http://hl7.org/fhir/ValueSet/repository-type|4.0.1 from the FHIR Standard

Differential View

This structure is derived from MolecularSequence

Nom	Drapeaux	Card.	Type	Description et contraintes
MolecularSequence		0..*	MolecularSequence	Information about a biological sequence
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	S	0..1	Reference(Oncology Patient)	Who and/or what this is about
referenceSeq
orientation	S	0..1	code	DNA strand orientation
referenceSeqId	S	1..1	CodeableConcept	Type of the referenced annotation Binding: Reference Type Value Set (extensible)
Slices pour repository		1..*	BackboneElement	External repository which contains detailed report related with observedSeq in this resource Slice: Unordered, Open by pattern:type
repository:reference-db		1..1	BackboneElement	External repository which contains detailed report related with observedSeq in this resource
type		1..1	code	directlink | openapi | login | oauth | other Required Pattern: other
name	S	1..1	string	Reference database name
datasetId	S	1..1	string	Identifier of the annotation in the database
repository:pfam-domain	S	0..1	BackboneElement	External repository which contains detailed report related with observedSeq in this resource
type		1..1	code	directlink | openapi | login | oauth | other Required Pattern: directlink
url		0..1	uri	URI of the repository Required Pattern: http://pfam.xfam.org/
name		0..1	string	Repository's name Required Pattern: pfam
datasetId	S	0..1	string	Pfam ID
readsetId	S	0..1	string	Pfam domain name
Documentation for this format

Terminology Bindings (Differential)

Path	Conformité	ValueSet	URI
MolecularSequence.referenceSeq.referenceSeqId	extensible	ReferenceType https://ig-osiris.cancer.fr/ig/osiris/ValueSet/ReferenceType 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: sequenceType (required): Type if a sequence -- DNA, RNA, or amino acid sequence.
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	SΣ	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	ΣC	0..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	Chromosome containing genetic finding Binding: chromosome-human (example): Chromosome number for human.
genomeBuild	Σ	0..1	string	The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
orientation	SΣ	0..1	code	DNA strand orientation Binding: orientationType (required): Type for orientation.
referenceSeqId	SΣ	1..1	CodeableConcept	Type of the referenced annotation Binding: Reference Type Value Set (extensible)
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.
windowStart	Σ	0..1	integer	Start position of the window on the reference sequence
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
Slices pour repository	Σ	1..*	BackboneElement	External repository which contains detailed report related with observedSeq in this resource Slice: Unordered, Open by pattern:type
repository:All Slices				Content/Rules for all slices
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
repository:reference-db	Σ	1..1	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. Required Pattern: other
url	Σ	0..1	uri	URI of the repository
name	SΣ	1..1	string	Reference database name
datasetId	SΣ	1..1	string	Identifier of the annotation in the database
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
repository:pfam-domain	SΣ	0..1	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. Required Pattern: directlink
url	Σ	0..1	uri	URI of the repository Required Pattern: http://pfam.xfam.org/
name	Σ	0..1	string	Repository's name Required Pattern: pfam
datasetId	SΣ	0..1	string	Pfam ID
variantsetId	Σ	0..1	string	Id of the variantset that used to call for variantset in repository
readsetId	SΣ	0..1	string	Pfam domain name
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	sequenceType http://hl7.org/fhir/ValueSet/sequence-type|4.0.1 from the FHIR Standard
MolecularSequence.referenceSeq.chromosome	example	chromosome-human http://hl7.org/fhir/ValueSet/chromosome-human from the FHIR Standard
MolecularSequence.referenceSeq.orientation	required	orientationType http://hl7.org/fhir/ValueSet/orientation-type|4.0.1 from the FHIR Standard
MolecularSequence.referenceSeq.referenceSeqId	extensible	ReferenceType https://ig-osiris.cancer.fr/ig/osiris/ValueSet/ReferenceType from this IG
MolecularSequence.referenceSeq.strand	required	strandType 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.repository:reference-db.type	required	Pattern: other http://hl7.org/fhir/ValueSet/repository-type|4.0.1 from the FHIR Standard
MolecularSequence.repository:pfam-domain.type	required	Pattern: directlink 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: 4 elements(1 nested mandatory element)
Must-Support: 8 elements

Structures

This structure refers to these other structures:

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

Slices

This structure defines the following Slices:

• The element 1 is sliced based on the value of MolecularSequence.repository

Other representations of profile: CSV, Excel, Schematron