Skip to content

Class: Sample

A biological sample used in structural biology experiments

URI: biostride_schema:Sample

classDiagram class Sample click Sample href "../Sample/" NamedThing <|-- Sample click NamedThing href "../NamedThing/" Sample : buffer_composition Sample --> "0..1" BufferComposition : buffer_composition click BufferComposition href "../BufferComposition/" Sample : concentration Sample : concentration_unit Sample --> "0..1" ConcentrationUnitEnum : concentration_unit click ConcentrationUnitEnum href "../ConcentrationUnitEnum/" Sample : description Sample : id Sample : molecular_composition Sample --> "0..1" MolecularComposition : molecular_composition click MolecularComposition href "../MolecularComposition/" Sample : molecular_weight Sample : parent_sample_id Sample --> "0..1" Sample : parent_sample_id click Sample href "../Sample/" Sample : preparation_method Sample : purity_percentage Sample : quality_metrics Sample : sample_code Sample : sample_type Sample --> "1" SampleTypeEnum : sample_type click SampleTypeEnum href "../SampleTypeEnum/" Sample : storage_conditions Sample --> "0..1" StorageConditions : storage_conditions click StorageConditions href "../StorageConditions/" Sample : title

Inheritance

Slots

Name Cardinality and Range Description Inheritance
sample_code 1
String		 Unique identifier code for the sample direct
sample_type 1
SampleTypeEnum		 Type of biological sample direct
molecular_composition 0..1
MolecularComposition		 Description of molecular composition including sequences, modifications, liga... direct
molecular_weight 0..1
Float		 Molecular weight in kDa direct
concentration 0..1
Float		 Sample concentration in mg/mL or µM direct
concentration_unit 0..1
ConcentrationUnitEnum		 Unit of concentration measurement direct
buffer_composition 0..1
BufferComposition		 Buffer composition including pH, salts, additives direct
preparation_method 0..1
String		 Method used to prepare the sample direct
storage_conditions 0..1
StorageConditions		 Storage conditions for the sample direct
parent_sample_id 0..1
Sample		 Reference to parent sample for derivation tracking direct
purity_percentage 0..1
Float		 Sample purity as percentage direct
quality_metrics 0..1
String		 Quality control metrics for the sample direct
id 1
Uriorcurie		 NamedThing
title 0..1
String		 NamedThing
description 0..1
String		 NamedThing

Usages

used by used in type used
Study samples range Sample
Sample parent_sample_id range Sample

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/biostride/

Mappings

Mapping Type Mapped Value
self biostride_schema:Sample
native biostride_schema:Sample

LinkML Source

Direct

name: Sample
description: A biological sample used in structural biology experiments
from_schema: https://w3id.org/biostride/
is_a: NamedThing
attributes:
  sample_code:
    name: sample_code
    description: Unique identifier code for the sample
    from_schema: https://w3id.org/biostride/
    rank: 1000
    domain_of:
    - Sample
    required: true
  sample_type:
    name: sample_type
    description: Type of biological sample
    from_schema: https://w3id.org/biostride/
    rank: 1000
    domain_of:
    - Sample
    range: SampleTypeEnum
    required: true
  molecular_composition:
    name: molecular_composition
    description: Description of molecular composition including sequences, modifications,
      ligands
    from_schema: https://w3id.org/biostride/
    rank: 1000
    domain_of:
    - Sample
    range: MolecularComposition
  molecular_weight:
    name: molecular_weight
    description: Molecular weight in kDa
    from_schema: https://w3id.org/biostride/
    rank: 1000
    domain_of:
    - Sample
    range: float
    unit:
      ucum_code: kDa
  concentration:
    name: concentration
    description: Sample concentration in mg/mL or µM
    from_schema: https://w3id.org/biostride/
    rank: 1000
    domain_of:
    - Sample
    range: float
  concentration_unit:
    name: concentration_unit
    description: Unit of concentration measurement
    from_schema: https://w3id.org/biostride/
    rank: 1000
    domain_of:
    - Sample
    range: ConcentrationUnitEnum
  buffer_composition:
    name: buffer_composition
    description: Buffer composition including pH, salts, additives
    from_schema: https://w3id.org/biostride/
    rank: 1000
    domain_of:
    - Sample
    range: BufferComposition
  preparation_method:
    name: preparation_method
    description: Method used to prepare the sample
    from_schema: https://w3id.org/biostride/
    rank: 1000
    domain_of:
    - Sample
  storage_conditions:
    name: storage_conditions
    description: Storage conditions for the sample
    from_schema: https://w3id.org/biostride/
    rank: 1000
    domain_of:
    - Sample
    range: StorageConditions
  parent_sample_id:
    name: parent_sample_id
    description: Reference to parent sample for derivation tracking
    from_schema: https://w3id.org/biostride/
    rank: 1000
    domain_of:
    - Sample
    range: Sample
  purity_percentage:
    name: purity_percentage
    description: Sample purity as percentage
    from_schema: https://w3id.org/biostride/
    rank: 1000
    domain_of:
    - Sample
    range: float
    minimum_value: 0
    maximum_value: 100
  quality_metrics:
    name: quality_metrics
    description: Quality control metrics for the sample
    from_schema: https://w3id.org/biostride/
    rank: 1000
    domain_of:
    - Sample
    - ExperimentRun

