Class: Experiment

Defines experimental context in which the subjects were studied. Covers environmental parameters like study counts, arena geometry, temperature, multi well plate details etc.

URI: BeStMeta:Experiment

 classDiagram
    class Experiment
    click Experiment href "../Experiment/"
      Experiment : arena_height

      Experiment : arena_height_unit





        Experiment --> "0..1 _recommended_" LengthUnitEnum : arena_height_unit
        click LengthUnitEnum href "../LengthUnitEnum/"



      Experiment : arena_length

      Experiment : arena_length_unit





        Experiment --> "0..1 _recommended_" LengthUnitEnum : arena_length_unit
        click LengthUnitEnum href "../LengthUnitEnum/"



      Experiment : arena_shape





        Experiment --> "0..1 _recommended_" ArenaShapeEnum : arena_shape
        click ArenaShapeEnum href "../ArenaShapeEnum/"



      Experiment : arena_type





        Experiment --> "0..1 _recommended_" ArenaTypeEnum : arena_type
        click ArenaTypeEnum href "../ArenaTypeEnum/"



      Experiment : arena_width

      Experiment : arena_width_unit





        Experiment --> "0..1 _recommended_" LengthUnitEnum : arena_width_unit
        click LengthUnitEnum href "../LengthUnitEnum/"



      Experiment : assay_description

      Experiment : assay_type

      Experiment : environmental_conditions





        Experiment --> "0..1 _recommended_" EnvironmentalConditions : environmental_conditions
        click EnvironmentalConditions href "../EnvironmentalConditions/"



      Experiment : experiment_end_datetime

      Experiment : experiment_start_datetime

      Experiment : light_cycle_detail

      Experiment : light_cycle_type





        Experiment --> "0..1 _recommended_" LightCycleTypeEnum : light_cycle_type
        click LightCycleTypeEnum href "../LightCycleTypeEnum/"



      Experiment : mortality

      Experiment : mortality_notes

      Experiment : n_individuals_end

      Experiment : n_individuals_per_arena

      Experiment : n_individuals_start

      Experiment : n_individuals_total

      Experiment : plate_well_count

      Experiment : temperature_celsius

      Experiment : well_shape_cross_section





        Experiment --> "0..1 _recommended_" WellCrossSectionShapeEnum : well_shape_cross_section
        click WellCrossSectionShapeEnum href "../WellCrossSectionShapeEnum/"

Slots

Name	Cardinality and Range	Description	Inheritance
n_individuals_total	1 Integer	Total number of individuals used in the experiment.	direct
n_individuals_per_arena	1 Integer	Number of individuals tested simultaneously in the arena.	direct
assay_type	1 String	Name of the behavioral assay paradigm or test paradigm.	direct
experiment_start_datetime	0..1 recommended Datetime	Date and time at which the experiment began.	direct
experiment_end_datetime	0..1 recommended Datetime	Date and time at which the experiment ended.	direct
arena_shape	0..1 recommended ArenaShapeEnum	Geometric shape of the test arena.	direct
arena_type	0..1 recommended ArenaTypeEnum	Type of the test arena, e.g., open field, multiwell plate or elevated plus maze.	direct
arena_length	0..1 recommended Float	Length of the arena along one axis.	direct
arena_length_unit	0..1 recommended LengthUnitEnum	Unit of measurement for arena_length.	direct
arena_width	0..1 recommended Float	Width of the arena along one axis.	direct
arena_width_unit	0..1 recommended LengthUnitEnum	Unit of measurement for arena_width.	direct
arena_height	0..1 recommended Float	Height of the arena, when applicable.	direct
arena_height_unit	0..1 recommended LengthUnitEnum	Unit of measurement for arena_height.	direct
plate_well_count	0..1 recommended Integer	Number of wells in the multiwell plate.	direct
well_shape_cross_section	0..1 recommended WellCrossSectionShapeEnum	Geometric cross section shape of the wells of a multiwell plate.	direct
temperature_celsius	0..1 recommended Float	Water or ambient temperature during the recording in degrees Celsius	direct
light_cycle_type	0..1 recommended LightCycleTypeEnum	Standardized category of the light-dark cycle.	direct
light_cycle_detail	0..1 recommended String	Free-text description of the light-dark cycle.	direct
mortality	0..1 recommended Boolean	Indicates whether a subject died during the course of the experiment.	direct
n_individuals_start	0..1 Integer	Number of individuals at the start of the experiment/trial.	direct
n_individuals_end	0..1 Integer	Number of individuals at the end of the experiment/trial.	direct
environmental_conditions	0..1 recommended EnvironmentalConditions	Environmental conditions during the experiment, including water chemistry, feed, and other details.	direct
assay_description	0..1 String	Free-text description of the assay protocol	direct
mortality_notes	0..1 String	Free-test notes on any deaths that occured during the trial. This can be used to provide additional context about mortality.	direct

