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Class: Molecule

More detailed information about individual molecules.

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

classDiagram class Molecule click Molecule href "../Molecule" Molecule : expression_system Molecule : gene_name Molecule : molecular_class Molecule --> "1" MoleculeClassEnum : molecular_class click MoleculeClassEnum href "../MoleculeClassEnum" 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 1
String		 Description of the overall molecular type, i direct
molecular_class 1
MoleculeClassEnum		 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 1
String		 Taxonomy ID of the natural source organism direct
expression_system 1
String		 Scientific name of the organism used to produce the molecule of interest direct
taxonomy_id_expression 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

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

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

Induced

name: Molecule
description: More detailed information about individual molecules.
from_schema: https://w3id.org/osc-em/oscem-schemas
slot_usage:
  name_mol:
    name: name_mol
    required: true
  molecular_type:
    name: molecular_type
    required: true
  molecular_class:
    name: molecular_class
    required: true
  sequence:
    name: sequence
    required: true
  natural_source:
    name: natural_source
    required: true
  taxonomy_id_source:
    name: taxonomy_id_source
    required: true
  expression_system:
    name: expression_system
    required: true
  taxonomy_id_expression:
    name: taxonomy_id_expression
    required: true
  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
    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
    rank: 1000
    alias: molecular_type
    owner: Molecule
    domain_of:
    - OverallMolecule
    - Molecule
    range: string
    required: true
  molecular_class:
    name: molecular_class
    description: Class of the molecule
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: molecular_class
    owner: Molecule
    domain_of:
    - Molecule
    range: MoleculeClassEnum
    required: true
  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
    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
    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
    rank: 1000
    alias: taxonomy_id_source
    owner: Molecule
    domain_of:
    - Molecule
    range: string
    required: true
  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
    rank: 1000
    alias: expression_system
    owner: Molecule
    domain_of:
    - Molecule
    range: string
    required: true
  taxonomy_id_expression:
    name: taxonomy_id_expression
    description: Taxonomy ID of the expression system organism
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: taxonomy_id_expression
    owner: Molecule
    domain_of:
    - Molecule
    range: string
    required: true
  gene_name:
    name: gene_name
    description: Name of the gene of interest
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: gene_name
    owner: Molecule
    domain_of:
    - Molecule
    range: string