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Class: StressorChemical

A chemical that elicits a response (a phenotype) in a subject when encountered through exposure.

URI: zebrafish_toxicology_atlas_schema:StressorChemical

classDiagram class StressorChemical click StressorChemical href "../StressorChemical/" ZappEntity <|-- StressorChemical click ZappEntity href "../ZappEntity/" StressorChemical : cas_id StressorChemical : chemical_id StressorChemical : comment StressorChemical : concentration StressorChemical --> "0..1" QuantityValue : concentration click QuantityValue href "../QuantityValue/" StressorChemical : id StressorChemical : manufacturer StressorChemical --> "0..1" ManufacturerEnum : manufacturer click ManufacturerEnum href "../ManufacturerEnum/" StressorChemical : synonym StressorChemical : unrecognized_chemical_name StressorChemical : unrecognized_manufacturer_name

Inheritance

Slots

Name Cardinality and Range Description Inheritance
chemical_id 0..1
Uriorcurie		 Chemical identifier (e direct
cas_id 0..1
String		 CAS identifier for the chemical direct
unrecognized_chemical_name 0..1
String		 Free-text name for a chemical or vehicle that could not be resolved to a stan... direct
synonym *
String		 Human-readable name(s) for the chemical (non-CURIE), used for display and sea... direct
manufacturer 0..1
ManufacturerEnum		 The manufacturer or supplier of the chemical direct
unrecognized_manufacturer_name 0..1
String		 Free-text name for a manufacturer or supplier that is not in the controlled M... direct
concentration 0..1
QuantityValue		 The dose or concentration of the chemical to which the subject was exposed to direct
comment 0..1
String		 Additional comments direct
id 1
Integer		 Auto-generated integer identifier ZappEntity

Usages

used by used in type used
ExposureEvent stressor range StressorChemical

Rules

Rule Applied Preconditions Postconditions Elseconditions

Rule Applied Preconditions Postconditions Elseconditions
slot_conditions {'manufacturer': {'equals_string': 'other_not_listed'}} {'unrecognized_manufacturer_name': {'required': True}}

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/sierra-moxon/zebrafish-toxicology-atlas-schema

Mappings

Mapping Type Mapped Value
self zebrafish_toxicology_atlas_schema:StressorChemical
native zebrafish_toxicology_atlas_schema:StressorChemical

LinkML Source

Direct

name: StressorChemical
description: A chemical that elicits a response (a phenotype) in a subject when encountered
  through exposure.
from_schema: https://w3id.org/sierra-moxon/zebrafish-toxicology-atlas-schema
is_a: ZappEntity
slots:
- chemical_id
- cas_id
- unrecognized_chemical_name
- synonym
- manufacturer
- unrecognized_manufacturer_name
- concentration
- comment
rules:
- postconditions:
    any_of:
    - slot_conditions:
        chemical_id:
          name: chemical_id
          required: true
    - slot_conditions:
        unrecognized_chemical_name:
          name: unrecognized_chemical_name
          required: true
  description: 'A chemical entry must be identifiable: at least one of chemical_id
    (a standardized identifier / CURIE) or unrecognized_chemical_name (the free-text
    fallback for a chemical that could not be resolved) must be present.'
- preconditions:
    slot_conditions:
      manufacturer:
        name: manufacturer
        equals_string: other_not_listed
  postconditions:
    slot_conditions:
      unrecognized_manufacturer_name:
        name: unrecognized_manufacturer_name
        required: true
  description: Picking the other_not_listed manufacturer escape hatch means the supplier
    has to be named in free text; without it the entry records no recoverable supplier
    at all.

