Class: Assembly

Assembly entity in the ENIGMA data model

classDiagram class Assembly click Assembly href "../Assembly/" Assembly : assembly_id Assembly : assembly_link Assembly : assembly_n_contigs Assembly : assembly_name Assembly : assembly_strain Assembly --> "0..1" Strain : assembly_strain click Strain href "../Strain/"

Slots

Name	Cardinality and Range	Description	Inheritance
assembly_id	1 String	id field for Assembly	direct
assembly_name	1 String	name field for Assembly	direct
assembly_strain	0..1 Strain	strain field for Assembly	direct
assembly_n_contigs	1 Count	n_contigs field for Assembly	direct
assembly_link	0..1 Link	link field for Assembly	direct

Usages

used by	used in	type	used
Bin	bin_assembly	range	Assembly

Identifier and Mapping Information

Annotations

property	value
term	DA:0000066
used_for_provenance	True
process_types	['PROCESS:0000023', 'PROCESS:0000024']
process_inputs	[['Reads'], ['Reads']]

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Assembly
annotations:
  term:
    tag: term
    value: DA:0000066
  used_for_provenance:
    tag: used_for_provenance
    value: true
  process_types:
    tag: process_types
    value:
    - PROCESS:0000023
    - PROCESS:0000024
  process_inputs:
    tag: process_inputs
    value:
    - - Reads
    - - Reads
description: Assembly entity in the ENIGMA data model
from_schema: https://w3id.org/enigma/enigma-cdm
slots:
- assembly_id
- assembly_name
- assembly_strain
- assembly_n_contigs
- assembly_link

Induced

name: Assembly
annotations:
  term:
    tag: term
    value: DA:0000066
  used_for_provenance:
    tag: used_for_provenance
    value: true
  process_types:
    tag: process_types
    value:
    - PROCESS:0000023
    - PROCESS:0000024
  process_inputs:
    tag: process_inputs
    value:
    - - Reads
    - - Reads
description: Assembly entity in the ENIGMA data model
from_schema: https://w3id.org/enigma/enigma-cdm
attributes:
  assembly_id:
    name: assembly_id
    annotations:
      type_term:
        tag: type_term
        value: ME:0000281
      microtype:
        tag: microtype
        value: ME:0000281
      microtype_data_type:
        tag: microtype_data_type
        value: object_ref
    description: id field for Assembly
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    identifier: true
    alias: assembly_id
    owner: Assembly
    domain_of:
    - Assembly
    range: string
    required: true
  assembly_name:
    name: assembly_name
    annotations:
      unique:
        tag: unique
        value: true
      type_term:
        tag: type_term
        value: ME:0000280
      microtype:
        tag: microtype
        value: ME:0000280
      microtype_data_type:
        tag: microtype_data_type
        value: object_ref
    description: name field for Assembly
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: assembly_name
    owner: Assembly
    domain_of:
    - Assembly
    range: string
    required: true
  assembly_strain:
    name: assembly_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 Assembly
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: assembly_strain
    owner: Assembly
    domain_of:
    - Assembly
    range: Strain
  assembly_n_contigs:
    name: assembly_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 Assembly
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: assembly_n_contigs
    owner: Assembly
    domain_of:
    - Assembly
    range: Count
    required: true
  assembly_link:
    name: assembly_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 Assembly
    comments:
    - Made optional because many Assembly records have empty or file path values instead
      of HTTP URLs
    from_schema: https://w3id.org/enigma/enigma-cdm
    rank: 1000
    alias: assembly_link
    owner: Assembly
    domain_of:
    - Assembly
    range: Link
    required: false