Class: Assay

A defined experimental method for measuring a biological change, structured so that its elements - the biological object measured, the process it takes part in, the detection technology, and the taxa and biological target families it applies to - can be matched against the Key Events the assay can inform. Assays are how New Approach Methodologies (NAMs) connect to Adverse Outcome Pathways, and an assay may be specified by one or more test guidelines. Some assays have an inherent directionality, meaning they are designed to detect change in a specific direction, such as an agonist or an antagonist effect on a specific molecular target.

URI: http://example.org/aopwiki-emod/Assay

classDiagram class Assay click Assay href "../Assay/" Assay : aops Assay --> "*" Aop : aops click Aop href "../Aop/" Assay : bio_target_families Assay --> "*" BioTargetFamily : bio_target_families click BioTargetFamily href "../BioTargetFamily/" Assay : biological_action_id Assay --> "0..1" BiologicalAction : biological_action_id click BiologicalAction href "../BiologicalAction/" Assay : citations Assay --> "*" Citation : citations click Citation href "../Citation/" Assay : classification Assay : created_at Assay : description Assay : detection_technology Assay : events Assay --> "*" Event : events click Event href "../Event/" Assay : external_assay_id Assay : id Assay : ke_relationships Assay --> "*" KeRelationship : ke_relationships click KeRelationship href "../KeRelationship/" Assay : objects Assay --> "*" BiologicalObject : objects click BiologicalObject href "../BiologicalObject/" Assay : processes Assay --> "*" BiologicalProcess : processes click BiologicalProcess href "../BiologicalProcess/" Assay : taxon_terms Assay --> "*" TaxonTerm : taxon_terms click TaxonTerm href "../TaxonTerm/" Assay : test_guidelines Assay --> "*" TestGuideline : test_guidelines click TestGuideline href "../TestGuideline/" Assay : title Assay : updated_at

Slots

Name	Cardinality and Range	Description	Inheritance
created_at	0..1 Datetime	Timestamp of when the record was created	direct
updated_at	0..1 Datetime	Timestamp of when the record was last updated	direct
id	1 Integer		direct
title	0..1 String		direct
description	0..1 String		direct
detection_technology	0..1 String		direct
biological_action_id	0..1 BiologicalAction		direct
external_assay_id	0..1 String		direct
classification	0..1 String		direct
objects	* BiologicalObject		direct
processes	* BiologicalProcess		direct
taxon_terms	* TaxonTerm		direct
events	* Event		direct
bio_target_families	* BioTargetFamily		direct
aops	* Aop		direct
citations	* Citation		direct
test_guidelines	* TestGuideline		direct
ke_relationships	* KeRelationship		direct

Usages

used by	used in	type	used
Aop	assays	range	Assay
Event	assays	range	Assay
KeRelationship	assays	range	Assay
Observation	assay_id	range	Assay
Citation	assays	range	Assay
BioTargetFamily	assays	range	Assay
ExperimentSetup	assay_id	range	Assay
TestGuideline	assays	range	Assay

Identifier and Mapping Information

Schema Source

from schema: http://example.org/aopwiki-emod

Mappings

Mapping Type	Mapped Value
self	http://example.org/aopwiki-emod/Assay
native	http://example.org/aopwiki-emod/Assay

