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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

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