Class: SequenceAlteration

A representation of a sequence alteration (so:0001059).

 classDiagram
    class SequenceAlteration
    click SequenceAlteration href "../SequenceAlteration"
      SequenceAlteration : has_alternate_allele




    SequenceAlteration --> "0..1" AlternateAllele : has_alternate_allele
    click AlternateAllele href "../AlternateAllele"


      SequenceAlteration : has_identifier




    SequenceAlteration --> "1" VariantIdentifier : has_identifier
    click VariantIdentifier href "../VariantIdentifier"


      SequenceAlteration : has_location




    SequenceAlteration --> "0..1" VariationSite : has_location
    click VariationSite href "../VariationSite"


      SequenceAlteration : has_reference_allele




    SequenceAlteration --> "0..1" ReferenceAllele : has_reference_allele
    click ReferenceAllele href "../ReferenceAllele"


      SequenceAlteration : has_zygosity




    SequenceAlteration --> "0..1" ZygosityType : has_zygosity
    click ZygosityType href "../ZygosityType"

Slots

Name	Cardinality and Range	Description	Inheritance
has_identifier	1 VariantIdentifier	A unique identifier for the sequence alteration	direct
has_reference_allele	0..1 ReferenceAllele	Links the sequence alteration to its reference allele	direct
has_alternate_allele	0..1 AlternateAllele	Links the sequence alteration to its alternate allele	direct
has_location	0..1 VariationSite	Links the sequence alteration to its location	direct
has_zygosity	0..1 ZygosityType	The zygosity of the sequence alteration	direct

Usages

used by	used in	type	used
Container	variantcatalog	range	SequenceAlteration

Identifier and Mapping Information

Schema Source

from schema: https://ican.fr/

Mappings

Mapping Type	Mapped Value
self	so:0001059
native	ican:SequenceAlteration
exact	geno:0000660

LinkML Source

Direct

name: SequenceAlteration
description: A representation of a sequence alteration (so:0001059).
from_schema: https://ican.fr/
exact_mappings:
- geno:0000660
attributes:
  has_identifier:
    name: has_identifier
    description: A unique identifier for the sequence alteration.
    from_schema: https://ican.fr/
    rank: 1000
    slot_uri: sio:000674
    domain_of:
    - SequenceAlteration
    range: VariantIdentifier
    required: true
  has_reference_allele:
    name: has_reference_allele
    description: Links the sequence alteration to its reference allele.
    from_schema: https://ican.fr/
    rank: 1000
    slot_uri: geno:0000385
    domain_of:
    - SequenceAlteration
    range: ReferenceAllele
    required: false
  has_alternate_allele:
    name: has_alternate_allele
    description: Links the sequence alteration to its alternate allele.
    from_schema: https://ican.fr/
    rank: 1000
    slot_uri: geno:0000382
    domain_of:
    - SequenceAlteration
    range: AlternateAllele
    required: false
  has_location:
    name: has_location
    description: Links the sequence alteration to its location.
    from_schema: https://ican.fr/
    rank: 1000
    slot_uri: faldo:location
    domain_of:
    - SequenceAlteration
    range: VariationSite
    required: false
  has_zygosity:
    name: has_zygosity
    description: The zygosity of the sequence alteration.
    from_schema: https://ican.fr/
    rank: 1000
    slot_uri: geno:0000139
    domain_of:
    - SequenceAlteration
    range: ZygosityType
    required: false
class_uri: so:0001059

Induced

name: SequenceAlteration
description: A representation of a sequence alteration (so:0001059).
from_schema: https://ican.fr/
exact_mappings:
- geno:0000660
attributes:
  has_identifier:
    name: has_identifier
    description: A unique identifier for the sequence alteration.
    from_schema: https://ican.fr/
    rank: 1000
    slot_uri: sio:000674
    alias: has_identifier
    owner: SequenceAlteration
    domain_of:
    - SequenceAlteration
    range: VariantIdentifier
    required: true
  has_reference_allele:
    name: has_reference_allele
    description: Links the sequence alteration to its reference allele.
    from_schema: https://ican.fr/
    rank: 1000
    slot_uri: geno:0000385
    alias: has_reference_allele
    owner: SequenceAlteration
    domain_of:
    - SequenceAlteration
    range: ReferenceAllele
    required: false
  has_alternate_allele:
    name: has_alternate_allele
    description: Links the sequence alteration to its alternate allele.
    from_schema: https://ican.fr/
    rank: 1000
    slot_uri: geno:0000382
    alias: has_alternate_allele
    owner: SequenceAlteration
    domain_of:
    - SequenceAlteration
    range: AlternateAllele
    required: false
  has_location:
    name: has_location
    description: Links the sequence alteration to its location.
    from_schema: https://ican.fr/
    rank: 1000
    slot_uri: faldo:location
    alias: has_location
    owner: SequenceAlteration
    domain_of:
    - SequenceAlteration
    range: VariationSite
    required: false
  has_zygosity:
    name: has_zygosity
    description: The zygosity of the sequence alteration.
    from_schema: https://ican.fr/
    rank: 1000
    slot_uri: geno:0000139
    alias: has_zygosity
    owner: SequenceAlteration
    domain_of:
    - SequenceAlteration
    range: ZygosityType
    required: false
class_uri: so:0001059