Introduction

In the GA4GH Phenopacket Schema, a phenopacket is an anonymous description of clinical data of an individual or biosample with potential genes of interest and/or diagnoses. It can be used for multiple use cases. For instance, it can be used to describe the phenotypic findings observed in an individual with a disease that is being studied or for an individual in whom the diagnosis is being sought. The phenopacket can contain information about genetic findings that are causative of the disease, or alternatively it can contain a reference to a VCF file if exome sequencing is being performed as a part of the differential diagnostic process. A phenopacket can also be used to describe the constitutional phenotypic findings of an individual with cancer (a Biosample should be used to describe the phenotypic abnormalities directly associated with an extirpated or biopsied tumor).

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

This structure is derived from Composition

Name	Flags	Card.	Type	Description & Constraints
Composition		0..*	Composition	A set of resources composed into a single coherent clinical statement with clinical attestation
identifier	S	1..1	Identifier	Version-independent identifier for the Composition
subject		0..1	Reference(Individual)	Who and/or what the composition is about
Slices for section		0..*	BackboneElement	Composition is broken into sections Slice: Ordered, Closed by value:code
section:phenotypic_features		0..*	BackboneElement	Composition is broken into sections
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: phenotypic_features
code		1..1	CodeableConcept	Classification of section (recommended) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: phenotypic_features
entry		0..*	Reference(Phenotypic Feature)	A reference to data that supports this section
section:measurements		0..*	BackboneElement	Composition is broken into sections
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: measurements
code		1..1	CodeableConcept	Classification of section (recommended) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: measurements
entry		0..*	Reference(Measurement)	A reference to data that supports this section
section:biosamples		0..*	BackboneElement	Composition is broken into sections
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: biosamples
code		1..1	CodeableConcept	Classification of section (recommended) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: biosamples
entry		0..*	Reference(Biosample)	A reference to data that supports this section
section:interpretations		0..*	BackboneElement	represent the interpretation of a genomic analysis, such as the report from a diagnostic laboratory.
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: interpretations
code		1..1	CodeableConcept	Classification of section (recommended) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: interpretations
entry		0..*	Reference(Phenopackets Genomic Interpretation)	A reference to data that supports this section
section:diseases		0..1	BackboneElement	Composition is broken into sections
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: diseases
code		1..1	CodeableConcept	Classification of section (recommended) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: diseases
entry		0..*	Reference(Disease profile)	A reference to data that supports this section
section:files		0..*	BackboneElement	relevant documents and files.
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: files
code		1..1	CodeableConcept	Classification of section (recommended) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: files
entry		0..*	Reference(DocumentReference)	A reference to data that supports this section
section:medicalActions		0..*	BackboneElement	relevant procedures, radiation therapies, therapeutic regimens, and treatments.
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: medicalActions
code		1..1	CodeableConcept	Classification of section (recommended) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: medicalActions
entry		0..*	Reference(Procedure | Medication | MedicationStatement | MedicationDispense | MedicationAdministration | MedicationRequest)	A reference to data that supports this section
Documentation for this format

