MolecularSequence R4 (FHIR) at fhirtruck

Path

MolecularSequence

Id

MolecularSequence

Cardinality

0 - *

Definition

Raw data describing a biological 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

msq-3 [error]

Only 0 and 1 are valid for coordinateSystem

Path

MolecularSequence.identifier

Id

MolecularSequence.identifier

Type

Identifier

Cardinality

0 - *

Definition

A unique identifier for this particular sequence instance. This is a FHIR-defined id.

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")

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).

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

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|4.0.1

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.coordinateSystem

Id

MolecularSequence.coordinateSystem

Type

integer

Cardinality

1 - 1

Definition

Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.patient

Id

MolecularSequence.patient

Type

Reference

Cardinality

0 - 1

Definition

The patient whose sequencing results are described by this resource.

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")

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.patient.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).

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

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")

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.patient.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).

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

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")

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).

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

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")

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).

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

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")

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).

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

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")

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).

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

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")

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).

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

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")

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).

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

display

string

Text alternative for the resource

display

string

Text alternative for the resource

Path

MolecularSequence.quantity

Id

MolecularSequence.quantity

Type

Quantity

Cardinality

0 - 1

Definition

The number of copies of the sequence of interest. (RNASeq).

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

value

decimal

Numerical value (with implicit precision)

comparator

code

< | <= | >= | > - 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.referenceSeq

Id

MolecularSequence.referenceSeq

Type

BackboneElement

Cardinality

0 - 1

Definition

A sequence that is used as a reference 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]

GenomeBuild 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 referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;

Path

MolecularSequence.referenceSeq.chromosome

Id

MolecularSequence.referenceSeq.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

example

Description

Chromosome number for human.

ValueSet

http://hl7.org/fhir/ValueSet/chromosome-human

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.referenceSeq.genomeBuild

Id

MolecularSequence.referenceSeq.genomeBuild

Type

string

Cardinality

0 - 1

Definition

The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.referenceSeq.orientation

Id

MolecularSequence.referenceSeq.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|4.0.1

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.referenceSeq.referenceSeqId

Id

MolecularSequence.referenceSeq.referenceSeqId

Type

CodeableConcept

Cardinality

0 - 1

Definition

Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.

Comment

Binding

Strength

example

Description

Reference identifier.

ValueSet

http://hl7.org/fhir/ValueSet/sequence-referenceSeq

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.referenceSeq.referenceSeqPointer

Id

MolecularSequence.referenceSeq.referenceSeqPointer

Type

Reference

Cardinality

0 - 1

Definition

A pointer to another MolecularSequence entity as reference sequence.

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")

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.referenceSeq.referenceSeqPointer.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).

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

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.referenceSeq.referenceSeqString

Id

MolecularSequence.referenceSeq.referenceSeqString

Type

string

Cardinality

0 - 1

Definition

A string like "ACGT".

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.referenceSeq.strand

Id

MolecularSequence.referenceSeq.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|4.0.1

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.referenceSeq.windowStart

Id

MolecularSequence.referenceSeq.windowStart

Type

integer

Cardinality

0 - 1

Definition

Start position of the window on the reference 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.referenceSeq.windowEnd

Id

MolecularSequence.referenceSeq.windowEnd

Type

integer

Cardinality

0 - 1

Definition

End position of the window on the reference 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.variant

Id

MolecularSequence.variant

Type

BackboneElement

Cardinality

0 - *

Definition

The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.variant.start

Id

MolecularSequence.variant.start

Type

integer

Cardinality

0 - 1

Definition

Start position of the variant on the reference 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.variant.end

Id

MolecularSequence.variant.end

Type

integer

Cardinality

0 - 1

Definition

End position of the variant on the reference 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.variant.observedAllele

Id

MolecularSequence.variant.observedAllele

Type

string

Cardinality

0 - 1

Definition

An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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.variant.referenceAllele

Id

MolecularSequence.variant.referenceAllele

Type

string

Cardinality

0 - 1

Definition

An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference 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.variant.cigar

Id

MolecularSequence.variant.cigar

Type

string

Cardinality

0 - 1

Definition

Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.variant.variantPointer

Id

MolecularSequence.variant.variantPointer

Type

Reference

Cardinality

0 - 1

Definition

A pointer to an Observation containing variant 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")

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.variant.variantPointer.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).