Induced

name: StressorChemical
description: A chemical that elicits a response (a phenotype) in a subject when encountered
  through exposure.
from_schema: https://w3id.org/sierra-moxon/zebrafish-toxicology-atlas-schema
is_a: ZappEntity
attributes:
  chemical_id:
    name: chemical_id
    description: Chemical identifier (e.g., a CHEBI or other ontology URI) for the
      chemical.
    from_schema: https://w3id.org/sierra-moxon/zebrafish-toxicology-atlas-schema
    rank: 1000
    owner: StressorChemical
    domain_of:
    - StressorChemical
    - VehicleOfTransmission
    - ChemicalCabinetEntry
    range: uriorcurie
  cas_id:
    name: cas_id
    description: CAS identifier for the chemical.
    from_schema: https://w3id.org/sierra-moxon/zebrafish-toxicology-atlas-schema
    rank: 1000
    owner: StressorChemical
    domain_of:
    - StressorChemical
    - VehicleOfTransmission
    range: string
  unrecognized_chemical_name:
    name: unrecognized_chemical_name
    description: Free-text name for a chemical or vehicle that could not be resolved
      to a standardized identifier.
    from_schema: https://w3id.org/sierra-moxon/zebrafish-toxicology-atlas-schema
    rank: 1000
    owner: StressorChemical
    domain_of:
    - StressorChemical
    - VehicleOfTransmission
    range: string
  synonym:
    name: synonym
    description: Human-readable name(s) for the chemical (non-CURIE), used for display
      and search. The canonical identity is chemical_id.
    from_schema: https://w3id.org/sierra-moxon/zebrafish-toxicology-atlas-schema
    rank: 1000
    owner: StressorChemical
    domain_of:
    - StressorChemical
    - VehicleOfTransmission
    range: string
    multivalued: true
  manufacturer:
    name: manufacturer
    description: The manufacturer or supplier of the chemical.
    from_schema: https://w3id.org/sierra-moxon/zebrafish-toxicology-atlas-schema
    rank: 1000
    owner: StressorChemical
    domain_of:
    - StressorChemical
    - VehicleOfTransmission
    range: ManufacturerEnum
  unrecognized_manufacturer_name:
    name: unrecognized_manufacturer_name
    description: Free-text name for a manufacturer or supplier that is not in the
      controlled ManufacturerEnum list.
    from_schema: https://w3id.org/sierra-moxon/zebrafish-toxicology-atlas-schema
    rank: 1000
    owner: StressorChemical
    domain_of:
    - StressorChemical
    - VehicleOfTransmission
    range: string
  concentration:
    name: concentration
    description: The dose or concentration of the chemical to which the subject was
      exposed to.
    from_schema: https://w3id.org/sierra-moxon/zebrafish-toxicology-atlas-schema
    rank: 1000
    owner: StressorChemical
    domain_of:
    - StressorChemical
    - VehicleOfTransmission
    range: QuantityValue
    inlined: true
    inlined_as_list: true
  comment:
    name: comment
    description: Additional comments.
    from_schema: https://w3id.org/sierra-moxon/zebrafish-toxicology-atlas-schema
    rank: 1000
    owner: StressorChemical
    domain_of:
    - Control
    - ExposureEvent
    - StressorChemical
    - VehicleOfTransmission
    range: string
  id:
    name: id
    description: Auto-generated integer identifier.
    from_schema: https://w3id.org/sierra-moxon/zebrafish-toxicology-atlas-schema
    rank: 1000
    identifier: true
    owner: StressorChemical
    domain_of:
    - ZappEntity
    range: integer
    required: true
rules:
- postconditions:
    any_of:
    - slot_conditions:
        chemical_id:
          name: chemical_id
          required: true
    - slot_conditions:
        unrecognized_chemical_name:
          name: unrecognized_chemical_name
          required: true
  description: 'A chemical entry must be identifiable: at least one of chemical_id
    (a standardized identifier / CURIE) or unrecognized_chemical_name (the free-text
    fallback for a chemical that could not be resolved) must be present.'
- preconditions:
    slot_conditions:
      manufacturer:
        name: manufacturer
        equals_string: other_not_listed
  postconditions:
    slot_conditions:
      unrecognized_manufacturer_name:
        name: unrecognized_manufacturer_name
        required: true
  description: Picking the other_not_listed manufacturer escape hatch means the supplier
    has to be named in free text; without it the entry records no recoverable supplier
    at all.