Name	Flags	Card.	Type	Description & Constraints
Composition		0..*	Composition	A set of resources composed into a single coherent clinical statement with clinical attestation
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	SΣ	1..1	Identifier	Version-independent identifier for the Composition
status	?!Σ	1..1	code	preliminary | final | amended | entered-in-error Binding: CompositionStatus (required): The workflow/clinical status of the composition.
type	Σ	1..1	CodeableConcept	Kind of composition (LOINC if possible) Binding: FHIRDocumentTypeCodes (preferred): Type of a composition.
subject	Σ	0..1	Reference(Individual)	Who and/or what the composition is about
date	Σ	1..1	dateTime	Composition editing time
author	Σ	1..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the composition
title	Σ	1..1	string	Human Readable name/title
Slices for section	C	0..*	BackboneElement	Composition is broken into sections Slice: Ordered, Closed by value:code cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
section:All Slices				Content/Rules for all slices
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
section:phenotypic_features	C	0..*	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: phenotypic_features
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: phenotypic_features
entry	C	0..*	Reference(Phenotypic Feature)	A reference to data that supports this section
section:measurements	C	0..*	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: measurements
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: measurements
entry	C	0..*	Reference(Measurement)	A reference to data that supports this section
section:biosamples	C	0..*	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: biosamples
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: biosamples
entry	C	0..*	Reference(Biosample)	A reference to data that supports this section
section:interpretations	C	0..*	BackboneElement	represent the interpretation of a genomic analysis, such as the report from a diagnostic laboratory. cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: interpretations
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: interpretations
entry	C	0..*	Reference(Phenopackets Genomic Interpretation)	A reference to data that supports this section
section:diseases	C	0..1	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: diseases
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: diseases
entry	C	0..*	Reference(Disease profile)	A reference to data that supports this section
section:files	C	0..*	BackboneElement	relevant documents and files. cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: files
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: files
entry	C	0..*	Reference(DocumentReference)	A reference to data that supports this section
section:medicalActions	C	0..*	BackboneElement	relevant procedures, radiation therapies, therapeutic regimens, and treatments. cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: medicalActions
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: medicalActions
entry	C	0..*	Reference(Procedure | Medication | MedicationStatement | MedicationDispense | MedicationAdministration | MedicationRequest)	A reference to data that supports this section
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet / Code	URI
Composition.status	required	CompositionStatus http://hl7.org/fhir/ValueSet/composition-status|4.0.1 from the FHIR Standard
Composition.type	preferred	FHIRDocumentTypeCodes http://hl7.org/fhir/ValueSet/doc-typecodes from the FHIR Standard
Composition.section:phenotypic_features.code	example	Pattern: phenotypic_features http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:measurements.code	example	Pattern: measurements http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:biosamples.code	example	Pattern: biosamples http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:interpretations.code	example	Pattern: interpretations http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:diseases.code	example	Pattern: diseases http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:files.code	example	Pattern: files http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:medicalActions.code	example	Pattern: medicalActions http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
cmp-1	error	Composition.section, Composition.section:phenotypic_features, Composition.section:measurements, Composition.section:biosamples, Composition.section:interpretations, Composition.section:diseases, Composition.section:files, Composition.section:medicalActions	A section must contain at least one of text, entries, or sub-sections : text.exists() or entry.exists() or section.exists()
cmp-2	error	Composition.section, Composition.section:phenotypic_features, Composition.section:measurements, Composition.section:biosamples, Composition.section:interpretations, Composition.section:diseases, Composition.section:files, Composition.section:medicalActions	A section can only have an emptyReason if it is empty : emptyReason.empty() or entry.empty()
dom-2	error	Composition	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Composition	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 : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Composition	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Composition	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Composition	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