LinkML Source

Direct

name: Assay
description: A defined experimental method for measuring a biological change, structured
  so that its elements - the biological object measured, the process it takes part
  in, the detection technology, and the taxa and biological target families it applies
  to - can be matched against the Key Events the assay can inform. Assays are how
  New Approach Methodologies (NAMs) connect to Adverse Outcome Pathways, and an assay
  may be specified by one or more test guidelines. Some assays have an inherent directionality,
  meaning they are designed to detect change in a specific direction, such as an agonist
  or an antagonist effect on a specific molecular target.
from_schema: http://example.org/aopwiki-emod
slots:
- created_at
- updated_at
attributes:
  id:
    name: id
    from_schema: http://example.org/aopwiki-emod
    identifier: true
    domain_of:
    - Aop
    - Event
    - KeRelationship
    - Assay
    - Observation
    - Evidence
    - Stressor
    - Citation
    - BiologicalAction
    - BiologicalObject
    - BiologicalProcess
    - LevelOfBiologicalOrganization
    - AopToEvent
    - AopToLifeStage
    - AopToKeRelationship
    - AopToSex
    - AopToPrototypicalStressor
    - AopToTaxon
    - AssignedLicense
    - BioTargetFamily
    - CellTerm
    - ConfidenceLevel
    - Directness
    - EventToLifeStage
    - EventToSex
    - EventToTaxon
    - ExperimentSetup
    - ExperimentType
    - Handbook
    - HarmonizedAop
    - HarmonizedEvent
    - License
    - LifeStageTerm
    - OecdStatus
    - OrganTerm
    - KeRelationshipToLifeStage
    - KeRelationshipToSex
    - KeRelationshipToTaxon
    - SexTerm
    - EventComponent
    - TaxonTerm
    - TestGuideline
    - User
    range: integer
    required: true
  title:
    name: title
    from_schema: http://example.org/aopwiki-emod
    domain_of:
    - Aop
    - Event
    - Assay
    - Citation
  description:
    name: description
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    domain_of:
    - Assay
    - BiologicalObject
    - BiologicalProcess
    - CellTerm
    - Directness
    - ExperimentSetup
    - License
    - OecdStatus
    - OrganTerm
  detection_technology:
    name: detection_technology
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    domain_of:
    - Assay
  biological_action_id:
    name: biological_action_id
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    domain_of:
    - Assay
    - Observation
    - EventComponent
    range: BiologicalAction
    inlined: true
  external_assay_id:
    name: external_assay_id
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    domain_of:
    - Assay
  classification:
    name: classification
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    domain_of:
    - Assay
  objects:
    name: objects
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    domain_of:
    - Assay
    range: BiologicalObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  processes:
    name: processes
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    domain_of:
    - Assay
    range: BiologicalProcess
    multivalued: true
    inlined: true
    inlined_as_list: true
  taxon_terms:
    name: taxon_terms
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    domain_of:
    - Assay
    range: TaxonTerm
    multivalued: true
    inlined: true
    inlined_as_list: true
  events:
    name: events
    from_schema: http://example.org/aopwiki-emod
    domain_of:
    - Aop
    - Assay
    - Observation
    - BioTargetFamily
    - TestGuideline
    range: Event
    multivalued: true
  bio_target_families:
    name: bio_target_families
    from_schema: http://example.org/aopwiki-emod
    domain_of:
    - Event
    - Assay
    - Citation
    range: BioTargetFamily
    multivalued: true
  aops:
    name: aops
    from_schema: http://example.org/aopwiki-emod
    domain_of:
    - Event
    - KeRelationship
    - Assay
    - Stressor
    range: Aop
    multivalued: true
  citations:
    name: citations
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    domain_of:
    - Assay
    - Observation
    - BioTargetFamily
    range: Citation
    multivalued: true
  test_guidelines:
    name: test_guidelines
    from_schema: http://example.org/aopwiki-emod
    domain_of:
    - Event
    - Assay
    range: TestGuideline
    multivalued: true
  ke_relationships:
    name: ke_relationships
    from_schema: http://example.org/aopwiki-emod
    domain_of:
    - Aop
    - Assay
    range: KeRelationship
    multivalued: true

