Class: Sample
Unifying class to describe the full sample.
URI: https://w3id.org/osc-em/oscem-schemas-spa/:Sample
erDiagram
Sample {
    string name  
    string description  
}
Grid {
    string manufacturer  
    string material  
    float mesh  
    boolean film_support  
    string film_material  
    string film_topology  
    string film_thickness  
    string pretreatment_type  
    string pretreatment_atmosphere  
}
QuantitySI {
    float valueSI  
    string unitSI  
    string unit  
    float value  
}
Specimen {
    string buffer  
    float ph  
    boolean vitrification  
    string vitrification_cryogen  
    boolean staining  
    boolean embedding  
    boolean shadowing  
}
Ligand {
    boolean present  
    string smiles  
    string reference  
}
Molecule {
    string name_mol  
    string molecular_type  
    string molecular_class  
    string sequence  
    string natural_source  
    string taxonomy_id_source  
    string expression_system  
    string taxonomy_id_expression  
    string gene_name  
}
OverallMolecule {
    MoleculeClassEnum molecular_overall_type  
    string name_sample  
    string source  
    AssemblyEnum assembly  
}
Sample ||--|o OverallMolecule : "overall_molecule"
Sample ||--}o Molecule : "molecule"
Sample ||--}o Ligand : "ligands"
Sample ||--|o Specimen : "specimen"
Sample ||--|o Grid : "grid"
Grid ||--|o QuantitySI : "pretreatment_time"
Grid ||--|o QuantitySI : "pretreatment_pressure"
Specimen ||--|o QuantitySI : "concentration"
Specimen ||--|o QuantitySI : "humidity"
Specimen ||--|o QuantitySI : "temperature"
OverallMolecule ||--|o QuantitySI : "molecular_weight"
Inheritance
- Sample
Slots
| Name | Cardinality and Range | Description | Inheritance | 
|---|---|---|---|
| name | 1 String | The name of the item | direct | 
| description | 1 String | The description of the item | direct | 
| overall_molecule | 0..1 OverallMolecule | Description of the overall molecule | direct | 
| molecule | * Molecule | List of molecule associated with the sample | direct | 
| ligands | * Ligand | List of ligands associated with the sample | direct | 
| specimen | 0..1 Specimen | Description of the specimen | direct | 
| grid | 0..1 Grid | Description of the grid used | direct | 
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/osc-em/oscem-schemas-spa
Mappings
| Mapping Type | Mapped Value | 
|---|---|
| self | https://w3id.org/osc-em/oscem-schemas-spa/:Sample | 
| native | https://w3id.org/osc-em/oscem-schemas-spa/:Sample | 
LinkML Source
Direct
name: Sample
description: Unifying class to describe the full sample.
from_schema: https://w3id.org/osc-em/oscem-schemas-spa
slots:
- name
- description
- overall_molecule
- molecule
- ligands
- specimen
- grid
slot_usage:
  name:
    name: name
    required: true
  description:
    name: description
    required: true
  overall_molecule:
    name: overall_molecule
    required: false
  molecule:
    name: molecule
    required: false
  ligands:
    name: ligands
  specimen:
    name: specimen
    required: false
  grid:
    name: grid
Induced
name: Sample
description: Unifying class to describe the full sample.
from_schema: https://w3id.org/osc-em/oscem-schemas-spa
slot_usage:
  name:
    name: name
    required: true
  description:
    name: description
    required: true
  overall_molecule:
    name: overall_molecule
    required: false
  molecule:
    name: molecule
    required: false
  ligands:
    name: ligands
  specimen:
    name: specimen
    required: false
  grid:
    name: grid
attributes:
  name:
    name: name
    description: The name of the item
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: name
    owner: Sample
    domain_of:
    - Detector
    - Sample
    range: string
    required: true
  description:
    name: description
    description: The description of the item
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: description
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: true
  overall_molecule:
    name: overall_molecule
    description: Description of the overall molecule
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: overall_molecule
    owner: Sample
    domain_of:
    - Sample
    range: OverallMolecule
    required: false
  molecule:
    name: molecule
    description: List of molecule associated with the sample
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: molecule
    owner: Sample
    domain_of:
    - Sample
    range: Molecule
    required: false
    multivalued: true
  ligands:
    name: ligands
    description: List of ligands associated with the sample
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: ligands
    owner: Sample
    domain_of:
    - Sample
    range: Ligand
    multivalued: true
  specimen:
    name: specimen
    description: Description of the specimen
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: specimen
    owner: Sample
    domain_of:
    - Sample
    range: Specimen
    required: false
  grid:
    name: grid
    description: Description of the grid used
    from_schema: https://w3id.org/osc-em/oscem-schemas-spa
    rank: 1000
    alias: grid
    owner: Sample
    domain_of:
    - Sample
    range: Grid