CanonicalAllele

Scope and Usage

A CanonicalAllele is a reference to a sequence change, independent of any particular representation relative to a ReferenceSequence. Since alleles are represented as a change (or no change) relative to a ReferenceSequence, a CanonicalAllele is composed of potentially multiple such representations (ContextualAlleles) that correspond to the same CanonicalAllele. One ContextualAllele is selected as the preferred representation of a CanonicalAllele

Resource Model

Related Conceptual Entities: CanonicalAllele, SimpleCanonicalAllele, SimpleNucleotideCanonicalAllele, SimpleAminoAcidCanonicalAllele, ComplexCanonicalAllele, ComplexNucleotideCanonicalAllele, ComplexAminoAcidCanonicalAllele

Notes

Definitions & Bindings

CanonicalAllele

Definition

The canonical representation of a set of equivalent sequence variants.

Control

1..1

CanonicalAllele.id

Definition

The logical identifier assigned by the source storage system.

Control

1..1

Type

Id

CanonicalAllele.version

Definition

The publicly stable version of the CanonicalAllele instance represented by the source system.

Control

0..1

Type

string

Requirements

Version changes may occur due to changes in the set of relatedContextualAlleles.

CanonicalAllele.meta

Definition

The metadata about a resource. This is content in the resource that is maintained by the infrastructure. Changes to the content may not always be associated with version changes to the resource.

Control

0..1

Type

Meta

Requirements

Version changes may occur due to changes in the set of relatedContextualAlleles.

CanonicalAllele.identifier

Definition

Business identifier(s) assigned by external authorities that represents the equivalent CanonicalAllele instance represented by the source system.

Control

0..*

Type

Identifier

CanonicalAllele.relatedIdentifier

Definition

Business identifier(s) assigned by external authorities that are not exactly representative of the CanonicalAllele instance, but provide a noteworthy alternative representation.

Control

0..*

Type

Identifier

CanonicalAllele.active

Definition

Is the CanonicalAllele active, or is it invalid or superceded by a different CanonicalAllele.

Control

0..1

Type

boolean

Requirements

The replacement property MUST contain one or more items if this is true, otherwise replacement MUST be empty.

CanonicalAllele.replacement

Definition

The CanonicalAllele to use instead in case it is found to describe the same allele as another CanonicalAllele

Control

0..*

Type

Replacement

Requirements

CanonicalAllele.canonicalAlleleType

Definition

TODO

Control

1..1

Binding

CanonicalAlleleType

Type

code

Requirements

CanonicalAllele.complexity

Definition

Is the CanonicalAllele represented by one ContextualAllele, or is it a composition of multiple CanonicalAlleles?

Control

1..1

Binding

CanonicalAlleleComplexity

Type

code

Requirements

If this allele is simple, then it can contain one or more ContextualAlleles in the relatedContextualAllele property. This value is immutable.

CanonicalAllele.nested

Definition

The set of CanonicalAlleles that compose this ComplexCanonicalAllele. The children CanonicalAlleles of a complex CanonicalAllele instance.

Control

0..*

Type

CanonicalAllele

Requirements

This is closely related to the CanonicalAllele.complexity and CanonicalAllele.relatedContextualAllele fields:

• if complexity is simple, then this list MUST be empty
• if complexity is complex, then this list MUST contain 2 or more CanonicalAlleles (each with complexity simple) AND relatedContextualAllele MUST be empty.

Notes: - the cardinality of this property is actually 0,2..* (i.e. anything but one) - currently, the idea of nesting complex CanonicalAlleles within other complex CanonicalAlleles is not supported.

CanonicalAllele.composite

Definition

The composite, parent or complex CanonicalAllele instance(s) that this Canonical Allele is part of.

Control

0..*

Type

CanonicalAllele

Requirements

• If this CanonicalAllele participates in one or more complex CanonicalAlleles then the complexity must be simple.
• It is not requirement to pass the association to the set of complex CanonicalAlleles unless it is useful to the receiving service.

CanonicalAllele.replacement

Definition

The CanonicalAllele instance(s) that subsequently replaced this CanonicalAllele.

Control

0..*

Binding

CanonicalAllele.Replacement

Requirements

If one or more replacement references exist then this CanonicalAllele should be active equal to false or inactive.

CanonicalAllele.replacement.replacementType

Definition

Code for the type of replacement that occurs when CanonicalAlleles are merged or split after being published.

Control

1..1

Binding

CanonicalAlleleReplacementType

Type

code

CanonicalAllele.replacement.split

Definition

A boolean indicating whether or not the target was replaced by more than one CanonicalAllele.

Control

0..1

Type

boolean

Requirements

It may be possible to conceptually split a pre-existing CanonicalAllele and replace it with more than one new CanonicalAllele, without actually creating all of the new replacements. This indicator provides a definitive value to represent whether the target represented more than one CanonicalAllele to begin with.

CanonicalAllele.replacement.target

Definition

A reference to either the CanonicalAllele that replaces or is replaced-by the primary CanonicalAllele with which it is associated.

Control

1..1

Type

CanonicalAllele

CanonicalAllele.relatedContextualAllele

Definition

The set of ContextualAlleles that are canonically equivalent.

Control

0..*

Requirements

If this set changes over time then the CanonicalAllele.version should be incremented to allow external references to maintain a stable representation of their original reference.

CanonicalAllele.relatedContextualAllele.contextualAllele

Definition

A reference to a ContextualAllele that is part of the set of CanonicalAllele.relatedContextualAlleles.

Control

1..1

Type

ContextualAllele

CanonicalAllele.relatedContextualAllele.preferred

Definition

An indicator as to whether this CanonicalAllele.relatedContextualAllele is the preferred representation for the CanonicalAllele.

Control

0..1

Type

boolean

Requirements

• The current design provides this indicator as a basic means to producing a simplified human-readable representation of the CanonicalAllele by allowing the source system to determine which related ContextualAllele is preferred over all the others.
• One and only one of the relatedContextualAlleles must be set as the preferred one. If a new related ContextualAllele is added or an existing one updated as preferred it would automatically override the prior related ContextualAllele that was set as preferred.

Schema

schema: CanonicalAllele.xsd

Examples