MolecularSequence R5 (FHIR) at fhirtruck

Path

MolecularSequence

Id

MolecularSequence

Cardinality

0 - *

Definition

Representation of a molecular sequence.

Comment

Constraint

dom-2 [error]

If the resource is contained in another resource, it SHALL NOT contain nested Resources

dom-3 [error]

If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource

dom-4 [error]

If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated

dom-5 [error]

If a resource is contained in another resource, it SHALL NOT have a security label

dom-6 [warning]

A resource should have narrative for robust management

Path

MolecularSequence.identifier

Id

MolecularSequence.identifier

Type

Identifier

Cardinality

0 - *

Definition

A unique identifier for this particular sequence instance.

Comment

Requirements

Allows sequences to be distinguished and referenced.

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

use

Summary: The element appears in the summary view

code

usual | official | temp | secondary | old (If known)

type

CodeableConcept

Description of identifier

coding

List: This element is a list and more than one value can be provided

Coding

Code defined by a terminology system

system

uri

Identity of the terminology system

version

string

Version of the system - if relevant

code

Symbol in syntax defined by the system

display

string

Representation defined by the system

userSelected

boolean

If this coding was chosen directly by the user

system

uri

The namespace for the identifier value

value

string

The value that is unique

period

Period

Time period when id is/was valid for use

start

dateTime

Starting time with inclusive boundary

end

dateTime

End time with inclusive boundary, if not ongoing

assigner

Reference

Organization that issued id (may be just text)

reference

string

Literal reference, Relative, internal or absolute URL

type

uri

Type the reference refers to (e.g. "Patient") - must be a resource in resources

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.identifier.Identifier.assigner.Reference.identifier

Id

Reference.identifier

Type

Identifier

Cardinality

0 - 1

Definition

An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.

Comment

When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any). This element only allows for a single identifier. In the case where additional identifers are required, use the [http://hl7.org/fhir/StructureDefinition/additionalIdentifier](http://hl7.org/fhir/extensions/StructureDefinition-additionalIdentifier.html) extension.

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Condition

ref-2

use

code

usual | official | temp | secondary | old (If known)

type

CodeableConcept

Description of identifier

system

uri

The namespace for the identifier value

value

string

The value that is unique

period

Period

Time period when id is/was valid for use

assigner

Reference

Organization that issued id (may be just text)

display

string

Text alternative for the resource

Path

MolecularSequence.type

Id

MolecularSequence.type

Type

code

Cardinality

0 - 1

Definition

Amino Acid Sequence/ DNA Sequence / RNA Sequence.

Comment

Binding

Strength

required

Description

Type if a sequence -- DNA, RNA, or amino acid sequence.

ValueSet

http://hl7.org/fhir/ValueSet/sequence-type|5.0.0

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.subject

Id

MolecularSequence.subject

Type

Reference

Cardinality

0 - 1

Definition

Indicates the subject this sequence is associated too.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

reference

string

Literal reference, Relative, internal or absolute URL

type

uri

Type the reference refers to (e.g. "Patient") - must be a resource in resources

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.subject.Reference.identifier

Id

Reference.identifier

Type

Identifier

Cardinality

0 - 1

Definition

An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.

Comment

When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any). This element only allows for a single identifier. In the case where additional identifers are required, use the [http://hl7.org/fhir/StructureDefinition/additionalIdentifier](http://hl7.org/fhir/extensions/StructureDefinition-additionalIdentifier.html) extension.

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Condition

ref-2

use

code

usual | official | temp | secondary | old (If known)

type

CodeableConcept

Description of identifier

system

uri

The namespace for the identifier value

value

string

The value that is unique

period

Period

Time period when id is/was valid for use

start

dateTime

Starting time with inclusive boundary

end

dateTime

End time with inclusive boundary, if not ongoing

assigner

Reference

Organization that issued id (may be just text)

reference

string

Literal reference, Relative, internal or absolute URL

type

uri

Type the reference refers to (e.g. "Patient") - must be a resource in resources

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.subject.Reference.identifier.Identifier.assigner.Reference.identifier

Id

Reference.identifier

Type

Identifier

Cardinality

0 - 1

Definition

An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.

Comment

When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any). This element only allows for a single identifier. In the case where additional identifers are required, use the [http://hl7.org/fhir/StructureDefinition/additionalIdentifier](http://hl7.org/fhir/extensions/StructureDefinition-additionalIdentifier.html) extension.

