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Class: GenomeInfo

information on a genome

URI: portable_microhaplotype_object:GenomeInfo

classDiagram class GenomeInfo click GenomeInfo href "../GenomeInfo" GenomeInfo : chromosomes GenomeInfo : genome_version GenomeInfo : gff_url GenomeInfo : name GenomeInfo : taxon_id GenomeInfo : url

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 name of the genome direct
genome_version 1
String		 the genome version direct
taxon_id 1..*
Integer		 the NCBI taxonomy number, can be a list of values if it's a genome file that ... direct
url 1
String		 a link to the where this genome file could be downloaded direct
chromosomes *
String		 a list of the chromosomes/contigs found within this genome direct
gff_url 0..1
String		 a link to the where this genome's annotation file could be downloaded direct

Usages

used by used in type used
PortableMicrohaplotypeObject targeted_genomes range GenomeInfo

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: GenomeInfo
description: information on a genome
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
attributes:
  name:
    name: name
    description: name of the genome
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - GenomeInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9]+$
  genome_version:
    name: genome_version
    description: the genome version
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - GenomeInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9]+$
  taxon_id:
    name: taxon_id
    description: the NCBI taxonomy number, can be a list of values if it's a genome
      file that has been created by combining gnomes from different species
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - GenomeInfo
    range: integer
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true
    minimum_value: 0
    pattern: ^[0-9]$
  url:
    name: url
    description: a link to the where this genome file could be downloaded
    examples:
    - value: https://plasmodb.org/common/downloads/release-65/Pfalciparum3D7/fasta/data/PlasmoDB-65_Pfalciparum3D7_Genome.fasta
    - value: ftp://ftp.ensemblgenomes.org/pub/protists/release-62/fasta/plasmodium_falciparum/dna/Plasmodium_falciparum.GCA000002765v3.dna.toplevel.fa.gz
    - value: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - GenomeInfo
    range: string
    required: true
    pattern: ^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$
  chromosomes:
    name: chromosomes
    description: a list of the chromosomes/contigs found within this genome
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - GenomeInfo
    range: string
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
    pattern: ^[A-z-._0-9]+$
  gff_url:
    name: gff_url
    description: a link to the where this genome's annotation file could be downloaded
    examples:
    - value: https://plasmodb.org/common/downloads/release-65/Pfalciparum3D7/fasta/data/PlasmoDB-65_Pfalciparum3D7.gff
    - value: ftp://ftp.ensemblgenomes.org/pub/protists/release-62/gff3/plasmodium_falciparum/Plasmodium_falciparum.GCA000002765v3.62.gff3.gz
    - value: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.gff.gz
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - GenomeInfo
    range: string
    required: false
    pattern: ^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$

Induced

name: GenomeInfo
description: information on a genome
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
attributes:
  name:
    name: name
    description: name of the genome
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: name
    owner: GenomeInfo
    domain_of:
    - GenomeInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9]+$
  genome_version:
    name: genome_version
    description: the genome version
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: genome_version
    owner: GenomeInfo
    domain_of:
    - GenomeInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9]+$
  taxon_id:
    name: taxon_id
    description: the NCBI taxonomy number, can be a list of values if it's a genome
      file that has been created by combining gnomes from different species
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: taxon_id
    owner: GenomeInfo
    domain_of:
    - GenomeInfo
    range: integer
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true
    minimum_value: 0
    pattern: ^[0-9]$
  url:
    name: url
    description: a link to the where this genome file could be downloaded
    examples:
    - value: https://plasmodb.org/common/downloads/release-65/Pfalciparum3D7/fasta/data/PlasmoDB-65_Pfalciparum3D7_Genome.fasta
    - value: ftp://ftp.ensemblgenomes.org/pub/protists/release-62/fasta/plasmodium_falciparum/dna/Plasmodium_falciparum.GCA000002765v3.dna.toplevel.fa.gz
    - value: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: url
    owner: GenomeInfo
    domain_of:
    - GenomeInfo
    range: string
    required: true
    pattern: ^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$
  chromosomes:
    name: chromosomes
    description: a list of the chromosomes/contigs found within this genome
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: chromosomes
    owner: GenomeInfo
    domain_of:
    - GenomeInfo
    range: string
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
    pattern: ^[A-z-._0-9]+$
  gff_url:
    name: gff_url
    description: a link to the where this genome's annotation file could be downloaded
    examples:
    - value: https://plasmodb.org/common/downloads/release-65/Pfalciparum3D7/fasta/data/PlasmoDB-65_Pfalciparum3D7.gff
    - value: ftp://ftp.ensemblgenomes.org/pub/protists/release-62/gff3/plasmodium_falciparum/Plasmodium_falciparum.GCA000002765v3.62.gff3.gz
    - value: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.gff.gz
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: gff_url
    owner: GenomeInfo
    domain_of:
    - GenomeInfo
    range: string
    required: false
    pattern: ^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$