Class: GenomicLocation

information on the genomic location of specific sequence

URI: portable_microhaplotype_object:GenomicLocation

classDiagram class GenomicLocation click GenomicLocation href "../GenomicLocation" GenomicLocation : chrom GenomicLocation : end GenomicLocation : ref_seq GenomicLocation : start GenomicLocation : strand

Slots

Name	Cardinality and Range	Description	Inheritance
chrom	1 String	the chromosome name	direct
start	1 Integer	the start of the location, 0-based positioning	direct
end	1 Integer	the end of the location, 0-based positioning	direct
strand	0..1 String	which strand the location is, either + for plus strand or - for negative stra...	direct
ref_seq	0..1 String	the reference sequence of this genomic location	direct

Usages

used by	used in	type	used
TargetInfo	insert_location	range	GenomicLocation
PrimerInfo	location	range	GenomicLocation

Identifier and Mapping Information

Schema Source

from schema: https://plasmogenepi.github.io/portable-microhaplotype-object

Mappings

Mapping Type	Mapped Value
self	portable_microhaplotype_object:GenomicLocation
native	portable_microhaplotype_object:GenomicLocation

LinkML Source

Direct

name: GenomicLocation
description: information on the genomic location of specific sequence
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
attributes:
  chrom:
    name: chrom
    description: the chromosome name
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - GenomicLocation
    range: string
    required: true
    pattern: ^[A-z-._0-9]$
  start:
    name: start
    description: the start of the location, 0-based positioning
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - GenomicLocation
    range: integer
    required: true
    pattern: ^[0-9]$
  end:
    name: end
    description: the end of the location, 0-based positioning
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - GenomicLocation
    range: integer
    required: true
    pattern: ^[0-9]$
  strand:
    name: strand
    description: which strand the location is, either + for plus strand or - for negative
      strand
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - GenomicLocation
    range: string
    required: false
    pattern: r'[+-]'
  ref_seq:
    name: ref_seq
    description: 'the reference sequence of this genomic location '
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - GenomicLocation
    range: string
    required: false
    pattern: ^[A-z-]$

Induced

name: GenomicLocation
description: information on the genomic location of specific sequence
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
attributes:
  chrom:
    name: chrom
    description: the chromosome name
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: chrom
    owner: GenomicLocation
    domain_of:
    - GenomicLocation
    range: string
    required: true
    pattern: ^[A-z-._0-9]$
  start:
    name: start
    description: the start of the location, 0-based positioning
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: start
    owner: GenomicLocation
    domain_of:
    - GenomicLocation
    range: integer
    required: true
    pattern: ^[0-9]$
  end:
    name: end
    description: the end of the location, 0-based positioning
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: end
    owner: GenomicLocation
    domain_of:
    - GenomicLocation
    range: integer
    required: true
    pattern: ^[0-9]$
  strand:
    name: strand
    description: which strand the location is, either + for plus strand or - for negative
      strand
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: strand
    owner: GenomicLocation
    domain_of:
    - GenomicLocation
    range: string
    required: false
    pattern: r'[+-]'
  ref_seq:
    name: ref_seq
    description: 'the reference sequence of this genomic location '
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: ref_seq
    owner: GenomicLocation
    domain_of:
    - GenomicLocation
    range: string
    required: false
    pattern: ^[A-z-]$