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Condition

ref-2

display

string

Text alternative for the resource

display

string

Text alternative for the resource

Path

MolecularSequence.focus

Id

MolecularSequence.focus

Type

Reference

Cardinality

0 - *

Definition

The actual focus of a molecular sequence when it is not the patient of record representing something or someone associated with the patient such as a spouse, parent, child, or sibling. For example, in trio testing, the subject would be the child (proband) and the focus would be the parent.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

reference

string

Literal reference, Relative, internal or absolute URL

type

uri

Type the reference refers to (e.g. "Patient") - must be a resource in resources

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.focus.Reference.identifier

Id

Reference.identifier

Type

Identifier

Cardinality

0 - 1

Definition

An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.

Comment

When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any). This element only allows for a single identifier. In the case where additional identifers are required, use the [http://hl7.org/fhir/StructureDefinition/additionalIdentifier](http://hl7.org/fhir/extensions/StructureDefinition-additionalIdentifier.html) extension.

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Condition

ref-2

use

code

usual | official | temp | secondary | old (If known)

type

CodeableConcept

Description of identifier

system

uri

The namespace for the identifier value

value

string

The value that is unique

period

Period

Time period when id is/was valid for use

start

dateTime

Starting time with inclusive boundary

end

dateTime

End time with inclusive boundary, if not ongoing

assigner

Reference

Organization that issued id (may be just text)

reference

string

Literal reference, Relative, internal or absolute URL

type

uri

Type the reference refers to (e.g. "Patient") - must be a resource in resources

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.focus.Reference.identifier.Identifier.assigner.Reference.identifier

Id

Reference.identifier

Type

Identifier

Cardinality

0 - 1

Definition

An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.

Comment

When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any). This element only allows for a single identifier. In the case where additional identifers are required, use the [http://hl7.org/fhir/StructureDefinition/additionalIdentifier](http://hl7.org/fhir/extensions/StructureDefinition-additionalIdentifier.html) extension.

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Condition

ref-2

display

string

Text alternative for the resource

display

string

Text alternative for the resource

Path

MolecularSequence.specimen

Id

MolecularSequence.specimen

Type

Reference

Cardinality

0 - 1

Definition

Specimen used for sequencing.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

reference

string

Literal reference, Relative, internal or absolute URL

type

uri

Type the reference refers to (e.g. "Patient") - must be a resource in resources

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.specimen.Reference.identifier

Id

Reference.identifier

Type

Identifier

Cardinality

0 - 1

Definition

An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.

Comment

When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any). This element only allows for a single identifier. In the case where additional identifers are required, use the [http://hl7.org/fhir/StructureDefinition/additionalIdentifier](http://hl7.org/fhir/extensions/StructureDefinition-additionalIdentifier.html) extension.

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Condition

ref-2

use

code

usual | official | temp | secondary | old (If known)

type

CodeableConcept

Description of identifier

system

uri

The namespace for the identifier value

value

string

The value that is unique

period

Period

Time period when id is/was valid for use

start

dateTime

Starting time with inclusive boundary

end

dateTime

End time with inclusive boundary, if not ongoing

assigner

Reference

Organization that issued id (may be just text)

reference

string

Literal reference, Relative, internal or absolute URL

type

uri

Type the reference refers to (e.g. "Patient") - must be a resource in resources

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.specimen.Reference.identifier.Identifier.assigner.Reference.identifier

Id

Reference.identifier

Type

Identifier

Cardinality

0 - 1

Definition

An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.

Comment

When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any). This element only allows for a single identifier. In the case where additional identifers are required, use the [http://hl7.org/fhir/StructureDefinition/additionalIdentifier](http://hl7.org/fhir/extensions/StructureDefinition-additionalIdentifier.html) extension.

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Condition

ref-2

display

string

Text alternative for the resource

display

string

Text alternative for the resource

Path

MolecularSequence.device

Id

MolecularSequence.device

Type

Reference

Cardinality

0 - 1

Definition

The method for sequencing, for example, chip information.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

reference

string

Literal reference, Relative, internal or absolute URL

type

uri

Type the reference refers to (e.g. "Patient") - must be a resource in resources

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.device.Reference.identifier

Id

Reference.identifier

Type

Identifier

Cardinality

0 - 1

Definition

An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.

Comment

When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any). This element only allows for a single identifier. In the case where additional identifers are required, use the [http://hl7.org/fhir/StructureDefinition/additionalIdentifier](http://hl7.org/fhir/extensions/StructureDefinition-additionalIdentifier.html) extension.