Name	Flags	Card.	Type	Description & Constraints
Composition		0..*	Composition	A set of resources composed into a single coherent clinical statement with clinical attestation
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. Additional Bindings Purpose AllLanguages Max Binding
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	SΣ	1..1	Identifier	Version-independent identifier for the Composition
status	?!Σ	1..1	code	preliminary | final | amended | entered-in-error Binding: CompositionStatus (required): The workflow/clinical status of the composition.
type	Σ	1..1	CodeableConcept	Kind of composition (LOINC if possible) Binding: FHIRDocumentTypeCodes (preferred): Type of a composition.
category	Σ	0..*	CodeableConcept	Categorization of Composition Binding: DocumentClassValueSet (example): High-level kind of a clinical document at a macro level.
subject	Σ	0..1	Reference(Individual)	Who and/or what the composition is about
encounter	Σ	0..1	Reference(Encounter)	Context of the Composition
date	Σ	1..1	dateTime	Composition editing time
author	Σ	1..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the composition
title	Σ	1..1	string	Human Readable name/title
confidentiality	Σ	0..1	code	As defined by affinity domain Binding: v3.ConfidentialityClassification (2014-03-26) (required): Codes specifying the level of confidentiality of the composition.
attester		0..*	BackboneElement	Attests to accuracy of composition
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
mode		1..1	code	personal | professional | legal | official Binding: CompositionAttestationMode (required): The way in which a person authenticated a composition.
time		0..1	dateTime	When the composition was attested
party		0..1	Reference(Patient | RelatedPerson | Practitioner | PractitionerRole | Organization)	Who attested the composition
custodian	Σ	0..1	Reference(Organization)	Organization which maintains the composition
relatesTo		0..*	BackboneElement	Relationships to other compositions/documents
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
code		1..1	code	replaces | transforms | signs | appends Binding: DocumentRelationshipType (required): The type of relationship between documents.
target[x]		1..1		Target of the relationship
targetIdentifier			Identifier
targetReference			Reference(Composition)
event	Σ	0..*	BackboneElement	The clinical service(s) being documented
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
code	Σ	0..*	CodeableConcept	Code(s) that apply to the event being documented Binding: v3 Code System ActCode (example): This list of codes represents the main clinical acts being documented.
period	Σ	0..1	Period	The period covered by the documentation
detail	Σ	0..*	Reference(Resource)	The event(s) being documented
Slices for section	C	0..*	BackboneElement	Composition is broken into sections Slice: Ordered, Closed by value:code cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
section: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
title		0..1	string	Label for section (e.g. for ToC)
code		0..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document.
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(Resource)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
section:phenotypic_features	C	0..*	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
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
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: phenotypic_features
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: phenotypic_features
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(Phenotypic Feature)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
section:measurements	C	0..*	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
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
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: measurements
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: measurements
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(Measurement)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
section:biosamples	C	0..*	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
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
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: biosamples
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: biosamples
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(Biosample)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
section:interpretations	C	0..*	BackboneElement	represent the interpretation of a genomic analysis, such as the report from a diagnostic laboratory. cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
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
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: interpretations
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: interpretations
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(Phenopackets Genomic Interpretation)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
section:diseases	C	0..1	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
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
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: diseases
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: diseases
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(Disease profile)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
section:files	C	0..*	BackboneElement	relevant documents and files. cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
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
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: files
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: files
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(DocumentReference)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
section:medicalActions	C	0..*	BackboneElement	relevant procedures, radiation therapies, therapeutic regimens, and treatments. cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
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
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: medicalActions
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: medicalActions
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(Procedure | Medication | MedicationStatement | MedicationDispense | MedicationAdministration | MedicationRequest)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet / Code	URI
Composition.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding http://hl7.org/fhir/ValueSet/languages from the FHIR Standard
Composition.status	required	CompositionStatus http://hl7.org/fhir/ValueSet/composition-status|4.0.1 from the FHIR Standard
Composition.type	preferred	FHIRDocumentTypeCodes http://hl7.org/fhir/ValueSet/doc-typecodes from the FHIR Standard
Composition.category	example	DocumentClassValueSet http://hl7.org/fhir/ValueSet/document-classcodes from the FHIR Standard
Composition.confidentiality	required	v3.ConfidentialityClassification http://terminology.hl7.org/ValueSet/v3-ConfidentialityClassification|2014-03-26 from the FHIR Standard
Composition.attester.mode	required	CompositionAttestationMode http://hl7.org/fhir/ValueSet/composition-attestation-mode|4.0.1 from the FHIR Standard
Composition.relatesTo.code	required	DocumentRelationshipType http://hl7.org/fhir/ValueSet/document-relationship-type|4.0.1 from the FHIR Standard
Composition.event.code	example	ActCode http://terminology.hl7.org/ValueSet/v3-ActCode
Composition.section.code	example	DocumentSectionCodes http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard
Composition.section:phenotypic_features.code	example	Pattern: phenotypic_features http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:phenotypic_features.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section:phenotypic_features.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section:phenotypic_features.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard
Composition.section:measurements.code	example	Pattern: measurements http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:measurements.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section:measurements.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section:measurements.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard
Composition.section:biosamples.code	example	Pattern: biosamples http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:biosamples.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section:biosamples.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section:biosamples.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard
Composition.section:interpretations.code	example	Pattern: interpretations http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:interpretations.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section:interpretations.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section:interpretations.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard
Composition.section:diseases.code	example	Pattern: diseases http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:diseases.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section:diseases.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section:diseases.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard
Composition.section:files.code	example	Pattern: files http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:files.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section:files.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section:files.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard
Composition.section:medicalActions.code	example	Pattern: medicalActions http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:medicalActions.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section:medicalActions.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section:medicalActions.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
cmp-1	error	Composition.section, Composition.section:phenotypic_features, Composition.section:measurements, Composition.section:biosamples, Composition.section:interpretations, Composition.section:diseases, Composition.section:files, Composition.section:medicalActions	A section must contain at least one of text, entries, or sub-sections : text.exists() or entry.exists() or section.exists()
cmp-2	error	Composition.section, Composition.section:phenotypic_features, Composition.section:measurements, Composition.section:biosamples, Composition.section:interpretations, Composition.section:diseases, Composition.section:files, Composition.section:medicalActions	A section can only have an emptyReason if it is empty : emptyReason.empty() or entry.empty()
dom-2	error	Composition	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Composition	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 : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Composition	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Composition	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Composition	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

