Class: Gene

Gene entity in the ENIGMA data model

classDiagram class Gene click Gene href "../Gene/" Gene : gene_aliases Gene : gene_contig_number Gene : gene_function Gene : gene_gene_id Gene : gene_genome Gene : gene_id Gene : gene_start Gene : gene_stop Gene : gene_strand

Slots

Name	Cardinality and Range	Description	Inheritance
gene_id	1 String	id field for Gene	direct
gene_gene_id	1 String	gene_id field for Gene	direct
gene_genome	1 String	genome field for Gene	direct
gene_aliases	* String	aliases field for Gene	direct
gene_contig_number	1 Integer	contig_number field for Gene	direct
gene_strand	1 String	strand field for Gene	direct
gene_start	1 Integer	start field for Gene	direct
gene_stop	1 Integer	stop field for Gene	direct
gene_function	0..1 String	function field for Gene	direct

Identifier and Mapping Information

Annotations

property	value
term	DA:0000040
process_types	['PROCESS:0000034']
process_inputs	[['Assembly']]

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Gene
annotations:
  term:
    tag: term
    value: DA:0000040
  process_types:
    tag: process_types
    value:
    - PROCESS:0000034
  process_inputs:
    tag: process_inputs
    value:
    - - Assembly
description: Gene entity in the ENIGMA data model
from_schema: https://w3id.org/enigma/enigma-cdm
slots:
- gene_id
- gene_gene_id
- gene_genome
- gene_aliases
- gene_contig_number
- gene_strand
- gene_start
- gene_stop
- gene_function

Induced

name: Gene
annotations:
  term:
    tag: term
    value: DA:0000040
  process_types:
    tag: process_types
    value:
    - PROCESS:0000034
  process_inputs:
    tag: process_inputs
    value:
    - - Assembly
description: Gene entity in the ENIGMA data model
from_schema: https://w3id.org/enigma/enigma-cdm
attributes:
  gene_id:
    name: gene_id
    annotations:
      type_term:
        tag: type_term
        value: ME:0000275
    description: id field for Gene
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    identifier: true
    alias: gene_id
    owner: Gene
    domain_of:
    - Gene
    range: string
    required: true
  gene_gene_id:
    name: gene_gene_id
    annotations:
      unique:
        tag: unique
        value: true
      type_term:
        tag: type_term
        value: ME:0000224
    description: gene_id field for Gene
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: gene_gene_id
    owner: Gene
    domain_of:
    - Gene
    range: string
    required: true
  gene_genome:
    name: gene_genome
    annotations:
      foreign_key:
        tag: foreign_key
        value: Genome.name
      type_term:
        tag: type_term
        value: ME:0000246
    description: genome field for Gene
    comments:
    - typedef.json has FK pointing to Genome without specifying target field
    - Assumed to reference Genome.name based on pattern
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: gene_genome
    owner: Gene
    domain_of:
    - Gene
    range: string
    required: true
  gene_aliases:
    name: gene_aliases
    annotations:
      type_term:
        tag: type_term
        value: ME:0000060
    description: aliases field for Gene
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: gene_aliases
    owner: Gene
    domain_of:
    - Gene
    range: string
    multivalued: true
  gene_contig_number:
    name: gene_contig_number
    annotations:
      units_term:
        tag: units_term
        value: UO:0000189
      type_term:
        tag: type_term
        value: ME:0000126
    description: contig_number field for Gene
    comments:
    - indexed starting at 1, as in KBase
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: gene_contig_number
    owner: Gene
    domain_of:
    - Gene
    range: integer
    required: true
  gene_strand:
    name: gene_strand
    annotations:
      type_term:
        tag: type_term
        value: ME:0000186
    description: strand field for Gene
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: gene_strand
    owner: Gene
    domain_of:
    - Gene
    range: string
    required: true
    pattern: '[+-]'
  gene_start:
    name: gene_start
    annotations:
      units_term:
        tag: units_term
        value: UO:0000244
      type_term:
        tag: type_term
        value: ME:0000242
    description: start field for Gene
    comments:
    - indexed starting at 1, as in KBase
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: gene_start
    owner: Gene
    domain_of:
    - Gene
    range: integer
    required: true
  gene_stop:
    name: gene_stop
    annotations:
      units_term:
        tag: units_term
        value: UO:0000244
      type_term:
        tag: type_term
        value: ME:0000243
    description: stop field for Gene
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: gene_stop
    owner: Gene
    domain_of:
    - Gene
    range: integer
    required: true
  gene_function:
    name: gene_function
    annotations:
      type_term:
        tag: type_term
        value: ME:0000250
    description: function field for Gene
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: gene_function
    owner: Gene
    domain_of:
    - Gene
    range: string