Scope and Usage
All alleles are described relative to a ReferenceSequence by way of the ContextualAllele.ReferenceCoordinate see ContextualAllele. Both the ContextualAllele position (or coordinate) and sequence at that postion are relative to the ReferenceSequence.
The current version of the model was based on four specific types of conceptual reference sequences; ChromosomeReferenceSequence, GeneReferenceSequence, TranscriptReferenceSequence and AminoAcidReferenceSequence.
Resource Model
Related Resources: ContextualAllele & Gene
Notes
- This version of the ReferenceSequence resource only considers the related reference sequence associations between amino acid and transcript reference sequences. This has constrained the scope of codes in the value set for the ReferenceSequence.related.relatedType attribute.
Definitions & Bindings
ReferenceSequence
- Definition
Stable, reliable, public consensus sequence of a portion of the genome against which alleles are aligned and described.
- Control
- 1..1
- Requirements
For every ContextualAllele.ReferenceCoordinate there must be a corresponding reference sequence.
ReferenceSequence.identifier
- Definition
The versioned accession that can be used to uniquely identify the sequence in a public database. All users of reference sequences SHALL be sure of the identity of the reference sequence. Often only one identifier will be used, but if more then one reference accession is used it's required to map the same sequence.
- Control
- 0..*
- Type
Identifier
- Requirements
For
ReferenceSequence, an identifier is valid unless the accession is withdrawn. If a new version of a sequence is created, it will be given a different versioned accession, and therefore a different identifier. In this case, the previous identifier is still valid: it can still be used to retrieve the given sequence, even if that sequence is no longer the most recent sequence associated with a given entity.
ReferenceSequence.referenceSequenceType
- Definition
The type of reference sequence.
- Control
- 1..1
- Binding
ReferenceSequenceType: reference-sequence-type (Codes identifying kinds of reference sequences)
- Type
code
- Requirements
Currently, the supported types are transcript, gene, chromosome and amino_acid (see Binding).
ReferenceSequence.chromosome
- Definition
The chromosome to which the reference sequence is naturally bound.
- Control
- 0..1
- Binding
ReferenceSequenceChromosome: reference-sequence-chromosome (Codes identifying human chromosomes.)
- Type
code
- Requirements
This should be provided when the sequence represents a 'chromosome'.
ReferenceSequence.cdsStart
- Definition
The offset of the start of the coding region from the start of the reference sequence. This should be provided when the sequence represents a 'transcript'.
NOTE: Unlike reference coordinates, this is a 1-based index representing the position of the nucleotide that starts the coding region.
- Control
- 0..1
- Type
integer
ReferenceSequence.cdsEnd
- Definition
The offset of the end of the coding region from the start of the reference sequence. This should be provided when the sequence represents a 'transcript'.
NOTE: Unlike reference coordinates, this is a 1-based index representing the position of the nucleotide that ends the coding region.
- Control
- 0..1
- Type
integer
ReferenceSequence.gene
- Definition
Identifies the gene related to a 'gene' or 'transcript' reference sequence.
- Control
- 0..1
- Type
Resource(Gene)
ReferenceSequence.referenceGenome
- Definition
The genome build in which the chromosomal reference sequence is referenced.
- Control
- 0..1
- Type
CodeableConcept
- Requirements
The current version of the model does not provide for the same version of a chromosomal reference sequence to be associated with more than one reference genome build.
ReferenceSequence.related
- Definition
The relationship between a different reference sequence to provide additional context.
- Control
- 0..1
- Requirements
The current version of the resource only defines relationship type terminology bindings to support the relationship between transcript and amino acid reference sequences.
ReferenceSequence.related.relatedType
- Definition
The type or relationship between an amino acid and transcript or vice versa.
- Control
- 0..1
- Binding
ReferenceSequenceRelationshipType: reference-sequence-relationship-type (Codes describing the relationships between ReferenceSequences)
- Type
code
ReferenceSequence.related.target
- Definition
The target reference sequence for the specified related.relatedType.
- Control
- 0..1
- Type
Resource(ReferenceSequence)
Schema
schema: ReferenceSequence.xsd