Differential View

This structure is derived from Composition

Name	Flags	Card.	Type	Description & Constraints
Composition		0..*	Composition	A set of resources composed into a single coherent clinical statement with clinical attestation
identifier	S	1..1	Identifier	Version-independent identifier for the Composition
subject		0..1	Reference(Individual)	Who and/or what the composition is about
Slices for section		0..*	BackboneElement	Composition is broken into sections Slice: Ordered, Closed by value:code
section:phenotypic_features		0..*	BackboneElement	Composition is broken into sections
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: phenotypic_features
code		1..1	CodeableConcept	Classification of section (recommended) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: phenotypic_features
entry		0..*	Reference(Phenotypic Feature)	A reference to data that supports this section
section:measurements		0..*	BackboneElement	Composition is broken into sections
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: measurements
code		1..1	CodeableConcept	Classification of section (recommended) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: measurements
entry		0..*	Reference(Measurement)	A reference to data that supports this section
section:biosamples		0..*	BackboneElement	Composition is broken into sections
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: biosamples
code		1..1	CodeableConcept	Classification of section (recommended) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: biosamples
entry		0..*	Reference(Biosample)	A reference to data that supports this section
section:interpretations		0..*	BackboneElement	represent the interpretation of a genomic analysis, such as the report from a diagnostic laboratory.
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: interpretations
code		1..1	CodeableConcept	Classification of section (recommended) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: interpretations
entry		0..*	Reference(Phenopackets Genomic Interpretation)	A reference to data that supports this section
section:diseases		0..1	BackboneElement	Composition is broken into sections
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: diseases
code		1..1	CodeableConcept	Classification of section (recommended) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: diseases
entry		0..*	Reference(Disease profile)	A reference to data that supports this section
section:files		0..*	BackboneElement	relevant documents and files.
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: files
code		1..1	CodeableConcept	Classification of section (recommended) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: files
entry		0..*	Reference(DocumentReference)	A reference to data that supports this section
section:medicalActions		0..*	BackboneElement	relevant procedures, radiation therapies, therapeutic regimens, and treatments.
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: medicalActions
code		1..1	CodeableConcept	Classification of section (recommended) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: medicalActions
entry		0..*	Reference(Procedure | Medication | MedicationStatement | MedicationDispense | MedicationAdministration | MedicationRequest)	A reference to data that supports this section
Documentation for this format