Induced

name: Assay
description: A defined experimental method for measuring a biological change, structured
  so that its elements - the biological object measured, the process it takes part
  in, the detection technology, and the taxa and biological target families it applies
  to - can be matched against the Key Events the assay can inform. Assays are how
  New Approach Methodologies (NAMs) connect to Adverse Outcome Pathways, and an assay
  may be specified by one or more test guidelines. Some assays have an inherent directionality,
  meaning they are designed to detect change in a specific direction, such as an agonist
  or an antagonist effect on a specific molecular target.
from_schema: http://example.org/aopwiki-emod
attributes:
  id:
    name: id
    from_schema: http://example.org/aopwiki-emod
    identifier: true
    alias: id
    owner: Assay
    domain_of:
    - Aop
    - Event
    - KeRelationship
    - Assay
    - Observation
    - Evidence
    - Stressor
    - Citation
    - BiologicalAction
    - BiologicalObject
    - BiologicalProcess
    - LevelOfBiologicalOrganization
    - AopToEvent
    - AopToLifeStage
    - AopToKeRelationship
    - AopToSex
    - AopToPrototypicalStressor
    - AopToTaxon
    - AssignedLicense
    - BioTargetFamily
    - CellTerm
    - ConfidenceLevel
    - Directness
    - EventToLifeStage
    - EventToSex
    - EventToTaxon
    - ExperimentSetup
    - ExperimentType
    - Handbook
    - HarmonizedAop
    - HarmonizedEvent
    - License
    - LifeStageTerm
    - OecdStatus
    - OrganTerm
    - KeRelationshipToLifeStage
    - KeRelationshipToSex
    - KeRelationshipToTaxon
    - SexTerm
    - EventComponent
    - TaxonTerm
    - TestGuideline
    - User
    range: integer
    required: true
  title:
    name: title
    from_schema: http://example.org/aopwiki-emod
    alias: title
    owner: Assay
    domain_of:
    - Aop
    - Event
    - Assay
    - Citation
    range: string
  description:
    name: description
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: description
    owner: Assay
    domain_of:
    - Assay
    - BiologicalObject
    - BiologicalProcess
    - CellTerm
    - Directness
    - ExperimentSetup
    - License
    - OecdStatus
    - OrganTerm
    range: string
  detection_technology:
    name: detection_technology
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: detection_technology
    owner: Assay
    domain_of:
    - Assay
    range: string
  biological_action_id:
    name: biological_action_id
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: biological_action_id
    owner: Assay
    domain_of:
    - Assay
    - Observation
    - EventComponent
    range: BiologicalAction
    inlined: true
  external_assay_id:
    name: external_assay_id
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: external_assay_id
    owner: Assay
    domain_of:
    - Assay
    range: string
  classification:
    name: classification
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: classification
    owner: Assay
    domain_of:
    - Assay
    range: string
  objects:
    name: objects
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: objects
    owner: Assay
    domain_of:
    - Assay
    range: BiologicalObject
    multivalued: true
    inlined: true
    inlined_as_list: true
  processes:
    name: processes
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: processes
    owner: Assay
    domain_of:
    - Assay
    range: BiologicalProcess
    multivalued: true
    inlined: true
    inlined_as_list: true
  taxon_terms:
    name: taxon_terms
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: taxon_terms
    owner: Assay
    domain_of:
    - Assay
    range: TaxonTerm
    multivalued: true
    inlined: true
    inlined_as_list: true
  events:
    name: events
    from_schema: http://example.org/aopwiki-emod
    alias: events
    owner: Assay
    domain_of:
    - Aop
    - Assay
    - Observation
    - BioTargetFamily
    - TestGuideline
    range: Event
    multivalued: true
  bio_target_families:
    name: bio_target_families
    from_schema: http://example.org/aopwiki-emod
    alias: bio_target_families
    owner: Assay
    domain_of:
    - Event
    - Assay
    - Citation
    range: BioTargetFamily
    multivalued: true
  aops:
    name: aops
    from_schema: http://example.org/aopwiki-emod
    alias: aops
    owner: Assay
    domain_of:
    - Event
    - KeRelationship
    - Assay
    - Stressor
    range: Aop
    multivalued: true
  citations:
    name: citations
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: citations
    owner: Assay
    domain_of:
    - Assay
    - Observation
    - BioTargetFamily
    range: Citation
    multivalued: true
  test_guidelines:
    name: test_guidelines
    from_schema: http://example.org/aopwiki-emod
    alias: test_guidelines
    owner: Assay
    domain_of:
    - Event
    - Assay
    range: TestGuideline
    multivalued: true
  ke_relationships:
    name: ke_relationships
    from_schema: http://example.org/aopwiki-emod
    alias: ke_relationships
    owner: Assay
    domain_of:
    - Aop
    - Assay
    range: KeRelationship
    multivalued: true
  created_at:
    name: created_at
    description: Timestamp of when the record was created
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: created_at
    owner: Assay
    domain_of:
    - Aop
    - Event
    - KeRelationship
    - Assay
    - Observation
    - Evidence
    - Stressor
    - Citation
    - BiologicalAction
    - BiologicalObject
    - BiologicalProcess
    - LevelOfBiologicalOrganization
    - AopToEvent
    - AopToLifeStage
    - AopToKeRelationship
    - AopToSex
    - AopToPrototypicalStressor
    - AopToTaxon
    - AssignedLicense
    - BioTargetFamily
    - CellTerm
    - ConfidenceLevel
    - Directness
    - EventToLifeStage
    - EventToSex
    - EventToTaxon
    - ExperimentSetup
    - ExperimentType
    - Handbook
    - HarmonizedAop
    - HarmonizedEvent
    - License
    - LifeStageTerm
    - OecdStatus
    - OrganTerm
    - KeRelationshipToLifeStage
    - KeRelationshipToSex
    - KeRelationshipToTaxon
    - SexTerm
    - EventComponent
    - TaxonTerm
    - TestGuideline
    range: datetime
  updated_at:
    name: updated_at
    description: Timestamp of when the record was last updated
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: updated_at
    owner: Assay
    domain_of:
    - Aop
    - Event
    - KeRelationship
    - Assay
    - Observation
    - Evidence
    - Stressor
    - Citation
    - BiologicalAction
    - BiologicalObject
    - BiologicalProcess
    - LevelOfBiologicalOrganization
    - AopToEvent
    - AopToLifeStage
    - AopToKeRelationship
    - AopToSex
    - AopToPrototypicalStressor
    - AopToTaxon
    - AssignedLicense
    - BioTargetFamily
    - CellTerm
    - ConfidenceLevel
    - Directness
    - EventToLifeStage
    - EventToSex
    - EventToTaxon
    - ExperimentSetup
    - ExperimentType
    - Handbook
    - HarmonizedAop
    - HarmonizedEvent
    - License
    - LifeStageTerm
    - OecdStatus
    - OrganTerm
    - KeRelationshipToLifeStage
    - KeRelationshipToSex
    - KeRelationshipToTaxon
    - SexTerm
    - EventComponent
    - TaxonTerm
    - TestGuideline
    range: datetime