Usages

used by	used in	type	used
ExperimentalConditions	experiment	range	Experiment

Rules

Rule Applied	Preconditions	Postconditions	Elseconditions
slot_conditions	`{'arena_length': {'value_presence': 'PRESENT'}}`	`{'arena_length_unit': {'required': True}}`

Rule Applied	Preconditions	Postconditions	Elseconditions
slot_conditions	`{'arena_width': {'value_presence': 'PRESENT'}}`	`{'arena_width_unit': {'required': True}}`

Rule Applied	Preconditions	Postconditions	Elseconditions
slot_conditions	`{'arena_height': {'value_presence': 'PRESENT'}}`	`{'arena_height_unit': {'required': True}}`

Rule Applied	Preconditions	Postconditions	Elseconditions
slot_conditions	`{'light_cycle_type': {'equals_string': 'cyclic_ld'}}`	`{'light_cycle_detail': {'required': True}}`

Rule Applied	Preconditions	Postconditions	Elseconditions
slot_conditions	`{'mortality': {'equals_expression': 'true'}}`	`{'n_individuals_start': {'required': True}, 'n_individuals_end': {'required': True}}`

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/bestmeta/schema

Mappings

Mapping Type	Mapped Value
self	BeStMeta:Experiment
native	BeStMeta:Experiment

LinkML Source

Direct

name: Experiment
description: Defines experimental context in which the subjects were studied. Covers
  environmental parameters like study counts, arena geometry, temperature, multi well
  plate details etc.
from_schema: https://w3id.org/bestmeta/schema
slots:
- n_individuals_total
- n_individuals_per_arena
- assay_type
- experiment_start_datetime
- experiment_end_datetime
- arena_shape
- arena_type
- arena_length
- arena_length_unit
- arena_width
- arena_width_unit
- arena_height
- arena_height_unit
- plate_well_count
- well_shape_cross_section
- temperature_celsius
- light_cycle_type
- light_cycle_detail
- mortality
- n_individuals_start
- n_individuals_end
- environmental_conditions
- assay_description
- mortality_notes
rules:
- preconditions:
    slot_conditions:
      arena_length:
        name: arena_length
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      arena_length_unit:
        name: arena_length_unit
        required: true
  description: arena_length requires arena_length_unit
- preconditions:
    slot_conditions:
      arena_width:
        name: arena_width
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      arena_width_unit:
        name: arena_width_unit
        required: true
  description: arena_width requires arena_width_unit
- preconditions:
    slot_conditions:
      arena_height:
        name: arena_height
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      arena_height_unit:
        name: arena_height_unit
        required: true
  description: arena_height requires arena_height_unit
- preconditions:
    slot_conditions:
      light_cycle_type:
        name: light_cycle_type
        equals_string: cyclic_ld
  postconditions:
    slot_conditions:
      light_cycle_detail:
        name: light_cycle_detail
        required: true
  description: If light_cycle_type is cyclic_ld, light_cycle_detail should be provided.
- preconditions:
    slot_conditions:
      mortality:
        name: mortality
        equals_expression: 'true'
  postconditions:
    slot_conditions:
      n_individuals_start:
        name: n_individuals_start
        required: true
      n_individuals_end:
        name: n_individuals_end
        required: true
  description: when mortality is true, counts of individuals at the start and end
    are required