Key Elements View

Name	Flags	Card.	Type	Description & Constraints
Composition		0..*	Composition	A set of resources composed into a single coherent clinical statement with clinical attestation
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	SΣ	1..1	Identifier	Version-independent identifier for the Composition
status	?!Σ	1..1	code	preliminary | final | amended | entered-in-error Binding: CompositionStatus (required): The workflow/clinical status of the composition.
type	Σ	1..1	CodeableConcept	Kind of composition (LOINC if possible) Binding: FHIRDocumentTypeCodes (preferred): Type of a composition.
subject	Σ	0..1	Reference(Individual)	Who and/or what the composition is about
date	Σ	1..1	dateTime	Composition editing time
author	Σ	1..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the composition
title	Σ	1..1	string	Human Readable name/title
Slices for section	C	0..*	BackboneElement	Composition is broken into sections Slice: Ordered, Closed by value:code cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
section:All Slices				Content/Rules for all slices
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
section:phenotypic_features	C	0..*	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: phenotypic_features
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: phenotypic_features
entry	C	0..*	Reference(Phenotypic Feature)	A reference to data that supports this section
section:measurements	C	0..*	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: measurements
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: measurements
entry	C	0..*	Reference(Measurement)	A reference to data that supports this section
section:biosamples	C	0..*	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: biosamples
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: biosamples
entry	C	0..*	Reference(Biosample)	A reference to data that supports this section
section:interpretations	C	0..*	BackboneElement	represent the interpretation of a genomic analysis, such as the report from a diagnostic laboratory. cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: interpretations
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: interpretations
entry	C	0..*	Reference(Phenopackets Genomic Interpretation)	A reference to data that supports this section
section:diseases	C	0..1	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: diseases
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: diseases
entry	C	0..*	Reference(Disease profile)	A reference to data that supports this section
section:files	C	0..*	BackboneElement	relevant documents and files. cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: files
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: files
entry	C	0..*	Reference(DocumentReference)	A reference to data that supports this section
section:medicalActions	C	0..*	BackboneElement	relevant procedures, radiation therapies, therapeutic regimens, and treatments. cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: medicalActions
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
code		1..1	code	Symbol in syntax defined by the system Fixed Value: medicalActions
entry	C	0..*	Reference(Procedure | Medication | MedicationStatement | MedicationDispense | MedicationAdministration | MedicationRequest)	A reference to data that supports this section
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet / Code	URI
Composition.status	required	CompositionStatus http://hl7.org/fhir/ValueSet/composition-status|4.0.1 from the FHIR Standard
Composition.type	preferred	FHIRDocumentTypeCodes http://hl7.org/fhir/ValueSet/doc-typecodes from the FHIR Standard
Composition.section:phenotypic_features.code	example	Pattern: phenotypic_features http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:measurements.code	example	Pattern: measurements http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:biosamples.code	example	Pattern: biosamples http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:interpretations.code	example	Pattern: interpretations http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:diseases.code	example	Pattern: diseases http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:files.code	example	Pattern: files http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:medicalActions.code	example	Pattern: medicalActions http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
cmp-1	error	Composition.section, Composition.section:phenotypic_features, Composition.section:measurements, Composition.section:biosamples, Composition.section:interpretations, Composition.section:diseases, Composition.section:files, Composition.section:medicalActions	A section must contain at least one of text, entries, or sub-sections : text.exists() or entry.exists() or section.exists()
cmp-2	error	Composition.section, Composition.section:phenotypic_features, Composition.section:measurements, Composition.section:biosamples, Composition.section:interpretations, Composition.section:diseases, Composition.section:files, Composition.section:medicalActions	A section can only have an emptyReason if it is empty : emptyReason.empty() or entry.empty()
dom-2	error	Composition	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Composition	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 : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Composition	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Composition	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Composition	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

