Class: Genome

Genome entity in the ENIGMA data model

classDiagram class Genome click Genome href "../Genome/" Genome : genome_id Genome : genome_link Genome : genome_n_contigs Genome : genome_n_features Genome : genome_name Genome : genome_strain Genome --> "0..1" Strain : genome_strain click Strain href "../Strain/"

Slots

Name	Cardinality and Range	Description	Inheritance
genome_id	1 String	id field for Genome	direct
genome_name	1 String	name field for Genome	direct
genome_strain	0..1 Strain	strain field for Genome	direct
genome_n_contigs	1 Count	n_contigs field for Genome	direct
genome_n_features	1 Count	n_features field for Genome	direct
genome_link	1 Link	link field for Genome	direct

Usages

used by	used in	type	used
Strain	strain_genome	range	Genome
Gene	gene_genome	range	Genome
TnSeqLibrary	tnseq_library_genome	range	Genome
DubSeqLibrary	dubseq_library_genome	range	Genome

Identifier and Mapping Information

Annotations

property	value
term	DA:0000039
used_for_provenance	True
process_types	['PROCESS:0000034', 'PROCESS:0000045']
process_inputs	[['Assembly'], ['Bin']]

Schema Source

from schema: https://w3id.org/enigma/enigma-cdm

Mappings

Mapping Type	Mapped Value
self	enigma:Genome
native	enigma:Genome

LinkML Source

Direct

name: Genome
annotations:
  term:
    tag: term
    value: DA:0000039
  used_for_provenance:
    tag: used_for_provenance
    value: true
  process_types:
    tag: process_types
    value:
    - PROCESS:0000034
    - PROCESS:0000045
  process_inputs:
    tag: process_inputs
    value:
    - - Assembly
    - - Bin
description: Genome entity in the ENIGMA data model
from_schema: https://w3id.org/enigma/enigma-cdm
slots:
- genome_id
- genome_name
- genome_strain
- genome_n_contigs
- genome_n_features
- genome_link

Induced

name: Genome
annotations:
  term:
    tag: term
    value: DA:0000039
  used_for_provenance:
    tag: used_for_provenance
    value: true
  process_types:
    tag: process_types
    value:
    - PROCESS:0000034
    - PROCESS:0000045
  process_inputs:
    tag: process_inputs
    value:
    - - Assembly
    - - Bin
description: Genome entity in the ENIGMA data model
from_schema: https://w3id.org/enigma/enigma-cdm
attributes:
  genome_id:
    name: genome_id
    annotations:
      type_term:
        tag: type_term
        value: ME:0000274
      microtype:
        tag: microtype
        value: ME:0000274
      microtype_data_type:
        tag: microtype_data_type
        value: object_ref
    description: id field for Genome
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    identifier: true
    alias: genome_id
    owner: Genome
    domain_of:
    - Genome
    range: string
    required: true
  genome_name:
    name: genome_name
    annotations:
      unique:
        tag: unique
        value: true
      type_term:
        tag: type_term
        value: ME:0000246
      microtype:
        tag: microtype
        value: ME:0000246
      microtype_data_type:
        tag: microtype_data_type
        value: object_ref
    description: name field for Genome
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: genome_name
    owner: Genome
    domain_of:
    - Genome
    range: string
    required: true
  genome_strain:
    name: genome_strain
    annotations:
      foreign_key:
        tag: foreign_key
        value: Strain.name
      type_term:
        tag: type_term
        value: ME:0000044
      microtype:
        tag: microtype
        value: ME:0000044
      microtype_data_type:
        tag: microtype_data_type
        value: object_ref
    description: strain field for Genome
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: genome_strain
    owner: Genome
    domain_of:
    - Genome
    range: Strain
  genome_n_contigs:
    name: genome_n_contigs
    annotations:
      units_term:
        tag: units_term
        value: UO:0000189
      type_term:
        tag: type_term
        value: ME:0000126
      microtype:
        tag: microtype
        value: ME:0000126
      microtype_data_type:
        tag: microtype_data_type
        value: int
    description: n_contigs field for Genome
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: genome_n_contigs
    owner: Genome
    domain_of:
    - Genome
    range: Count
    required: true
  genome_n_features:
    name: genome_n_features
    annotations:
      units_term:
        tag: units_term
        value: UO:0000189
      type_term:
        tag: type_term
        value: ME:0000126
      microtype:
        tag: microtype
        value: ME:0000126
      microtype_data_type:
        tag: microtype_data_type
        value: int
    description: n_features field for Genome
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: genome_n_features
    owner: Genome
    domain_of:
    - Genome
    range: Count
    required: true
  genome_link:
    name: genome_link
    annotations:
      type_term:
        tag: type_term
        value: ME:0000203
      microtype:
        tag: microtype
        value: ME:0000203
      microtype_data_type:
        tag: microtype_data_type
        value: string
    description: link field for Genome
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: genome_link
    owner: Genome
    domain_of:
    - Genome
    range: Link
    required: true