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Class: GenomeCoordinatesSource

Represents the source of a sequence that is identified by genome coordinates, requested from NCBI

URI: opencloning_linkml:GenomeCoordinatesSource

classDiagram class GenomeCoordinatesSource click GenomeCoordinatesSource href "../GenomeCoordinatesSource" Source <|-- GenomeCoordinatesSource click Source href "../Source" GenomeCoordinatesSource : assembly_accession GenomeCoordinatesSource : database_id GenomeCoordinatesSource : end GenomeCoordinatesSource : gene_id GenomeCoordinatesSource : id GenomeCoordinatesSource : input GenomeCoordinatesSource --> "*" SourceInput : input click SourceInput href "../SourceInput" GenomeCoordinatesSource : locus_tag GenomeCoordinatesSource : output_name GenomeCoordinatesSource : sequence_accession GenomeCoordinatesSource : start GenomeCoordinatesSource : strand GenomeCoordinatesSource : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
assembly_accession 0..1
String		 The accession of the assembly direct
sequence_accession 1
String		 The accession of the sequence direct
locus_tag 0..1
String		 The locus tag of the sequence direct
gene_id 0..1
Integer		 The gene id of the sequence direct
start 1
Integer		 The starting coordinate (1-based) of the sequence in the sequence accession direct
end 1
Integer		 The ending coordinate (1-based) of the sequence in the sequence accession direct
strand 1
Integer		 The strand of the sequence in the sequence accession, should be 1 or -1 direct
type 0..1
String		 Designates the class Source
output_name 0..1
String		 Used to specify the name of the output sequence Source
database_id 0..1
Integer		 The id of an entity in a database Source
input *
SourceInput		 The inputs to this source Source
id 1
Integer		 A unique identifier for a thing NamedThing

Identifier and Mapping Information

Schema Source

  • from schema: https://opencloning.github.io/OpenCloning_LinkML

Mappings

Mapping Type Mapped Value
self opencloning_linkml:GenomeCoordinatesSource
native opencloning_linkml:GenomeCoordinatesSource

LinkML Source

Direct

name: GenomeCoordinatesSource
description: Represents the source of a sequence that is identified by genome coordinates,
  requested from NCBI
from_schema: https://opencloning.github.io/OpenCloning_LinkML
is_a: Source
attributes:
  assembly_accession:
    name: assembly_accession
    description: The accession of the assembly
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    domain_of:
    - GenomeCoordinatesSource
    range: string
    required: false
  sequence_accession:
    name: sequence_accession
    description: The accession of the sequence
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    domain_of:
    - GenomeCoordinatesSource
    range: string
    required: true
  locus_tag:
    name: locus_tag
    description: The locus tag of the sequence
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    domain_of:
    - GenomeCoordinatesSource
    range: string
    required: false
  gene_id:
    name: gene_id
    description: The gene id of the sequence
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    domain_of:
    - GenomeCoordinatesSource
    range: integer
    required: false
  start:
    name: start
    description: The starting coordinate (1-based) of the sequence in the sequence
      accession
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    domain_of:
    - GenomeCoordinatesSource
    range: integer
    required: true
  end:
    name: end
    description: The ending coordinate (1-based) of the sequence in the sequence accession
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    domain_of:
    - GenomeCoordinatesSource
    range: integer
    required: true
  strand:
    name: strand
    description: The strand of the sequence in the sequence accession, should be 1
      or -1
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    domain_of:
    - GenomeCoordinatesSource
    - PlannotateAnnotationReport
    range: integer
    required: true

Induced

name: GenomeCoordinatesSource
description: Represents the source of a sequence that is identified by genome coordinates,
  requested from NCBI
from_schema: https://opencloning.github.io/OpenCloning_LinkML
is_a: Source
attributes:
  assembly_accession:
    name: assembly_accession
    description: The accession of the assembly
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: assembly_accession
    owner: GenomeCoordinatesSource
    domain_of:
    - GenomeCoordinatesSource
    range: string
    required: false
  sequence_accession:
    name: sequence_accession
    description: The accession of the sequence
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: sequence_accession
    owner: GenomeCoordinatesSource
    domain_of:
    - GenomeCoordinatesSource
    range: string
    required: true
  locus_tag:
    name: locus_tag
    description: The locus tag of the sequence
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: locus_tag
    owner: GenomeCoordinatesSource
    domain_of:
    - GenomeCoordinatesSource
    range: string
    required: false
  gene_id:
    name: gene_id
    description: The gene id of the sequence
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: gene_id
    owner: GenomeCoordinatesSource
    domain_of:
    - GenomeCoordinatesSource
    range: integer
    required: false
  start:
    name: start
    description: The starting coordinate (1-based) of the sequence in the sequence
      accession
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: start
    owner: GenomeCoordinatesSource
    domain_of:
    - GenomeCoordinatesSource
    range: integer
    required: true
  end:
    name: end
    description: The ending coordinate (1-based) of the sequence in the sequence accession
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: end
    owner: GenomeCoordinatesSource
    domain_of:
    - GenomeCoordinatesSource
    range: integer
    required: true
  strand:
    name: strand
    description: The strand of the sequence in the sequence accession, should be 1
      or -1
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: strand
    owner: GenomeCoordinatesSource
    domain_of:
    - GenomeCoordinatesSource
    - PlannotateAnnotationReport
    range: integer
    required: true
  type:
    name: type
    description: Designates the class
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    designates_type: true
    alias: type
    owner: GenomeCoordinatesSource
    domain_of:
    - Sequence
    - SourceInput
    - Source
    - CollectionOptionInfo
    - AnnotationReport
    - AssociatedFile
    range: string
  output_name:
    name: output_name
    description: Used to specify the name of the output sequence
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: output_name
    owner: GenomeCoordinatesSource
    domain_of:
    - Source
    range: string
    required: false
  database_id:
    name: database_id
    description: The id of an entity in a database
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    slot_uri: schema:identifier
    alias: database_id
    owner: GenomeCoordinatesSource
    domain_of:
    - Primer
    - Source
    - DatabaseSource
    range: integer
    required: false
  input:
    name: input
    description: The inputs to this source. If the source represents external import
      of a sequence, it's empty.
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    slot_uri: schema:object
    alias: input
    owner: GenomeCoordinatesSource
    domain_of:
    - Source
    range: SourceInput
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
  id:
    name: id
    description: A unique identifier for a thing
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    slot_uri: schema:identifier
    identifier: true
    alias: id
    owner: GenomeCoordinatesSource
    domain_of:
    - NamedThing
    - Sequence
    range: integer
    required: true