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" NCBISequenceSource <|-- GenomeCoordinatesSource click NCBISequenceSource href "../NCBISequenceSource" GenomeCoordinatesSource : assembly_accession GenomeCoordinatesSource : coordinates GenomeCoordinatesSource : database_id GenomeCoordinatesSource : gene_id GenomeCoordinatesSource : id GenomeCoordinatesSource : input GenomeCoordinatesSource --> "*" SourceInput : input click SourceInput href "../SourceInput" GenomeCoordinatesSource : locus_tag GenomeCoordinatesSource : output_name GenomeCoordinatesSource : repository_id GenomeCoordinatesSource : type

Inheritance

NamedThing
- Source
  - RepositoryIdSource
    - NCBISequenceSource
      - GenomeCoordinatesSource

Slots

Name	Cardinality and Range	Description	Inheritance
assembly_accession	0..1 String	The accession of the assembly	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
coordinates	0..1 SimpleSequenceLocation	If provided, represents the location of a subsequence within the sequence ide...	NCBISequenceSource
repository_id	1 String	The sequence accession (e	RepositoryIdSource
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: NCBISequenceSource
slot_usage:
  location:
    name: location
    required: true
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
  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

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: NCBISequenceSource
slot_usage:
  location:
    name: location
    required: true
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
  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
  coordinates:
    name: coordinates
    description: If provided, represents the location of a subsequence within the
      sequence identified by the sequence accession.
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    alias: coordinates
    owner: GenomeCoordinatesSource
    domain_of:
    - UploadedFileSource
    - NCBISequenceSource
    range: simple_sequence_location
    required: false
  repository_id:
    name: repository_id
    description: The sequence accession (e.g. X60065.1)
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: repository_id
    owner: GenomeCoordinatesSource
    domain_of:
    - RepositoryIdSource
    range: string
    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