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Class: Molecule

More detailed information about individual molecules.

URI: https://w3id.org/osc-em/oscem-schemas-subtomo/:Molecule

classDiagram class Molecule click Molecule href "../Molecule" Molecule : expression_system Molecule : gene_name Molecule : molecular_class Molecule : molecular_type Molecule : name_mol Molecule : natural_source Molecule : sequence Molecule : taxonomy_id_expression Molecule : taxonomy_id_source

Slots

Name Cardinality and Range Description Inheritance
name_mol 1
String		 Name of an individual molecule (often protein) in the sample direct
molecular_type 0..1
String		 Description of the overall molecular type, i direct
molecular_class 0..1
String		 Class of the molecule direct
sequence 1
String		 Full sequence of the sample as in the data, i direct
natural_source 1
String		 Scientific name of the natural host organism direct
taxonomy_id_source 0..1
String		 Taxonomy ID of the natural source organism direct
expression_system 0..1
String		 Scientific name of the organism used to produce the molecule of interest direct
taxonomy_id_expression 0..1
String		 Taxonomy ID of the expression system organism direct
gene_name 0..1
String		 Name of the gene of interest direct

Usages

used by used in type used
Sample molecule range Molecule
SampleMolecular molecule range Molecule

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/osc-em/oscem-schemas-subtomo

Mappings

Mapping Type Mapped Value
self https://w3id.org/osc-em/oscem-schemas-subtomo/:Molecule
native https://w3id.org/osc-em/oscem-schemas-subtomo/:Molecule

LinkML Source

Direct

name: Molecule
description: More detailed information about individual molecules.
from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
slots:
- name_mol
- molecular_type
- molecular_class
- sequence
- natural_source
- taxonomy_id_source
- expression_system
- taxonomy_id_expression
- gene_name
slot_usage:
  name_mol:
    name: name_mol
    required: true
  molecular_type:
    name: molecular_type
    required: false
  molecular_class:
    name: molecular_class
    required: false
  sequence:
    name: sequence
    required: true
  natural_source:
    name: natural_source
    required: true
  taxonomy_id_source:
    name: taxonomy_id_source
    required: false
  expression_system:
    name: expression_system
    required: false
  taxonomy_id_expression:
    name: taxonomy_id_expression
    required: false
  gene_name:
    name: gene_name

Induced

name: Molecule
description: More detailed information about individual molecules.
from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
slot_usage:
  name_mol:
    name: name_mol
    required: true
  molecular_type:
    name: molecular_type
    required: false
  molecular_class:
    name: molecular_class
    required: false
  sequence:
    name: sequence
    required: true
  natural_source:
    name: natural_source
    required: true
  taxonomy_id_source:
    name: taxonomy_id_source
    required: false
  expression_system:
    name: expression_system
    required: false
  taxonomy_id_expression:
    name: taxonomy_id_expression
    required: false
  gene_name:
    name: gene_name
attributes:
  name_mol:
    name: name_mol
    description: Name of an individual molecule (often protein) in the sample
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: name_mol
    owner: Molecule
    domain_of:
    - Molecule
    range: string
    required: true
  molecular_type:
    name: molecular_type
    description: Description of the overall molecular type, i.e., a complex
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: molecular_type
    owner: Molecule
    domain_of:
    - Molecule
    range: string
    required: false
  molecular_class:
    name: molecular_class
    description: Class of the molecule
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: molecular_class
    owner: Molecule
    domain_of:
    - Molecule
    range: string
    required: false
  sequence:
    name: sequence
    description: Full sequence of the sample as in the data, i.e., cleaved tags should
      also be removed from sequence here
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: sequence
    owner: Molecule
    domain_of:
    - Molecule
    range: string
    required: true
  natural_source:
    name: natural_source
    description: Scientific name of the natural host organism
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: natural_source
    owner: Molecule
    domain_of:
    - Molecule
    range: string
    required: true
  taxonomy_id_source:
    name: taxonomy_id_source
    description: Taxonomy ID of the natural source organism
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: taxonomy_id_source
    owner: Molecule
    domain_of:
    - Molecule
    range: string
    required: false
  expression_system:
    name: expression_system
    description: Scientific name of the organism used to produce the molecule of interest
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: expression_system
    owner: Molecule
    domain_of:
    - Molecule
    range: string
    required: false
  taxonomy_id_expression:
    name: taxonomy_id_expression
    description: Taxonomy ID of the expression system organism
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: taxonomy_id_expression
    owner: Molecule
    domain_of:
    - Molecule
    range: string
    required: false
  gene_name:
    name: gene_name
    description: Name of the gene of interest
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: gene_name
    owner: Molecule
    domain_of:
    - Molecule
    range: string