Class: Manipulation

Treatment and chemical exposure information decribing pharmacological, toxicological and/or any other interventions that subjects went through. This sub-class can be omitted where no interventions were used.

URI: BeStMeta:Manipulation

 classDiagram
    class Manipulation
    click Manipulation href "../Manipulation/"
      Manipulation : control_type





        Manipulation --> "0..1" ControlTypeEnum : control_type
        click ControlTypeEnum href "../ControlTypeEnum/"



      Manipulation : exposure_compound_chebi_id

      Manipulation : exposure_compound_name

      Manipulation : exposure_concentration

      Manipulation : exposure_concentration_unit





        Manipulation --> "0..1 _recommended_" ConcentrationUnitEnum : exposure_concentration_unit
        click ConcentrationUnitEnum href "../ConcentrationUnitEnum/"



      Manipulation : exposure_duration_h

      Manipulation : exposure_route





        Manipulation --> "0..1" ExposureRouteEnum : exposure_route
        click ExposureRouteEnum href "../ExposureRouteEnum/"



      Manipulation : exposure_type





        Manipulation --> "0..1 _recommended_" ExposureTypeEnum : exposure_type
        click ExposureTypeEnum href "../ExposureTypeEnum/"



      Manipulation : habituation_duration_min

      Manipulation : habituation_protocol

      Manipulation : housing_conditions

      Manipulation : solvent_vehicle

      Manipulation : treatment_description

      Manipulation : treatment_name

      Manipulation : well_shape_bottom





        Manipulation --> "0..1" WellBottomShapeEnum : well_shape_bottom
        click WellBottomShapeEnum href "../WellBottomShapeEnum/"

Slots

Name	Cardinality and Range	Description	Inheritance
treatment_name	0..1 recommended String	Short label identifying the experimental treatment group, condition, or regimen.	direct
treatment_description	0..1 recommended String	Full description of the treatment protocol.	direct
exposure_compound_name	0..1 recommended String	Name of the chemical, drug, or substance used in the treatment or exposure.	direct
exposure_compound_chebi_id	0..1 recommended String	ChEBI identifier for the test substance.	direct
exposure_concentration	0..1 recommended Float	Nominal exposure concentration (numeric value only; use unit field).	direct
exposure_concentration_unit	0..1 recommended ConcentrationUnitEnum	Unit for exposure concentration.	direct
exposure_type	0..1 recommended ExposureTypeEnum	It indicates the type of exposure (Acute or chronic)	direct
well_shape_bottom	0..1 WellBottomShapeEnum	Geometric bottom shape of the wells of a multiwell plate.	direct
habituation_duration_min	0..1 Float	Duration of habituation period before recording, in minutes	direct
habituation_protocol	0..1 String	Description of habituation or acclimation prior to testing.	direct
housing_conditions	0..1 String	Free-text description of animal housing conditions prior to assay.	direct
exposure_route	0..1 ExposureRouteEnum	Route of chemical or treatment administration.	direct
exposure_duration_h	0..1 Float	Duration of chemical or treatment exposure in hours.	direct
solvent_vehicle	0..1 String	Solvent or vehicle used to dissolve the test substance.	direct
control_type	0..1 ControlTypeEnum	Type of control group used.	direct

Usages

used by	used in	type	used
ExperimentalConditions	manipulation	range	Manipulation

Rules

Rule Applied	Preconditions	Postconditions	Elseconditions
slot_conditions	`{'exposure_concentration': {'value_presence': 'PRESENT'}}`	`{'exposure_concentration_unit': {'required': True}}`

Rule Applied	Preconditions	Postconditions	Elseconditions
slot_conditions	`{'exposure_compound_chebi_id': {'value_presence': 'PRESENT'}}`	`{'exposure_compound_name': {'recommended': True}}`

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Manipulation
description: Treatment and chemical exposure information decribing pharmacological,
  toxicological and/or any other interventions that subjects went through. This sub-class
  can be omitted where no interventions were used.
from_schema: https://w3id.org/bestmeta/schema
slots:
- treatment_name
- treatment_description
- exposure_compound_name
- exposure_compound_chebi_id
- exposure_concentration
- exposure_concentration_unit
- exposure_type
- well_shape_bottom
- habituation_duration_min
- habituation_protocol
- housing_conditions
- exposure_route
- exposure_duration_h
- solvent_vehicle
- control_type
rules:
- preconditions:
    slot_conditions:
      exposure_concentration:
        name: exposure_concentration
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      exposure_concentration_unit:
        name: exposure_concentration_unit
        required: true
  description: exposure_concentration requires exposure_concentration_unit.
- preconditions:
    slot_conditions:
      exposure_compound_chebi_id:
        name: exposure_compound_chebi_id
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      exposure_compound_name:
        name: exposure_compound_name
        recommended: true
  description: exposure_compound_name is recommended when exposure_compound_chebi_id
    is provided.

