Class: Sequence

A sequence of nucleotides or amino acids.

classDiagram class Sequence click Sequence href "../Sequence/" Table <|-- Sequence click Table href "../Table/" Sequence : checksum Sequence : entity_id Sequence : length Sequence : sequence_id Sequence : type Sequence --> "0..1" SequenceType : type click SequenceType href "../SequenceType/"

Inheritance

Table
- Sequence

Slots

Name	Cardinality and Range	Description	Inheritance
sequence_id	1 CdmSequenceId	Internal (CDM) unique identifier for a sequence. From the Entity table: entity_id where entity_type == 'Sequence'.	direct
entity_id	1 CdmId	The entity to which this sequence belongs.	direct
type	0..1 SequenceType	The type of the sequence, either "Nucleotide" or "Amino Acid".	direct
length	0..1 Integer	The length of the sequence in base pairs (for nucleotide sequences) or amino acids (for amino acid sequences).	direct
checksum	0..1 String	The checksum of the sequence, used to verify its integrity.	direct

Usages

used by	used in	type	used
Schema	sequences	range	Sequence

Identifier and Mapping Information

Schema Source

from schema: http://kbase.github.io/cdm-schema/linkml/cdm_schema

Mappings

Mapping Type	Mapped Value
self	kb_cdm:Sequence
native	kb_cdm:Sequence

LinkML Source

Direct

name: Sequence
description: A sequence of nucleotides or amino acids.
from_schema: http://kbase.github.io/cdm-schema/linkml/cdm_schema
is_a: Table
slots:
- sequence_id
- entity_id
slot_usage:
  entity_id:
    name: entity_id
    description: The entity to which this sequence belongs.
attributes:
  type:
    name: type
    description: The type of the sequence, either "Nucleotide" or "Amino Acid".
    from_schema: http://kbase.github.io/cdm-schema/linkml/cdm_bioentity
    domain_of:
    - AttributeValue
    - EncodedFeature
    - Feature
    - Sample
    - Sequence
    range: SequenceType
  length:
    name: length
    description: The length of the sequence in base pairs (for nucleotide sequences)
      or amino acids (for amino acid sequences).
    from_schema: http://kbase.github.io/cdm-schema/linkml/cdm_bioentity
    domain_of:
    - Contig
    - Protein
    - Sequence
    range: integer
  checksum:
    name: checksum
    description: The checksum of the sequence, used to verify its integrity.
    from_schema: http://kbase.github.io/cdm-schema/linkml/cdm_bioentity
    rank: 1000
    domain_of:
    - Sequence
    range: string

Induced

name: Sequence
description: A sequence of nucleotides or amino acids.
from_schema: http://kbase.github.io/cdm-schema/linkml/cdm_schema
is_a: Table
slot_usage:
  entity_id:
    name: entity_id
    description: The entity to which this sequence belongs.
attributes:
  type:
    name: type
    description: The type of the sequence, either "Nucleotide" or "Amino Acid".
    from_schema: http://kbase.github.io/cdm-schema/linkml/cdm_bioentity
    alias: type
    owner: Sequence
    domain_of:
    - AttributeValue
    - EncodedFeature
    - Feature
    - Sample
    - Sequence
    range: SequenceType
  length:
    name: length
    description: The length of the sequence in base pairs (for nucleotide sequences)
      or amino acids (for amino acid sequences).
    from_schema: http://kbase.github.io/cdm-schema/linkml/cdm_bioentity
    alias: length
    owner: Sequence
    domain_of:
    - Contig
    - Protein
    - Sequence
    range: integer
  checksum:
    name: checksum
    description: The checksum of the sequence, used to verify its integrity.
    from_schema: http://kbase.github.io/cdm-schema/linkml/cdm_bioentity
    rank: 1000
    alias: checksum
    owner: Sequence
    domain_of:
    - Sequence
    range: string
  sequence_id:
    name: sequence_id
    description: 'Internal (CDM) unique identifier for a sequence.

      From the Entity table: entity_id where entity_type == ''Sequence''.

      '
    from_schema: http://kbase.github.io/cdm-schema/linkml/cdm_schema
    rank: 1000
    alias: sequence_id
    owner: Sequence
    domain_of:
    - Sequence
    range: cdm_sequence_id
    required: true
  entity_id:
    name: entity_id
    description: The entity to which this sequence belongs.
    from_schema: http://kbase.github.io/cdm-schema/linkml/cdm_schema
    rank: 1000
    alias: entity_id
    owner: Sequence
    domain_of:
    - ClusterMember
    - Entity
    - Identifier
    - Name
    - EntityMixin
    - Sequence
    - Association_x_SupportingObject
    range: cdm_id
    required: true