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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 --> "*" Sequence : input click Sequence href "../Sequence" GenomeCoordinatesSource : locus_tag GenomeCoordinatesSource : output GenomeCoordinatesSource --> "0..1" Sequence : output click Sequence href "../Sequence" 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
input *
Sequence		 The sequences that are an input to this source Source
output 0..1
Sequence		 Identifier of the sequence that is the output of this source Source
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
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
  input:
    name: input
    description: The sequences that are an input 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: Sequence
    required: false
    multivalued: true
    inlined_as_list: false
  output:
    name: output
    description: Identifier of the sequence that is the output of this source.
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    slot_uri: schema:result
    alias: output
    owner: GenomeCoordinatesSource
    domain_of:
    - Source
    range: Sequence
    required: false
    inlined: false
  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
    - 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
  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