Induced

name: Experiment
description: Defines experimental context in which the subjects were studied. Covers
  environmental parameters like study counts, arena geometry, temperature, multi well
  plate details etc.
from_schema: https://w3id.org/bestmeta/schema
attributes:
  n_individuals_total:
    name: n_individuals_total
    description: Total number of individuals used in the experiment.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: integer
    required: true
  n_individuals_per_arena:
    name: n_individuals_per_arena
    description: Number of individuals tested simultaneously in the arena.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: integer
    required: true
    minimum_value: 1
  assay_type:
    name: assay_type
    description: Name of the behavioral assay paradigm or test paradigm.
    examples:
    - value: open field test
    - value: light-dark transition
    - value: elevated plus maze
    - value: locomotor activity assay
    - value: chemobehavioral assay
    from_schema: https://w3id.org/bestmeta/schema
    broad_mappings:
    - OBI:0000070
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: string
    required: true
  experiment_start_datetime:
    name: experiment_start_datetime
    description: Date and time at which the experiment began.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: datetime
    required: false
    recommended: true
  experiment_end_datetime:
    name: experiment_end_datetime
    description: Date and time at which the experiment ended.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: datetime
    required: false
    recommended: true
  arena_shape:
    name: arena_shape
    description: Geometric shape of the test arena.
    from_schema: https://w3id.org/bestmeta/schema
    broad_mappings:
    - OBI:0000968
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: ArenaShapeEnum
    required: false
    recommended: true
  arena_type:
    name: arena_type
    description: Type of the test arena, e.g., open field, multiwell plate or elevated
      plus maze.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: ArenaTypeEnum
    required: false
    recommended: true
  arena_length:
    name: arena_length
    description: Length of the arena along one axis.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: float
    required: false
    recommended: true
  arena_length_unit:
    name: arena_length_unit
    description: Unit of measurement for arena_length.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: LengthUnitEnum
    required: false
    recommended: true
  arena_width:
    name: arena_width
    description: Width of the arena along one axis.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: float
    required: false
    recommended: true
  arena_width_unit:
    name: arena_width_unit
    description: Unit of measurement for arena_width.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: LengthUnitEnum
    required: false
    recommended: true
  arena_height:
    name: arena_height
    description: Height of the arena, when applicable.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: float
    required: false
    recommended: true
  arena_height_unit:
    name: arena_height_unit
    description: Unit of measurement for arena_height.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: LengthUnitEnum
    required: false
    recommended: true
  plate_well_count:
    name: plate_well_count
    description: Number of wells in the multiwell plate.
    examples:
    - value: '24'
    - value: '96'
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - AFR:0002231
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: integer
    required: false
    recommended: true
    minimum_value: 1
  well_shape_cross_section:
    name: well_shape_cross_section
    description: Geometric cross section shape of the wells of a multiwell plate.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: WellCrossSectionShapeEnum
    required: false
    recommended: true
  temperature_celsius:
    name: temperature_celsius
    description: Water or ambient temperature during the recording in degrees Celsius
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: float
    required: false
    recommended: true
    unit:
      ucum_code: Cel
  light_cycle_type:
    name: light_cycle_type
    description: Standardized category of the light-dark cycle.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: LightCycleTypeEnum
    required: false
    recommended: true
  light_cycle_detail:
    name: light_cycle_detail
    description: Free-text description of the light-dark cycle.
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - MESH:D017440
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: string
    required: false
    recommended: true
  mortality:
    name: mortality
    description: Indicates whether a subject died during the course of the experiment.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: boolean
    required: false
    recommended: true
  n_individuals_start:
    name: n_individuals_start
    description: Number of individuals at the start of the experiment/trial.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: integer
  n_individuals_end:
    name: n_individuals_end
    description: Number of individuals at the end of the experiment/trial.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: integer
  environmental_conditions:
    name: environmental_conditions
    description: Environmental conditions during the experiment, including water chemistry,  feed,
      and other details.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: EnvironmentalConditions
    required: false
    recommended: true
  assay_description:
    name: assay_description
    description: Free-text description of the assay protocol
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: string
    required: false
  mortality_notes:
    name: mortality_notes
    description: Free-test notes on any deaths that occured during the trial.  This
      can be used to provide additional context about mortality.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: string
rules:
- preconditions:
    slot_conditions:
      arena_length:
        name: arena_length
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      arena_length_unit:
        name: arena_length_unit
        required: true
  description: arena_length requires arena_length_unit
- preconditions:
    slot_conditions:
      arena_width:
        name: arena_width
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      arena_width_unit:
        name: arena_width_unit
        required: true
  description: arena_width requires arena_width_unit
- preconditions:
    slot_conditions:
      arena_height:
        name: arena_height
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      arena_height_unit:
        name: arena_height_unit
        required: true
  description: arena_height requires arena_height_unit
- preconditions:
    slot_conditions:
      light_cycle_type:
        name: light_cycle_type
        equals_string: cyclic_ld
  postconditions:
    slot_conditions:
      light_cycle_detail:
        name: light_cycle_detail
        required: true
  description: If light_cycle_type is cyclic_ld, light_cycle_detail should be provided.
- preconditions:
    slot_conditions:
      mortality:
        name: mortality
        equals_expression: 'true'
  postconditions:
    slot_conditions:
      n_individuals_start:
        name: n_individuals_start
        required: true
      n_individuals_end:
        name: n_individuals_end
        required: true
  description: when mortality is true, counts of individuals at the start and end
    are required