Snapshot View

Name	Flags	Card.	Type	Description & Constraints
Composition		0..*	Composition	A set of resources composed into a single coherent clinical statement with clinical attestation
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. Additional Bindings Purpose AllLanguages Max Binding
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	SΣ	1..1	Identifier	Version-independent identifier for the Composition
status	?!Σ	1..1	code	preliminary | final | amended | entered-in-error Binding: CompositionStatus (required): The workflow/clinical status of the composition.
type	Σ	1..1	CodeableConcept	Kind of composition (LOINC if possible) Binding: FHIRDocumentTypeCodes (preferred): Type of a composition.
category	Σ	0..*	CodeableConcept	Categorization of Composition Binding: DocumentClassValueSet (example): High-level kind of a clinical document at a macro level.
subject	Σ	0..1	Reference(Individual)	Who and/or what the composition is about
encounter	Σ	0..1	Reference(Encounter)	Context of the Composition
date	Σ	1..1	dateTime	Composition editing time
author	Σ	1..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the composition
title	Σ	1..1	string	Human Readable name/title
confidentiality	Σ	0..1	code	As defined by affinity domain Binding: v3.ConfidentialityClassification (2014-03-26) (required): Codes specifying the level of confidentiality of the composition.
attester		0..*	BackboneElement	Attests to accuracy of composition
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
mode		1..1	code	personal | professional | legal | official Binding: CompositionAttestationMode (required): The way in which a person authenticated a composition.
time		0..1	dateTime	When the composition was attested
party		0..1	Reference(Patient | RelatedPerson | Practitioner | PractitionerRole | Organization)	Who attested the composition
custodian	Σ	0..1	Reference(Organization)	Organization which maintains the composition
relatesTo		0..*	BackboneElement	Relationships to other compositions/documents
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
code		1..1	code	replaces | transforms | signs | appends Binding: DocumentRelationshipType (required): The type of relationship between documents.
target[x]		1..1		Target of the relationship
targetIdentifier			Identifier
targetReference			Reference(Composition)
event	Σ	0..*	BackboneElement	The clinical service(s) being documented
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
code	Σ	0..*	CodeableConcept	Code(s) that apply to the event being documented Binding: v3 Code System ActCode (example): This list of codes represents the main clinical acts being documented.
period	Σ	0..1	Period	The period covered by the documentation
detail	Σ	0..*	Reference(Resource)	The event(s) being documented
Slices for section	C	0..*	BackboneElement	Composition is broken into sections Slice: Ordered, Closed by value:code cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
section: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
title		0..1	string	Label for section (e.g. for ToC)
code		0..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document.
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(Resource)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
section:phenotypic_features	C	0..*	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
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
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: phenotypic_features
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: phenotypic_features
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(Phenotypic Feature)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
section:measurements	C	0..*	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
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
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: measurements
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: measurements
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(Measurement)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
section:biosamples	C	0..*	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
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
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: biosamples
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: biosamples
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(Biosample)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
section:interpretations	C	0..*	BackboneElement	represent the interpretation of a genomic analysis, such as the report from a diagnostic laboratory. cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
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
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: interpretations
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: interpretations
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(Phenopackets Genomic Interpretation)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
section:diseases	C	0..1	BackboneElement	Composition is broken into sections cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
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
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: diseases
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: diseases
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(Disease profile)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
section:files	C	0..*	BackboneElement	relevant documents and files. cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
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
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: files
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: files
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(DocumentReference)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
section:medicalActions	C	0..*	BackboneElement	relevant procedures, radiation therapies, therapeutic regimens, and treatments. cmp-1: A section must contain at least one of text, entries, or sub-sections cmp-2: A section can only have an emptyReason if it is empty
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
title		0..1	string	Label for section (e.g. for ToC) Fixed Value: medicalActions
code		1..1	CodeableConcept	Classification of section (recommended) Binding: DocumentSectionCodes (example): Classification of a section of a composition/document. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: medicalActions
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
author		0..*	Reference(Practitioner | PractitionerRole | Device | Patient | RelatedPerson | Organization)	Who and/or what authored the section