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

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.observedSeq

Id

MolecularSequence.observedSeq

Type

string

Cardinality

0 - 1

Definition

Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality

Id

MolecularSequence.quality

Type

BackboneElement

Cardinality

0 - *

Definition

An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.type

Id

MolecularSequence.quality.type

Type

code

Cardinality

1 - 1

Definition

INDEL / SNP / Undefined variant.

Comment

Binding

Strength

required

Description

Type for quality report.

ValueSet

http://hl7.org/fhir/ValueSet/quality-type|4.0.1

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.standardSequence

Id

MolecularSequence.quality.standardSequence

Type

CodeableConcept

Cardinality

0 - 1

Definition

Gold standard sequence used for comparing against.

Comment

Binding

Strength

example

Description

Reference identifier of the sequence that used to mark the quality of tested samples.

ValueSet

http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence

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.quality.start

Id

MolecularSequence.quality.start

Type

integer

Cardinality

0 - 1

Definition

Start position of the 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.quality.end

Id

MolecularSequence.quality.end

Type

integer

Cardinality

0 - 1

Definition

End position of the 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.quality.score

Id

MolecularSequence.quality.score

Type

Quantity

Cardinality

0 - 1

Definition

The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

value

decimal

Numerical value (with implicit precision)

comparator

code

< | <= | >= | > - 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.quality.method

Id

MolecularSequence.quality.method

Type

CodeableConcept

Cardinality

0 - 1

Definition

Which method is used to get sequence quality.

Comment

Binding

Strength

example

Description

The method used to evaluate the numerical quality of the observed sequence.

ValueSet

http://hl7.org/fhir/ValueSet/sequence-quality-method

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.quality.truthTP

Id

MolecularSequence.quality.truthTP

Type

decimal

Cardinality

0 - 1

Definition

True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.queryTP

Id

MolecularSequence.quality.queryTP

Type

decimal

Cardinality

0 - 1

Definition

True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.truthFN

Id

MolecularSequence.quality.truthFN

Type

decimal

Cardinality

0 - 1

Definition

False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.queryFP

Id

MolecularSequence.quality.queryFP

Type

decimal

Cardinality

0 - 1

Definition

False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.gtFP

Id

MolecularSequence.quality.gtFP

Type

decimal

Cardinality

0 - 1

Definition

The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.precision

Id

MolecularSequence.quality.precision

Type

decimal

Cardinality

0 - 1

Definition

QUERY.TP / (QUERY.TP + QUERY.FP).

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.recall

Id

MolecularSequence.quality.recall

Type

decimal

Cardinality

0 - 1

Definition

TRUTH.TP / (TRUTH.TP + TRUTH.FN).

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.fScore

Id

MolecularSequence.quality.fScore

Type

decimal

Cardinality

0 - 1

Definition

Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.roc

Id

MolecularSequence.quality.roc

Type

BackboneElement

Cardinality

0 - 1

Definition

Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.roc.score

Id

MolecularSequence.quality.roc.score

Type

integer

Cardinality

0 - *

Definition

Invidual data point representing the GQ (genotype quality) score threshold.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.roc.numTP

Id

MolecularSequence.quality.roc.numTP

Type

integer

Cardinality

0 - *

Definition

The number of true positives if the GQ score threshold was set to "score" field value.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.roc.numFP

Id

MolecularSequence.quality.roc.numFP

Type

integer

Cardinality

0 - *

Definition

The number of false positives if the GQ score threshold was set to "score" field value.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.roc.numFN

Id

MolecularSequence.quality.roc.numFN

Type

integer

Cardinality

0 - *

Definition

The number of false negatives if the GQ score threshold was set to "score" field value.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.roc.precision

Id

MolecularSequence.quality.roc.precision

Type

decimal

Cardinality

0 - *

Definition

Calculated precision if the GQ score threshold was set to "score" field value.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.roc.sensitivity

