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Class: Sample

Unifying class to describe the full sample.

URI: https://w3id.org/oscem-schemas/latest/spa/Sample

erDiagram Grid { string film_material boolean film_support string film_thickness string film_topology string manufacturer string material float mesh string pretreatment_atmosphere string pretreatment_type } Ligand { boolean present string reference string smiles } Molecule { string expression_system string gene_name string molecular_class string molecular_type string name_mol string natural_source string sequence string taxonomy_id_expression string taxonomy_id_source } OverallMolecule { AssemblyEnum assembly MoleculeClassEnum molecular_overall_type string name_sample string source } QuantitySI { string unitSI float valueSI string unit float value } Sample { string name string description } Specimen { string buffer boolean embedding float ph boolean shadowing boolean staining boolean vitrification string vitrification_cryogen } Grid ||--|o QuantitySI : "pretreatment_pressure, pretreatment_time" OverallMolecule ||--|o QuantitySI : "molecular_weight" Sample ||--|o Grid : "grid" Sample ||--|o OverallMolecule : "overall_molecule" Sample ||--|o Specimen : "specimen" Sample ||--}o Ligand : "ligands" Sample ||--}o Molecule : "molecule" Specimen ||--|o QuantitySI : "concentration, humidity, temperature"

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/oscem-schemas/latest/spa

Mappings

Mapping Type Mapped Value
self https://w3id.org/oscem-schemas/latest/spa/Sample
native https://w3id.org/oscem-schemas/latest/spa/Sample

LinkML Source

Direct

name: Sample
description: Unifying class to describe the full sample.
from_schema: https://w3id.org/oscem-schemas/latest/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/oscem-schemas/latest/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/oscem-schemas/latest/spa
    rank: 1000
    owner: Sample
    domain_of:
    - Detector
    - Sample
    range: string
    required: true
  description:
    name: description
    description: The description of the item
    from_schema: https://w3id.org/oscem-schemas/latest/spa
    rank: 1000
    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/oscem-schemas/latest/spa
    rank: 1000
    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/oscem-schemas/latest/spa
    rank: 1000
    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/oscem-schemas/latest/spa
    rank: 1000
    owner: Sample
    domain_of:
    - Sample
    range: Ligand
    multivalued: true
  specimen:
    name: specimen
    description: Description of the specimen
    from_schema: https://w3id.org/oscem-schemas/latest/spa
    rank: 1000
    owner: Sample
    domain_of:
    - Sample
    range: Specimen
    required: false
  grid:
    name: grid
    description: Description of the grid used
    from_schema: https://w3id.org/oscem-schemas/latest/spa
    rank: 1000
    owner: Sample
    domain_of:
    - Sample
    range: Grid