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Condition

ref-2

use

code

usual | official | temp | secondary | old (If known)

type

CodeableConcept

Description of identifier

system

uri

The namespace for the identifier value

value

string

The value that is unique

period

Period

Time period when id is/was valid for use

start

dateTime

Starting time with inclusive boundary

end

dateTime

End time with inclusive boundary, if not ongoing

assigner

Reference

Organization that issued id (may be just text)

reference

string

Literal reference, Relative, internal or absolute URL

type

uri

Type the reference refers to (e.g. "Patient") - must be a resource in resources

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.device.Reference.identifier.Identifier.assigner.Reference.identifier

Id

Reference.identifier

Type

Identifier

Cardinality

0 - 1

Definition

An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.

Comment

When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any). This element only allows for a single identifier. In the case where additional identifers are required, use the [http://hl7.org/fhir/StructureDefinition/additionalIdentifier](http://hl7.org/fhir/extensions/StructureDefinition-additionalIdentifier.html) extension.

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Condition

ref-2

display

string

Text alternative for the resource

display

string

Text alternative for the resource

Path

MolecularSequence.performer

Id

MolecularSequence.performer

Type

Reference

Cardinality

0 - 1

Definition

The organization or lab that should be responsible for this result.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

reference

string

Literal reference, Relative, internal or absolute URL

type

uri

Type the reference refers to (e.g. "Patient") - must be a resource in resources

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.performer.Reference.identifier

Id

Reference.identifier

Type

Identifier

Cardinality

0 - 1

Definition

An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.

Comment

When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any). This element only allows for a single identifier. In the case where additional identifers are required, use the [http://hl7.org/fhir/StructureDefinition/additionalIdentifier](http://hl7.org/fhir/extensions/StructureDefinition-additionalIdentifier.html) extension.

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Condition

ref-2

use

code

usual | official | temp | secondary | old (If known)

type

CodeableConcept

Description of identifier

system

uri

The namespace for the identifier value

value

string

The value that is unique

period

Period

Time period when id is/was valid for use

start

dateTime

Starting time with inclusive boundary

end

dateTime

End time with inclusive boundary, if not ongoing

assigner

Reference

Organization that issued id (may be just text)

reference

string

Literal reference, Relative, internal or absolute URL

type

uri

Type the reference refers to (e.g. "Patient") - must be a resource in resources

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.performer.Reference.identifier.Identifier.assigner.Reference.identifier

Id

Reference.identifier

Type

Identifier

Cardinality

0 - 1

Definition

An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.

Comment

When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any). This element only allows for a single identifier. In the case where additional identifers are required, use the [http://hl7.org/fhir/StructureDefinition/additionalIdentifier](http://hl7.org/fhir/extensions/StructureDefinition-additionalIdentifier.html) extension.

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Condition

ref-2

display

string

Text alternative for the resource

display

string

Text alternative for the resource

Path

MolecularSequence.literal

Id

MolecularSequence.literal

Type

string

Cardinality

0 - 1

Definition

Sequence that was observed.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.formatted

Id

MolecularSequence.formatted

Type

Attachment

Cardinality

0 - *

Definition

Sequence that was observed as file content. Can be an actual file contents, or referenced by a URL to an external system.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

contentType

code

Mime type of the content, with charset etc.

data

base64Binary

Data inline, base64ed

url

Uri where the data can be found

size

integer64

Number of bytes of content (if url provided)

hash

base64Binary

Hash of the data (sha-1, base64ed)

title

string

Label to display in place of the data

creation

dateTime

Date attachment was first created

height

positiveInt

Height of the image in pixels (photo/video)

width

positiveInt

Width of the image in pixels (photo/video)

frames

positiveInt

Number of frames if > 1 (photo)

duration

decimal

Length in seconds (audio / video)

pages

positiveInt

Number of printed pages

Path

MolecularSequence.relative

Id

MolecularSequence.relative

Type

BackboneElement

Cardinality

0 - *

Definition

A sequence defined relative to another sequence.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.relative.coordinateSystem

Id

MolecularSequence.relative.coordinateSystem

Type

CodeableConcept

Cardinality

1 - 1

Definition

These are different ways of identifying nucleotides or amino acids within a sequence. Different databases and file types may use different systems. For detail definitions, see https://loinc.org/92822-6/ for more detail.

Comment

Binding

Strength

extensible

Description

Genomic coordinate system.

