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Class: Specimen

Description of specimen handling.

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

classDiagram class Specimen click Specimen href "../Specimen" Specimen : buffer Specimen : concentration Specimen --> "0..1" QuantityValue : concentration click QuantityValue href "../QuantityValue" Specimen : embedding Specimen : humidity Specimen --> "0..1" QuantityValue : humidity click QuantityValue href "../QuantityValue" Specimen : ph Specimen : shadowing Specimen : staining Specimen : temperature Specimen --> "0..1" QuantityValue : temperature click QuantityValue href "../QuantityValue" Specimen : vitrification Specimen : vitrification_cryogen

Slots

Name Cardinality and Range Description Inheritance
buffer 0..1
String		 Name/composition of the (chemical) sample buffer during grid preparation direct
concentration 0..1
QuantityValue		 Concentration of the (supra)molecule in the sample, in mg/ml direct
ph 1
Float		 pH of the sample buffer direct
vitrification 1
Boolean		 Whether the sample was vitrified direct
vitrification_cryogen 1
String		 Which cryogen was used for vitrification direct
humidity 0..1
QuantityValue		 Environmental humidity just before vitrification, in % direct
temperature 0..1
QuantityValue		 Environmental temperature just before vitrification, in K direct
staining 1
Boolean		 Whether the sample was stained direct
embedding 1
Boolean		 Whether the sample was embedded direct
shadowing 1
Boolean		 Whether the sample was shadowed direct

Usages

used by used in type used
Sample specimen range Specimen

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/:Specimen
native https://w3id.org/osc-em/oscem-schemas/:Specimen

LinkML Source

Direct

name: Specimen
description: Description of specimen handling.
from_schema: https://w3id.org/osc-em/oscem-schemas
slots:
- buffer
- concentration
- ph
- vitrification
- vitrification_cryogen
- humidity
- temperature
- staining
- embedding
- shadowing
slot_usage:
  buffer:
    name: buffer
  concentration:
    name: concentration
  ph:
    name: ph
    required: true
  vitrification:
    name: vitrification
    required: true
  vitrification_cryogen:
    name: vitrification_cryogen
    required: true
  humidity:
    name: humidity
  temperature:
    name: temperature
  staining:
    name: staining
    required: true
  embedding:
    name: embedding
    required: true
  shadowing:
    name: shadowing
    required: true

Induced

name: Specimen
description: Description of specimen handling.
from_schema: https://w3id.org/osc-em/oscem-schemas
slot_usage:
  buffer:
    name: buffer
  concentration:
    name: concentration
  ph:
    name: ph
    required: true
  vitrification:
    name: vitrification
    required: true
  vitrification_cryogen:
    name: vitrification_cryogen
    required: true
  humidity:
    name: humidity
  temperature:
    name: temperature
  staining:
    name: staining
    required: true
  embedding:
    name: embedding
    required: true
  shadowing:
    name: shadowing
    required: true
attributes:
  buffer:
    name: buffer
    description: Name/composition of the (chemical) sample buffer during grid preparation
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: buffer
    owner: Specimen
    domain_of:
    - Specimen
    range: string
  concentration:
    name: concentration
    description: Concentration of the (supra)molecule in the sample, in mg/ml
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: concentration
    owner: Specimen
    domain_of:
    - Specimen
    range: QuantityValue
  ph:
    name: ph
    description: pH of the sample buffer
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: ph
    owner: Specimen
    domain_of:
    - Specimen
    range: float
    required: true
  vitrification:
    name: vitrification
    description: Whether the sample was vitrified
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: vitrification
    owner: Specimen
    domain_of:
    - Specimen
    range: boolean
    required: true
  vitrification_cryogen:
    name: vitrification_cryogen
    description: Which cryogen was used for vitrification
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: vitrification_cryogen
    owner: Specimen
    domain_of:
    - Specimen
    range: string
    required: true
  humidity:
    name: humidity
    description: Environmental humidity just before vitrification, in %
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: humidity
    owner: Specimen
    domain_of:
    - Specimen
    range: QuantityValue
  temperature:
    name: temperature
    description: Environmental temperature just before vitrification, in K
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: temperature
    owner: Specimen
    domain_of:
    - Specimen
    range: QuantityValue
    minimum_value: 0.0
  staining:
    name: staining
    description: Whether the sample was stained
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: staining
    owner: Specimen
    domain_of:
    - Specimen
    range: boolean
    required: true
  embedding:
    name: embedding
    description: Whether the sample was embedded
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: embedding
    owner: Specimen
    domain_of:
    - Specimen
    range: boolean
    required: true
  shadowing:
    name: shadowing
    description: Whether the sample was shadowed
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: shadowing
    owner: Specimen
    domain_of:
    - Specimen
    range: boolean
    required: true