focus		0..1	Reference(Resource)	Who/what the section is about, when it is not about the subject of composition
text	C	0..1	Narrative	Text summary of the section, for human interpretation
mode		0..1	code	working | snapshot | changes Binding: ListMode (required): The processing mode that applies to this section.
orderedBy		0..1	CodeableConcept	Order of section entries Binding: ListOrderCodes (preferred): What order applies to the items in the entry.
entry	C	0..*	Reference(Procedure | Medication | MedicationStatement | MedicationDispense | MedicationAdministration | MedicationRequest)	A reference to data that supports this section
emptyReason	C	0..1	CodeableConcept	Why the section is empty Binding: ListEmptyReasons (preferred): If a section is empty, why it is empty.
section	C	0..*	See section (Composition)	Nested Section
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet / Code	URI
Composition.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding http://hl7.org/fhir/ValueSet/languages from the FHIR Standard
Composition.status	required	CompositionStatus http://hl7.org/fhir/ValueSet/composition-status|4.0.1 from the FHIR Standard
Composition.type	preferred	FHIRDocumentTypeCodes http://hl7.org/fhir/ValueSet/doc-typecodes from the FHIR Standard
Composition.category	example	DocumentClassValueSet http://hl7.org/fhir/ValueSet/document-classcodes from the FHIR Standard
Composition.confidentiality	required	v3.ConfidentialityClassification http://terminology.hl7.org/ValueSet/v3-ConfidentialityClassification|2014-03-26 from the FHIR Standard
Composition.attester.mode	required	CompositionAttestationMode http://hl7.org/fhir/ValueSet/composition-attestation-mode|4.0.1 from the FHIR Standard
Composition.relatesTo.code	required	DocumentRelationshipType http://hl7.org/fhir/ValueSet/document-relationship-type|4.0.1 from the FHIR Standard
Composition.event.code	example	ActCode http://terminology.hl7.org/ValueSet/v3-ActCode
Composition.section.code	example	DocumentSectionCodes http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard
Composition.section:phenotypic_features.code	example	Pattern: phenotypic_features http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:phenotypic_features.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section:phenotypic_features.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section:phenotypic_features.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard
Composition.section:measurements.code	example	Pattern: measurements http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:measurements.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section:measurements.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section:measurements.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard
Composition.section:biosamples.code	example	Pattern: biosamples http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:biosamples.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section:biosamples.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section:biosamples.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard
Composition.section:interpretations.code	example	Pattern: interpretations http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:interpretations.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section:interpretations.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section:interpretations.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard
Composition.section:diseases.code	example	Pattern: diseases http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:diseases.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section:diseases.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section:diseases.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard
Composition.section:files.code	example	Pattern: files http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:files.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section:files.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section:files.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard
Composition.section:medicalActions.code	example	Pattern: medicalActions http://hl7.org/fhir/ValueSet/doc-section-codes from the FHIR Standard
Composition.section:medicalActions.mode	required	ListMode http://hl7.org/fhir/ValueSet/list-mode|4.0.1 from the FHIR Standard
Composition.section:medicalActions.orderedBy	preferred	ListOrderCodes http://hl7.org/fhir/ValueSet/list-order from the FHIR Standard
Composition.section:medicalActions.emptyReason	preferred	ListEmptyReasons http://hl7.org/fhir/ValueSet/list-empty-reason from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
cmp-1	error	Composition.section, Composition.section:phenotypic_features, Composition.section:measurements, Composition.section:biosamples, Composition.section:interpretations, Composition.section:diseases, Composition.section:files, Composition.section:medicalActions	A section must contain at least one of text, entries, or sub-sections : text.exists() or entry.exists() or section.exists()
cmp-2	error	Composition.section, Composition.section:phenotypic_features, Composition.section:measurements, Composition.section:biosamples, Composition.section:interpretations, Composition.section:diseases, Composition.section:files, Composition.section:medicalActions	A section can only have an emptyReason if it is empty : emptyReason.empty() or entry.empty()
dom-2	error	Composition	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Composition	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 : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Composition	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Composition	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Composition	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

This structure is derived from Composition

Summary

Mandatory: 1 element(7 nested mandatory elements)
Must-Support: 1 element
Fixed: 7 elements

Structures

This structure refers to these other structures:

• Individual (http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Individual)
• Phenotypic Feature (http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature)
• Measurement (http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Measurement)
• Biosample (http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Biosample)
• Phenopackets Genomic Interpretation (http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/phenopackets-genomic-interpretation)
• Disease profile (http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Disease)

Slices

This structure defines the following Slices:

• The element 1 is sliced based on the value of Composition.section (ordered, Closed)