ValueSet

http://loinc.org/LL5323-2/

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

coding

Coding

Code defined by a terminology system

system

uri

Identity of the terminology system

version

string

Version of the system - if relevant

code

Symbol in syntax defined by the system

display

string

Representation defined by the system

userSelected

boolean

If this coding was chosen directly by the user

Path

MolecularSequence.relative.ordinalPosition

Id

MolecularSequence.relative.ordinalPosition

Type

integer

Cardinality

0 - 1

Definition

Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.relative.sequenceRange

Id

MolecularSequence.relative.sequenceRange

Type

Range

Cardinality

0 - 1

Definition

Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

low

Quantity

Low limit

value

decimal

Numerical value (with implicit precision)

comparator

code

< | <= | >= | > | ad - how to understand the value

unit

string

Unit representation

system

uri

System that defines coded unit form

code

Coded form of the unit

high

Quantity

High limit

value

decimal

Numerical value (with implicit precision)

comparator

code

< | <= | >= | > | ad - how to understand the value

unit

string

Unit representation

system

uri

System that defines coded unit form

code

Coded form of the unit

Path

MolecularSequence.relative.startingSequence

Id

MolecularSequence.relative.startingSequence

Type

BackboneElement

Cardinality

0 - 1

Definition

A sequence that is used as a starting sequence to describe variants that are present in a sequence analyzed.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

msq-5 [error]

Both genomeAssembly and chromosome must be both contained if either one of them is contained

msq-6 [error]

Have and only have one of the following elements in startingSequence: 1. genomeAssembly; 2 sequence

Path

MolecularSequence.relative.startingSequence.genomeAssembly

Id

MolecularSequence.relative.startingSequence.genomeAssembly

Type

CodeableConcept

Cardinality

0 - 1

Definition

The genome assembly used for starting sequence, e.g. GRCh38.

Comment

Binding

Strength

extensible

Description

Human reference sequence NCBI build ID.

ValueSet

http://loinc.org/LL1040-6/

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Condition

msq-6

msq-5

coding

Coding

Code defined by a terminology system

Path

MolecularSequence.relative.startingSequence.chromosome

Id

MolecularSequence.relative.startingSequence.chromosome

Type

CodeableConcept

Cardinality

0 - 1

Definition

Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340)).

Comment

Binding

Strength

required

Description

The chromosome containing the sequence.

ValueSet

http://loinc.org/LL2938-0/|5.0.0

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Condition

msq-5

coding

Coding

Code defined by a terminology system

Path

MolecularSequence.relative.startingSequence.sequence[x]

Id

MolecularSequence.relative.startingSequence.sequence[x]

Type

CodeableConcept

Cardinality

0 - 1

Definition

The reference sequence that represents the starting sequence.

Comment

A starting sequence may be represented in one of three ways: 1. CodeableConcept, using NCBI, LRG or other appropriate code systems 1. a simple string of IUPAC codes 1. a reference to another MolecularSequence resource.

Binding

Strength

example

Description

Multiple bindings acceptable (NCBI or LRG)

ValueSet

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Condition

msq-6

coding

Coding

Code defined by a terminology system

Path

MolecularSequence.relative.startingSequence.windowStart

Id

MolecularSequence.relative.startingSequence.windowStart

Type

integer

Cardinality

0 - 1

Definition

Start position of the window on the starting sequence. This value should honor the rules of the coordinateSystem.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.relative.startingSequence.windowEnd

Id

MolecularSequence.relative.startingSequence.windowEnd

Type

integer

Cardinality

0 - 1

Definition

End position of the window on the starting sequence. This value should honor the rules of the coordinateSystem.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.relative.startingSequence.orientation

Id

MolecularSequence.relative.startingSequence.orientation

Type

code

Cardinality

0 - 1

Definition

A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.

Comment

Binding

Strength

required

Description

Type for orientation

ValueSet

http://hl7.org/fhir/ValueSet/orientation-type|5.0.0

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.relative.startingSequence.strand

Id

MolecularSequence.relative.startingSequence.strand

Type

code

Cardinality

0 - 1

Definition

An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.

Comment

Binding

Strength

required

Description

Type for strand

ValueSet

http://hl7.org/fhir/ValueSet/strand-type|5.0.0

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.relative.edit

Id

MolecularSequence.relative.edit

Type

BackboneElement

Cardinality

0 - *

Definition

Changes in sequence from the starting sequence.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.relative.edit.start

Id

MolecularSequence.relative.edit.start

Type

integer

Cardinality

0 - 1

Definition

Start position of the edit on the starting sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.relative.edit.end

Id

MolecularSequence.relative.edit.end

Type

integer

Cardinality

0 - 1

Definition

End position of the edit on the starting sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.relative.edit.replacementSequence

Id

MolecularSequence.relative.edit.replacementSequence

Type

string

Cardinality

0 - 1

Definition

Allele that was observed. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.relative.edit.replacedSequence

Id

MolecularSequence.relative.edit.replacedSequence

Type

string

Cardinality

0 - 1

Definition

Allele in the starting sequence. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the starting sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children