Class: Specimen

Description of specimen handling.

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

erDiagram Specimen { string buffer float ph boolean vitrification string vitrification_cryogen boolean staining boolean embedding boolean shadowing } QuantitySI { float valueSI string unitSI string unit float value } Specimen ||--|o QuantitySI : "concentration" Specimen ||--|o QuantitySI : "humidity" Specimen ||--|o QuantitySI : "temperature"

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 QuantitySI	Concentration of the (supra)molecule in the sample, in mg/ml	direct
ph	0..1 Float	pH of the sample buffer	direct
vitrification	0..1 Boolean	Whether the sample was vitrified	direct
vitrification_cryogen	0..1 String	Which cryogen was used for vitrification	direct
humidity	0..1 QuantitySI	Environmental humidity just before vitrification, in %	direct
temperature	0..1 QuantitySI	Environmental temperature just before vitrification, in K	direct
staining	0..1 Boolean	Whether the sample was stained	direct
embedding	0..1 Boolean	Whether the sample was embedded	direct
shadowing	0..1 Boolean	Whether the sample was shadowed	direct

Usages

used by	used in	type	used
Sample	specimen	range	Specimen
SampleMolecular	specimen	range	Specimen

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/osc-em/oscem-schemas-subtomo

Mappings

Mapping Type	Mapped Value
self	https://w3id.org/osc-em/oscem-schemas-subtomo/:Specimen
native	https://w3id.org/osc-em/oscem-schemas-subtomo/:Specimen

LinkML Source

Direct

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

Induced

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