Id

MolecularSequence.quality.roc.sensitivity

Type

decimal

Cardinality

0 - *

Definition

Calculated sensitivity if the GQ score threshold was set to "score" field value.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.quality.roc.fMeasure

Id

MolecularSequence.quality.roc.fMeasure

Type

decimal

Cardinality

0 - *

Definition

Calculated fScore if the GQ score threshold was set to "score" field value.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.readCoverage

Id

MolecularSequence.readCoverage

Type

integer

Cardinality

0 - 1

Definition

Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.repository

Id

MolecularSequence.repository

Type

BackboneElement

Cardinality

0 - *

Definition

Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.repository.type

Id

MolecularSequence.repository.type

Type

code

Cardinality

1 - 1

Definition

Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.

Comment

Binding

Strength

required

Description

Type for access of external URI.

ValueSet

http://hl7.org/fhir/ValueSet/repository-type|4.0.1

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.repository.url

Id

MolecularSequence.repository.url

Type

uri

Cardinality

0 - 1

Definition

URI of an external repository which contains further details about the genetics data.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.repository.name

Id

MolecularSequence.repository.name

Type

string

Cardinality

0 - 1

Definition

URI of an external repository which contains further details about the genetics data.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.repository.datasetId

Id

MolecularSequence.repository.datasetId

Type

string

Cardinality

0 - 1

Definition

Id of the variant in this external repository. The server will understand how to use this id to call for more info about datasets in external repository.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.repository.variantsetId

Id

MolecularSequence.repository.variantsetId

Type

string

Cardinality

0 - 1

Definition

Id of the variantset in this external repository. The server will understand how to use this id to call for more info about variantsets in external repository.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.repository.readsetId

Id

MolecularSequence.repository.readsetId

Type

string

Cardinality

0 - 1

Definition

Id of the read in this external repository.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.pointer

Id

MolecularSequence.pointer

Type

Reference

Cardinality

0 - *

Definition

Pointer to next atomic sequence which at most contains one variant.

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")

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.pointer.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).

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

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")

identifier

Identifier

Logical reference, when literal reference is not known

Path

MolecularSequence.pointer.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).

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

display

string

Text alternative for the resource

display

string

Text alternative for the resource

Path

MolecularSequence.structureVariant

Id

MolecularSequence.structureVariant

Type

BackboneElement

Cardinality

0 - *

Definition

Information about chromosome structure variation.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.structureVariant.variantType

Id

MolecularSequence.structureVariant.variantType

Type

CodeableConcept

Cardinality

0 - 1

Definition

Information about chromosome structure variation DNA change type.

Comment

Binding

Strength

required

Description

DNA change type.

ValueSet

http://loinc.org/vs/LL379-9|4.0.1

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.structureVariant.exact

Id

MolecularSequence.structureVariant.exact

Type

boolean

Cardinality

0 - 1

Definition

Used to indicate if the outer and inner start-end values have the same meaning.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.structureVariant.length

Id

MolecularSequence.structureVariant.length

Type

integer

Cardinality

0 - 1

Definition

Length of the variant chromosome.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.structureVariant.outer

Id

MolecularSequence.structureVariant.outer

Type

BackboneElement

Cardinality

0 - 1

Definition

Structural variant outer.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.structureVariant.outer.start

Id

MolecularSequence.structureVariant.outer.start

Type

integer

Cardinality

0 - 1

Definition

Structural variant outer start. 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.structureVariant.outer.end

Id

MolecularSequence.structureVariant.outer.end

Type

integer

Cardinality

0 - 1

Definition

Structural variant outer end. 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.structureVariant.inner

Id

MolecularSequence.structureVariant.inner

Type

BackboneElement

Cardinality

0 - 1

Definition

Structural variant inner.

Comment

Constraint

ele-1 [error]

All FHIR elements must have a @value or children

Path

MolecularSequence.structureVariant.inner.start

Id

MolecularSequence.structureVariant.inner.start

Type

integer

Cardinality

0 - 1

Definition

Structural variant inner start. 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.structureVariant.inner.end

Id

MolecularSequence.structureVariant.inner.end

Type

integer

Cardinality

0 - 1

Definition

Structural variant inner end. 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