Induced

name: Sample
description: A biological sample used in structural biology experiments
from_schema: https://w3id.org/biostride/
is_a: NamedThing
attributes:
  sample_code:
    name: sample_code
    description: Unique identifier code for the sample
    from_schema: https://w3id.org/biostride/
    rank: 1000
    alias: sample_code
    owner: Sample
    domain_of:
    - Sample
    range: string
    required: true
  sample_type:
    name: sample_type
    description: Type of biological sample
    from_schema: https://w3id.org/biostride/
    rank: 1000
    alias: sample_type
    owner: Sample
    domain_of:
    - Sample
    range: SampleTypeEnum
    required: true
  molecular_composition:
    name: molecular_composition
    description: Description of molecular composition including sequences, modifications,
      ligands
    from_schema: https://w3id.org/biostride/
    rank: 1000
    alias: molecular_composition
    owner: Sample
    domain_of:
    - Sample
    range: MolecularComposition
  molecular_weight:
    name: molecular_weight
    description: Molecular weight in kDa
    from_schema: https://w3id.org/biostride/
    rank: 1000
    alias: molecular_weight
    owner: Sample
    domain_of:
    - Sample
    range: float
    unit:
      ucum_code: kDa
  concentration:
    name: concentration
    description: Sample concentration in mg/mL or µM
    from_schema: https://w3id.org/biostride/
    rank: 1000
    alias: concentration
    owner: Sample
    domain_of:
    - Sample
    range: float
  concentration_unit:
    name: concentration_unit
    description: Unit of concentration measurement
    from_schema: https://w3id.org/biostride/
    rank: 1000
    alias: concentration_unit
    owner: Sample
    domain_of:
    - Sample
    range: ConcentrationUnitEnum
  buffer_composition:
    name: buffer_composition
    description: Buffer composition including pH, salts, additives
    from_schema: https://w3id.org/biostride/
    rank: 1000
    alias: buffer_composition
    owner: Sample
    domain_of:
    - Sample
    range: BufferComposition
  preparation_method:
    name: preparation_method
    description: Method used to prepare the sample
    from_schema: https://w3id.org/biostride/
    rank: 1000
    alias: preparation_method
    owner: Sample
    domain_of:
    - Sample
    range: string
  storage_conditions:
    name: storage_conditions
    description: Storage conditions for the sample
    from_schema: https://w3id.org/biostride/
    rank: 1000
    alias: storage_conditions
    owner: Sample
    domain_of:
    - Sample
    range: StorageConditions
  parent_sample_id:
    name: parent_sample_id
    description: Reference to parent sample for derivation tracking
    from_schema: https://w3id.org/biostride/
    rank: 1000
    alias: parent_sample_id
    owner: Sample
    domain_of:
    - Sample
    range: Sample
  purity_percentage:
    name: purity_percentage
    description: Sample purity as percentage
    from_schema: https://w3id.org/biostride/
    rank: 1000
    alias: purity_percentage
    owner: Sample
    domain_of:
    - Sample
    range: float
    minimum_value: 0
    maximum_value: 100
  quality_metrics:
    name: quality_metrics
    description: Quality control metrics for the sample
    from_schema: https://w3id.org/biostride/
    rank: 1000
    alias: quality_metrics
    owner: Sample
    domain_of:
    - Sample
    - ExperimentRun
    range: string
  id:
    name: id
    from_schema: https://w3id.org/biostride/
    rank: 1000
    identifier: true
    alias: id
    owner: Sample
    domain_of:
    - NamedThing
    - OntologyTerm
    range: uriorcurie
    required: true
  title:
    name: title
    from_schema: https://w3id.org/biostride/
    rank: 1000
    slot_uri: dcterms:title
    alias: title
    owner: Sample
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    from_schema: https://w3id.org/biostride/
    rank: 1000
    alias: description
    owner: Sample
    domain_of:
    - NamedThing
    range: string