Induced

name: Manipulation
description: Treatment and chemical exposure information decribing pharmacological,
  toxicological and/or any other interventions that subjects went through. This sub-class
  can be omitted where no interventions were used.
from_schema: https://w3id.org/bestmeta/schema
attributes:
  treatment_name:
    name: treatment_name
    description: Short label identifying the experimental treatment group, condition,
      or regimen.
    examples:
    - value: diazepam 1 mg/kg
    - value: atrazine 10 ug/L
    - value: vehicle control
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - NCIT:C82542
    rank: 1000
    owner: Manipulation
    domain_of:
    - Manipulation
    range: string
    required: false
    recommended: true
  treatment_description:
    name: treatment_description
    description: Full description of the treatment protocol.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Manipulation
    domain_of:
    - Manipulation
    range: string
    required: false
    recommended: true
  exposure_compound_name:
    name: exposure_compound_name
    description: Name of the chemical, drug, or substance used in the treatment or
      exposure.
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - EDAM.DATA:0997
    rank: 1000
    owner: Manipulation
    domain_of:
    - Manipulation
    range: string
    required: false
    recommended: true
  exposure_compound_chebi_id:
    name: exposure_compound_chebi_id
    description: ChEBI identifier for the test substance.
    examples:
    - value: CHEBI:15930
    - value: CHEBI:49575
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - EDAM.DATA:1174
    rank: 1000
    owner: Manipulation
    domain_of:
    - Manipulation
    range: string
    required: false
    recommended: true
    pattern: ^CHEBI:\d+$
  exposure_concentration:
    name: exposure_concentration
    description: Nominal exposure concentration (numeric value only; use unit field).
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - EDAM.DATA:2140
    rank: 1000
    owner: Manipulation
    domain_of:
    - Manipulation
    range: float
    required: false
    recommended: true
  exposure_concentration_unit:
    name: exposure_concentration_unit
    description: Unit for exposure concentration.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Manipulation
    domain_of:
    - Manipulation
    range: ConcentrationUnitEnum
    required: false
    recommended: true
  exposure_type:
    name: exposure_type
    description: It indicates the type of exposure (Acute or chronic)
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Manipulation
    domain_of:
    - Manipulation
    range: ExposureTypeEnum
    required: false
    recommended: true
  well_shape_bottom:
    name: well_shape_bottom
    description: Geometric bottom shape of the wells of a multiwell plate.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Manipulation
    domain_of:
    - Manipulation
    range: WellBottomShapeEnum
    required: false
  habituation_duration_min:
    name: habituation_duration_min
    description: Duration of habituation period before recording, in minutes
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Manipulation
    domain_of:
    - Manipulation
    range: float
    required: false
    unit:
      ucum_code: min
  habituation_protocol:
    name: habituation_protocol
    description: Description of habituation or acclimation prior to testing.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Manipulation
    domain_of:
    - Manipulation
    range: string
    required: false
  housing_conditions:
    name: housing_conditions
    description: Free-text description of animal housing conditions prior to assay.
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - XCO:0000033
    rank: 1000
    owner: Manipulation
    domain_of:
    - Subject
    - Manipulation
    range: string
    required: false
  exposure_route:
    name: exposure_route
    description: Route of chemical or treatment administration.
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - MESH:D004333
    rank: 1000
    owner: Manipulation
    domain_of:
    - Manipulation
    range: ExposureRouteEnum
    required: false
  exposure_duration_h:
    name: exposure_duration_h
    description: Duration of chemical or treatment exposure in hours.
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Manipulation
    domain_of:
    - Manipulation
    range: float
    required: false
    unit:
      ucum_code: h
  solvent_vehicle:
    name: solvent_vehicle
    description: Solvent or vehicle used to dissolve the test substance.
    examples:
    - value: DMSO 0.01%
    - value: ethanol 0.1%
    - value: water
    from_schema: https://w3id.org/bestmeta/schema
    rank: 1000
    owner: Manipulation
    domain_of:
    - Manipulation
    range: string
    required: false
  control_type:
    name: control_type
    description: Type of control group used.
    from_schema: https://w3id.org/bestmeta/schema
    exact_mappings:
    - NCIT:C178849
    rank: 1000
    owner: Manipulation
    domain_of:
    - Manipulation
    range: ControlTypeEnum
    required: false
rules:
- preconditions:
    slot_conditions:
      exposure_concentration:
        name: exposure_concentration
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      exposure_concentration_unit:
        name: exposure_concentration_unit
        required: true
  description: exposure_concentration requires exposure_concentration_unit.
- preconditions:
    slot_conditions:
      exposure_compound_chebi_id:
        name: exposure_compound_chebi_id
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      exposure_compound_name:
        name: exposure_compound_name
        recommended: true
  description: exposure_compound_name is recommended when exposure_compound_chebi_id
    is provided.